Mysore Proceeding

1
2
CENTRAL SERICULTURAL RESEARCH & TRAINING INSTITUTE

Introduction

Ever since the human genome has been deciphered, it has emerged that bioinformatics
will become increasingly important for many areas in the life sciences. This era has seen an
explosion of information discovered from the areas of molecular biology and genetics. The focus
of bioinformatics is dealing with this flood of information turning it into useful knowledge. The
flow of information has revolutionized many fields of biosciences. It is also important for the
improvement of genomes of economically important crops and animals. Full understanding and
application of this new data requires a large and growing body of intelligent, creative and
experienced scientists with strong understanding of both computation and biology. The post-
genomic era has thrown great challenges for the scientists to create, manage and interpret the
massive sets of complex biological data. Rapid advances in information technology, computer
science, structural biology and development of sophisticated computational software and tools
have played a key role in deciphering the structure and function of biological molecules, which
has great relevance to agriculture, human health and environment. It is befitting to state that the
increased significance of bioinformatics can no longer be overemphasized.

The Department of Biotechnology, Govt. of India has reacted to this development with
the establishment of a special research focus on bioinformatics. The department has established a
nation wide network of bioinformatics centres spread across the country even the farthest corners.
This network has established a link between diverse groups of scientists working in various R &
D institutions and universities engaged in specified areas of biotechnology. I am proud to state
that Central Sericultural Research & Training Institute, Mysore, which is the premier research
institute for sericulture in the country, is a part of this prestigious network. The bioinformatics
centre of this institute was established in 1999 to primarily support biotechnological research in
sericulture.

The annual meeting of the coordinators of BTISnet is held to review the progress and
activities of all the centres. It is highly overwhelming to host such an important event of this
year in this institute. The progress reports of all the centres compiled in this volume is a valuable
document for taking stock of the activities and achievements of the BTISnet. I earnestly foresee
that these two days congregation of ignited brains will provide an excellent platform for
meaningful interaction, exchange of valuable ideas and new thoughts, which will lead to new
breakthroughs. I am confident that this will further enable us to conquer greater heights in the
field of Bioinformatics.

Dr. Chandrakant K. Kamble
DIRECTOR
BI OI NFORMATI CS CENTRE
Central Silk Board (Ministry of Textiles Govt. of India)
Srirampura, Manandavadi Road, Mysore 570 008
Dr. C. K. Kamble
Director & Coordinator

Ph. 0821-2362547 Fax : 2362845
E-mail : btis_csrti@yahoo.com
3
CONTENTS

1. Advanced Centre for Treatment, Resarch, & Education in Cancer,
Mumbai
01
2. Aligarh Muslim University, Aligarh 05
3. All India Institute of Medical Sciences, New Delhi 09
4. Anna University, Chennai 12
5. Assam Agricultural University, Jorhat 16
6. Banaras Hindu University, Varanasi 21
7. Banasthali Vidyapith, Banasthali 27
8. Barkatullah University, Bhopal 32
9. Bharathidasan University, Tiruchirappalli 38
10. Biotech Consortium India Limited, New Delhi 43
11. Biotech Park, Lucknow 50
12. Birla Institute of Scientific Research, Jaipur 56
13. Birla Institute of Technology, Mesra, Ranchi 61
14. Bose Institute, Kolkata 66
15. Central Agricultural Research Institute, Port Blair 72
16. Central Drug Research Institute, Lucknow 77
17. Central Institute of Freshwater Aquaculture, Bhubaneswar 84
18. Central Institute of Medicinal and Aromatic Plants, Lucknow 89
19. Central Plantation Crops Research Institute, Kasaragod, Kerala 94
20. Central Sericultural Research and Training Institute, Mysore 99
21. Centre for Cellular & Molecular Biology, Hyderabad 104
22. CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur 110
23. Devi Ahilya University, Indore 114
24. Dr.Y S Parmar University of Horticulture and Forestry, H.P. 119
25. G. B. Pant University of Agriculture & Technology, Pantnagar 125
26. Guru Nanak Dev University, Amritsar 129
27. Himachal Pradesh University, Summer Hill, Shimla 134
28. Indian Agricultural Research Institute, New Delhi 138
29. Indian Institute of Science, Bangalore 143
30. Indian Institute of Spices Research, Calicut, Kerala 148
31. Indian Institute of Technology, New Delhi 152
32. Indian Institute of Technology, Kharagpur 157
33. Indian Veterinary Research Institute, Izatnagar 162
34. Indian Institute of Advanced Research, Gandhinagar, Gujarat 167
35. Indian Institute of Integrative Medicine, Canal Road, Jammu 171
36. Indian Institute of Chemical Biology, Kolkata 176
37. Institute of Bioresources and Sustainable Development, Imphal 180
38. Institute of Microbial Technology, Chandigarh 184
39. Karnataka Veterinary, Animal & Fisheries Sciences University, Mangalore 192
40. Kerala Agricultural University, Thrissur 201
41. Madurai Kamaraj University, Madurai 205
42 Mahatma Gandhi Institute of Medical Sciences, Sevagram (Wardha) 211
43. M.S. University of Baroda, Baroda 217
44. National Brain Research Centre, Manesar, Haryana 223
45. National Dairy Research Institute, Karnal 229
46. National Institute of Immunology, New Delhi 233
47. National Institute of Oceanography, Goa 237
48. National Institute for Plant Genome Research, New Delhi 241
49. National Institute of Technology, Raipur 243
50. North-Eastern Hill University, Shillong 246
4
51. Pondicherry University, Pondicherry 255
52. Punjab Agricultural University, Ludhiana 262
53. Rajiv Gandhi Centre for Biotechnology, Trivandrum 268
54. State Council of Science & Technology for Sikkim 273
55. T. M. Bhagalpur University, Bhagalpur 278
56. Tamilnadu Veterinary and Animal Sciences University, Chennai 283
57. Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 288
58. Tropical Botanic Garden and Research Institute Palode, Kerala 293
59. University of Calcutta, Kolkata 299
60. University of Kashmir, Hazratbal, Srinagar, J&K 303
61. University of Pune, Pune

307
Bioinformatics Infrastructure Facility Centres (BIFs)

1. Assam Agricultural University, Khanapara, Guwahati 320
2. Alagappa University, Karaikudi, Tamil Nadu 323
3. Bharathiar University, Coimbatore 328
4. CCS Haryana Agricultural University, Hisar 330
5. Dr. B. R. Ambedkar Center for Biomedical Research,
Delhi
333
6. Fakir Mohan University, Balasore, 337
7. Forest Research Institute - Dehradun 339
8. Guru Jambheshwar University of Science & Technology,
Hisar
343
9. HNB Garhwal University, Garhwal 347
10. Holy Cross College, Tiruchirappalli, Tamil Nadu 350
11. Indira Gandhi Krishi Vishwavidyalaya, Raipur 354
12. Indian Institute of Technology, Madras 357
13. Jamia Millia Islamia, New Delhi 360
14. Jiwaji University, Gwalior 364
15. Kannur University, Kannur 367
16. Karnatak University, Dharwad 371
17. Kumaun University, Nainital 373
18. Lady Doak College, Madurai 375
19. Lucknow University, Lucknow 378
20. Madras Christian College, Chennai 381
21. Maharanis Science College for Women, Bangalore 384
22. Maulana Azad National Institute of Technology, Bhopal 387
23. Narendra Deva University of Agriculture & Technology,
Faizabad
391
24. National Institute of Pharmaceutical Education and
Research, Chandigarh
396
25. Orissa University of Agriculture and Technology,
Bhubaneswar
399
26. Presidency College, Chennai 402
27. Presidency College, Kolkata 406
28. Sardar Vallabh Bhai Patel University of Agriculture &
Technology, Meerut
409
29. Sant Gadge Baba Amravati University, Amravati 411
30. Sanjay Gandhi Postgraduate Institute of Medical
Sciences, Lucknow
414
31. Shri Mata Vaishno Devi University (SMVDU), Katra,
Jammu
418
5
32. Sri Padmavati Mahila Visvavidyalayam, Tirupati 422
33. Sri Venkateswara College, (University of Delhi) 425
34. Sri Venkateshwara Institute of Medical Sciences,
Tirupati
428
35. Tezpur University, Tezpur 432
36. University of Allahabad, Allahabad 435
37. University of Bangalore, Bangalore 438
38. University of Calicut, Kerala 441
39. University of Hyderabad, Hyderabad 443
40. University of Jammu, Jammu 446
41. University of Kalyani, Kalyani, West Bengal 451
42. University of Madras, Chennai 455
43. University of North Bengal 458
44. University of Rajasthan, Jaipur 461
45. Vidyasagar University, Midnapur, West Bengal 464
46. West Bengal University of Technology, Kolkata 469
47. COE, Jawaharlal Nehru University, New Delhi 472

6
Advanced Centre for Treatment, Research, & Education in Cancer, Mumbai.
Coordinator : Robin Mukhopadhyaya

1. Summary of the progress made by the centre from its inception.

The Department of Biotechnology (DBT), Government of India, funded the
establishment of a Biotechnology Information Service (BTIS)/Bioinformatics Centre
at the Cancer Research Institute in 1989. Since then DBT has maintained its support
and TMC has also provided necessary inputs as and when required for gradual
maturation of the facility.

Along with expansion of the institutional infrastructure, advanced data/information
dissipation with higher level of security to increasing number of users is an ongoing
process. During this period quite a few hardware additions took place.

BTIS organizes every year a two-day workshop primarily targeting
College/University faculties/Ph.D. students (15-16 nos) to provide basic knowledge
of applications in bioinformatics using data/information on cancer biology and
proteomics, gene expression analysis using Micro arrays etc along with lectures on
computer basics, literature mining followed by hands on training sessions. A
bioinformatics expert usually is invited from other national institute to deliver a
special lecture. BTIS staff supports the scientists/students for all
bioinformatics/biostatistics related queries and additionally was also responsible for
initial development, updating and maintenance of the website that is hosted on our
server. Computerized repository of cell line maintenance, a small software, was
developed (available on the ACTREC web site) by a basic research scientist in
association with BTIS staff.

2. Major research activities in Biotechnology and its related fields at your
institution: Focus is on basic and translational research in cancer biology.
All details are available at www.actrec.gov.in/Research/Basic Research. In
relation to use of bioinformatics thrust is on genomics and proteomics of oral
cancer, cervical cancer and a hematological malignancy in keeping with the
wet lab thrust areas.

3. Area of Specialization of the centre. Cancer Biology: Basic and
Translational.

4. Major activities of the centre during the year 2007-08: Significant addition
of computational infrastructure contributed by the institute; Organization of
training course; Training new Ph.D. students in use of bioinformatics
resources; Uploading of a new database developed in-house.
Infrastructure facilities in the Bioinformatics Centre
i. Computer & Communication facility:
Two Linux based IBM servers, purchased on DBT grant, and are used as the Internet
and mail servers. The high end X-225 server is configured as mail server and X-205
is the proxy+web server and the Trend Antivirus is being used on the gateway as well
as mail server. The old ACER PII server, procured long back also through DBT, is
being used for deploying MS security patches as well as anti-virus software at
7
desktop level (recently switched from Symantec corporate edition to Trend Micro
client-server messaging security). A Linux based IBM Intellistation Z Pro
workstation for a molecular modelling study was acquired in recent times. Hundred-
user license patch-easy software was deployed for patch management and additional
40-user license of MS Office 2003 was also procured. To ease net connectivity on
demand avoiding additional civil work, Wi-Fi facility was implemented in certain
areas with high volume users/laptop users within the institute and a NAS server (1 TB
capacity) was deployed for online back up.
We have a 1Mbps shared (1/4) leased line from VSNL through MTNL OF
connectivity. Additionally a 250 Kbps last mile wire less internet connectivity from
M/S Tulip Inc has recently been commissioned. Internet is connected to ~150 PC
terminals.

ii. Scientific Software packages: None
iii. Databases & other information resources: Database on oral cancer
genes and chromatin ( See 11 below)
5. Details about staff members working in the centre (Name of the staff,
Designation, Specialization and period of working. Please indicate their
absorption status)

All staff on DBT funding was absorbed by the institute way back in 1994.
The centre has one Scientist C, Mr. NK Gadewal, with a post graduate
degree in Biotechnology and a diploma in Bioinformatics; the facility is
actively supported by staff from IT and biostatistics personnel who are
permanent staff of the Centre.

6. Types of services provided:
Training in basics of bioinformatics to scientific staff/doctoral students; special
emphasis is to train scientific staff, and post graduate students of biology from
resource poor academic institutes in the state.

7. Educational activities with details of placement: Nil
8. Initiative to validate the outcome of bioinformatics resources: Each year
there are about 40 short term trainees from different parts of the country who
undertake their M Sc dissertation with faculty at ACTREC and utilize these
facilities. Fairly good numbers of students/academic staff members from
Mumbai and nearby institutes also regularly access the facility/take
suggestions relevant to their work from BTIS staff.

9. Collaborative works/ initiatives: Nil

Databases/ Software packages developed:

A major focus of this group, in keeping with the wet lab thrust area, is to
develop meaningful database related to genomics/ proteomics of oral cancer.
A new database was developed here and uploaded on our website (URL-
http://www.actrec.gov.in/oralcancer/GeneHome.htm).
This year a new Histone database was uploaded on our website (URL
http://www.actrec.gov.in/histone/infobase.htm)

Papers published or presented in the conferences with reference:
8
Database and interactome map of genes involved in oral cancer. Gadewal
NS, Zingde SM. Online J Bioinfo 8: 41-44, 2007.

Initiation of R&D activities in Bioinformatics: Bioinformatics is now an
integral component of several queries in this centre. It is required for analysis
of the genomics and proteomics related programs on oral cancer, cervical
cancer, brain cancer and hematological malignancies. In 2007 Structural
Biology has been introduced as a thrust area at the Centre. The scientific
inquiries in this include proteosomal dynamics, structure activity relationships
of apoptotic proteins and X-ray crystallography of cancer- associated proteins
all of which will require extensive mining of data from different bases using
relevant bioinformatics software. Structure-based drug design and molecular
modeling.

10. Details of Training/ Workshop organized and total no. of user trained.

A DBT sponsored workshop on Bioinformatics was held on 22-23 March 2007
at this centre. The 11 participants from other institutes were lecturers as well
as doctoral students. The Workshop included lectures on different topics like
Applications in bioinformatics, Cancer biology and proteomics, Micro array
data analysis, Computer/networking basics, Database concept and usage
followed by hands on training sessions. Dr. Surekha Zingde, Dr. Chandan
Kumar, Mr. N. Gadewal, Mrs. S. Kannan, and Mrs O. Upasani delivered the
lectures; the Hands-on Training session involved the members of the Bio-
informatics/Biostatistics section and one doctoral student, Mr. Santhosh VC,
explained genome sequencing/annotation. All course materials were provided
to the participants on CD. A guest lecture was delivered during the workshop
by Dr. Urmila Kulkarni-Kale from Bioinformatics Centre, University of Pune.
One student was provided short term training on Database development
(Meenakshi Sharma, M.Sc Bionformatics, Banasthali Vidyapith, Rajasthan,
January 8-June 7).
11. Impact shown by your centre on the growth of biotechnology and allied
areas. Papers published from the center-45; Invited lectures by the staff of
BTIS in neighboring institutes. There is a growing demand from many city
colleges/institutes to hold the bioinformatics workshop twice in a year.
12. Future activities: Infrastructure and expertise development in molecular
modeling.

Additional Details: Nil

Name of the Coordinator: R. Mukhopadhyaya

Postal Address: Bioinformatics Centre, Advanced Centre for Treatment,
Research & Education in Cancer (ACTREC), Kharghar, Navi Mumbai - 410
210.
Phone Number: 022-2740 5000 Fax No.: 022-2740 5085

Email: btis@actrec.gov.in Website: www.actrec.gov.in

Name of Contact Person: Dr. Ashok Varma.
Email: avarma@actrec.gov.in
9
Aligarh Muslim University, Aligarh
Coordinator : Professor M. Saleemuddin

1. Summary of the progress made by the centre from its inception
The Distributed Information Sub-Centre was established by the DBT, New
Delhi at Aligarh Muslim University, Aligarh in the academic session 1988-89.
The main function of the Centre is to act as a member of Bioinformatics
Network System for providing information to the interested users on topics
pertaining to the relevant areas of Biotechnology specially protein folding and
design, protein structure and protein engineering. The functions of the Centre
include, among others, acquisition, creation and development of programmes
and databases needed by the users. For the last several years, Centre is
contributing significantly for the manpower development by organizing
workshops and courses in the field of bioinformatics. Since its inception the
Centre has organized 14 national level bioinformatics workshops and trained
more than 325 participants from different universities and institutions. Centre
is regularly organizing seminar lecture for the benefit of students, researchers
and scientists working the area of biotechnology or in the areas related to
biotechnology. Centre is regularly providing Internet facility for its users since
1994. Recently a dedicated 512 kbps BSNL leased line and a 2 mbps
broadband connection has been installed and is functioning satisfactorily in
providing online literature search etc.

institution
Right from its establishment, the unit has been concentrating on research in
various aspects of protein biotechnology and efforts continue in this direction,
in addition to those in immunology and molecular biology. One aspect that is
being actively pursued is the stabilization of enzymes with the help of
polyclonal antibodies. Attempts are currently being made to identify regions of
the enzyme that are crucial for enzyme stability and raise antibodies against
the regions in experimental animals. Another group is actively engaged in the
study of pathways leading to various folding intermediate of proteins, which
involves the characterization of various intermediates. Moreover development
of liposome-based vaccines to project against various antifungal diseases are
also in pipeline. Studies on isolation of T4 nrdB mutants for the investigation
of the structure-function relationship in RNA splicing of group I introns on a
model with view to understand the requirement of secondary and tertiary
structure of RNA in the autocatalytic splicing of intron is also being
investigated. Molecular Biology and Yeast genetics exploring Transcription
factors and their interaction with 3 RNA processing machinery. Transcription
regulation and gene silencing versus histone methylation .

3. Area of Specialization of the centre : Basic Biotechnology

4. Major activities of the centre during the year 2007- 08
Distributed Informatics Sub-center is involved in bioinformatics research in the fields
of genome and proteome analysis. The genome of Arabidopsis thaliana was
analyzed to determine the position and frequency of simple sequence repeats
(SSRs). Simple sequence repeats or microsatellite repeats are defined as regions
within DNA sequences where short sequences (1-6 bp; monomers to hexamers) are
repeated in tandem array. We have developed a perl program (SSRscanner) for this
10
analysis. The work was published in the journal Bioinformation (Anwar, T & Khan,
A.U., 2005. Mapping and analysis of Simple Sequence Repeats in the Arabidopsis
thaliana Genome. Bioinformation 1(2):64-68.) At present research work is going on
the in silico analysis of proteome of a deadly virus i.e., Influenza A virus (Bird flu
virus). This program will be very helpful to Influenza researchers who wish to do
analysis of Influenza sequences or any other sequence by comparison of two
sequences.
Workshops on Bioinformatics : Workshop on Genome analysis: A bioinformatics
was organised during February 24-25, 2007 in which 22 participants were trained.
E-Mail and Internet Facility : The Centre is regularly providing INTERNET facility to
the users through BSNL dedicated 512 kbps leased line and BSNL 2 mbps Broad
Band Connection which has recently been procured by the Centre.
CD-ROM Databases Facility : The CD-ROM databases facility of the Centre is being
regularly used by the students, researchers and teachers of this University for the
retrieval of scientific information.
Scientific Software Facility : Among others, Centre has procured few scientific
softwares like Sigma Plot, DTMM, Reference Manager, Enzfitter, Instat, Peakfit,
which are being regularly used by the students and researchers of this University.
Bioinformatics teaching: A paper entitled Computational methods and
bioinformatics has been introduced in the curriculum offered to M.Sc. Biotechnology
and the bioinformatics part is being taught by the BTIS staff of this Centre.
Inhouse Databases: These are Proteolytic enzyme database, Immobilized metal
affinity chromatography database, Human Vaccine database.

5. Infrastructure facilities in the Bioinformatics Centre:
i. Computer & Communication facility
The Bioinformatics Centre is now fully equipped with BSNL dedicated 512 kbps leased line
and BSNL 2 mbps Broad Band Connection, One servers, fourteen Pentium IV systems,
three Pentium 2 systems and one Pentium 1 system with two dot matrix printers, three
laser printers, two scanners, one photocopier and a fax machine.
ii. Scientific Software packages
iii. Databases & other information resources
Medline, Biotechnology Abstracts, Agricola, and Life Science Collection
Journals: European Journal of Biochemistry, Science, New Scientist, Trends in Biochemical
Sciences and Trends in Biotechnology, Nature, New Scientist, Nature Biotechnology etc.

absorption status)
Name of the staff Designation Period of Work
S. Faisal Maqbool Sr. Scientific Officer 18 years
Parveen Salahuddin Sr. Res. Assistant 17 years
S. Aqtedar Husain Data Entry Operator 17 years
All above have already absorbed by the University

7. Types of services provided
Workshops on Bioinformatics, E-Mail and Internet Facility, CD-ROM
Databases Facility, Scientific Software Facility,In-house Databases. The
following databases have been developed and upgraded regularly for the
routine use of the biotechnologists.
(a) Proteolytic enzyme database
(b) Immobilized metal affinity chromatography database
(c) Human Vaccine database

8. Educational activities with details of placement
Bioinformatics teaching:
11
Multimedia and E-learning initiatives:

9. Initiative to validate the outcome of bioinformatics resources
Organizing workshop in bioinformatics for manpower development.
Providing online services through BSNL dedicated 512 kbps leased line and
BSNL 2 mbps Broad Band Connection for literature search etc.
Providing offline services using CD-ROM database (Medline, Life Science
Collection and Biotechnology Abstracts).
Providing scientific softwares like Sigma plot, Grafit, Reference Manager,
DTMM, Instat, Buffer Maker and a number of word processing softwares for the
routine use of researchers and teachers.

10. Collaborative works/ initiatives Nil

11. Databases/ Software packages developed
Databases: (i) Proteolytic enzyme database (ii) Immobilized metal affinity
chromatography database (iii) Human Vaccine database
Software: AMACAN: An hydrophobicity analysing software for protein and
amino acid sequences developed in visual basic and MS-Access for the
routine use of students and teachers.

12. Papers published or presented in the conferences with reference
During the year (2007-2008) years more than 35 papers were published using
bioinformatics facilities

13. Initiation of R&D activities in Bioinformatics: Nil

14. Details of Training/ Workshop organized and total no. of user trained
The centre has organized 14 workshops since 1994 and has trained more
than 325 users so far.

areas. In this you may highlight the details like number of paper
published/ number of papers published with the help of your centre,
how your centre is promoting various activities of your organization and
neighboring institutions, manpower trained, tools developed, patents &
copyrights acquired and other services offered etc.

Centre is involved in bioinformatics research in the fields of genome and
proteome analysis. The genome of Arabidopsis thaliana was analyzed to
determine the position and frequency of simple sequence repeats (SSRs).
Simple sequence repeats or microsatellite repeats are defined as regions
within DNA sequences where short sequences (1-6 bp; monomers to
hexamers) are repeated in tandem array. We have developed a perl program
(SSRscanner) for this analysis. At present research work is going on the in
silico analysis of proteome of a deadly virus i.e., Influenza A virus (Bird flu
virus). The avian influenza (bird flu) caused by Influenza virus is an infectious
disease of birds, ranging from a mild to a severe form of illness. Influenza
viruses pose significant challenges to both human and animal health. Highly
pathogenic avian influenza virus infection

can result in huge economic loss.
The proteins Nucleoprotein (NP), Neuraminidase (NA) and Hemagglutinin
12
(HA) of Influenza A Virus (Bird flu virus) sub-type A/Hatay/2004/(H5N1) from
chicken are being analyzed to check the mutations and to find out the protein
that is responsible for causing the disease, secondary structure prediction,
etc. A perl program MAPMUTATION that compares two sequences and
report the exact location of mutation in the sequence and change in amino
acid/nucleotide was also developed for this study. This program will be very
helpful to Influenza researchers who wish to do analysis of Influenza
sequences or any other sequence by comparison of two sequences. More
than 38 papers have been published using bioinformatics facilities(see
attached list).

16. Future activities
Analysis of eukaryotic genomic DNA and its organization using gene
finder program.
Development of databases in the areas actively investigated at this
University such as on vaccines against human diseases, chemokines,
Enzyme immobilisation. etc.
Organising workshops on bioinformatics.
Organising seminar lecture programmes in the areas of bioinformatics and
biotechnology
Online access to E-journals, softwares etc.

Additional details:
Name of the Coordinator:Professor M. Saleemuddin
Postal Address: Coordinator, Distributed Information Sub-Centre,
Interdisciplinary Biotechnology Unit, Aligarh Muslim University,
Aligarh 202 002.
Phone: 0571-2720388, Fax: 0571-2721776
E-mail: alg_btisamua@sancharnet.in

13
All India Institute of Medical Sciences, New Delhi
Co-ordinator: Prof. Y.D. Sharma

The progress made by BTIS is reflected in modern methods of M.Biotech.
teaching and ready access of bioinformatics tools The research scholars and
students in our department have become more adept in handling various
scientific packages and their efforts in this direction have led to the
development of two software packages Spectral Repeat Finder and My
Pattern Finder. The manpower trained by us has found placement in
government and private sectors both in India and abroad.

All our research labs are connected through a local area network afforded by
BTIS and provided with internet connectivity. The BTIS facility provides strong
support to all research projects of the department and 24hours of internet
connectivity is utilized effectiviley for accessing various online databases and
for online submission of manuscripts and sequences.

institution.

The research laboratories in the department of biotechnology at AIIMS are
carrying out active research in the fields of molecular and immunological
aspects of infectious diseases like Malaria and Tuberculosis, tumor biology
and cardiac diseases. PCR based diagnostic methods have been developed
for TB and closely related mycobacteria and they have also been patented.
Research is also being carried out to identify potential drug and vaccine target
antigens for TB and Malara. Basic research is being carried out to decipher
the role of DevR-DevS signal transduction system in pathogenesis and
virulence of M. tuberculosis. Mutations in cytokine genes and their receptors
are also being studied in different categories of cancer patients for providing a
better diagnostic tool. In the field of cardiac diseases, modulation of endothelin in blood
plasma of patients undergoing coronary artery bypass surgery imparted with relaxation
therapy in the form of meditation is being studied.

3. Area of Specialization of the centre:
Infectious diseases, tumor biology, cardiac diseases.

4. Major activities of the centre during the year 2007-08.
BTIS provided support for three major activities of our department namely (i)
Teaching: The bioinformatics module for M.Biotech. students was further
strengthened to a 3.0 credit point course (ii) Research: Active research was
carried out in the field of infectious diseases including malaria & tuberculosis,
cancer and cardiac diseases culminating in (iii) Publications, diagnostics
and patents.
5. Infrastructure facilities in the Bioinformatics Centre
Computer & Communication facility
Tetronix color laser printer (1), laser Printers (5), Deskjet Printer (1),
Modem (2), UPS (1), Fax Machine (2), Modi Xerox (1), Electronic Type
Writer (1), Server Netfinity (1), Windows NT Server (1), CD Writer (2), Zip
14
Drive (2), Router DI-1162 (1), HP Scanners (2), OHP (1)Lap Top &
LCD Projector (1), Gel Doc System (1).

Scientific Software packages (procured):
Labwork for Gel Analysis on UVP system
Graph Pad
End Note Version 7.0

Databases & other information resources: NIL
absorption status)

7. Types of services provided.
Access to computers and accessories including round the clock internet facility
for teaching, scientific research and publication to students, research scholars,
office staff and faculty

8. Educational activities with details of placement.
A 3.0 credit point course module in bioinformatics is being run for M.Biotech.
students. The students are imparted with hands on training in the use of
various bioinformatics tools and packages. Experts are invited from other
departments, institutes (TCGA) and universities (JNU). The details of the
placement of individual candidates may be viewed in Appendix-I

9. Initiative to validate the outcome of bioinformatics resources.
The two-software packages developed by us are being used by students for
in silico analysis of research hypotheses and are finding support in
experimental results.

10. Collaborative works/ initiatives.
Interactions with Other Institutions/Centres: Experts are invited from various
academic institutes/centres for delivering lectures on various topics in
Bioinformatics to M.Biotech. students. Some of the collaborating
institutes/centres include IGIB, New Delhi, SIT, JNU New Delhi, IIT Delhi,
Deptt. of Biophysics, AIIMS, Deptt. of Computer facility, AIIMS and Deptt. Of
NMR, AIIMS.
11. Databases/ Software packages developed.
Two software packages developed by us are
1. Spectral Repeat Finder
2. My Pattern Finder
In 2007 16 papers have been published in peer-reviewed (Pub-Med indexed)
journals. (See Appendix-II for references).

13. Initiation of R&D activities in Bioinformatics.
Name Of The
Staff
Designation Specialization Working
Since
Absorption
Status
Shalini Narang Data entry
operator
M.Sc. Computer
Science
April 2000
( 7 yrs.)
AIIMS
employee
15
In silico analysis of wet-lab. Data and hypothesis formulation using
bioinformatics tools available on-line is an integral part of all R&D activity
being carried out in our department.

BTIS is providing support to the M.Biotech. Teaching Programme, PhD
scholars, MD/MS trainees, WHO fellows, DBT Associates and summer
trainees. The total strength of manpower trained is, therefore, greater than
332.

areas.
No. of M.Biotech students trained: > 168
No. of PhD scholars passed out 27
No. of PhD scholars enrolled currently 18
No. of Post MD/MS professionals trained > 15
No. of summer trainees > 90
No. of WHO fellows trained 14
No. of papers published in 2007 16
No. of patents 14

The conditions for learning and teaching of Bioinformatics shall be optimized
based on the articulated needs and concerns of the students carrying out
research in the field of biomedical sciences. Upgradation Infrastructure
Facility shall be carried out for teaching purposes

Additional Details:
Name of the Coordinator: Prof. Y.D.Sharma
Postal Address: Department of Biotechnology,
All India Institute of Medical Sciences
Ansari Nagar, New Delhi -110029
Phone Number: 26594609 Mobile: 9868397964 Fax: 26589286
Email: ydsharma@hotmail.com
Website: www.aiims.edu/aiims/departments/biotech.
16
Anna University, Chennai
Coordinator : Prof. P. Gautam

The Distributed Information Centre, Centre for Biotechnology, Anna University
has good infrastructure facility with a Apple cluster for parallel computing, a high
end SGI Server and SGI Fuel Workstations and IBM PCs. These facilities are
used for research activities in Molecular dynamics, Molecular modeling, Docking,
Cluster computing, Database creation, Protein Structure Studies, Genomics and
Systems Biology. A three Credit course in bioinformatics is offered to the
Undergraduate students and a 3 Credit course in Computational Biology is
offered to Postgraduate and Doctoral students of the University.
We also provide guidance on Projects in Bioinformatics for our Undergraduates,
Postgraduates and students from other Universities. Information dissemination
and training is one of the mandates of the centre. Regular workshops and
training programmes are conducted by the centre for familiarizing College
Professors and Lecturers with the latest trends in Bioinformatics and
Computational biology.
institution
Tissue Culture and Drug Discovery, Immunotechnology, Bioorganic Chemistry
and Bioremediation, Computational Biology & Bioinformatics, Protein
Biotechnology, Molecular Biology, Bioprocess engineering.
3. Area of Specialization of the centre
Areas of specialization of the BTIS DIC, CBT, Anna University include Molecular
Dynamics, Molecular modeling and docking, Cluster Computing, Protein
Structure Prediction and Genomics.
4. Major activities of the centre during the year 2007-08
Research at the Centre is mainly focused in the areas of Molecular dynamics,
Molecular modeling, Protein structural analyses, Genomics and Systems Biology.
17
Infrastructure facilities in the Bioinformatics Centre
A High End SGI Origin Server with the following specification: Dual
R14000 @600 MHz, 1GB ECC Ram, 18GB Ultra SCSI Internal hard disk
Silicon Graphics Fuel Systems - 2 Nos.
IBM Intel Pentium IV 2.4GHz with 512cache 256MB RAM, 40GB HDD - 4 Nos.
in Cluster and 2 Nos. as Workstations
Dual 2GHz PowerPC G5 Apple Mac - 1 No.
IBM Netvista Pentium III 88 MhZ, 20 GB HDD - 7 Numbers
HP 24 port 100Mbps Switch
Colour Laserjet Printers - 1 no.
Apple Mac - 1 No
Apple G5 64Bit Cluster Computing System With Accessories- 1 No.
B. Scientific Software packages
Oracle Database 10g and Internet Application Server, GROMACS (Parallel
Molecular Dynamics), AutoDock, Dock, Whatif, Delphi, VectorNTI Ver 4.0,
Matlab, EMBOSS, Rasmol, Molscript, Phylip, Dotter, ClustalW,
absorption status)
Dr. Sharmila
Anishetty
Member Research
Staff
Protein Structure
Prediction,
Comparative
Genomics, Databases,
Systems Biology
2003 onwards
Contract Basis
Ms. T.Kothai
Member Research
Staff
Molecular Dynamics
Simulation
1996 onwards
Contract Basis
Mrs.
Vijaylakshmi
Narayanan
Documentation
Officer
Digital Library
2006 Onwards
Contract Basis

Types of services provided
Educational activities with details of placement
Teaching Bioinformatics to the Undergraduate B.Tech Industrial Biotechnology,
Postgraduate M.Tech Biotechnology and Doctoral students. We also provide
Summer term Projects and Curriculum Based Projects for Undergraduates and
students from other Universities.

Initiative to validate the outcome of bioinformatics resources
We are working on protein protein interaction networks. The results obtained in this
study will be validated through single molecule studies using FRET.
18
Papers published or presented in the conferences
1) FEBS Lett. 2007 Sep 18;581(23):4377-83. Epub 2007 Aug 14.
Activation of Candida rugosa lipase at alkane-aqueous interfaces: a
molecular dynamics study.
James JJ, Lakshmi BS, Seshasayee AS, Gautam P.

2) Protein Pept Lett. 2007;14(6):552-6.
Distribution of tripeptides in MHC binding peptides.
Sharmila Anishetty, Gautam Pennathur

3) Bioinformatics. 2007 Feb 1;23(3):267-71.
In silico identification of putative metal binding motifs.
Thilakaraj R, Raghunathan K, Anishetty S, Pennathur G.

Initiation of R&D activities in Bioinformatics:
B. Tech and M. Tech Projects:
Areas of Research:
Molecular dynamics simulations of phospholipases and lipases,
Respiratory tract pathogens, Molecular level studies of multidrug
resistance, Protein protein interactions, Alpha beta hydrolases,
Metalloproteins, Quorum sensing pathways, Metabolic flux analysis of
aromatic amino acid pathways, Modeling of phenylketonuria.
Ph.D. students:
We have six Ph.D. students in Computational Biology working on
Modeling quorum sensing pathways in Pseudomonas aeruginosa,
Cell wall biosynthetic pathway inhibitors in pathogenic bacteria,
Protein protein interactions, Comparative genomics and systems biology
studies of marine organisms,
Molecular dynamics simulations of lipases and acetylases.
Details of Training/ Workshop organized and total no. of user trained
No. Workshop Title Period No.of
Participants
1. Workshop on Sequence Analysis and
Molecular Simulation
5
th
8
th

December 2007

15
Impact shown by your centre on the growth of biotechnology and allied areas. In
this you may highlight the details like number of paper published/ number of
papers published with the help of your centre, how your centre is promoting
various activities of your organization and neighboring institutions, manpower
trained, tools developed, patents & copyrights acquired and other services
offered etc
In the last three years we have published about eight papers in bioinformatics. One
person has finished a Ph.D. in Computational Biology and one person has completed a
19
M.S. degree. Currently six students are registered for a Ph.D. in Computational Biology.
The facilities of the center are used by students from different colleges in and around
Chennai.

Future activities Research:
1) Molecular Dynamics simulation of enzymes immobilized on surfaces.
2) Understand Quorum sensing in Pathogens through a Systems Biology
and a Comparative genomics approach
3) Understand the mechanism of metal ion transport in bacteria by optical
imaging and develop tools for the process.
4) We are in the process of developing an algorithm for identification of
conserved protein interaction network motifs.
5) Systems Biology approach to model phenylalanine metabolism related
disorders.
Education:
We would like to start a M.Sc. ( Computational Biology ) Course with the
bioinformatics Centres of Madurai Kamaraj University and Pondicherry
University.

Additional Details:
Name of the Coordinator: Prof. P. Gautam, Centre for Biotechnology,
Anna University, Chennai 600025.
Phone Number:091-44-22350772 Fax No.: 091-44-22350299
Email: pgautam@annauniv.edu, gpennathur@yahoo.com
Website: http://www.annauniv.edu/biotech/boc/
Name of Contact Person(s): Dr. Sharmila Anishetty, Ms.T.Kothai
Email: s_anishetty@yahoo.co.uk, tkothai@annauniv.edu

20
Assam Agricultural University, Jorhat
Coordinator : Dr. Mahendra K. Modi

1. Summary of the progress made by the centre from its inception :
The Assam Agricultural University is a Premier University in the North-East-
India engaged in teaching, research and extension activities of Agricultural
and Allied Sciences. At present the university has four faculties viz.
Agriculture, Veterinary, Home Science and Fisheries with six constituent
colleges. The center successfully bridged the interdisciplinary gaps on
information and links in the area of Agricultural Biotechnology in the North-
East India. The center is also providing information via Reference Retrieval
system and facilities like computational analysis of the research data,
Internet/Email facilities and imparting teaching and organizing training
programmes on Bioinformatics for the teachers and researchers involved in
different Universities, educational institutes and R & D centers of North-east
India. The centre since its inception, have been organizing regular National
Workshops/Training on Bioinformatics to make entry and mid-level scientist
familiar to the basic fundamentals of bioinformatics as well as ways of utilizing
Information Technology in Life Science Research. A two hour credit course
on Application of Computers in Biotechnology has been introduced for
the Post Graduate students of this University since 1990. This course was
found very useful and effective for the students. From 2004-05 a new post-
graduate course on Introduction to Bioinformatics has been introduced,
in which the students are exposed to various softwares and techniques in
Bioinformatics. The Centre also actively engaged in the preparation of
different databases and successfully completed database like 1. Citrus
Germplasm Database which include citrus germplasm available in India
along with their detaled morphological and biochemical characteristics. 2.
Tea germplasm database which include different tea gerplasm available in
north-east India along with their detailed morphological and biochemical
characteristics.

2. Major research activities in Biotechnology and its related fields in your
institution

The major research activities in Biotechnology are :

a. Development of an EST library in Tea (camellia sinensis)
b. Genetic transformation of chickpea mediated through Agrobacterium for
development transgenic chickpea against stored grain pest.
c. Genetic transformation of black gram mediated through Agrobacterium for
development transgenic chickpea against pod borer.
d. Genetic transformation of Citrus mediated through Agrobacterium for
development of transgenic Citrus reticulata cv. Khasi mandarin and Citrus
limon cv Assam lemon against stem/trunk borer.
e. Genetic transformation of rice mediated through Agrobacterium for
development of transgenic indica rice varieties of Assam.
3. Area of Specialization of the centre :
a. Broad : Agricultural Biotechnology
21
b. Specific : Plant Tissue Culture, Plant Molecular Biology, Plant Genetic
Engineering and Microbial Biotechnology.

4. Major activities of the centre during the year 2007-08: No major activity
could be taken up during this year as the Information Officer has gone on a
years study leave. The databases on citrus and tea are being converted
from stand-alone to network mode and efforts are being made to publish
the databases once the conversion is completed.


A. Computer & Communication facility :

i. Computer Hardware :
LAN Server, 2 Unit; PC-Pentium II, III & IV, 10 Units; Workstation 1 Unit,
Notebook, 1 Unit; Multimedia Projector, 2 Unit; Network Printer 1 Unit
Other Inkjet & Laser Printer, 7 Unit, various UPSs, Scanners, Networking
equipments etc.

ii. Communication Facilities :
1. 512 Kbps dedicated leased line Internet Port facility has been obtained
from BSNL.
2. SCPC VSAT link (256 Kbps) from ERNET subscribed by the university
and ICAR. The facility is shared by the center through a fibre- optic
campus LAN However This link is being upgraded to 2 MBPS leaswed
line
3. FAX /Telephone

SPSS 12.0.1, Vector NTI Advance for PC version 9.1, EMBOSS software
suit, BioEdit, Rapidistance, Phylip, DNASIS, pDRAW, DNAClub, ClustalW
etc, Exome, Exome-ED, PDQuest Gel analysis software

C. (i) Databases & other information resources
Name of
Database
Broad Subject
area
Broad
functional
area
Developed
or acquired
Status of
completion
Network
Availa-
bility
Agricola Agricultural
Science
Bibliographical
database
Acquired Yes
Agris Agricultural
Science
Bibliographical
database
Acquired Yes
CABCD Agricultural
Science
Bibliographical
database
Acquired Yes
Citrus
Germplasm
Database
Morphological,
biochemical and
molecular
biological
information
Research/
Teaching
Developed Completed No
Tea
Germplasm
Database
Varietal
information,
Tissue culture and
Molecular biology
Research/
Teaching
Developed Completed No
Rice
Germplasm
Varietal
information,
Research/
Teaching
Developed Under
Progress
No
22
Breeding
Weed
Database
Morphological,
biochemical and
molecular
biological
information
Research/
Teaching
Developed Under
Progress
No
ii. Journals and other information sources

Name of
Journal/
Online
service
Broad Subject
area
Network
Availability
Online/Pri
nt based
Remarks
Blackwell-
Synergy
Plant Science Yes Online 40 journals are
available. Acquired from
DBT resources
Springer-Link Agricultural
Sciences
Yes Online 180 journals are
available. Acquired
through university
resources (ICAR)
Science
Direct
Plant Science Yes Online 160 journals are
available. Acquired
through university
resources (ICAR)
Print
Journals
Related to
Biotechnology,
Bioinformatics &
Computer Science

No Print 8 journals from
NISCAIR and few other
journals are subscribed
by the center.

Designation, Specialization and period of working)

Sl.
No.
Designation Num-
ber
Educational
qualification
Area of
specialization
Status of
manpower
absorption
Anticipated
future
requirement
1. Salvinder
Singh
Information
Officer
1 M.Sc. (Agri) Agricultural
Biotechnology
Filled -
2. Technical
Asstt.
1 B.Sc. Biology Vacant 1
3. Data Entry
Operator
1 Graduate English Vacant 1
4. Research
Associate
1 Graduate &
Diploma in
Computer
Sc.
B.Sc. and
Diploma in
Computer Sc.
Filled -

23
7. Types of services provided :

Analysis of Research Data; Retrieval of bibliographic information, both online
and offline; Training in the field of Bioinforamtics etc.

8. Educational activities with details of placement :
Our Centre has not introduced one year Advanced Post Diploma or M.Tech
courses. Alternatively, a two-hour credit course on, Application of
Computers in Biotechnology was introduced for the Post-graduate
students of this University since 1990.The present course for the PG students
shall be continued. A separate course on Bioinformatics, viz.
Introduction to Bioinformatics , was introduced for the Post-Graduate
students in 2004-05.

9. Initiative to validate the outcome of bioinformatics resources:
No initiatives have been taken to validate outcome of bioinformatics
resources

10. Collaborative works/ initiatives
The centre has collaboration with the Department of Plant Breeding &
Genetics, Biochemistry & Agricultural Chemistry, Horticulture, Tea Husbandry
& Technology, Agronomy and Regional Agricultural Research Station, Titabar
of Assam Agricultural University for the development of Databases. We have
also initiated collaboration with the Bioinformatics Facility (BIF) established at
College of Veterinary Sciences, Khanapara, Guwahati. The centre is also
collaborating with the Agricultural Research Information System (ARIS)
programme of this University, which is being supported by ICAR, Govt. of
India, New Delhi. The Centre is also associated with the scientists of North
Eastern Institute of Technology (Formerly Regional Research Laboratory),
Jorhat; Tocklai Experimental Station, Jorhat; Rain Forest Research Institute,
Jorhat and Central Muga & Eri Research Institute, Jorhat.

11. Databases/ Software packages developed : Same as mentioned above in
section 5(c)

12. Papers published or presented in the conferences with reference: Nil

13. Initiation of R&D activities in Bioinformatics:
The center is developing of an expert system for detection of Weed seeds in
the field. The system will have a detailed database detailing the
morphological attributes with photographs and DNA fingerprints. This system
will help the seed certification agencies and quarantine agencies to identify
contaminating weed seeds in seed lots of crop plants.


1993 : National workshop on Bioinformatics.*
1995 : National workshop on Bioinformatics and its application in Life
Sciences.*
1996 : National workshop on Computers in Scientific Communication.*
1997 : National workshop on Applications of Computers in Biological
Sciences.*
24
1999 : National workshop on Application of Computers in Agriculture and
Allied Sciences. *
2000 : National workshop on Application on Computers in Scientific
Communications. *
2001 : National workshop on Bioinformatics in Agriculture. *
2003 : National Workshop on Use of Computers and Internet in
Biological Sciences *
2004 : National workshop on Use of Linux in Bioinformatics.*
2005 : National Workshop on Bioinformatics Tools and Applications.*
2006 : National Workshop on Basics of Bioinformatics and its application
in Biological Sciences
* Number of Participants in each Workshop : 30 (Thirty). The deta

15. Future activities:
1. To provide services to the scientific community of NE India
2. Organize National Workshop on Bioinformatics for teachers, scientists and
research scholars of this region.
3. To complete the databases under progress.
4. A new database with the parentages of modern rice varieties is proposed
and work will be initiated in the near future. The database will allow the
breeders to know the parentages of varieties quickly and help in planning
breeding programmes.
5. The existing databases will be converted to web-accessible format so that
these can be made available online.

16. Additional Details:

Name of the Coordinator: Dr. Mahendra K. Modi
Postal Address: Department of Agricultural Biotechnology, Assam
Agricultural University, Jorhat-785013
Phone Number:0376-2340095 Fax No.: 0376-2340001
Email: mkmodi@aau.ac.in mohan_aau@yahoo.com
Website: http://www.aau.ac.in, http://www.aau.ac.in/btis

Name of Contact Person(s):
1. Dr. M.K. Modi, Coordinator, Bioinformatics Sub-Centre, Department of
Agricultural Biotechnology, AAU, Jorhat-785013,
Email: mkmodi@aau.ac.in, mkmodi@gmail.com
25
Banaras Hindu University, Varanasi
Coordinator : Prof. Ashok Kumar

1. Summary of the progress made by the Centre from its inception:
The Bioinformatics Centre was setup in 1989 at the School of Biotechnology, Faculty
of Science, Banaras Hindu University, Varanasi, as one of the Distributed
Information Sub-Centres (Sub-DICs) under the Biotechnology Information System
(BTIS). The main function of the Centre is to act as a member of Bioinformatics
Network System for providing information to the interested users in the area of
Bioinformatics and Biotechnology. A separate room attached to the School of
Biotechnology was built in 1998 which had been housing all the facilities of the
Bioinformatics Centre. Now the Centre has got additional two rooms (12ftX28ft and
9ftX15ft). The posts of Data Entry Operator (grade II) and Programmer (grade II)
were filled up in 1995 and the employees appointed have been absorbed by
University in 2005 and made permanent. The Internet facility through VSAT became
operational during the year 1997. In addition Fiber optics connectivity has also been
provided by the University and is functioning for providing online literature search.
The Centre has been providing internet, data search and other facilities to all the users
of the university and neighboring institutes. The facilities of the centre are utilized for
teaching of M.Sc. Biotechnology courses in general and one course namely Computer
Applications, Bioinformatics and Biostatistics is taught and covered by the staff of
the centre. The centre has become an independent unit under Faculty of Science since
August 1998. The posts of Information officer and Data Entry Operator are yet to be
filled. For the last several years, the centre has been organizing various training
courses regularly for the manpower development in the area of Bioinformatics and
Biotechnology. The Centre has acquired a number of software and databases for the
use of researchers.

2. Major research activities in Biotechnology and its related fields at
your institution:
The faculty members of the School are focusing their efforts in the
following areas:

A. Development of Regional Biofertilizer Strain Collection and Research
Centre:
Our School has developed the facilities and competence in the molecular and
applied aspects of Biofertilizer technology. On molecular side, the genes
responsible for nitrogen fixation, dicarboxylate transport, osmoregulation in
the plant growth promoting bacterium, Azospirillum were cloned and
characterized. On applied side, the technology for large scale production and
field application of cyanobacterial biofertilizer were developed and
demonstrated to farmers. We have collected a number of bacterial isolates
which could be used for biofertilizer purposes.

B. Environmental Microbiology and Enzyme Technology:
The School has demonstrated its ability to address some of the environmental
problems via bioremediation. Several bacterial strains have been isolated and
characterized for their ability to degrade sodium dodecyl sulphate,
acrylamide, tannins and recalcitrant carbon compounds present in distillary
and explosive factory effluent. Some of the isolates seem to be potential for
26
bioremediation studies. With the success in application of PCR fingerprinting
techniques on clinically important bacteria such as Salmonella typhi and
Helicobacter pylori, the School plans to develop programme for surveillance
and forecasting of bacterial and viral (infectious/epidemic) isolates causing
diseases. The School has also developed competence in enzyme technology
and is capable of producing industrially and clinically important enzymes such
as urease, -galactosidase and -amylase.

C. Development of insect resistant chickpea and pigeonpea:
Attempts have been made to develop a regeneration protocol amenable to
genetic transformation for insect resistant chickpea and pigeonpea.
Decapitated embryo axis has been used to develop a genotype-independent
high frequency and highly reproducible shoot regeneration protocol. These
regeneration systems were used for genetic transformation mediated by
Agrobacterium tumefaciens.

D. Cellular & Molecular immunology, and Tumour immunology:
The School has excellent expertise in the area of animal cell culture and
immunology. The main focus of research in these disciplines has been the study of
the mechanisms of anti-cancer defense operating in the body and the study of the
tumor growth dependent immuno-suppression with an aim to generate effective
immuno-therapeutic strategies for locating cancer.

3. Area of Specialization of the Centre: Bioinformatics & Agriculture.

4. Major activities of the centre during 2007-2008:
The major activities of the Centre during the year 2006-2007 are;
a. 512 kbps leased line connection has been installed in the Centre for
providing the better connectivity of internet.
b. The University has also provided a Optical Fiber connectivity to the centre
for access of free online important Journals related to biotechnology and
bioinformatics.
c. Networking (Local Area Network) of Internet facility to all the teachers and
their research laboratory has been completed.
d. Imparted regular theory and practical classes to the M.Sc. Biotechnology
students on Computer Applications, Bioinformatics and Biost course.
e. Provided literature searches online and through CD (Medline Abstract and
Biotechnology Abstract) to Teaching staff and Research Scholars.

A. Computer and Communication facility:
Sl. NO. Particulars
Quantity
1. 512 kbps Leased Line connection
1 No.
2. HP Proliant ML 350 Server
1 No.
3. Optical Fiber Internet Connection (University)
1.No.
4. Xeon based 2.4 GHz Server with color monitor
1 No.
5. Lap top Computer System
1 No.
6. Pentium IV Computer System with color monitor
13 Nos.
7. Pentium III Computer System with color monitor
2 No.
27
8. HP Laser Jet Color Printer
1 No.
9. HP Laser Jet Printer
3 Nos.
10. Dot matrix Printer
3 No.
11. Hp Laserjet (all in one)
1 No.
12. Fax (Samsung SF 4500)
1 No.
13. Telephone /Fax (STD/ISD)
1 No.
14. UPS 10KVA, 5KVA
2 No.

B. Scientific Software packages: The Centre has acquired software packages
viz., Windows-95, Windows-98,MS Windows NT4, Windows XP, MS Office
2000 Professional, MS Office 2007, Norton Anti Virus 2007, MS Visual Studio
2005, Sigma Plot 10, Sigma State 3.5, SPSS, WIN/ISIS, Exome Version 1.3,
Accelrys Gene 2.5 for various types of analysis related to bioinformatics

C. Databases and other information resources:
Sl. No. Name of Data base Acquired/Developed
1. Medline Abstracts Acquired
2. Biotechnology Abstracts Acquired

Designation, Specialization, and period of working. Please indicate
their absorption status):
Name of the staff Designation Specialization
Period of working
Mr.Dinesh
Chaudhary
Data Entry
Operator
Data Entry March- 1995 to till date*
Mrs. Savita Rani Programmer Programming June 1995 to till date*
* The post of Data Entry Operator Gr.II and Programmer Gr.II has been
absorbed by the University in June 2005.

7. Types of services provided: The following types of services are provided
by the centre:
a. E-Mail and Internet Services: Provided to all the Teaching staff,
Research Scholars and other scientific staffs for their R& D works.
b. Databases Services: The Bioinformatics Centre provides database
accessibility online and through CD (Medline Abstracts and
Biotechnology Abstracts) to all the interested users.
c. Communication Services: The Centre provides the communication
facilities like Internet, Fax and Phone etc. to all the staff, students
and other members belonging to Faculty of Science/other faculties
of the university.
d. Other services: Xerox facility.

8. Educational activities with details of placement:
Ongoing teaching programmes: A course on Computer Applications,
Bioinformatics and Biostatistics for M.Sc. Biotechnology students.

9. Initiative to validate the outcome of Bioinformatics resources:
Attempts are being made to have Industry- University collaboration.
28

10. Collaborative works/initiative:
Mahila Mahavidlaya, BHU, has started two years course in Bioinformatics
where our centre is getting involved in organization of the course.
Furthermore Faculty of Science, BHU, is also going to start PG and
Diploma course in Bioinformatics involving our centre. The centre has
established collaborations with other institutions such as IIVR, Varanasi
and IIT, Roorkee.

11. Databases/software packages developed:
Sl. No. Name of Data base Acquired/Developed
1 Cytokine Developed
2. Plant Growth Promoting Rhizobacteria Developed

12. Papers published or presented in conferences with reference:
Jha, P.N. and Kumar, A. (2007). Endophytic colonization of Typha
australis by a plant growth promoting bacterium klebsiella oxytoca Strain
GR -3. Journal of Applied Microbiology (Published on-line June 2007).
Nagarajan, T., Vanderleyden, J. and Tripathi, A.K. (2007). Identification of
salt stress induscible genes that control cell envelope related functions
in Azosplreillum brasilense SP 7. Molecular Genetics and Genomics 278:
43-51.
Tripathi, P., Leggio, L.L., Mansfeld, J., Ulbrich-Hofmann, R., and
Kayastha, A.M. (2007). -amylase from mung beans (Vigna radiata)-
Correlation of biochemical properties and tertiary structure by homology
modelling. Phytochemistry 68:1623-1631.
Sebnem Unlu, Kumar Arvind, Wayne R. Waterman, Junichi Tsukada, Kent
Z. Q. Wang, Deborah L Galson, Philip E. Auron (2007). Phosphorylation of
IRF8 in a pre associated complex with Spi-1/ PU. 1 and non-
phosphorylated Stat 1 is critical for LPS induction of the ILI1B gene.
Molecular Immunology 44: 3364-3379.
Alahari, A., Tripathi, A.K. and Le Rudulier, D. (2006) Cloning and
characterization of a fur homolog from Azospirillum brasilense Sp7.
Current Microbiology 52:123-127.
Tripathi, A. K., Verma, S.C., Paul Chowdhury, S., Lebuhn, M., Gattinger,
A. and Schloter, M. (2006) Ochrobacterum oryzae sp. nov, a novel
endophytic bacterial species isolated from deep-water rice in India.
International Journal of Systematic and Evolutionary Microbiology
56:1677-1680.
Paul Chowdhury, S., Schmid, S., Hartmann, A. and Tripathi, A.K. (2006)
Identification of diazotrophs in the culturable bacterial community
associated with roots of Lasiurus sindicus, a perennial grass of Thar
Desert, India. Microbial Ecology 54: 82-90.

The School has acquired an Automated DNA Sequencer, which has been linked to
the internet facility of the Bioinformatics centre. This has facilitated and speed up
direct analysis of the nucleotide sequence data for comparison with databases such
as GenBank, swissprot etc.
Recently, researches have been initiated on comparative and functional
genomics of plant growth promoting bacteria (Azospirillum and Rhizobium).
29
Genome of Azospirillum brasilense is being analyzed by random
mutagenesis and transposon flanking regions have been sequenced to
identify the genes and their promoters. Identification of genes by database
searches gives an idea about the function/phenotype of the mutated genes.

14. Details of Training workshop organized and total no. of users
trained:
I. Organized a Short Training Course on L
A
T
E
X for Ph.D. students and
M.Tech. students from Feb. 17, to March 5, 2005. Total No. of
participants: 34.
II. Organized a short training course on Computer Application on Office
Automation from 4-9
th
July, 2005 for technical and administrative staff of
Mahila Mahavidlaya of the University. Total No. of participants: 16.
III. Organized a Short Training Course on L
A
T
E
M.Tech. students from September 26 to October 1, 2005. Total No. of
participants: 18.
IV. Organized a Short Training Course on L
A
T
E
M.Tech. students from February 6 to Feabruary 11, 2007. Total No. of
participants: 16.

15. Impact shown by your centre on the growth of biotechnology and
allied areas.
The centre has provided excellent facilities in literature survey, getting
accession number and online submission of research papers. Sequence
homology search, primer designing etc. are routinely done with the facilities
available in the Centre. More than 20 research papers have been published
in Journals of repute with the tools available in the Centre. A number of
teachers and research scholars both from this university and other
neighboring institutions have been trained in the training programs
organized by the Centre for collecting and generating data bases

The Centre proposes to organize at least four short training and one
workshop annually for the benefits of researchers involved in
biotechnological research. It is planed to develop teaching package in
biology with particular reference to the courses of M.Sc. Biotechnology.
Attempts are also being made to start two years M.Sc. teaching course in
Bioinformatics under the Faculty of Science, utilizing the facilities available
at the Centre. The Centre also plans to develop more databases in
Agricultural Biotechnology and other.

Additional Details:

Name of the Coordinator:Prof. Ashok Kumar
Postal Address: School of Biotechnology, Faculty of Science
Banaras Hindu University, Varanasi 221 005
Phone Number: 0542-2368364 Fax No.0542- 2368693/2368174
Email: kasokbt@rediffmail.com
Website: http://bioinformaticsbhu.tripod.com
Name of Contact Person(s): Prof. Ashok Kumar
30
Email: kasokbt@rediffmail.com
31
Banasthali Vidyapith, banasthali
Coordinator : Dr. Vinay Sharma

The Centre for Bioinformatics at Banasthali University is being extensively
used by PG students in Biotechnology & Bioscience, Ph.D. students, faculty
of the Department of Bioscience & Biotechnology. In addition, the research
students, teachers/scientists of many other departments, especially Home
Science, Chemistry, Krishi Vigyan Kendra etc. The services of the Centre for
Bioinformatics include analysis of biological data, bibliographic references to
published literature in science and technology (including databases and
patents). Some of the important databases and softwares of biological
importance are acquired as well as developed for the users. Training
programmes are also organized to train manpower.
institution
The Ph.D. students carry out research in various disciplines of Biotechnology,
Bioscience and Bioinformatics. There are sponsored research projects with
teaching faculty of the department. Some of the Agricultural Biotechnology
related research topics are: Phytoalexins; Immobilization of enzymes;
Fluoride toxicity; Reclamation of desert soils using plants; Tissue culture of
arid zone species etc.
Collaborative work with local/nearby institutions as Krishi Vigyan Kendra,
Banasthali University, Durgapura (Jaipur) Agriculture Research Station and
others is being carried out.
A research collaboration of a few faculty members with laboratories in
Germany and USA. Prof. Vinay Sharma has been a Visiting Professor at the
Department of Molecular Biology and Microbiology, University of Florida, USA
(January to May, 2006).
Dr. Bhumi Nath Tripathi lecturer was awarded the prestigious DBT Young
Scientist Overseas Associateship and visited the laboratory of Prof. Karl-
Josef Dietz, University of Bielefeld, Germany (July to November, 2006)
Dr. Bhumi Nath Tripathi Senior Lecturer is a Visiting Scientist at the Research
institute of Bioresources, Okayama University, Japan (October 07-March 08).

Information Dissemination in Biotechnology
Bioinformatics Education & Human Resource Development
Environment and Diversity
The Major activities of the Centre of Bioinformatics at Banasthali:
The total number of users utilizing the bioinformatics facilities has increased,
currently, it is more than 500.
To cater the regional and national needs, the Centre has also developed
databases on Biotechnological Industries of Rajasthan, SSR Database of
Citrus sinensis, Database for Simple Sequence Repeats of Takifugu rubripus
and Database of Diterpene Synthase Gene. The work on the other database,
Flora of Indian Desert and Plant Host-Pathogen Interaction is in progress.
The Centre has a website link at <www.banasthali.ac.in> (website of the
institution).
32

A. Computer & Communication facility
Servers & PCs :HP Proliant DL 385 G2 Server 1 No.; HP NET E60 Server 1
No.; HP Proliant ML 150 Server 1 No.; Wipro super genius 6100 2 Nos. ; Vinitron
Celeron @300A MHz 2 Nos.; HP Brio Celeron @300A MHz 2 Nos.; Zenith P-IV 1
No.; Ingram Micro VESTA PC 5 Nos.; IBM Thinkcentre P-IV 13 Nos.; IBM
ThinkPad 2 Nos.; HP scanner 6300c 1 No.
Printers :HP Laserjet (color) 2550 1 No; HP Laserjet (color) 2500 1 No; HP
Laserjet 4200n 1 No; HP LaserJet 2100m 1 No; HP Deskjet 5160 1 No; HP
Deskjet 3500c 1 No; HP LaserJet 1015 2 No; TVSE MSP345 1 No
UPS : Vinitek 3 KVA UPS 1 No.; Vinitek 5 KVA UPS 1 No.; Vinitek 10 KVA UPS
1 No.
Communication Facilities :Modem 56.6 KBPS 1 No.; Sony LCD Projector 1
No.; Desktop Photocopier Model K-1212 1 No.; External CD Writer 1 No.; Kodak
6330 Digital Camera 1 No.; Creative Web Camera 2 Nos.; Switch 8 port 2 Nos ;
Switch 16 port 2 Nos.; Switch 24 port 1 No.
Insight II (Homology); Genocluster ver 1.0; Chrome Circle Application; HPLC
Software; TLC Manual; Crash Proof Instant Data Recovery Software
C. Databases & other information resources
Biotechnology Abstract; Medline; Indian Forester Information System; Agris;
Agricola
absorption status)
Sr.
No
Name of the
Staff
Designation Educational
Qualification/
Specialization
Period of
Working
Absorption
Status
1) Ms. Saroj
Yadav
Information
Officer
M.Sc.
Bioinformatics
1 Year
(Contract)
----
2) Mrs. Kiran
Shanti
Technical
Assistant
P.G.D.C.A. 11 Years
(Permanent)
----
3) Mr. S. R.
Choudhary
Computer
Operator
A.D.C.A.,
P.G.D.C.T.A.
I.T.
7 Years
(Contract)
----
4) Mr. K. M.
Jangid
Computer
Operator
A Level
C++
3 Years
(Contract)
----
5) Mr. Amit
Goyal
Data Entry
Operator
O Level,
MCSE, CCNA
3 Years
(Contract)
----

Please also see S.No. 4
The services of the Centre for Bioinformatics include analysis of biological data,
bibliographic references to published literature in Science and Technology (including
databases and patents) and access to Internet.
Some of the currently available important databases in Biological sciences are: Medline
Standard, Agris, Agricola, Chrome Circle Application, Biotechnology Abstracts and
Indian Forester Information System.
To generate trained manpower in Bioinformatics, National Workshops with participation
of University level teaching faculty/ Scientists are regularly organized by the Centre.
33
Educational activities: To generate trained manpower in Bioinformatics,
National Workshops with participation of University level teaching faculty /
Scientists are regularly organized by the Centre.
Placement: -Not applicable-
The information on various hardware and the related equipments, software,
databases; both acquired and developed that are available with this
Bioinformatics Centre is available on the web site of this institution and these
facilities are open to access by academic and para academic organizations. If the
need be, the databases developed by the centre will be made available to the
DBT for further suitable action.
Collaborative work with local/nearby institutions as Krishi Vigyan Kendra,
Banasthali University, Central Sheep Wool Research Institute, Avikanagar,
Durgapura (Jaipur) Agriculture Research Center and others is being carried
out.
As in S.No. 2
S.
No
Name of Database Broad Subject
Area
Broad
Functional Area
Developed/
Acquired
Completion
Status
1. Biotechnological
Industries of
Rajasthan
Bioinformatics
/Biotechnology
Biotechnology Developed Completed
2. SSR Database of
Citrus sinensis
Bioinformatics Bioinformatics Developed Completed
3. Database for Simple
Sequence Repeats
of Takifugu rubripus
4. Database of
Diterpene Synthase
Gene
5. Database of Flora of
Indian Desert
Bioinformatics/
Plant Science
Biodiversity Developed In Progress
6. Database of Plant
Host-Pathogen
Interaction
Bioinformatics/
Plant Science
Biodiversity Developed In Progress

Research Papers published in peer reviewed journals by using
Bioinformatics Support
Ten Important Research Publications in 2006 & 2007
1. Anamika, Saxena J. and Sharma V. (2007). J. Pure & Applied
Microbiology 1: 269-280.
2. Joshi G.K. and Sharma V. (2007). Research Journal of Biotechnology, 2:
50 - 56.
3. Joshi, G. K., Kumar, S. and Sharma V. (2007). Brazilian J. Microbiology,
38: 773-779.
4. Tripathi, A., Sharma, N. and Sharma, V. (2007). Biochemical and Cellular
Archives (accepted, In Press)
5. Joshi G.K., Kumar S., Tripathi B.N. and Sharma V. (2006). Current
Microbiology (Springer) 52: 354-358.
34
6. Tripathi B.N., Mehta S.K., Anshu Amar and Gaur J.P. (2006).
Chemosphere 62: 538-544.
7. Shanker A., Bhargava A., Bajpai R., Singh S., Srivastava S. and Sharma
V. (2007). Sci. Horti. 113: 353-361.
8. Shanker A., Singh A. and Sharma V. (2007). Microbiological Research
162: 250-256.
9. Grover A. and Sharma P.C. (2007). In Silico Biol. 7: 0021.
10. Grover A., Aishwarya V., and Sharma P.C. (2007). Mol Gen Genomics
277:469-480.
Book Published:
Tripathi B. N., Shekhawat G. S. and Sharma V. (2007). Applications in
Biotechnology. Avishkar Publisher, Jaipur.
Sharma V., Munjal A. and Shanker A. (2007). Textbook of
Bioinformatics. Rastogi Publications, Meerut (in press).

13. Initiation of R&D activities in Bioinformatics
Bioinformatics related problems are regularly given to M.Sc. Biotechnology
and M.Sc. Bioinformatics students for their project work.
The facilities of the Centre are regularly used for various R & D activities in
Biotechnology carried in the Dept. of Bioscience & Biotechnology at this
University.
Workshops are regularly organized by the Centre to generate trained manpower in
Bioinformatics.
A three days workshop on Biological Databases and Data Mining was
organized by the Centre for Bioinformatics, Dept. of Bioscience & Biotechnology
from 22
nd
Dec. to 24
th
Dec., 2007 with 66 participants.
areas.
Number of publications is very high in Biotechnology and Bioinformatics as
seen in column 12 (Appendix A).
Intensive use of the Centre by PG, PhD. Students and faculty.
Workshops are regularly organized by the Centre to generate trained
manpower in Bioinformatics. Several databases have been developed/are
being developed by the centre.
More than 200 teachers/scientists from Colleges, Universities and scientific
institutions have been trained.

To cater to the regional and national needs, the work on the developing
specific databases being currently developed by the Center will continue.
The R & D activities will be strengthened in Bioinformatics.
The PG courses in Bioinformatics will be focalized towards offering
specializations in future.

Additional Details:

35
Name of the Coordinator: Dr. Vinay Sharma
Postal Address: Dr. Vinay Sharma
Prof. & Head
Department of Bioscience & Biotechnology
Banasthali University
P.O. Banasthali Vidyapith 304 022
(Rajasthan)
Phone Number: 01438-228302 (O)
01438-228533 (R)
Email: ban_bioinfo@yahoo.com
vinaysharma30@yahoo.co.uk
Website: www.banasthali.org
Name of Contact Person(s): Dr. Vinay Sharma
Email: ban_bioinfo@yahoo.com
vinaysharma30@yahoo.co.uk.

36
Barkatullah University, Bhopal
Coordinator: Dr. Anil Prakash

1. Summary of the progress made by the centre from its inception:
10 days Training was organized IN THE Department of Biotechnology and
Bioinformatics Center during 9
th
Jan to 18
th
Jan 2008, which was sponsored by the
Madhya Pradesh Council of Science and Technology. 21 participants were enrolled
for this hand on training program. Total 4152 genes of Bacillus licheniformis are
analyzed. 4 students will join the Center for dissertation to work further on the other
species of Bacilli. Center has written one article title as Bioinformatics and
Personalized medicine for the Industrial & Academic meet going to be held at
BMHRC, Bhopal and one poster will be presented on the work done on Bacillus
licheniformis. Fish diversity database is in progress and initiative has been taken to
develop the database of Medicinal plant diversity database of Madhya Pradesh.
institution
i. Selection of Bio-inoculants for the growth promotion of J. curcus (MNES
projects)
ii. Inventorisation of Medicinal and Aromatic plant resources of selected areas of
Madhya Pradesh
iii. Secondary metabolites of Fluorescent Pseudomonads and other Rhizobacteria (Indo-
German project)
iv. Rhizobacterial inoculants for low input Wheet based cropping system. (Indo-
Swiss Project)
v. PGPR operative ISR in Soyabean (Glycine max)

i. Sequence analysis and Annotations of Fungi and Bacterial Genome
ii. Database creation: Fish biodiversity of Madhya Pradesh
iii. Medicinal Plant diversity database of Madhya Pradesh
i. Total 10 research publications and 3 oral presentations, during the 2007-
08 in the field of Biotechnology
ii. One Article and one poster presentation in Bioinformatics
iii. Three Bacilli species are analyzed for codon usage preferences.
iv. Organized 10 days Hands on Training in Bioinformatics, title as
Bioinformatics Tool and data analysis during 9 - 18 Jan 2008.
2 Servers (DNA- Windows Server 2003 & RNA Linux Fedora Core 4) of
Intel Xeon Processor 400 GB, 4 GB SDRAM
1 Server (Cell Fedora Core 4): Intel P-III, 40 GB, 512 RAM by Wipro
Infotech Pvt. Ltd.
26 Clients Desktop: - 8 from Bioinformatics grant: Compaq P IV, 40 GB and
256 DDRAM and 18 from Biotechnology grant: Wipro, P-IV, 20 GB, 128 RAM
37
2 Client Workstation for Hyperchem and ExomED of 40 GB HDD, 512 MB
DDRAM
Printer: 5 in No. (HP Laser Color 1, Laser HP 1200 series 2, Dot-matrix
Wipro 2)
Scanner: 3 No.
External CD Writer: 1, Laptop: IBM ThinkPad (P IV, 20 GB), OHP (Over Head
Projector): 1, LCD projector (In progress): 1
Networking Equipments Internet Facility: Router Cisco 1751 series with
Interface cards, Switches: 1 manageable 24 port, 2 non-manageable- 16 port,
Modem: 4 external (3 56 kbps Dialup, 1 128 kbps ISDN), 8 internal (56
kbps Dial up),.
Internet Connection:
a. 512 KBPS Leased Line Internet connection
b. 64 kbps ISDN line separate for Web site updatation
Uninterrupted Power Supply: UPS: 5 in no. (1 KVA 2, 3 KVA 1, 5 KVA
2),
Scientific Software packages
Licensed Bioinformatics Software: Hyperchem Release 7.5 (1 user) and ExomED
research (1 user)
Free Software OS and Packages: Linux Fedora Core 4, MySQL Windows and
Linux based
Licensed Software OS and Packages: Windows server Standard 2003 (2 User) with
CAL, Visual studio .NET (1 User), MS-Office 2003 (12 User), Adobe Creative Suite
Premium (1 user), Macromedia Dreamweaver MX 2004 Education (1 user), SQL
Server 2000(1 server & 5 client)
Databases & other information resources
Developed Database:
1. FISH Biodiversity database of Madhya Pradesh developed in collaboration
with Limnology department of Barkatullah University
2. Library Book Database using E-Grantahalay
Acquired Database: PDB Protein Structure database and EMBL
Nucleotide Sequence database in CD form
absorption status)
Name Designation Specialization Period of
Working
Absorption
Status
Mr. Kishor K.
Shende
Information
Officer
Bioinformatics &
Biotechnology
4 years Not
Absorbed
Mr. Durgesh Technical
Assistant
Bioinformatics & Botany 2 years Not
Absorbed
Mrs. Archana
Nema
Computer
Professional
Windows OS and DBMS
(MS Access, SQL server
2000 and MySQL),
2 years 6
months
Not
Absorbed
Mr. Chandan
Bisht
Data Entry
Operator
Data entry and Official
Work
4 years &
1 month
Not
Absorbed

Phylogenetic analysis using Bioinformatics Tools as PHYLIP
38
Training in Bioinformatics to students, research scholars and staff related
with various field of bioinformatics like Sequence analysis, Structural
analysis, molecular modeling, Database creation and front end designing
and software development.
Providing the Internet and Library facility to the students, research
scholars and staff of Life science department of Barkatullah University
Organizing a workshop in Bioinformatics
Solving the Hardware & Software related problems of the staff and
research scholars of Life Science departments Barkatullah University

M.Sc. in Biotechnology: 2 year master degree course in Biotechnology divided in
4 semesters
Ph.D. in Biotechnology
Placements: Last year students are placed Government and Private
Organizations
Government Organization: Students are working as Lecturer, Research
associates, project assistant or research fellow some of the following institutes
1. High Secure Animal Disease Laboratory, Bhopal
2. Jawaharlal Nehru University, New Delhi
3. Central Drug Research Institute, Lucknow
4. The Energy Resource Institute, New Delhi
5. Carrier college, Bhopal
Most of the Students are doing their 6 months project from Government
organizations
1. National Institute of Immunology
2. Institute of Genomics and Integrative Biology, New delhi
3. National Environmental Engineering and Research Institute, Nagpur
4. IIT, New Delhi
9. Initiative to validate the outcome of bioinformatics resources: Nil
Biotechnology:
1. Project through Indo-Swiss Collaboration in Biotechnology
2. Collaborative work CIMAP, Lucknow for the project on Medicinal Plants
of Madhya Pradesh
Bioinformatics:
1. Organizing the training in Bioinformatics in collaboration with the
MPCST.
2. Department of Limnology, Barkatullah University, Bhopal for FISH
Biodiversity database of Madhya Pradesh
Database:
i. FISH Biodiversity database of Madhya Pradesh
ii. Medicinal Plant Databases
Biotechnology:
39
1). D. K. Chaudhary and B. N. Johri, Anil Prakash; 2008; Volatiles as priming
agents that induce plant growth and defense response; Current Science
(Accepted)
2). D. K. Chaudhary, Anil Prakash and B. N. Johri; 2007; Induced systemic
resistance (ISR) in plants: Mechanism of action; Indian Journal of Microbiology,
Vol 47, 289-297
3). B. N. Johri, D. K. Chaudhuri and S. Chaudhuri; 2007, Dr. U.
Ashwathanarayana (Ed); How to use soil microorganisms to optimize soil
productivity; Chapter in Book: Food and Water Security, page 51-62; Publication:
Taylor & Francis, Netherland
4). Alok Sharma, A. Pathak, M. Sahgal, J. M. Meyer, V. Wrey and B. N. Johri;
2007; Molecular characterization of plant growth promoting rhizobacteria that
enhance peroxidase and pheny-alanine ammonia lyase activity in chilly
(Capsicum annum L.) and tomato ( Lycopersicon esculantum L.); Archive
Microbiology Vol 188 : 887-894
5). Sharma, V. Wrey, and B. N. Johri; 2007; Rhizosphere Pseudomonas sp.
Strain reduce occurrence of pre- and post emergence damping off in chilly and
tomato in Central Himalayan Region; Archive Microbiology, Vol 187 : 321-335
6). P. K. Sharma, M. Kukreja, K. K. Sahu and Ragini Gothalwal; Texo-ethano-
botanical value of some plants from Chattisgarh; Advances in Biological
Sciences, Volume: 6 (102), page 37-38
7). Chakroborty, S. S. Nadi and Ragini Gothalwal; 2007; Periplasmic high level
expression and single step purification of fusion MBP- Human ranulocyte colony
stimulating factor protein in E. coli; Applied Microbiology and Biotechnology (on
line version no ID AMB-07-14996.RI)
8). Sweta Sao, Ragini Gothalwal, L. K. Thetwar and N. D. Deshmukh; 2007;
Effect of flyash and plant harmones treated soil on the increased protein and
amino acid content in the seed of ground nut.; Asian Journal of Chemistry, Vol
19: 1017-1022
9). P. K. Sharma and Ragini Gothalwal; 2007; Supplimentation: Enhances the
growth and biological efficiency of Pleurotus sajor-caju grown in different
Lignocellulosic wastes; Advances in Biological Sciences, Vol 6: 19-23
10). P. K. Sharma and Ragini Gothalwal; 2007; Comparative study of grains on
spawn development of two Pleurotus sp. Journal of Basic and Applied Mycology

Oral Presentation in Bhartiya Vigyan Sammelam 2007 held in Bhopal on 23- 25
Nov, 07
1. Atul V.Singh, Pavan K. Agarwal, Anil Prakash and B. N. Johri; 2007; Influence
of Rhizobacteria and Arbuscular Mycorrhizal Fungi (AMF) on the soil and crop
in Wheat- Legume Cropping System.
2. Rubina Begum and Anil Prakash; 2007; Diversity of endophytic fungi in Stevia
rebaudiana Bartoni leaves
3. Puja Uppal and Anil Prakash; 2007; Effect of Bioinoculants on growth
promotion of Jatropa caucas

Bioinformatics
1. Kishor Shende and Anil Prakash; Article, Bioinformatics and Personalized
Medicine presentation in MEDBIO-2008 & 3
rd
Industry-Academia Meet,
organized by BMHRC, Bhopal during 14
th
16
th
Feb 2008
40
2. Kishor Shende, Leena Agrawal, Priyanka Johri, Durgesh Gupta, Ragini
Gothalwal and Anil Prakash; Poster presentation Compositional bias in
codon usage preferences among the 4152 genes of Bacillus licheniformis
ATCC 14580 in National Symposium organized by School of Biotechnology,
GGU, Bilaspur (Date 28-29 Jan 2008).

1. Genome analysis of Bacterial Genome is in progress
2. Creation of Databases using the data made available by various Life
Science departments

Workshop Title of the Workshop Date No.
Participants
Workshop
1
Bioinformatics tools and
data analysis
9 18 Jan
2008
20
Workshop
2
Structural Bioinformatics 12-14 Feb
2008
20
Workshop
3
Proteomics and Drug
designing
10-12 Mar
2008
20

1. The Ph.D. students of Barkatullah University are using the Bioinformatics
Center Library and the Internet connection and help for reference searching.
Students are also using the Bioinformatics Center to learn the applications of
Bioinformatics tools in basic research work in Life science and finding the
study materials: 50 users per day
2. Bioinformatics awareness spread through the Departmental website and by
organizing workshop and Training in Bioinformatics
1. Web Sever development and Web site hosting at Departmental server.
2. Organizing the 15 days Training on Phylogenetic analysis using the
various techniques in Wet Lab and Dry lab.
3. Two workshops will be organized in Bioinformatics
4. Development of FISH Biodiversity Database of Madhya Pradesh and
making available online.
5. Task oriented six month training in Bioinformatics for students from other
institute
6. Further analysis of Bacilli gene for the codon usage frequency and its
role in gene regulations

Additional Details:
41
Name of the Coordinator: Dr. Anil Prakash
Postal Address: Department of Biotechnology & Bioinformatics Center,
Barkatullah University, Bhopal
Phone Number: 755-2677748-102
Mobile: Email: bicbubhopal@hotmail.com
Website: http://bioinfobubpl.nic.in
Name of Contact Person(s): Dr. Anil Prakash
Email: bicbubhopal@hotmail.comv
42
Bharathidasan University, Tiruchirappalli
Coordinator : Dr. L. Uma

The Centre was launched in April 2001 as a special purpose centre meant for
cyanobacteriology. The centre is equipped with Servers, an SGI Fuel
Workstation, Desktops, LCD Projector, scanner, printers and photocopier with
a small library. The centre has a round-the-clock 512 kbps leased line
internet connectivity. A dozen ASM online journals, and the magazine
PCQuest have been subscribed. Training workshops (Workshop On
Bioinformatics for Cyanobacteriologists - WOBIC) on the basics of
bioinformatics are being conducted every year during the month of February /
March. A database on cyanobacteriology has been developed. News letter
on cyanobacteriology with information about scientific meetings, research
positions available is posted in the National Facility for Marine Cyanobacteria
(NFMC) and University websites and the activities of the NFMC, is maintained
online. The literature collection of more than three thousand reprints on
cyanobacteriology available in NFMC has been digitized. The Centre assists
the Facility and the Department of National Facility for Marine Cyanobacteria
(DBT, Sponsored Facility) to all faculty and scholars by providing
infrastructural facilities like internet, email, printing and also conducts
bioinformatics theory and lab courses for M.Sc. programme. The
Bioinformatics Centre at this institute, supported by DBT, has created
awareness in cyanobacteria, the primordial organism. The Centre focuses on
database generation, data mining and its application in wet lab research.
institution
Our Bioinformatics Centre research activities aids as a platform for our wet
lab analysis. Our study is focused on superoxide dismutase, cytochrome
P450 & CN splitting enzyme, toxin genes and sequencing of plasmid from
Indian isolates.
Our Centre is assisting the NFMC in the biotechnological exploitation of
marine cyanobacteria through genome wide hunt for its biotechnological
potential in the areas of food, feed, fertilizer, fuel, fine chemicals, colorant,
pharmaceuticals and waste treatment.
3. Area of specialization of the centre
Cyanobacteriology
The leased line internet facility has been upgraded to 512 kbps, and a pair of
2 mbps capable modems has been added to the centre.
As part of human resource development, Workshop On Bioinformatics for
Cyanobacteriologists and Workshop on Research Techniques in
Cyanobacteria (WOBIC is conducted every year and this year between March
3
rd
to 7
th
2008).
The participants are made familiar with wet and dry hands on experiments.
Bioinformatics exercise includes database search, analysis at nucleic acid
and protein level and phylogeny analysis.
Research in Cyanobacterial bioinformatics:
43
_ The Bioinformatics centre has paved way for multidisciplinary approach
resulting in one of the esteemed chemistry journals Journal of Chemical
Society along with Dept. of Chemistry, Bharathidasan University.
_ DATA MINING
At present our research areas include
Superoxide dismutases - the first line of defense antioxidant against
oxidative damage.
Cytochrome P450 known to play a role in xenobiotic degradation
CN splitting enzymes nitrilase, rhodanase and cyanate lyase
involved in nitrile and cyanide degradation.
PCD genes unique with much similarity to eukaryotic caspases.
Toxin gene as marker for cyanobacterial identification
Comparison of plasmid genes
Initiation of RNAi work.
_ GENOMICS
Cyanobacteria exhibit tremendous biotechnological potentials but one
of the major hurdles in exploiting them for industrial application is the non-
availability of multi-host expression systems. Vectors developed with
Escherichia coli or other bacterial replicons are not functional in the
cyanobacteria. As a preliminary step, the Centre has partially sequenced a
marine cyanobacterial plasmid pbdu02 from Phormidium sp. of from our
germplasm is submitted in NCBI (Genome Accession No: AAZV00000000). The
genes identified are: hypothetical protein, P-loop linked to ATPase
acetyltransferase, Aldo/keto reductase, hypothetical protein, NifZ, Pseudouridine
synthase, Peptide deformylase, Pyrimidine regulatory protein, ATP-dependent
Clp protease adaptor protein, 2-tRNA, and 1-rRNA. This sequence analysis of
cyanobacterial plasmid has given an insight into their functional organization, and
facilitates its possible use as cloning vectors.
Our online database, Blue Green Database (BGBASE) is being
updated constantly and is being accessed by cyanobacteriologists around the
world. This searchable database contains information regarding literature,
germplasm and scientists working on cyanobacteriology. An online newsletter,
BGNEWS serves as a portal for cyanobacteriologists in providing information
regarding the updates of our site, scientific meetings, conferences, workshops
etc., conducted on cyanobacteriology, and research positions available in
cyanobacteriology. The Centre is helping Marine Biotechnology students in
conducting courses in Bioinformatics paper at the Post Graduate level. The
students and scholars are given the facilities like email, internet on all 365 days.
Online journals subscribed - 12 (American Society for Microbiology)
Reprints on cyanobacteria - 3100
Website usage - @ 800 day-
1
Alpha Servers - 2
Xeon Server - 1
SGI FUEL Workstation - 1
Pentium IV Computers - 16
44
Scanner - 1
Printers - 5 (4 + 1 Large format printer)
7.5 KVA UPS - 1
LCD Projector - 1
Photocopier - 1
Router - 1
Leased Line Modems - One Pair
Further, 512 kbps Leased-line internet connection is available round the clock.
B. Scientific software packages
1) CHROMOSOB : For identification of secondary metabolities
Blue Green Database - BGBASE, a database on Cyanobacteriology has
been developed at the centre and is available online at www.nfmc.res.in. The database is
constantly being updated.
A library with about 250 books on bioinformatics and computer science is
available for the researchers. Twelve online journals of the American Society for
Microbiology, and the magazine PC-Quest are also available in the library.
6. Details about staff members working in the centre
Name and
Designation
Specialization Period of
working
Whether
Absorbed
Mr. K. Ganesan
Information Officer
Cyanobacteriology
and Bioinformatics
Till June
2007
No
Mrs. R. Renganayagi
Technical Assistant
Computer
Application
3.3 yrs. No
Mr. B. Venkatesh Moorthy
Data Entry Operator
Computer
Application
Till June
2007.
No
Internet access and Email facilities are provided round the clock to the
needy. The facilities are also extended to other departments and colleges
whenever required. Copies of the reprints available at the centre are made
available to these researchers.
8. Educational activities & details of placement
Human Resource Development Cyanobacterial Bioinformatics
9. Initiative to validate outcome of bioinformatics resources - Our
center is focusing on Cyanobacterial Bioinformatics and shares its knowledge
with faculties, researchers and students.
10. Collaborative works / initiatives
Initiated research on genome wide hunt on cyanobacteriology.
11. Databases / software packages developed
An internationally accessible online database Blue Green Database BGBASE
(www.nfmc.res.in/bgbase/) has been developed at the Centre. The database is searchable
45
and consists information on culture collections, cyanobacteriologists, literature /
publications in the field of cyanobacteriology.
12. Papers published / presented in conferences with reference
1. Saha K., Das R., Bora K.N., UMA. L. (2007) Biodiversity epilithic
Cyanobacteria from freshwater streams of Kakoijana reserve forest, Assam,
India. Indian Journal of Microbiology. 47: 219-232
2. Rajendiran V., Palaniandavar M., Swaminathan P., UMA L.. (2007) Cleavage
of proteins by a mixed ligand copper (II)-phenolate complex: Hydrophobocity
od diimine co-liand promotes cleavage. Inorganic Chemistry (communication).
3. Subramanian G., UMA L., Priya B., Prabaharan D (2007) Utilization of
microalgae to address pollution problems. Indian Hydrobiology 10(2): 1- 25
4. Balakrishnan Priya, Jagadeesan Premanandh, Raman T Dhanalakshmi,
Thangaraj Seethalakshmi, Lakshmanan Uma, Dharmar Prabaharan,
Gopalakrishnan Subramanian (2007) Comparative analysis of cyanobacterial
superoxide dismutases to discriminate canonical forms. BMC Genomics 8: 435
13. Initiation of R&D activities in bioinformatics
Completed - Short term bioinformatics projects on the topics 1) Caspases,
metal Transportors
On going: Superoxide dismutases, Cytochrome P
450
, Microcystin
The Workshop is conducted as a continuation of a wet lab workshop on
cyanobacteriology conducted by NFMC, enabling researchers to get trained in both in
vitro and in silico methods.
15. Impact shown by your centre on the growth of biotechnology and allied areas
a) Number of paper published/ presented.
Three presented at National conferences.
Two international publications.
b) Promoting various activities of your organization and neighboring
institutions
Infrastructure and expertise provided to the University for conducting the
Bioinformatics Theory and Practicals to Marine Biotechnology courses.
c) Manpower trained
14 researchers through workshops and 14 students are trained in the 2007 -
08.
d) Tools developed
Online database on cyanobacteriology available at www.nfmc.res.in
A database booklet for workshop.
e) Patents & copyrights acquired - Nil
f) Other services offered - Nil
Completion of whole plasmid sequencing
ADDITIONAL DETAILS :
46
Coordinator :
Dr. L. UMA
Bioinformatics Centre, NFMC
Bharathidasan University
Tiruchirappalli 620 024
Email: uma@nfmc.res.in
Phone/Fax. : 0431 2407084
Website : www.nfmc.res.in
47
Biotech Consortium India Limited, New Delhi
Coordinator : Dr. Purnima Sharma

Since its inception in 1992, the Distributed Information Sub Centre (DISC)
at Biotech Consortium India Limited (BCIL) has taken up various activities
to facilitate commercialisation of biotechnology. It has brought out a
number of publications and periodicals, databases and status reports and
has organized several seminars/workshops, events, entrepreneurs meets
etc. for promotion of commercial biotechnology. Current activities include
compilation of databases and directories, preparation of industry specific
status reports on different aspect of biotechnology and organizing national
and international workshops, seminars, conferences and entrepreneurs
meets to create awareness on issues relevant to commercialization of
biotechnology.

The DISC also runs a Biotechnology Club. The biotech club membership
is being offered on annual and life memberships basis to individuals,
institutions and corporate bodies interested in biotechnology. Members
receive BCILs publications and, participate in events organized by BCIL,
either free of cost or at a discount.

2. Major research activities in biotechnology and its related fields in your
institution:
BCILs main objective is to provide linkages to facilitate commercialization of
biotechnology. BCIL has been engaged in technology transfer, consultancy, fund
syndication, information dissemination, and manpower training related to
biotechnology. In these areas, it has assisted over 200 clients including scientists,
technologists, research institutions, universities, first generation entrepreneurs, the
corporate sector, government, banks and financial institutions.

3. Area of specialization of the centre:
Technology assessment, valuation and transfer, preparation of commercial
databases, biotechnology project specific updates, publication of journals and
organization of national and international workshops, seminars, and training
programmes.

Focussing on commercial biotechnology, in the year under review, DISC
continued to bring out publications and organize events primarily of relevance to
industry. The major projects completed were:

I. Directory of Biotechnology industries and institutions in India-5
th

Edition
The 5th edition of the Directory of Biotechnology Industries and
Institutions in India covering profiles of more than 1000 industries
and institutions has been compiled during the year. The directory is
being received very well by industry, institutions and academia. The
directory was circulated to all the bioinformatics centres (DICs and
DISCs) on complementary basis.
48

II. Maintenance of following websites :
The following websites containing value added information on R&D
and commercialization of GMOs were developed during the
previous year and are being continuously updated by DISC:

a) Indian Biosafety Clearing House (BCH) website
(http://indbch.nic.in) as part of Indias commitment to the
Cartagena Protocol on Biosafety
b) Updation & Maintenance of DBT Biosafety websiteThe website
(http://dbtbiosafety.nic.in) has a public domain for guidelines,
acts and rules on GMOS as well as a confidential domain in
providing online tracking of regulatory clearance of applications
to RCGM and e-monitoring of 328 IBSCs on personalized web
features.
c) Web-based database on Indian GMO Research Information
System (IGMORIS) (http://igmoris.nic.in)
d) GEF- World Bank Website for MoEF
(http://www.envfor.nic.in/divisions/csurv/biosafety/default.htm)
e) BCIL website (parent organization)
www.bcil.nic.in
f) Website for National Certification Systems for Tissue Culture
Raised Plants (NCS-TCP) was developed and maintained by
DISC (http://dbtncstcp.nic.in/)

III. Conferences, workshops, seminar-cum-training
programmes :
DISC has played an important role by providing both manpower
and information support to BCIL in organizing several national and
international events. The events where DISC has assisted BCIL
range from entrepreneurs development programmes in
biotechnology, workshop on commercilisation of biotechnology,
workshop on management of IPR in biotechnology, workshop on
biosafety issues and investors meet on current topics of interest.
Some of the important events organized during the year are
highlighted as under:

a) Workshop on Management of Intellectual Property Rights in
Biotechnology : DISC at BCIL under the sponsorship from the
Department of Biotechnology (DBT) had organized 3 workshops
on Management of IPR in Biotechnology at Chennai, Lucknow
and Hyderabad. Around 350 participants from academia and
research institutions attended these programmes.

b) Entrepreneurship Development Programme (EDP) in
Biotechnology: Entrepreneurship Development Programmes
(EDP) in Biotechnology sponsored by Department of
Biotechnology (DBT), Ministry of Science and Technology,
Government of India and the Office of the Development
Commissioner, Ministry of Micro, Small and Medium Enterprises
(MSME) were organized at Kolkata, Pune, Shimla, Indore,
49
Chennai and Agartala. The objective of these programmes was
to train the prospective entrepreneurs on different aspects of
business management in biotechnology and to encourage them
to set up commercially viable biotech ventures in small and
medium scale sector. Around 300 participants attended these
events.

c) Workshop on Commercialisation of Biotechnology: As part of
the DISC activity, a workshop on Commercialisation of
Biotechnology was organized during the year with a focus on
business opportunities, issues in biotechnology
commercialization such as technology evaluation, valuation and
financing, regulatory requirements and issues related to
patenting of biotechnology products.

IV. Biotechnology club
The Biotechnology Club managed by DISC at BCIL has more than
200 members including life members, annual members and VATIS
Update subscribers. Many leading biotech companies are
members of the club. The members of the club receive host of
privileges such as complimentary copies of BCIL publications,
discount on reference directories published by BCIL, participation in
events organized by BCIL either free of cost or at discounted fees,
copies of proceedings of various workshops and seminars
organized by BCIL.

V. Publication
The following periodicals and journals are being published by DISC:

a) Vatis Update: Biotechnology
The Value Added Technology Information Services (VATIS)
Update, Biotechnology a bimonthly publication in association
with Asian and Pacific Centre for Transfer of Technology
(APCTT) was continued during the year.
b) Biotech Bulletin
The in-house bimonthly publication from DISC, Biotech
Bulletin, consisting of compilation of interesting news clippings
on biotechnology from newspapers, magazines and journals for
apprising industry on current national/international
developments in the area of biotechnology was also continued.
c) Biosafety Newsletter (Quarterly)
The quarterly newsletter introduced in association with Ministry
of Environment and Forests, Govt. of India to update on various
developments and issues in the area of biosafety, was
circulated to the Biotech Club Members of BCIL.


(i) Computer & Communication facility:
The Centre has two servers, an IBM LAN server and Linux based
proxy server. A 512 kbps Internet Lease Line (ILL) (wireless radio
50
link) has been installed at the centre from SIFY. Besides, the
centre has Pentium 4 Laptops, Pentium 4 desktops, CISCO Router,
HP color laser printer, HP scanner and related peripherals required
for its functioning.

(ii) Scientific Software Packages: Nil

(iii) Databases and other information resources
In-house databases developed as detailed under 11.

6. Details about staff members working in the centre:

Name Designation Specialization Period
(years)
Dr. Vibha Ahuja Dy. General
Manager
Ph.D in industrial
Biotechnology

14
(Absorbed in
BCIL)
Dr. Jeevan
Kumar
Manager Ph.D. in Agri
Biotechnology
2
(Absorbed in
BCIL)
Anita Sharma Deputy
Manager
Management of Sub-DIC
activities
13
(Absorbed in
BCIL)
Dr. Vivek Dixit Sr. Project
Executive
(Information
Officer)
Ph.D. in Plant
Biochemistry
6 months
Contractual
Vinod Kumar Assistant
Manager
Management of BCIL
Biotech Club & VATIS
Update
6
Absorbed
(in BCIL)
Arvind Kumar System
Administrator
Database Development,
Website Maintenance
2
Contractual
Deepanshu
Sharma
Computer
Operator
Data processing, Data
entry
2
Contractual
Mr. Mukesh
Raja
Project
Executive
Information collection and
compilation
2 months
Contractual

51
7. Types of Services provided
DISC provided information to scientists, academia and industry through its
website and various journals/publications on biotechnology. The
publications include:
a) Vatis Update: Biotechnology
b) Biotech Bulletin
c) Biosafety Newsletter (Quarterly)
d) Organization of Workshops
In addition, the DISC continued to support the activities of BCIL by
providing information support for preparation of various reports and
publications.

8. Educational activities with details of placement : NA

9. Initiative to validate the outcome of bioinformatics resources: NA

10. Collaborative works/initiatives
DISC at BCIL worked in close collaboration with Ministry of Environment
and Forests (MoEF), Department of Biotechnology (DBT), Ministry of Agriculture
and The Development Commissioner, Ministry of Micro, Small and Medium
Enterprises, Government of India, for organizing various workshops on
biotechnology issues, status studies, market surveys during the year.

11. Databases/Software packages developed
The following databases were prepared to support ongoing activities of
BCIL.
(a) Database of IBSC members and DBT nominees
(b) Directory of Biotechnology Industries and Institutions in India
(5
th
Edition)
(c) Online database (web-enabled) for accepting application from
PG students across the country applying under Biotechnology
Industrial Training Programme (BITP) of DBT for 6 months
industrial training.
(d) Online database for accepting feedback forms from students
placed for training in industry and also from trainer industry. This
database is capable for accessing individual information of the
trainee student and trainers industry.

12. Papers published or presented in the conferences with reference: In
almost all the workshops, conferences and training programmes, BCIL officers
have been presenting papers on various issues related to biotech
commercialization such as status of biotech industry in India, IPR issues in
biotechnology, regulatory requirements, biosafety issues, business opportunities
in biotechnology.

13. Initiation on R&D activities in Bioinformatics: NA

14. Details of Training / Workshop organized and total no. of user trained
DISC at BCIL has organized the following workshops during the year.

S. Workshops/seminars organized Participants
52
No.
1. Workshop on Management of Intellectual Property
Rights in Biotechnology
350
2. Entrepreneurship Development Programme (EDP) in
Biotechnology
300
3. Workshop on Commercialisation of Biotechnology 100
Total 750

15. Impact shown by your centre on the growth of biotechnology
The DISC at BCIL is promoting activities related to commercial
biotechnology by organizing workshops in key issues related to
commercialization of biotechnology, assisting (providing database support) in
identifying suitable licensees for transfer of technologies and bringing out
publications in biotechnology.

1) During the year more than 750 stake holders belonging to diverse
background i.e. scientists, industry, academicians and students
were trained on different aspects of commercial biotechnology.
2) A Plant extract based biopesticide formulation Bollcure effective
against cotton bollworm Helicoverpa armigera was transferred to a
leading company
3) The Directory of Biotechnology Industries and Institutions in India-
5
th
Edition covering more than 1000 records was updated and
released.
4) Provide support service to the parent organization in placing more
than 400 post graduate students in biotechnology for 6 months
industrial training in leading biotech companies under BITP of DBT.

The DISC at BCIL proposes to take up the following activities:
i. Creation of Databases which can further promote and facilitate
networking between the academia and the industry e.g. list of
resource persons in biotechnology, sector specific databases etc.
ii. Organizing workshops on Commercialisation of Biotechnology
iii. Updation of technology profiles
iv. Establishment and maintenance of websites
v. Organizing technically intensive training programmes in the
following areas such as technology transfer and licensing,
management of ntellectual Property Rights, Biosafety issues,
Enhancing skills of biotech industry
vi. Providing value added services to the members of Biotechnology
Club of DISC at BCIL

Additional Details
Name of the Coordinator : Dr. Purnima Sharma
Executive Director & CEO
Postal Address : Biotech Consortium India Limited
5
th
Floor, Anuvrat Bhawan
210, Deen Dayal Upadhyaya Marg
New Delhi 110 002
53
Phone No. : 011-2321 9064/65/66/67
Fax No. : 011-2321 9063
Email : bcildelhi@vsnl.com
Website : www.bcil.nic.in

Name of the contact person : Dr. Jeevan Kumar, Manager, BCIL
bcildelhi@vsnl.com
54
Biotech Park, Lucknow
Coordinator: Dr. P. K. Seth

1. Summary of the progress made by the centre from its inception :-
The Bioinformatics Centre, Biotech City was set up in November 2001 at
Industrial Toxicology Research Centre (ITRC), Lucknow as networking site.
Subsequently it has started functioning since August 25
th
, 2003 from the site
office of the Biotech Park at Sector-G, Jankipuram, Kursi Road, Lucknow
from June 2006 from its Biobusiness Centre. The Major Objective of the
Bioinformatics Centre is to showcase the R & D and academic strength of the
Lucknow in the area of Biotechnology and serve as nodal point for industry-
academia-U.P. Government interactions.
The Centre is extensively involved in popularizing the application of
Bioinformatics in R & D by providing training to the scientists Research
Scholars and students. It has established a close network with the
neighboring Academic and R&D institutions to provide information to
industries, entrepreneurs and farmers regarding technologies, facilities and
expertise available with them in the area of Biotechnology. The centre has 1
Mbps. Radio link internet connectivity through Software Technology Park of
India (STPI), Lucknow. It proves to be a valuable resource in providing upto
date information about expertise and facilities available in various local
institutions for entrepreneurs through its website.

2. Major research activities in Biotechnology and its related field at your
institution:- The Biotech Park offers common integration facilities for
knowledge based bio-business and state of the art infrastructure facilities in
the area of industrial biotechnology. The thrust areas are Health Care:
Human and animal health care products including therapeutic aids,
immunodiagnostics, and vaccines etc Agriculture: Micro propagation (Tissue
Culture), biofertilizers and biopesticides, vermicompost, floriculture crops,
Energy: Biofuel from Jatropha curcas, renewable energy resources. The
Park has GLP/GMP compliant facilities for the startup companies in the area
of industrial biotechnology which includes common instrumentation facilities,
tissue culture facilities, diagnostic and drug delivery facilities, upscaling/
processing of plant based lead molecules, pilot plant for
biofertilizers/biopesticides, hardening and macro propagation facilities.

3. Area of Specialization of the BTISnet centre:-
Development of Interactive websites, Databases and Softwares.

4. Major activities of the centre during the year 2007-08:-
The centre has organized four DBT sponsored training programme/workshop
and the total number of candidates participated are 85. These
workshop/training programme were design to expose scientists, doctors,
research scholars, technical assistants and students working in teaching and
research institutions in the country with the operation of personal computers
and scientific software that are being routinely used in the modern biological
research.
In addition to the training programmes, the training on Database/Software
Development, Phylogenetic Analysis, Primer Designing, Protein Modeling,
55
and Orthologous Clustering was provided to approximately 178 M.Sc.
Bioinformatics / Biotechnology /B.Tech /MCA /M.Tech students.
Research work concerned with Molecular Modeling, Protein Structure
Prediction and Analysis, Proteomics and Genomics such as modeling of
pExp53 membrane bound protein of mycobacterium tuberculosis,
Phylogenetic analysis of envelope Glycoprotein gp160 of HIV1 virus in Asian
Countries, structure prediction of mannose binding lectine protein of
Convovolus arvensis has been done.
The centre has established the video conferencing facility and the DBT
sponsored training workshop held on 10-11 December, 2007 was inaugurated
through video conferencing from CIMAP.
Infrastructure has been improved by the addition of 8 computer systems
having TFT monitors.
Creating and maintaining websites for the other companies placed inside the
park.

5. Infrastructure facilities in the Bioinformatics centre :-
A. Computer & Communication Facility :-
Bioinformatics centre has 1 Mbps radio link internet connectivity through
Software Technology Park of India, Lucknow.
Server Campaq Proliant ML 370 - 1 No.
HP Campaq Proliant ML 370 - 1 No.
Computers (HP Compaq d330ut) - 5 Nos.
HP Computer (IV D 820 dual core 2.8 Ghz) - 8 Nos.
Computers (IBM. T.C.) - 3 Nos.
Computers (Compaq Deskpro ENL) - 5 Nos.
Network Lazer Printer(HP 2200 DN) - 1 No.
HP Network Color Laser Printer (3700 DN) - 1 No.
HP psc 2210 all-in-one - 2 Nos.
HP Officejet 4255 all-in-one - 2 Nos.
HP Scanner - 1 No.
UPS (5 KVA) online - 1 Nos.
UPS (3 KVA & 2 KVA) online - 1 Each
UPS (1 KVA) online - 2 Nos.
External CD Writer (HP 9600E) - 1 No.
Internal CD Writer (LG) - 2 Nos.
Canon 1600 Photo Copier - 1 No.
HP Digital Camera - 1 No.
HP Compaq Laptop - 1 No.
Projector (Toshiba) - 1 No.
Tablet PC - 1 No.
Video Conferencing System. - 1 No.
SGI machine - 1 No.
Scientific Software packages - Macromedia Studio 8, Corel Draw x3,
Microsoft Windows Server 2003 R2 Standard x64 Edition, Microsoft SQL
Server 2005 Standard Edition, Microsoft Office Professional Plus 2007,
McAfee Managed Virus Scan plus Anti Spyware.
56
B. Databases & other information resources-
1. Bio-diesel Database.
2. Database on Biofertilizers/Biopesticides.
3. Database on hemophelia.
4. Database on Educational Institutes in UP.
5. Database on Antidibetic plants based on clinical/experimental trial.
6. Details of Staff members working in the centre:-
S. No Name of
Staff
Designation Specialization Period of
working
Absorption
Status
1. Mr. Sunil
Kumar
Gupta
System
Network
Administrator
Bioinformatics 19
th
June,
2007 to till
date
Non-Regular
2. Ms. Shipra
Gupta
Senior
Programmer
Bioinformatics 31
th
Jan,
2007 to till
date
Non-Regular
3. Ms. Sarita
Singh
Programmer Bioinformatics 19
th
June,
2007 to till
date
Non-Regular
4. Mr. Gulam
Sabir
Data Entry
Operator cum
Office Assistant
Diploma in
Computer
Application
18
th
Oct,
2006 to till
date
Non-Regular

7. Types of Services Provided: - Development of profile CD for Biotech Park,
Development of Video CD showcasing the facilities available with Biotech Park
and near by Research Labs, Educational Institutions, Development of application
softwares and databases, Network management, Website management, Data
retrieval and analysis, Email management, Development of human resources in
Bioinformatics, Radio link internet connectivity, Video conferencing facility and
Management of Web & Mail Server.

8. Educational activities with detail of placements: - Nil.

9. Initiative to validate the outcome of bioinformatics resources: - Nil.

10. Collaborative Works/Initiatives: - Jalaja Technologies Pvt. Ltd
demonstrated Genocluster software which contains different modules for genome
analysis and putative function of any predicted protein. Modalities for further
collaborations are being worked out.
11. Databases/Software packages developed:-
1. Database on Biofertilizers/Biopesticides.
2. Database for hemophelia.
3. Database on Bio-Diesel.
4. Database on Fruits in UP.
5. Database on Educational Institutes in UP.
6. Database on Shizidata surviving, schizophrenia A database on
Gene & Drug.
7. Database on Organic Farming.
8. Database on Pathways of Neurological disorder.
57
12. Paper published or presented in the conferences with references:-
Presented in Conferences :-
1. Somvanshi P, Mishra B N., Seth P K(2006). Dengue virus 2 Envelope
protein and its Phylogenetics Correlation by Bioinformatics Approach.
Proceeding of National Seminar on Recent Advances in Biotechnology &
Bioinformatics 24-25
th
July, Hyderabad, India.
2. Somvanshi P, Mishra B N, Seth P K(2006). Genome wide identification of
vaccine candidates in consensus sequence of antigenically distinct
variants of Dengue virus. Proceeding of GSM, Advanced Centre for
Treatment Research and Education in Cancer, Tata Memoria Centre 23
rd

September, Navi Mumbai, India.
3. Somvanshi P, Mishra B N, Seth P K(2006). Genome wide identification of
vaccine candidates in Antigenically Distinct Variants of Dengue Virus: A
Bioinformatics Approach Proceeding of international Symposium on
computational Biology & Bioinformatics ISBB,15-17
th
December,
Bhubaneswar, India.
4. Rathi B, Somvanshi P, Seth PK (2006). Prediction of the promoter region
in Unregulated genes of macrophagic stage in Mycobacterium
tuberculosis Proceeding of International conference on Bioinformatics
INCOB, 18-20
th
December, New Delhi, India.
5. Mehrotra M, Somvanshi P,Seth P K(2007). Development of Neuro
Toxicology biomarkers Database Proceeding of International Conference
on Biomarkers in Health and Environmental Management & XXXII Annual
Meet of Environmental Mutagen Society of India 10-12
th
January,
Coimbatore, India.
6. Somvanshi P, Rastogi O, Seth P K(2007). Phylogenetic Analysis of nif A
gene in Nitrogenous Bacteria Proceeding of national Conference on
Microbial Diversity: Avenues and Application 17-18
th
March, Dehradun,
India.
7. Somvanshi P, Seth P K(2007).Insilico analysis of antigenic diversity of T
cell epitopes in the prediction of Hepatitis virus polyprotein. Proceeding of
BIOCONVENE international Conference on Bioinformatics and Drug
Discovery: 16-22
th
December, Hyderabad, India.
8. Singh Sarita, Gupta Sunil Kr., Gupta Manish Kr., Dr. Seth P. K.(2007).
Phylogenetic analysis of envelope Glycoprotein gp160 of HIV1 virus in
Asian Countries. Presented in Proceeding of iCAB international
Conference on Applied Bioengineering: 5-7 December, Chennai, India.

13. Initiation of R&D activities in Bioinformatics:- Research and development
activities of the centre is focused in the area of Molecular Modeling, Protein
Structure Prediction and Analysis, Proteomics and Genomics such as modeling
of matrix protein of Chandipura virus, Mechanism of action of Anti diabetic herbs,
clinical and experimental trails of anti-diabetic herbs, Database on Medicinal and
Aromatic plants .

14. Detail of Training/Workshop organized and total number of user
trained:-
58
The centre has organized four DBT sponsored training programmes /workshops
and the total no. of candidates participated are 85.
S. No. Training
Programmes/Workshops
No. of
Participants
Duration
1.
Genomics: Databases &
Web Technologies
24 18
th
20
th
May,
2006
2.
Proteomics & Drug
Development
25 22
nd
24
th
August,
2006
3.
Tools & Languages for
Database Development
24 9
th
10
th
November,
2006
4.
Bioinformatics Tools & Their
Applications in Biological
Research
12 15
th
-17
th
February,
2007

The centre provided training to 178 students in the year 2006-07 and overall
persons trained by the centre are 263.

area:
The Biotech Centre has made a significant impact about the
Biotechnology as evident by increasing number of hits on website. It is also
attracting the Entrepreneurs through its website and it helped in development of
human resource through short and long term training programmes.

16. Future activities:-
To extend facility of SGI Work Station for Computational Biology and Drug
Development applications to researchers of different institutions.
To organize long-term Training Programmes in the field of Bioinformatics.
Process scheduling of Biotech Park facilities and activities.
Updating and modifying facilities and website of the centre.
Developing of databases on Anti-Diabetic Plants and Medicinal &
Aromatic Plants.

17. Additional details :-
Name of the Coordinator: Dr. P. K. Seth
Chief Excutive Officer
Postal Address: Biotech Park , Lucknow
Sector-G, Jankipuram, Kursi Road,
Lucknow-226021
Phone Number: +91-522-2365050,4012076/77,4012091.
Fax No: +91-522-4012081
Email: info@biotechpark.org.in
ceo.biotech@gmail.com
Website: www.biotechpark.org.in
59
Name of the contact person(s): Dr. P. K. Seth
Email: ceo.biotech@gmail.com
ceo@biotechpark.org.in

60
Birla Institute of Scientific Research, Jaipur
Coordinator : Dr P Ghosh

Birla Institute is a leading renowned center for Biotechnology research in
Rajasthan. The institute undertakes goal-oriented applied research in the
frontier areas of industrial biotechnology sponsored by government and
industries as well as in-house research. Recognizing the importance of IT for
pursuing advanced research in modern biology and biotechnology, DBT had
started a Bioinformatics program envisaged as a distributed database and
network organization. BISR has been identified as one such centre. This
Centre was established in 1999. This is one of the core facilities in the field of
Biotechnology providing access to the latest information of the world
databases. Internet/E-mail facility at this centre is extensively used by the
researchers of our institute and by other nearby academic institutes and
universities. Recently, BISR has initiated research in Proteomics and
Genomics area of Biotechnology. Besides, efforts are directed towards
development of quality information resources in the form of databases and
software for professionals in the area of biotechnology and Bioinformatics. In
addition to research, training programs, workshops and scientific meetings
are organized regularly.
2. Major research activities in Biotechnology and its related fields in your institution
Birla Institute of Scientific Research (BISR) is involved in fostering and
promoting various aspects of science and technology and has multi functional
activities. The research programs of the BISR are concerned primarily with
Biotechnology and Natural Resource Management.

Major Activities:
Conduct basic and applied research in established and emerging areas of
science and technology.
Organize quality improvement and customer specific training programs in
Biotechnology.
Establish and maintain effective linkages with industry, educational and
research organizations.

Industrial Biotechnology,
Microbial and Bioprocess Technology
Genomics and Proteomics
Applied Plant Biotechnology

a) National workshop on advance areas of Bioinformatics
o Algorithms in Bioinformatics, 15-17 November 2007
o Biological Sequence Analysis, 17-21 December 2007
b) Research training to 5 students from different universities was imparted.
c) Developed a database on Interaction-Specificity in Protein-Ligand
Complex (DisProlic)
d) Developed the interface of Virtual Proteomics Workbench.
e) Developed an intranet mailing facility in the center.
61
f) Guest visit - Invited guest scientist from renowned bioinformatics centre
like JNU, MASCON, University of Bergen, Norway.
HP Proliant ML350 Server (double xeon )
Windows NT Server HP Netserver E200
IBM Intellistation (AIX 5) Graphics Workstation
One Laptop IBM PIV 2.4 GHz with 40 GB HDD, 256 MB RAM
Five numbers HP XE310 Celeron 1.1 GHz, Five number IBM Pentium III
500 MHz, Two numbers Acer Power 4100 Pentium II 333 MHz, Three
numbers Acer power 4000 Intel Celeron 333 MHz,
One Iomega External Zip Drive, One HP External CD-WRITER
LCD Projector Infocus LP500
One number HP 2100TN LAN Laser Printer, Two number HP LaserJet 6L
Gold Printer, RICOH FT 3513 Photocopier
Three numbers TVS UPS 1.5 KVA Line Interactive, Eight numbers 500 VA
UPS, two numbers APC UPS 1.5 KVA line interactive.

a) Exome Horizon, Vector NTI, Reference Manager, Library Management
Software, Visual Studio, Discovery Studio Package


S. No.
Name of Staff
working
1 Dr M krishnamohan Scientist Microbial
Biotechnology
9 years
2 P. S Solanki

Information
Analyst
Bioinformatics 6 years
3 Shivani Chandra

Research
Associate
Genomics 2 years
4 Radhakishan Technical
Assistant
Networking 4 years
5 Rakesh ojha Project
Assistant
Information
Technology
2 years
6 Neha Sharma Project
Assistant
Web
Technolgy
1 year
7 Sonia Gabhrani Project
Associate
Maths & Stats 1 year
8 Vanita Parashar Project
Associate
IT 1 year
9 Amit Nagal Project
Associate
CADD 1 year
The Institute works on Research projects in the frontier areas of Biotechnology
with direct relevance to the Industry. It is important to be in contact with the latest
happenings. A modern library with facilities for literature search, access to other
62
information centres, in-house development of databases etc. is essential.
Towards this end an Integrated Information Centre has been setup.

The Bioinformatics Centre at BISR has created an infrastructure for providing
facilities to the users working in the field of Biological Sciences. The users of
Rajasthan, Jaipur in particular, are using facilities available at the Bioinformatics
Centre extensively. Following is the brief description of the services offered by
this centre:

E-mail and Internet facility: The Bioinformatics Centre has leased line Internet
connection. The center has been providing E-mail facilities since 1997. The
facilities have been used not only by the institute staff but also by personnel
working in the area of life sciences from the neighboring institutions and
organizations.
Other functions of the centre include:
b) Installing, implementing and maintaining software on computer.
c) Preventive maintenance of computers.
d) Updating the users with recent advances in computers/internet.

A) Name of Database: DOMAP
Broad Subject Area: Plant Biotechnology
Broad Functional Area: Medicinal and Aromatic Plants of Rajasthan
Whether developed or acquired: Developed
Status of completion: Complete
Whether the database is accessible over the network: Yes
B) Name of the software: Library management system
Function: Library automation
Acquired or developed: Developed
Status of completion: Completed
System requirement for running the package: Windows, Visual
Basic Package
C) Name of the Database: Database of Interaction-Specificity in Protein-
Ligand Complex ( DISProLiC)
Broad Subject Area: Structural Biology
Broad Functional Area: Interaction Specificity in Complexes
Whether developed or acquired: Developed
Status of completion: About to Complete

D) Name of the Software: Virtual Proteomics Workbench
Broad Subject Area: Proteomics
Broad Functional Area: Proteomics Data Analysis
Whether developed or acquired: Under development
Status of completion: About to Complete

The Research activities at the center involve two areas related to evolutionary
biology. The structural aspects as well as the comparative genomics are being
63
used for studying evolutionary Genomics of micro-organisms. Besides, the centre
works in the area of database and software development specifically related to
life sciences.

10. Details of Training/ Workshop organized
In order to educate the users on latest advances in the field of computer and
Information Technology the Bioinformatics Centre conducts workshops regularly.
This year our center conducted two workshops of three days.

A) Algorithms in Bioinformatics (15 -17 November 2007)
A three-day workshop was organized on the above topic and 40
participants were selected for the training from various institutes and
universities in India. We invited guest speakers from leading
Bioinformatics Institutes and Industries.

B) Biological Sequence Analysis ( 17 21 December 2007)
A five-day workshop was organized on the above topic and 40 participants
were selected for the training from various institutes and universities in
India. We invited guest speakers from leading Bioinformatics Institutes
and Industries.

C) Research Project and Summer Training:
The center has imparted six-month research projects to 5 students from
different universities in India. Some of the research topics include:
Virtual Proteomics Workbench Development using LAMP
Designed and developed improved algorithm of PCR primers
HMM based prediction for predicting post translation modifications

areas
The institute is engaged in various research activities and centre provides the
Bioinformatics support to the scientists. All scientists and researchers in the
institute working in the different areas of Biotechnology and Natural Resource
Management used the internet facility provided by the Bioinformatics centre.
During 2006-07 institutes has published 14 research papers in peer reviewed
journals. 119 nucleotide sequences were deposited in the Genbank during
2006-07.

Since our research work is mainly related with the biotechnology, Biochemical
engineering, applied geology and Microbiology, the current work we can
implement Bioinformatics in the following fronts:
a) Sequence analysis software development related to molecular biology. It will
involve the development of software for the quantitative analysis of the biological
systems.
b) Computer aided molecular designing and modeling of proteins to study the cause
of their thermostability and adaptability in extremophiles.
c) Whole genome sequence analysis of Rhizobium species to carry out comparative
genomic studies.
64
d) Development of Virtual Proteomics Workbench.
e) Construction of bioinformatics resource Meta server
The goal of such server is to provide bioinformatics services to the
international biology community by executing various bioinformatics tools,
some of them locally, other remotely at other servers around the world,
and to store, organize and present the results using a web oriented
interface.

Additional Details:
Coordinators Name: Dr P Ghosh
Postal Address:
Birla Institute of Scientific Research,
Statue Circle, Jaipur 302001 Rajasthan
Phone Number: 0141-2385283, 2385094;
Fax No.: 0141-2385121 Website: www.bisr.res.in
Email: bioinfo@bisr.res.in , pghosh9@yahoo.com


1. Dr M Krishnamohan
Mobile: +91-9314509942
mkrishnamohan@gmail.com,

2. Mr. P S Solanki
Mobile : +91-9928365838
pooransingh@gmail.com

65
Birla Institute of Technology, Mesra, Ranchi
Coordinator: Dr. A. S. Vidyarthi

1. Summary of the progress made by the center from its inception
The Distributed Information Sub-Center (Sub-DIC) was established by the
Department of Biotechnology, Government of India at Department of Biotechnology,
Birla Institute of Technology, Mesra, Ranchi in the year of 2005. The center is
involved in distributing information on various aspects of biology, providing access
to different databases through internet, as well as some specialized databases,
softwares and online bioinformatics journals used by the staff of our department. The
center has a wireless Local-Area-Network with connectivity 512Kbps. All the major
software packages (SYSTAT 11.0, SIGMAPLOT 9.0, GCG11.0, INSIGHT II, DS
Gene scan etc.) were installed in the workstation successfully and working well.
Organization of training programs, workshops and scientific meetings in order to
create awareness of bioinformatics in the local community is among its regular
activities. The database of medicinal and aromatic plants available at Jharkhand was
developed and upgraded on regular basis. Efforts are directed towards development of
quality databases and software for useful purpose in the area of medicinal and
aromatic plants. The development of two software PROMET for structural mapping
metal of ion bindings proteins and PROANA for protein sequence analysis including
all aspects are in progress. Study of HIV dynamics, Microbial (Flu virus and
Mycobacterium tuberculosis) and plant Gene analysis (CVOMT, Ocimum sanctum)
and annotations is going on.

institution
Development of Database for medicinal and aromatic plants available in
Jharkhand.
Study of HIV dynamics using Fuzzy Logic.
Phenetic and phylogenetic analysis of wild Commiphora wightii population.
Phylogenetic analysis of Chavicol-O-methyl transferase (CVOMT) gene in
the family Labiatae.
Comparative modeling of CVOMT protein in the family Labiatae.
Chemo-informatics of Catharanthus roseus, Ocimum sanctum, Withania
somnifera (Ashwagandha), Cassia angustifolia (Senna), Chlorophytum
borivillianum (Safed Musli), brahmi Bacopa monnieri
Drug discovery by high through put screening against target molecules and
known homologs from different medicinal plants.
Modification of Artemisinin (a compound extracted from the Artemisia
annua, sweet wormwood artemisinin used as antimalarial drug) drug
structure for better binding at target sitr of protein.
Analysis of differential gene expression in wheat plants induced by the leaf
rust fungus: A Trancriptomic Approach
Analysis of differentially expressed proteins induced by the drought in rice
plants: A Proteomics Approach
Analysis of Synonymous codon usage bias in Mycobacterium tuberculosis
phages and its Implication in phage therapy.
Analysis of adaptive molecular evolution of Avian Influenza A Virus
Subtype H5N1.
66
A homology based approach for modification of ampicillin structure for its
stability using Insight II.
Insilico prediction of 3-D structure of important metal bindings proteins for
findings of structure function relationship.
Genomic analysis of HIV viral gene.
Scanning of HIV viral genome and proteome for potential drug targeting.
Designing of small peptides for antigenic response in human and
optimization of the same for human system.
Fruit & Vegetable Processing (Post Harvest Technology)
Species Identification and Strain Differentiation of Dermatophytes from
tribal dominated regions of Jharkhand
Bio Fuels
Development & Evaluation of Herbal Medicines against Mycoses
Production of Industrial Enzymes
Production of Biopolymers from wastewater
Microbial community analysis of rhizosphere soil & Microbial Interaction
Protein structure function relationships and Effect of high pressure and
temperature (Cereal and legume protein)

3. Area of specialization of the center
Medicinal and Aromatic Plants, Molecular Modeling, drug designing and
Computational Bioinformatics.

4. Major activities of the center during the year 2007- 08
Upgradation of bioinformatics laboratory with new softwares (installation of
server, installation of workstations and software packages installation)
Development of database of medicinal and aromatic plants available at Jharkhand
is in progress.
Drug discovery by high through put screening against target molecules and
known homologs from different medicinal plants
Phenetic and phylogenetic analysis of wild Commiphora wightii population,
Phylogenetic analysis of Chavicol-O-methyl transferase (CVOMT) gene in the
family Labiatae, Comparative modeling of CVOMT protein in the family
Labiatae, Chemo-informatics of Catharanthus roseus, Ocimum sanctum,
Withania somnifera (Ashwagandha), Cassia angustifolia (Senna), Chlorophytum
borivillianum (Safed Musli), brahmi Bacopa monnieri
Departmental projects for B. E. (Biotechnology) and M. Sc. Bioinformatics
students (Phylogenetic analysis of a viral gene, in silico drug designing, 3D
structure prediction of proteins etc.) were assigned in this lab.
A network (LAN) has setup within the bioinformatics lab as well as department
with the server for fast transferring data among different lab within the
biotechnology department.
The development of two softwares (PROMET and PROANA) for structural
mapping metal ion bindings proteins and protein sequence analysis was
developed.
Genome analysis and annotations of Microbial (Flu virus and Mycobacterium
tuberculosis) is going on.
512 Kbps internet connectivity was established at the center.
67

5. Infrastructure facilities in the Bioinformatics Center

A. Computer and Communication facility
Computer and peripherals:
SERVER: DELL PowerEdgeTM 1800(Processor Intel Xeon
processor at 3.2GHz/2MB Cache, 800MHz FSB, Operating System
Windows Server 2003, Standard Edition, Includes 5 CALs and
LINUX)
28 clients workstations: DELL Pentium IV workstations, 80GB HDD,
512 RAM, 3.8GHz, Operating System Windows XP.
2 clients workstations: DELL Pentium IV workstations, 380GB HDD,
1GB RAM, 3.8 GHz Operating System LINUX WS.
Networking Equipments:
Modem: 3 external (2 512 kbps, 1 512 kbps Lease Line),
30 nodes.
Internet connection: 512 kbps (dedicated) BSNL, Lease line
512 Kbps ISDN line.
Power supply: UPS: 10KVA 2.
Printer:
Network Printer: HP Color LaserJet 4700dn (Print speed, color (best
quality mode), Up to 31 ppm, Processor speed 533 MHz
HP LaserJet 3050 All-in-One, (Print, color scan, copy, and fax ),
Automatic document feeder (30 pages), Incoming fax memory: 110
pages
GCG 11.0 (Sequence Analysis)
Insight II (Molecular Modeling)
SYSTAT 11.0, SIGMAPLOT 9.0 (Statistical Analysis)
HOMOLOGY (Comparative modeling and alignment)
DS GENE STATIC (Sequence search on Internet)
BIOPOLYMER (Protein and peptide designing)
BIOPERL (Programming Tools for bioinformatics)
Various molecular display programs (such as RASMOL, spdb
Viewer, Qmol etc.)
PDB database of proteins CDROM (from accelrys and rcsb).

6. Details about staff members working in the center
Sr. Number

Name of the
Staff
working
1. Dr. A. S.
Vidyarthi
Professor &
HOD
Bioprocess
Engineering
4 years
2. Mr. Raju
Poddar
Lecturer Molecular
modeling
17 months
3. Mr.
Shakaracharya
Technical
Assistant
Computer
networking
12months

68
Sequence analysis
Molecular modeling and drug designing
Homology modeling of protein structures
Internet facility for the study, research and reference searching purpose to
students, research scholar and faculties
Computer education and training in bioinformatics

M. Sc. in Bioinformatics (2 years), PG Diploma in Bioinformatics (1 year) and B.E.
in Biotechnology (4 years). Placement of the students in the institute is more than 70%.

-NIL-

One collaborative research work is going on in host pathogen interaction during
leaf rust infection in wheat: a transcriptomics approach, with IARI, New Delhi
and CCSU, Meerut.
Initiatives has taken to make a database of insects and plant diseases related to
LAC plant in collaboration with INDIAN LAC RESEARCH INSTITUTE
(Indian Council of Agricultural Research) Namkum, Ranchi - 834 010, INDIA
Another project is proteomics and genomics analysis of tasar with Central Tasar
Research & Training Institute, Piska nagri, Ranchi - 835 303, India.
Another initiative was taken to upgrade medicinal and aromatic plant database
with other BTIS center like CIMAP Lucknow.

11. Databases/ Softwares packages developed
Database for medicinal and aromatic plants available in Jharkhand,
Software packages (developed by your centre with application).
ProMET (A platform for findings of metal bindings site of a protein).
ProANA (A platform for analysis of new protein sequences including all aspects)

12. Papers published or presented in the conferences with references
Rocky Kumar, Partho Halder and Raju Poddar, Adaptive molecular evolution of
virulence genes of avian influenza - A virus subtype H5N1: An analysis of host
radiation, Bioinformation, 2006, 1(8): 321-326.
Ashutosh Ranjan, A. S. Vidyarthi and Raju Poddar, Codon bias perspectives in
phage therapy of Mycobacterium tuberculosis, In silico Biology, 2007, 7 (30), 21-
30.
S. Srivastava, P. Shukla and Raju Poddar, In sillico study of sequence homology
of Xylenase family 11.0 , Journal of Applied Sciences, 2007 (Accepted).
Ashutosh Ranjan, and Raju Poddar, Potential Therapeutic Targets of Salmonella
typhi: A Subtractive Genomics Approach, JBMC, 2007 (Accepted).
Raju Poddar, Modification of ampicillin structure for better bindings and stability,
Current Drug Targets, 2007 (commun.).
S. Sharma and Raju Poddar, Synonymous codon usage bias in Pseudomonas
syringe phages: implication in Phage Therapy, Journal of Bioinformatics and
computational Biology (JBCB), 2007 (commun.).
69
S. Srivastava, P. Shukla and Raju Poddar, Study of codonbais perspectives of
fungal xylanase gene by multivariate analysis, presented at 48
th
AMI annual
conference, IIT Chennai, 18-21, December, 2007.
13. Initiation of R & D activities in Bioinformatics
Bioinformatics tool has been applied to analysis of differentially expressed
proteins induced by the drought in rice plants, Phylogenetic and sequence
homology studies of Microbial community of rhizosphere soil and dermatophytes
etc.

14. Details of training/ Workshop organized and total no. of user trained

National Workshop on Functional Genomics of Prokaryotes held on
September 10-15, 2007 (number of participants 30).
Potential and areas of growth in Biotechnology to be held on March, 2008.
15. Impact shown by your center on the growth of biotechnology and allied fields.
In this you may highlight the details number of paper published/number of paper
published with the help of your center, How your center is promoting various
activities of your organization and neighboring institution, Manpower trained tools
developed patents & copyrights acquired and other services offered etc.
a. Paper Published: 5
b. Center Activities regarding the promotion of Departmental Activities: Guiding the
students, research scholars about the Application of Bioinformatics in the Field of
Life Science, Helping them to find online Research papers, using different analytical
tools, conducting the workshop.
c. Patents & Copyrights: nil

16. Future activities : Research
Microbial Genome analysis and annotations
Medicinal plant database
Molecular modeling
Medicinal plant gene analysis
Workshop: A workshop will be conducted on structural and knowledge based
Bioinformatics.
Training: Students will be allotted under the scheme traineeship and studentship to
accomplish the tasks in Bioinformatics
Infrastructure: Department plans to make centralized data storage system and make the
data available to all the departments through Local Area Network.

Additional details

Name of the Coordinator: Dr. A. S. Vidyarthi
Postal Address: Prof. & Head
Dept. of Biotechnology
Birla Institute of Technology,
Mesra 835 215
Ranchi, Jharkhand
Phone Number: + 91-651- 2276223, 2276590
Fax No.: + 91-651- 2275401
Email: btis_bit@bitmesra.ac.in
asvidyarthi@bitmesra.ac.in
70
Website: www.bitmesra.ac.in
Name of the contact person: Mr. Raju Poddar
E-mail: rpoddar@bitmesra
71
Bose Institute, Kolkata
Coordinator : Professor Pinak Chakrabarti

Since its inception in 1988 the Bioinformatics Centre at Bose Institute has fulfilled
multiple tasks for the service of the scientific community in Eastern India. Its main
activities have been:
Information Distribution: Meeting the objective of the BTIS program, the Centre is
involved in distributing information on various aspects of biology, providing access
to different databases through internet, as well as purchasing some specialized
databases, softwares and journals. Crossing the boundaries of the host institute, the
service has been provided to the whole of the eastern region, reaching places like
Tripura, Andaman Islands, Almora etc.
Networking and Communications: In 1997 we have established a Local-Area-
Network in both the campuses of Bose Institute and subsequently linked the two
through Wide-Area-Network. A 1 mbps (that has been upgraded to 2mbps in 2006-
07) internet connectivity is used for the activities of the Centre and also serves as a
backup resource to the ERNET connectivity used by the scientists in the Institute.
Research Activities: The computational infrastructure developed at the
Centre has provided the impetus for thriving research activities in
bioinformatics and computational biology, as can be seen from a large
number of publications made over the years and its recognition as the Centre
of Excellence in Bioinformatics by DBT in 2004 and awards received by staff
and students working at the Centre.

Awards/Recognition:
Dr. T.C. Ghosh was awarded Biotechnology Overseas Associateships by DBT
for the year 2000-01 and 2005-06 and was invited by UNESCO, European Office
to give lectures in a course on Bioinformatics for East-European students during
October 20-24, 2003. Based on their doctoral work in Bioinformatics Dr. D. Pal,
was awarded INSA Medal for Young Scientist in the year 2000. Prof. B.B. Biswas
outstanding Student Award of Bose Institute was awarded to Dr. D. Pal in 1999,
Dr. U. Samanta in 2000, Dr. R. Bhattacharyya in 2002, Dr. R. P. Bahadur in 2003
and Mr. Mainak Guha Roy in 2007. The Nilratan Sarkar Award of the Institute
was awarded to Dr. R. Saha 2006 and to Dr. S. Basak in 2007. Dr. R.
Bhattacharyya has been awarded the JBS Haldane Memorial Prize 2006 by the
Indian Statistical Institute, Kolkata. Prof. P. Chakrabarti has been awarded the JC
Bose National Fellowship in 2007.

2. Major research acti vities in Biotechnology and its related fields at your
institution
In addition to carrying out independent lines of work, many of the activities in
the Centre are directly related to and supplement the biotechnology
programmes that are being carried out in the different departments of the
institute.
The following research activities are being actively carried out:
+ Genome analysis
+ Analysis and prediction of three-dimensional structures of proteins
+ Plant and mycobacterial genomics and proteomics
72
+ Homology modeling of protein structures
+ Biomolecular structure determination using NMR and Xray crystallography
+ Protein-protein interaction, docking and molecular recognition
+ Protein folding and threading
+ Dynamics and protein networks

Genome analysis; genetic engineering and molecular modeling.

4. Major activities of the centre during the year 2007
One Research Scientist, one Research Associate and eight JRFs/SRFs are
working in the COE in Bioinformatics. For topics of research see item no. 2; list of
publication in the year is provided in item no. 12 and the workshop arranged in
item no. 14.

Computer Hardware (functional): Sun E420R Server, SGI O2 Desktop
Workstation (three nos), SGI Octane Workstation, IBM PCs (thirty five nos),
IBM X206(4 servers), IBM 226 (two servers), IBM X255 (two servers), IBM
Color MFP, Pentium III PC (twenty nos), HP Scanner, HP Laser Printer, Cisco
Router and Cisco Switch, Linksys Switches, HP photo printer, HP All-in-one
printer, Xerox photocopier.

Communication Facilities: Since 1997 BIC has established LAN in both the
campuses of the institute and subsequently linked them to the internet by a
1mbps leased line (ERNET). In December 2006, a 2 mbps internet
connectivity has been made operational (through VSNL).


A web-server, ProFace has been developed for dissecting protein-protein
interfaces and deriving various physicochemical parameters. It is available at
http://www.boseinst.ernet.in/resources/bioinfo/stag.html.

A web-server, IntGeom has been developed for calculating the geometry of
interaction between planar side chains in protein structures. It is available at
http://www.boseinst.ernet.in/resources/bioinfo/stag.html.

An online version of the standalone version of ConfPlot (reference: Pal D and
Chakrabarti P (1999) Graphical representation of the salient conformational
features of protein residues. Protein Engng. 12, 523-526) has been made and
put on the web.

Most of the commercial softwares (such as Bio-suite, Accelyrs, etc.) and graphics
and docking programs are available at the Centre.

73
Three different databases on interfaces in homodimers, protein-protein
complexes and those in the crystal of monomeric proteins are available at the
web-site, http://www.boseinst.ernet.in/resources/bioinfo/stag.html. These have
been used in the analysis of protein-protein interaction.

A database on the conservation of some high priority medicinal plants of India,
PlantCon, has been developed, and available at
http://www.boseinst.ernet.in/resources/bioinfo/plantcon.html.

absorption status)
Name of the Staff Designation Specialization Period of Working

a) Dr. Tapash Chandra Ghosh Sr. Lecturer Genome analysis From 1993
b) Mr. Tushar Kanti Bhattacharya Technical officer Computer software From 1991
c) Mrs. Sujata Roy(Majumder) S.T.A. Bibliography From 1993
d) Mr. Sanjib Kumar Gupta S.T.A Networking From1994
e) Dr. Debjani Roy Research Scientist Molecular modeling From 2005
f) Mr. J.N. Mandal Sr. attendant From 1988

All, other than Dr. Debjani Roy, who was hired in the COE grant, are institute
employees.

7. Types of services provided : Data retrieval, Sequence analysis, Molecular
modelling and drug design, Ligand docking and virtual drug screening,
Homology modeling of protein structures
BIC personnel are involved in teaching and supervising projects in the
Bioinformatics MSc/MTech courses being conducted by the Calcutta
University, W B University of Technology.

BIC provides project work to students undergoing B.Tech/Mtech/MCA/DCA
courses from a large number of institutes/universities. It offers a one-
semester course in bioinformatics to the PhD students in the institute.
Eight students have been selected under the studentship/traineeship
programme for a period of 6 months. They are: Maitrayee Dasgupta, Baisakhi
Halder, Sraani Chattopadhyay, Tina Begum, Priyanka Shah, Bipulesh
Bhowmick, Manidipa Paul and Roopsha Brahma. Six students who finished
their traineeship last year have all been well placed, joining an engineering
college in Mumbai as a lecturer, PhD programmes at IIIT-Hyderabad and
Bose Institute, MTech programme at IIIT-Allahabad, and IBM as a
programmer.
One of the earlier PhD students (Dr. Debnath Pal) is now a faculty of the
Bioinformatics Centre, IISc. Two students (Mr. Anshuman Bagchi and Ms.
Tania Banerjee), who finished their PhD theses, have been recruited as a
faculty in the Biochemistry Department of Kalyani University and TCS,
Kolkata, respectively.

74
The softwares developed at the Centre have been put on the net, so that these can be
used worldwide, and people can use/validate the scientific output from the Centre.
Besides, all the work are published (or under submission) in peer-reviewed international
journals.

P. Chakrabarti and Prof. J. Janin of Universite Paris-Sud, Orsay, France have
been collaborating for the past six years and a new project has been submitted to
IFCPAR for funding.
Collaborative work between T.C. Ghosh and G. DOnofrio of Stazione Zoologica,
Italy has been continuing.

Details provided under item nos. 5B and 5C.
12. Papers published or presented in the conferences with reference (2007-
08)
- DOnofrio, G., and T.C. Ghosh and S. Saccone. 2007. Different
functional classes of genes are characterized by different compositional
properties. FEBS Letters (in press).
- Basak, S., S. Roy, and T.C. Ghosh. 2007. On the origin of synonymous
codon usage divergence between thermophilic and mesophilic
prokaryotes. FEBS Letters (in press).
- Bagchi, A., and T.C. Ghosh. 2007. Homology modeling and molecular
dynamics study of the interactions of SoxY and SoxZ: The central player
of biochemical oxidation of sulfur anions in Pseudaminobacter
salicylatoxidans. Res. J.Microbiol. 2: 569-576.
- Mukhopadhyay, P., S. Basak, and T. C. Ghosh. 2007. Synonymous
codon usage in different protein secondary structural classes of human
genes: Implication for increased non-randomness of GC
3
rich genes
towards protein stability. J Biosciences 32: 947-963.
- Mukhopadhyay, P., S. Basak, and T. C. Ghosh. 2007. Nature of
selective constraints on synonymous codon usage of rice differs in GC-
poor and GC-rich genes. Gene 400: 71-81.
- Kahali, B., S. Basak, and T. C. Ghosh. 2007. Reinvestigating the codon
and amino acid usage of S. cerevisiae genome: A new insight from protein
secondary structure analysis. Biochem. Biophys. Res. Commun. 354:
693-699.
- Sau, K., S.K. Gupta, S. Sau, S.C. Mandal, and T.C. Ghosh. 2007.
Studies on synonymous codon and amino acid usage biases in the broad-
host range bacteriophage KVP40. J. Microbiol. 45: 58-63.
- Banerjee, M., D.Roy, B. Bhattacharyya and G. Basu. 2007. Differential
colchicine-binding across eukaryotic families: the role of highly conserved
Pro268beta and Ala248beta residues in animal tubulin. FEBS Lett.581:
5019-5023.
- Janin, J., F. Rodier, P. Chakrabarti and R. Bahadur. 2007.
Macromolecular recognition in the Protein Data Bank. Acta Crystallogr.
D63, 1-8.
75
- Pal, A., P. Chakrabarti, R.P. Bahadur, F. Rodier, and J. Janin. 2007.
Peptide segments in protein-protein interfaces. J. Biosci. 32, 101-111.
- Saha, R.P., R. Bhattacharyya and P. Chakrabarti. 2007. Interaction
geometry involving planar groups in protein-protein interfaces. Proteins.
67, 84-97.
- Dasgupta, B. P., P. Chakrabarti and G. Basu. 2007. Enhanced stability
of cis Pro-Pro peptide bond in Pro-Pro-Phe sequence motif. FEBS Lett.
581:4529-4532.
- Guharoy, M and P. Chakrabarti. 2007. Secondary structure based
analysis and classification of biological interfaces: identification of binding
motifs in protein-protein interactions. Bioinformatics, 23: 1909-1918.
- Chakrabarti, P. and R. Bhattacharyya. 2007. Geometry of nonbonded
interactions involving planar groups in proteins. Prog. Biophys. Mol. Biol.
95: 83-137.
- Vidyasagar et al. 2007. BioSuite: a comprehensive bioinformatics
software package (A unique industry-academia collaboration). The
NMITLI-BioSuite Team Curr. Sci. 92:29-38.
- Kundu, S., and D. Roy. 2007. Computational study of glyceraldehyde-3-
phosphate dehydrogenase of Entamoeba histolytica: implications for
structure-based drug design. 25:25-33.
- Pal, A., A. Chakrabarti and J. Basak 2007. New motifs within the NB-
ARC domain of R proteins: probable mechanisms of integration of
geminiviral signatures within the host species of Fabaceae family and
implications in conferring disease resistance. J. Theo. Biol 246: 564-573.
- Chattopadhyaya, R. and A. Pal. 2008. Three dimensional models of NB-
ARC domains of disease resistance proteins in tomato, Arabidopsis and
flax, J Biomol Struct and Dyna 25: 357-572.
- Kundu, S. and D. Roy. 2007. Structural considerations for designing
adenosine analogs as selective inhibitors of Trichomonas sp.
glyceraldehyde-3-phosphate dehydrogenase. In Silico Biology 7: 0051.

The on-going research activities will be continued.
A workshop on Application of bioinformatics in molecular and structural
biology was organized during February 23-24, 2007. There were more than
100 participants.

areas. In this you may highlight the details like number of paper published/
number of papers published with the help of your centre, how your centre is
promoting various activities of your organization and neighboring institutions,
manpower trained, tools developed, patents & copyrights acquired and other
services offered etc.
In 2007, nineteen papers dealing with different aspects of bioinformatics have
been published by people working at the Centre Many other publications have
taken the services of the Centre.

76
Research activities given in item no. 2 will be continued. The staff strength and the
number of students will be increased.
Additional Details:
Name of the Coordinator: Professor Pinak Chakrabarti
Postal Address: Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M,
Kolkata 700 054
Phone Number: +91 33 2355 6626 Fax No.: +91 33 2355 3886
Email: dicdbt@boseinst.ernet.in Website:www.boseinst.ernet.in/bic
Name of Contact Person(s): Prof. Pinak Chakrabarti
Email: dicdbt@boseinst.ernet.in
77
Central Agricultural Research Institute, Port Blair
Coordinator: Dr. M. Balakrishnan

The Distributed Information Sub Centre (Sub-DIC) was established at Central
Agricultural Research Institute Port Blair, in the year 2005 with the support
from DBT, Govt. of India. The Sub-DIC has been made well equipped with
hardware including computers, proxy server, mail server, database server
and VSAT (Institutional Facility).
The mission of Bioinformatics Centre, CARI is to develop databases on
Biodiversity of Andaman & Nicobar Islands, which would provide information
to taxonomists, ecologists, biodiversity management specialists, policy
makers, planners & related entrepreneurs to store, manage, and exchange
electronically published scientific information in standard format. It also serves
as an active site for bioinformatics research and development in the remote
union territory of Andaman and Nicobar Islands.This centre has created both
off-line and On-line database on biodiversity of Andaman and Nicobar
Islands.
2. Major research activity in biotechnology ad its related fields at your
institution
A. Major Activities:
Biotechnology Section of CARI, conceptualized, designed and developed
during 1992, cell technology and molecular biology research including
transgenic development and gene tagging for excess salt tolerance are
undergoing currently. Cell and tissue culture, molecular analysis, transgenic
development, transgenic rearing facility (DBT approved, Type II facility), dark
room photography, microscopes (trinocular, florescence and inverted
microscopes), electrophoresis and gel documentation, molecular marker,
quantification facilities, radioisotope lab (Type II, BARC approved) are the
major facilities available in this section. In addition, to screen saline/metal
toxicity tolerant lines, a simulated screening facility and a mini repository of
medicinal plants indigenous to Bay Islands have also been developed. Along
with this various technology developed includes semi-dwarf salt tolerant
Pokkali lines viz. BTS 24, BTS 28 and BTS-13 having productivity of ~3.5
tons/ha through exploitation of In vitro culture induced variations, AI & Fe
toxicity tolerant lines in IR72 & C 14-8, transgenic lines carrying osmotine, cry
IA(b), cry IA(b), cry IA(c), AmSOD & chitinase in indica rice through
Agrobacterium mediated genetic transformation, Production technology for
tetraploid, gynogenetic & transgenic stocks (rtgh gene) in Indian major carps
(IMC)- rohu, catla & mrigal and Efficient in vitro micropropagation protocols
for mass production of planting materials in pineapple, banana. Cymbidium,
Gerbera jamesonii & Bacopa monnieri (under grotek culture system)
developed to undertake profitable agribusiness.
Patent application for Protocol for producing large number of viable plantlets
of Bacopa monneri vitro gro-tek system system under liquid culture Mass
Production System. has been submitted to Indian Patent Office, New Delhi.

3. Area of specialization of the centre.

Development of database for the Biodiversity of A & N Islands.

78
The Centre during this year has been actively indulged in the creation of
database for the biodiversity. IFS and mango along with training students of
various universities in the field of molecular modeling and structure based
drug designing from mainland. Apart from this databases such rice genome,
PDB and Pfam are maintained. The centre has also successfully conducted a
national conference on Bioinformatics tools for gene and protein analysis in
collaboration with SIGC, Trichy.
5. Infrastructure facility at the Bioinformatics centre.

A. Computer and Communication Facility
The hardware includes Pentium desktop computer (10 nos.). LAN,
proxy server, mail server, database server and VSAT (Institutional
Facility), digital photocopier, Network Printer, UPS 7.5 kw (2 nos)

B. Scientific & Software Packages
Scientific software packages for Molecular modeling ( Modeller9v2,
JACKAL, ICM Pro, CAChe, Discover studio), Sequence analysis
(GeneDoc, Accelrys gene, CLC work bench 2, Bioedit.), In silico cloning
tools (Gene Constriction kit 2, Vector NTI 9.1 and Plasmid draw 3.2) and
phylogenetic analysis tools (PHYLIP, MEGA, Tree Viewer) are available.

6. Details about staff members working in the centre.

7. Types of service provided.
Bioinformatics Centre at Central Agricultural Research Institute, Port Blair is
focused on providing qualify consultancy services in the field of website
development, database management and manpower training.Our team here
at Bioinformatics centre can assist any progressive organization / institute in
developing, integrating and maintaining valuable biological data so that it can
be accessible in a safe and comfortable manner.

8. Educational activity with details of placement.
6 M.Sc. (Biotechnology) final year students along with 3 summer training
students from mainland universities viz. Bangalore University, Bharathidasan
University had successfully completed their dissertation work in field of
molecular modeling, structure based drug designing and gene annotation.
Currently a total of 11 students from Bharthidasan and Bharathiar University
are undergoing their project work.

Name of the
Staff
working
Absorption
Status
Mr. Mayank
Pokhriyal
RA M.Sc.
Microbiology
August,
2007
nil
Ms. Soma
Mondal
SRF M.Sc. Computer
Science
March,
2007
nil
Ms. S.
Thenmozhi
JRF M.Sc.
Microbiology
October,
2007
nil
Mr. Rajiv
Ranjan
Studentship B.C.A August,
2007
nil
79
9. Initiative to validate the outcome of bioinformatics resources. N.A

10. Collaborative works/initiatives.
A national level conference on Bioinformatics tools for gene and protein
analysis was conducted in association with Shrimati Indira Gandhi College of
Arts and Science (SIGC) , Trichy, T.N was successfully conducted . A total of
450 participants including research scholars, scientists and students from
various institutions with in India attended the conference. Also initiative has
been taken for further scope of collaboration with ICMRs regional centre here
in the islands and Anna university in the area of molecular modeling and
database development.

11. Databases / Software package developed.
Along with databases of medicinal plants, economically important pants, rice
cultivars, orchids etc, recently Sub-DIC has also developed 4 more databases
which include database for Integrated farming system models in A & N
Islands, database of Biodiversity of A & N Islands, database for Mango and
medicinal plant database.

12. Papers published or presented in the conference with references.

Balakrishnan, M and K.Meena (2006). A back-propagation algorithm applied to forecast
coconut yield, AMSE international journal, 69160, tassin la demi-lune (France), Modeling
D, Vol.27 n
0
2 : pp.75-85.

Balakrishnan, M, 2007. Recent trends in Networking Concepts and communication
technologies chapter in Bioinformatics and Statistics in Fisheries research Vol.III, CIFA,
Bhubaneshwar, Orissa Vol(3): pp:124-132.

Balakrishnan, M., K.Meena, S.Sethi and A.N. Sarangi, 2007. Neural Network and its
Application in Aquaculture chapter in Bioinformatics and Statistics in Fisheries research
Vol.III, CIFA, Bhubaneshwar, Orissa Vol (3): pp: 145-151.

Balakrishnan, M., R.C Srivastava and Mayank Pokhriyal (2007). Databases and
Browsing Tools for Gene Prediction, Bioinformatica Journal, National institute of
Science & Technology, Orissa. Vol.1, Vol.4: pp.16-22.

Balakrishnan, M. Recent trends in networking concepts and communication
technologies 2006, In Proc. of National workshop cum Training on Bioinformatics and
statistics in Aquaculture Research organized by CIFA,(ICAR, Kausalyaganga,
Bhubaneswar-751 002, on 7- 10 February 2006, pp.122-129.

Balakrishnan, M., R.Elanchezhian, R.C. Srivastava, Mayank Pokhriyal and Soma
Mondal (2007), Database for Rice cultivars of Andaman and Nicobar Islands. In Proc. of
International Symposium on Management of Coastal Ecosystem: Technological
Advancement and Livelihood Security to organized by ISCAR at Science City, Kolkata,
from 27-30 October, 2007, P.19

Balakrishnan, M., R.Elanchezhian, R.C. Srivastava, Mayank Pokhriyal and Soma
Mondal (2007), Database for Indigenous Orchids in Andaman and Nicobar Islands. In
Proc. of International Symposium on Management of Coastal Ecosystem: Technological
Advancement and Livelihood Security to organized by ISCAR at Science City, Kolkata,
from 27-30 October, 2007, P.41
80

Balakrishnan, M., N.Ravisankar, K.Meena, R.Elanchezhian, S.K Zamir Ahmed
(2007).Yield Prediction through Feed Forward Neural Network Approach for Direct
Seeded Rice (Oryza sativa) in Bay Islands. In Proc. of 3
rd
Indian International
Conference on Artificial Intelligence (IICAI-07) NIA, Pune, India from 17-19, December,
PP.1533-1541, 2007

13. Initiation of R & D activities in bioinformatics.
Sub-DIC is actively indulged in research activities like application of
bioinformatics in nucleotide and protein sequence alignment, gene prediction,
protein structure prediction and homology modeling, fishing out gene
responsible stress tolerance in crop plants and development of ANN model
for gene prediction / classification

14. Details of training / workshop organized and total no. of user trained.

areas.
The Sub-DIC is assisting research scholars and scientists from neighboring
departments / institutes in updating their knowledge in bioinformatics through
softwares available in the centre. The centre is also providing training on
bioinformatics tools for gene and protein sequence analysis, gene annotation,
database designing, web technology to M.Sc. students. Seven M. Sc.
(Biotechnology) and 2 B.Tech students from mainland universities viz.
Bangalore University, Bharthidasan University had undergone dissertation
work and currently 11 M.Sc. (Bioinformatics) and two M.Sc students of
Biotechnology and Microbiology are undergoing dissertation work in the Sub-
DIC for partial fulfillment of M.Sc. degree.

16. Future activities.
Creation of database for stress responsive genes in agricultural crops
Gene expression studies related to agricultural crops of prime importance in
A & N Islands
To design and develop database on plant genetic resources of Bay Islands
Development of Protein Prediction models (computer models) using the
concept of Artificial Neural Network (ANN) and Data mining
Sl.No Topic Duration No. of
Participants
From
To

1 One day workshop on
bioinformatics and its
application
1 day 30 27
th
Mar
2008
2 Bioinformatics tools for
gene and protein Analysis
4 days 27

26
th
29
th

July,2006
3 Database Development
and its Application in
Biodiversity
5 days 27 19
th
23
rd

February,
2007
4 National Conference on
Bioinformatics Tools for
Gene and Protein
Analysis in collaboration
with SIGC, Trichy
2 days 450
7
th
8
th

Sept,
2007
81
To establish an agriculture information system for villages in A & N Islands
Development of ANN model for disease prediction

Address
Central Agricultural Research Institute
Coordinator: Dr. M. Balakrishnan
Bioinformatics Centre
Biotechnology Section
Port Blair
E-mail: mbkrishnan@hotmail.com

82
Central Drug Research Institute, Lucknow
Coordinator : Dr. Prodyut K Roy

Right afer the creation of the Centre, The BTIS Centre at CDRI, Lucknow
styartyed to create a state of the art infrastructure and environment to carry
out R& D work in Bioinformatics in the area of drug development. Collection,
retrieval and dissemination of Information on biomedical research has been
among the missions of the BTIS Centre at the Central Drug Research
Institute, Lucknow. BTIS centre has been catering to the information
requirements of the users working in the area of Biotechnology. CDRI library
which is the base of the BTIS user Centre has been functioning as the
National Information Centre for Drugs And Pharmaceuticals (NICDAP) of the
department of Science and Technology, Government of India for the last
twenty eight years. As such this center has been serving the research
community in the area of Drugs and Pharmaceuticals for quite some time.
With the establishment of BTIS Center, the user profile of the center has
widened to those working in the area of Biotechnology in Drug Research and
Pharmaceutical Industry. User profile of the center include:

Drugs & Pharmaceutical Industry
R&D Institution, CSIR, ICAR, DBT, DOD, State Science &
Technology Councils, etc.
Universities/Departments of Biotechnology
Small Entrepreneurs
Students Pursuing Courses in Biotechnology And Bio-
informatics

institution
The institute has a major programme in the area of Biotechnology and in
all the research projects; Biotechnology is one of the main components.
The research Activities of the Institute include:

Development of Drugs, Vaccines and Diagnostics
Cellular and Molecular Studies to understand Diseases
Cellular and Molecular Studies to understand Disease processes
and reproductive physiology
Development of Contraceptive Devices and Agents
Systematic Evaluation of Medicinal properties of Natural products
including terrestrial plants and marine flora and fauna
Development of Technology for drugs, intermediates and
biologicals
Dissemination of information in the field of drug research,
development and production
Consultancy and development of manpower.
2. To create and maintain infrastructure for R& work to be carried out in the
Bioinformatic studies by the Centre as well as the scientists of the institute
working in the area of drug design and development. Acquisition,
83
Compilation and Dissemination of information on Biotechnology to the
people working in the area of Drugs and Pharmaceuticals.


4. Major Activities

Bioinformatics
BTIS at CDRI initiated Bioinformatics work with the induction of traineesl
research students in collaboration with the Molecular and Structural
Biology research group of the institute. Two works carried out by the
Centre during the year were :
. StructuralBioinformatics Studies of Dihydrofolate Reductase Enzyme
from Toxoplasma gondii
. StructuralBioinformatics Studies of Putative Ubiquitin Conjugating
Enzyme from Toxoplasma gondii

Information Services

Being a National Information on Drugs and Pharmaceuticals, our library
caters to the information needs os the students, researchers of
institutions/ universities involved in biomedical Research all over the
country.

More than five hundred queries from universities, Pharmaceutical
industry, R & D organizations etc. are received annually and
replied to with the help of available resources.

Student pursuing postgraduate/ postdoctoral courses in
Biotechnology, Pharmacy, Medicinal and Pharmaceutical
Chemistry in various universities/ institutions visit the Centre
regularly and utilize our resources. More than two hundred visitors
from outside Lucknow visit the center every month. They are
provided with required information and are helped to retrieve
required information from available resources.

A large number of local users including researchers in local
universities and students of biotechnology, pharmacy, Chemical
Engineering etc. visit the library on a daily basis to make use of the
information resources and infrastructure available in the center.

On an average two thousand online searches were made monthly
by outside users to get information on drugs and pharmaceuticals
and biotechnology.

Current Awareness services
Current awareness service in the area of drugs and
Pharmaceuticals research and pharmaceutical industry has been one of
the main activities of the CDRI library, we have, from 2005 onwards,
started publishing the two journals under the BTIS banner. The journals
84
are:

Drugs & Pharmaceuticals - Industry Highlights (Monthly)
Drugs & Pharmaceuticals - Current R&D Highlights (Quarterly)

The biotechnology aspects of Pharmaceutical industry are given special
emphasis in the two bulletins. From 2005 onwards, our emphasis is to
cover biotechnology as much as possible in these bulletins. We have also
decided to expand our clientele of information seekers among more and
more academic institutions and smaller colleges where library and
information facility is not very adequate and the bulletins could possibly fill
the void. The small entrepreneurs in this field of biotechnology based
pharmaceutical industry are also being targeted.

(A) We have few computers attached to a server to cater to the users.
However, with the grant made available by the BTIS in the year 2004-
2005 we are in process of acquiring more P4 computers and latest version
of server.
(B) Libsys for Library Networking
R&D Insight online & CD
Science direct (1800 journals)
Pharmacopoeias on CD
About 3400 online journals of all major publishers
More than 350 journals majority of which are foreign journals.

6. Staff Members associated with the center:
Dr. P.K. Roy, Coordinator
Dr. Sheela Tandon
Mr. A.K. Srivastava
Mr. S.K. Mallik
Mrs. Seema Mehrotra
Mr. Zafar A. Zaidi
Mr. V.K. Vohra
Mr. W. F. Rahman
They are all working as regular employees of the institute for the last 15-20
years.

Current Awareness service in the Area of Biotechnology in Drug
Development.
Information Dissemination
Query Service
Full text Delivery Service

8. Educational activities with details of placement -


85
Many Services were provided to the outside users on payment. The
continuance at the users with the center and continuous inflow of information
requests from existing users validate the resources.

Efforts are on to carry out more collaborative initiatives on the pattern of
Lucknow Special Libraries Consortium. The Centre is a part of DELNET and
would like to join hands with other BTIS Centres.

Database already completed :
Natural Products And Medicinal Plants
Scientific serials available in Lucknow
Papers published by CDRI since 1951
Databases in progress:
Profile of Drugs under newly approved Drugs
Indian Patents

Ahmed, S Dul Qui, BX and Walworth, N Msc1 Acts through Histone H2A.Z to Promote
chromosome stability in Schizosacchromyces pombe Genetics 177,1487-1497
Akhtar, MS and Bhakuni, V Role of ionic interactions and linker in the domain interaction
and modulation of functional activity of hyaluronate lyases Biochemical And Biophysical
Research Communications 353,286-292
Avasthi, Kamlakar Farooq, Sheikh M Bal, Chandralata, Kumar, Rishi Tewari, Ashish K
and Maulik, Prakas, R Design and synthesis of pyrazolo[3,4-d]pyrimidine and triazolo[4,5-
d]pyrimidine based dissymmetrical Leonard linker compounds: 1H NMR and
crystallographic evidence for folded conformation due to arene interactions Journal of
Molecular Structure 842, 100-108
Avasthi, Kamlakar Farooq, Sheikh M Aswal, Sangeeta Raghunandan, Resmi and Maulik,
Prakas R
1
H NMR and crystallographic evidence for tolerance of bulky electron
withdrawing methanesulfonyl group on robustness of the U-motif in pyrazolo[3,4-
d]pyrimidine core based Leonard linker compounds and formation of plus (+) motif
Journal of Molecular Structure 827, 88-94
Bal, NC Agrawal, H Meher, AK and Arora, A Characterization of peptidyi-tRNA hydrolase
encoded by open reading frame Rv1014c of Mycobacterium tuberculosis H37Rv
Biological Chemistry 388, 467-479
Bhadauria, S Singh, G Sinha, N and Srivastava, S Isoniazid Induces Oxidative Stress,
Mitochondrial Dysfunction And Apoptosis In Hep G2 Cells Cellular and Molecular
Biology 53, 102-114
Guha, Mithu Choubey, Vinay Maity, Pallab Kumar, Sanjay Shrivastava Kumkum Puri,
Sunil K and Bandyopadhyay, Uday Overexpression, purification and localization of
apoptosis related protein from Plasmodium falciparum Protein Expression And
Purification 52, 363-372
Gupta, R Chakrabarti, P Dikshit, M and Dash, D Late signaling in the activated platelets
up regulates tyrosine phosphatase SHP1 and impairs platelet adhesive functions:
Regulation by calcium and Src kinase Biochimica Et Biophysica Acta (BBA) -
Molecular Cell Research 1773131-140
Gupta, SK Sisodia, BS Sinha, S Hajela, K Naik, S Shasany, AK and Dube, A Proteomic
approach for identification and characterization of novel immunostimulatory proteins from
soluble antigens of Leishmania donovani promastigotes Proteomics 7, 816-23
Gupta, Subash Chandra Siddique, Rahman Hifzur, Mathur, Neeraj Vishwakarma, Lal
Achchhe Mishra, Ranjit Kishore, Saxena, Krishna Daya and Chowdhuri, Debapratim Kar
Induction of hsp70, alterations in oxidative stress markers and apoptosis against
dichlorvos exposure in transgenic Drosophila melanogaster: Modulation by reactive
oxygen species Biochimica et Biophysica Acta(BBA) - General Subjects 1382-1394
86
Gupta, Swati Dube, Anuradha and Vyas, Suresh P Antileishmanial efficacy of
amphotericin B bearing emulsomes against experimental visceral Journal of Drug
Targeting 15, 437-44
Jain, Akhlesh K Chalasani, KB Khar, RK Ahmed, FJ and Diwan, PVMuco-adhesive
multivesicular liposomes as an effective carrier for transmucosal insulin delivery Journal
of Drug Targeting 15, 417 427
Laughton, CA Luisi, BF Pratap, JV and Calladine, CR potential molecular switch in an
alpha helical coiled coil Proteins 70, 25-30 A
Lella, RK and Sharma, C EIS (enhanced intracellular survival) protein of mycobacterium
tuberculosis disturbs the cross regulation of T-cells J Biol Chem 282, 18671-75
Lundsen, T Hunt, MC Nilsson, LM Sanyal, S Angelin, B Alexson, SE and Rudling, M
PPARalpha is a key regulator of hepatic FGF21 Biochemical and Biophysical
Research Communications 360, 437-440
Meher, Akshaya K Lella, Ravi K Sharma, Charu and Arora, Ashish Analysis of complex
formation and immune response of CFP-10 and ESAT-6 mutants Vaccine 25, 6098-
6106
Misra, Gauri Aggarwal, Anita Mittal, Sonia Singh, Yogendra and Ramachandran,
Ravishankar Purification, crystallization and preliminary structural analysis of nucleoside
diphosphate kinase from Bacillus anthracis Acta. Cryst. Sect F 63, 1084-1086
Naim, M Bhat, Sathesh Rakin, KN Dennis, S Choudhury, SF Siddiqi, M Imran Drabik, P
Sulea, T Bayly, C Jakalian, A and Purisima, EO Solovated interaction energy (SIE) for
scoring protein ligand binding affinities.1. Exploring the parameter space J Chemical
Information & Modeling 47, 122-133
Raghu Ram, EVS Kumar, Biswas, A Kumar, S Chaubey, AS Siddiqui, MI and Habib, S
Nuclear gyr B encodes a functional subunit of the Plasmodium falciparum gyrase that is
involved in apicoplast DNA replication Molecular & Biochemical Parasitology 154, 30-
39
Rawal, Ravindra K Kumar, Ashutosh Siddiqi, Mohammad Imran and Katti, Setu B
Raza, S, Sahasrabuddhe, AA and Gupta, CM Nuclear localization of an actin-related
protein (ORF LmjF21.0230) in Leishmania (+) Molecular & Biochemical Parasitology
153, 216-219
Sanyal, S Bvner, A Haroniti, A Nilsson, LM, Lundsen, T Rehnmark, S Witt, MR
Einarsson, C Talianidis, I Gustafsson, JA and Treuter, E Involvement of corepressor
complex subunit GPS2 in transcriptional pathways governing human bile acid
biosynthesis Proceedings of the National Academy of Sciences USA104, 15665-
15670
Shagufta, Kumar Ashutosh, Panda, Gautam and Siddiqi, Mohammad Imran CoMFA and
CoMSIA 3D-QSAR analysis of diaryloxy-methano-phenanthrene derivatives as anti-
tubercular agents Journal of Molecular Modeling (Online) 13, 99-109

Sharma, Sarita and Bhakuni, Vinod Cloning and structural analysis of Mycobacterium
leprae serine hydroxymethyltransferase Protein Expression and Purification 55, 189-
197

Sharma, Sharad Kumar Gupta, Chittarmal, Dwivedi, Varun Misra-Bhattacharya, Shaija
and Owais, Mohammad Prophylactic potential of liposomized integral membrane protein
of Plasmodium yoelii nigeriensis against blood stage infection in BALB/c mice Vaccine
25, 2103-2111

Singh, Ashok Chandra, Saurabh Gupta, Shrawan Kumar Chauhan, LKS and Rath,
Srikanta Kumar Mutagenicity of leachates from industrial solid wastes using Salmonella
reverse mutation assay Ecotoxicology And Environmental Safety 66, 210-216
Singh, K and Bhakuni, V Cation induced differential effect on structural and functional
properties of Mycobacterium tuberculosis alpha-isopropylmalate synthase BMC Struct
Biol 9, 39
Singh, R Shasany, AK Aggarwal, A Sinha, Sudhir Sisodia, BS Khanuja, SPS and Misra,
R Low molecular weight proteins of outer membrane of Salmonella typhimurium are
immunogenic in Salmonella induced reactive arthritis revealed by proteomics Clinical
and Experimental Immunology 148, 486-493
87
Song, GY Gibson, G Haq, W Huang, EC Srivastava, T Hollstein, M Daftarian, P Wang, Z
Diamond, D and Ellenhorn, JD An MVA vaccine overcomes tolerance to human p53 in
mice and humans Cancer Immunol Immunother 56, 1193-205
Srivastava, Sandeep Kumar Dube, Divya Kukshal, Vandana Jha, Ashok Kumar Hajela,
Kanchan and Ravishankar, Ramachandran NAD+ -dependent DNA ligase (Rv3014c)
from Mycobacterium tuberculosis : Novel Structure-function relationship and identification
of a specific inhibitor Proteins : Structure, Function And Bioinformatics 69, 97-111
Srivastava, V Rouanet, C Srivastava, R Ramalingam, B Locht, C and Srivastava, BS
Tripathi, T Rahlfs, S Becker, K and Bhakuni, V Glutathione mediated regulation of
oligomeric structure and functional activity of Plasmodium falciparum glutathione S-
transferase BMC Struct Biol 17, 67
Vatsyayan, Rit and Roy, Uma Molecular cloning and biochemical characterization of
Leishmania donovani serine hydroxymethyl transferase Protein Expression And
Purification 52, 433-440
Yadav, Sharada Prasad Ahmad, Aqeel and Ghosh, Jimut Kanti Addition of a small
hydrophobic segment from the head region to an amphipathic leucine zipper like motif of
E. coli toxin hemolysin E enhances the peptide-induced permeability of zwitterionic lipid
vesicles Biochimica Et Biophysica Acta (BBA) Biomembranes 6, 1574-1582

Structurebased antiTB and antileishmania design Leishmania
denovani serine hydroxyonethytransferase [SHMT] and chrosimate
synathase [MTCS] have been identified for understanding mechanistic
and structural information
Training provided to 13 students of students of information science giving
them on-the-job training facility for a period of 6 months to 1 year.
One MSc. Biotechnology is undergoing studentship under the BTIS
programme.

areas
With the acquisition of the hardware and other information resources made
available with the fund of BTIS, the center plans to:
Modernize the information base of the center with introduction of state of
the art hardware facilities.
To subscribe to the more user friendly and broader coverage databases to
cater to the changing needs of users.
To develop in-house databases in the areas hitherto untouched by others.
(Mostly information on work being carried out in Indian institutions and
Indian Biotechnology based pharmaceutical companies.)
To have a network within the institute where Biotechnology information will
be available on-line.
Procure state of the art information dissemination techniques and
resources.
To bring out a monthly Newsletter (on-line) of the Biotechnology
Information and activities of the BTIS Centre.

Additional Details:

Name of the coordinator: Dr. Prodyut K Roy
Dy. Director & Scientist-in-Charge
88
Doc. & Library Services Division
Central Drug Research Institute
Lucknow-226001

Phone No.: 522-2613812
Fax. No. 522-623405
Email prodyutr@yahoo.com
Website: www.cdriindia.org
Name of the Contact Person S K Mallik
Email: sumanmallik@rediffmail.com

89
Central Institute of Freshwater Aquaculture, Bhubaneswar
Coordinator : A.K. Roy

The Central Institute of Freshwater Aquaculture (ICAR), Kausalyaganga,
Bhubaneswar established during 1990-91 is a Distributed Information Sub-
Centre (Sub-DIC) under Biotechnology Information System (BTIS) Network of
the Department of Biotechnology, Ministry of Science & Technology,
Government of India. The centre is specialized in the field of Aquaculture and
serves as an information source in the country.

2. Major research activities in Biotechnology and its related fields in
your Institution

Statistical Analysis of Genomic sequence of Carps viz. Labeo and Cyprinus
using SPSS package.
Sustainable genetic improvement of Rohu (Lebeo rohita) for growth through
selective breeding.
DNA fingerprinting of fish microbial pathogens using RAPD-PCR.
Development of DNA markers in Indian major carp, Labeo rohita for studying
population genetic variation and identification of trait associated genes

3. Area of Specialization of the Centre: Aquaculture

4. Major acti vi ties of the Center during the year 2007-08

(A) Organisation of National Workshop:

Workshop: On Bioinformatics and Statistics in Aquaculture Research during 22
nd

to 25
th
January, 2007
Inaguration: By Mr.Amiteshwar Dayal Seth, Manager, Infosys.
Participants and resource persons: 51 participants comprising research scholars,
scientists, associate lecturers, project Assistants and 30 Resource Persons
Organisations/Institutes: IIT-Kharagpur, CDAC, Kolkata, ISI, Kolkata, CIFRI,
Kolkata, BCKV, Kalyani, CRIDA, NAARM, Hyderabad, VIT, Vellore, CIBA,
Chennai, IASRI, New Delhi, NCAP, New Delhi, RRL, Bhubaneswar, OUAT,
Bhubaneswar, CIFRI, Berrackpore etc.
Course content: Data Warehousing, Reverse Engineering of Gene Regulatory
Network by Neural Network, Data mining and Databases, Modeling and
Forecasting and Genetic Statistics, Econometric Analysis, Knowledge Discovery,
etc.

(B) Genomic Sequence, Micro array Analysis and Modeling:

Correspondence Analysis of relative synonymous codon usage values of
nucleotide sequences of Labeo rohita and genes of Cyprinus carpio
Statistical Analysis of Microarray data of Common carp.
Modeling and Forecasting of Fish Production in India.


90
(A) Computer & Communication facility
Hardware: PC's; Multimedia PC; Server; CD Mirror server; Macintosh SE;
1 KVA UPS; Dot Matri, HP DeskJet, HP LaserJet Printers; Cannon Bubble
jet Printers; LCD; Color Scanner; Modem; CD Writer; 5.5 KVA Generator.
Software: MS Office 97, 2000; Novel Netware 4.1; SPAR1; FoxPro;
QPRO; Oracle; M.S. Project; Visual Studio.
Operating System: DOS; Windows 95, 98, XP; UNIX; Linux.
Communication and Network Linkage: The centre has acquired
upgraded and maintenance the following communication facilities:
BSNL Lease Line 512 kbps.
Local Area Network (LAN): More than 100 Computers are distributed to
different scientists, researchers and officers of the Institute and connected
with the BTIS centre through LAN and IP based.

(B) Scientific Software Packages
Statistical Analysis System (SAS); Statistical Package for Social Science
(SPSS) version14.0; Quantity one (gel analysis); DNA Star; UVI
Software (gel analysis).

(C) Databases & Other Information Resources
Renewed Aquatic Sciences and Fisheries Abstracts (ASFA) online of
CSA; The FAO Fisheries Atlas; Diagnosis of Shrimp Disease FAO; FAO
- ICLARM (Stock assessment tool); FishstatPlus (V 2.3) FAO, 2006;
Archives of the Bay of Bengal Programme; Fish Base. FAO.

Sl.
No.
Name Designation Specialisation Period of working
1. Mr. A. K. Roy Pr. Scientist Ag. Statistics Sept. 96 to till date
2. Mrs. N. Panda T-6 Statistics Feb,2005 to till date
3. Mr. D. P. Rath T-4 Comp.
Application
12.10.1990 to till date
4. Mr. S. N. Rath Studentship Bioinformatics Dec 2007 to 01.04.2007
5. Ms. S. R. Martha Studentship Bioinformatics 14.04.2007 to till date


The services include, internet browsing, online and offline bibliographic
databases search, statistical data analysis, creation of presentations, Photo
scanning, printing, loading of software packages and trouble shooting.

Students (M.F.Sc) are regularly trained on application of Computers,
software packages and Bioinformatics in Aquaculture Research.
The training facilities are availed to research workers of various reputed
organizations viz., Utkal University, ICMR, RRL, Regional College of
Education.
By the studentship and traineeship programmes students are regularly
trained in Bioinformatics.
91


Feed back through evaluation and impact of various workshops on ICT application
indicated that Research workers from around the country are showing lots of
enthusiasm in using on-line bibliographic search facilities of ASFA and use of
statistical packages for multivariate data analysis. Lack of infrastructure facilities at
various fisheries colleges/institutions in the country is retarded by the use of modern
technologies by the trained researchers. Hands on training programme of longer
duration are in demand.


The Centre collaborates with various National and International Organizations like
IASRI, NBFGR, CIBA, CMFRI, CIFRI, FAO/UNDP, NACA, World Fish Centre,
etc. for exchange of information related to fisheries in the form of CD ROM database,
software, etc.


Database system on socio-economic status of fish farmers is developed to provide in-
depth details of socio-economic conditions of fish farmers of Kolleru Lake, which
will support in boosting up the result oriented research and development of fish
farmers.


Roy, A. K, S. R. Martha and S. N. Rath. 2007. Correspondence Analysis
of Codon Usage in Labeo rohita, International Symposium on
Chromosome to Genomes (c2g), held during 3-5 July 2007 at CCMB,
Hyderabad, India. 9 -10 (Abs.).
Roy, A. K. and Martha. 2007. Correspondence Analysis in Study of
Genomic Sequence of Labeo rohita, 8
th
Asian Fisheries Forum (8aff),
Kochi held during 20 - 23 November 2007. 317 318 (Abs.GMO 008).
Roy, A. K. and Martha. 2007. Multivariate Statistical Analysis of Codon
Usage values of L. rohita. International Conference on Applied
Bioengineering held at Chennai during 5
th
-7
th
December 2007(Abs.).
Roy, A. K. and N. Panda, 2007. Study on Trend of Growth of Fish
Production in North Eastern States in India. National seminar on Recent
Advances and Rebuilding of Fish and Fisheries in North East India. Dept.
of Pisci cult., St. Antonys College, Shillong-793001.
Roy, A.K., N. Sarangi and G. S. Saha, 2007. Estimation of Impact of
Socio-economic and Farm specific variables on Technical Efficiency of
Carp Culture Farms of Kolleru Lake, Andhra Pradesh, India. 8
th
Asian
Fisheries Forum held at Cochi, India during 20-23 Nov., 2007.
Roy, A. K. and N. Panda, 2007. Projection of Freshwater Aquaculture Fish
Production in India. 8
th
Asian Fisheries Forum held at Cochi, India during
20-23 Nov., 2007.
Roy, A. K., N. Panda and D.P. Rath, 2007. Forecasting of Culture Fishries
Production in India. National symposium on Ecosystem health and fish for
92
tomorrow held at Bartackpore during 14-16 Dec., 2007 organised by IFSI,
Barrackpore


Application of Statistics in Bio informatics related to Aquaculture.
Genomic Sequence and Microarray Analysis of Carps.

14. Details of Training/ Workshop organized and total no. of users trained

Sl
No
Name of the Training/Workshop Duration No. of
participants
1 National Workshop on Perspectives in Bioinformatics and
Its Application to Aquaculture
February
22-26, 1994.
11
2 National Workshop on Networking and Biological Data
Analysis
February
4-6, 1997
23
3 National Workshop on Information Technology in
Aquaculture Research
February
10-13, 1998
49
4 National workshop cum Training Programme on
Bioinformatics and Statistics in Aquaculture Research
February
2-5, 1999.
28
February
8-11, 2000
33
January
16-19, 2001
43
January
08-11, 2002.
34
Application of Bioinformatics and Statistics in Aquaculture
February
4 - 7, 2003
51
9 National Training Programme on Application of
Bioinformatics and Statistics in Aquaculture
June
03 - 06,2003
15
10 National workshop cum Training Programme on Recent
Development in Bioinformatics and Statistics in
Aquaculture,
February
10-13, 2004
52
February
7-10,2006
39
January 22-
25,2007
51
Total 429
15. Impact shown by your center on the growth of biotechnology and allied areas. In
this you may highlight the details like number of papers published with the help
of your center, how your center is promoting various activities of your
organization and neighboring institutions, manpower trained, tools developed,
patents & copyrights acquired and other services offered etc.
Over five hundred researchers representing various organizations (State &
Central) spread all over the country have been trained in application of
Bioinformatics & Statistics in Aquaculture Research.
Bibliographic literature search from ASFA are frequently provided to
people.
Analysis of Genomic and Microarray data using codon usage and SPSS
package.
93
Web Publication: Web site of CIFA (http://www.cifa.in) has been hosted
and updated from time to time with relevant resources on
fisheries/aquaculture for sharing of knowledge.
Books published:
1. Roy, A.K. and N. Sarangi. 2007. Bioinformatics and Statistics in Fisheries
Research, Vol-III. Central Institute of Freshwater Aquaculture (CIFA),
Kausalyaganga, Bhubaneswar. Pp. 558.
2. Roy, A.K. and N. Sarangi. 2007. Applied Bioinformatics, Statistics and
Economics in Fisheries Research. NIPA, New Delhi. Pp. 550.(In Press).


Statistical Analysis of Microarray data in Fisheries
Development of Biophysical and Econometric model through input-output
analysis
Modernisation of the present infrastructure
Modelling and forecasting

Additional Details:
Name of the Coordinator A.K. Roy
Postal Address: Bioinformatics Centre,
Central Institute of Freshwater Aquaculture,
Kausalyaganga, Bhubaneswar - 751002
Phone Number: 0674-2465430 Fax No.: 0674-2465407
Email: cifa@ori.nic.in
94
Central Institute of Medicinal and Aromatic Plants, Lucknow
Coordinator: Dr. Ashok Sharma


Bioinformatics Centre, since its inception in 1999 is the backbone of
information need of all research activities in CIMAP, Lucknow. The centre
started its R&D activities in the areas of Bioinformatics and research activities
undertaken include database development, Software development and
computational analysis in areas such as Genomics, Transcriptomics,
Proteomics, Metabolomics, microsatellite markers identification, drug target
identification, lead molecules identification and computer aided drug
designing in Medicinal & Aromatic Plants. Apart from R&D activities,
Bioinformatics Centre continues to provide facility and technical support for all
IT and internet based services to scientific staff onto their desktop and to
research scholars of CIMAP and nearby institutions. Centre continued to
provide Human Resource Development through its summer and winter
training programs.

institution:

Characterization of biodiversity and conservation of genetic resources of
medicinal and aromatic plants (MAPs) and other plants of interest; Defining of
genes relating to the yield determining steps of metabolic pathways
concerned with chemicals of interest and their modulation; Construction of
transgenic plants; Detection and characterization of new anti-microibal, anti-
cancer/ or pesticidal chemicals of herbal origin and their commercialization;
Building up of MAP related databases; Development of human resources for
R&D in the basic and applied areas of MAP science.


Bioinformatics of Medicinal & Aromatic Plants (MAPs).

4. Major activities of the centre during the year 2007-08:

In Silico analysis of SSRs in ESTs corresponding to alkaloid,
phenylpropenoid and terpenoid biosynthetic pathways in medicinal and
aromatic plants; In Silico analysis of cytochrome P450 in medicinal plants; In
Silico analysis of metal binding sites to study phytoremediation in medicinal
plants; In Silico designing of oligonucleotides using ESTs of Mentha species;
In Silico studies of alkaloid biosynthetic pathways in medicinal and aromatic
plants; In Silico study of distribution and functional characterization of
terpenes in plants; dbAlkaloid: A comprehensive database of alkaloid
biosynthesizing genes; DbAlBioPath: A database on alkaloid biosynthesis
pathways; DBMDR: A comprehensive database of MDR genes; dbTerpene: A
comprehensive database of Terpenes; Database on menthol biosynthetic
pathway

95

Fiber optic based LAN with managed switches (>350 nodes) 2 MBPS radio
link internet connectivity, Silicon Graphics Interface fuel station package, Sun
Microsystems, IBM Pentium 4 with HT technology system, HP systems.


GenoCluster package, SYSSTAT package, VMD 1.8.2 Viewer, Rasmol
Viewer, Swiss PDB viewer, Pymol View, BioEdit, AutoSignal V.1.7, MGL
Tools Autodock tools, PMV, Sigmaplot, Cygwin, Modeller 7V7, DTMM,
VeGA ZZ, Clustal X, Matlab V. 7.0, NAMD 2.4, Bioperl 0.7.2, Biojava 1.20,
hmmer 2.1.1, Phylip, Python 2.5, Python 2.4, Emboss, Win pep 1.0,
Threader, Octave, MDL Chime SP6, TurboC2, Tree View 32, Procheck_NT,
blast-2.2.14-ia32-win32, modeller9v1, ActivePerl-5.8.8.822-MSWin32-x86-
280952, Cn3D-4.1, ACDLAB 8.0, Cluster, D2OL, MDL ISIS Draw 2.5
MS Visual Studio. Net, OCR Fine Reader, Macromedia MX, Oracle 9i,
Application Server, Adobe Acrobat, MS Back Office Server 2000.

C. Database & other information resources:

a. Bibliographic Databases on CD-ROM
Agris, Agricola, Medline, Biotechnology Abstract, Altmedex
b. E-Journal Gateway Platform
J-Gate (Agricultural & Biological Sciences)
c. In Diskettes
Current contents (Agriculture, Biology & Environmental Sciences), Abstract
Edition from Vol.34 onwards.
d. E-Journals
(Through CSIR e-journals Consortium)
Elsevier, Blackwell, Springer-Kluwer, Oxford University Press, Wiley, Royal
Society of Chemistry, American Chemical Society, Cambridge University
Press.

6. Details about Staff members working in the centre (Name of Staff,
Designation, Specialization and period of working):
Name of the Staff Designation Specialization Period of
working
Absorption
status
Dr. Ashok Sharma Scientist-F & Head Bioinformatics Permanent Permanent
Feroz Khan Scientist-C Bioinformatics Permanent Permanent
Kumar Parijat
Tripathi
Project Assistant Bioinformatics 6-6-2006 Contractual
Sudeep Roy Project Assistant Bioinformatics 16-10-2006 Contractual
Akansha Saxena Research Intern Bioinformatics 12-3-2007 Contractual
Sanchita Project Assistant Bioinformatics 17-9-2007 Contractual
Manoj Mishra Project Assistant IT 10-11-2006 Contractual
Naresh Sen Project Assistant IT 20-9-2007 Contractual

96

E-mailing, Internet access, LAN management, System management, Web
designing & hosting, Software development, Database development on
MAPs, Digitization of MAPs information, Human Resource Development in
Bioinformatics of MAPs, R&D and S&T Publications, Computational services,
Information support.


CIMAP-JNU Ph.D Programme in Life Sciences (Biotechnology and
Bioinformatics)
Students placed as scientists in CSIR labs- ITRC, NBRI, as Faculty in
University Banasthali Vidyapeeth, Banasthali, as R&D staff SGPGI,
Lucknow and several others organizations like TCS, Mumbai

9. Initiatives to validate the outcome of Bioinformatics resources:

The activities of the centre has helped in popularizing the concept, utilities
and tools of Bioinformatics among the user organizations and individuals.
Centre has successfully met their information requirements. New databases
in the areas of MAPs has been generated. The network and services created
is playing instrumental role in communication, database research, patent
searches and market search.

10. Collaborative work/initiatives:

Lucknow University, Lucknow, Bundelkhand University, Jhansi, Jawaharlal
Nehru University, New Delhi, Allahabad Agricultural Institute, Allahabad, Veer
Bahadur Singh Purvanchal University, Jaunpur, Mother Teresa Womens
University, Kodaikanal, Choudhary Charan Singh University, Meerut,
Banasthali Vidyapeeth, Banasthali, Barktullah University, Bhopal.

11. Databases/Softwares packages developed:
DbAlBioPath: A database on alkaloid biosynthesis pathways
dbTerpene: A comprehensive database of Terpenes
MBiopath: A database on menthol biosynthesis pathway

Ashok Sharma, Tanuja Rastogi, Menakshi Bhartiya, AK Shasany, SPS
Khanuja. 2007. Type 2 diabetes mellitus: phylogenetic motifs for predicting
protein functional sites. Journal of Biosciences 32(5): 999-1004.
Khanduri S, Roy S, Tripathi KP, Saxena A, Saxena A, Sharma A, Khanuja
SPS. 2007. Putative metal binding motifs: An in silico analysis to study
phytoremediation in medicinal plants. International Conference on
Bioinformatics and Drug Designing (BIOCONVENE 2007), Hyderabad, 20-
22 December, 2007.
Tripathi KP, Khanduri S, Sudeep Roy, Saxena A, Sharma A, Khanuja
SPS. 2007. Functional perspectives of SSRs corresponding to alkaloid,
terpenoid and phenylpropanoid biosynthesis. International Conference on
97
Bioinformatics and Drug Designing (BIOCONVENE 2007), Hyderabad, 20-
22 December, 2007.
A Saxena, Sudeep Roy, KP Tripathi, A Saxena, Sanchita, Manoj Mishra, J
Singh and Ashok Sharma. 2007. Biopiracy of traditional knowledge: IPR
protection. National Convention & Seminar on Business Enabling of
Aromatic Plants Products (BEAP-2007), DehraDun, 21-22 November,
2007.


Genomics, Transcriptomics, Proteomics & Metabolomics (Omics sciences)
studies in the area of MAPs.

14. Details of Training/Workshop organized and total no. of user trained:
One month CIMAP Summer Training on Techniques and Tools of
Biotechnology and Bioinformatics (CST-2007) held during June-July,
2007. Trained 30 students.
One month CIMAP Winter Training on Techniques and Tools of
Biotechnology and Bioinformatics (CWT-2007) from January February,
2008. 24 students are likely to participate.
Dissertation/project work: Ten students trainees (B.Tech./M.Sc.)
completed their six months training/dissertation at our centre.

15. Impact shown by the Centre:

Bioinformatics Centre of CIMAP, Lucknow is continuously progressing
towards the centre of Excellence in the R&D of MAPs Bioinformatics. The
extensive research is going on the secondary metabolism of MAPs, genomic
sequence analysis (ESTs) for SSRs markers development on various MAPs
plants e.g. Mentha, Catharanthus etc. Beside this, some of the impacts
shown by the Centre are: Strengthen the ongoing research projects;
Successfully organized the Bioinformatics training & teaching & contributed to
manpower development.


Bioinformatics R&D in metabolic pathway modeling, computer-aided drug
design, genomics, proteomics, protein structure prediction, phylogenetics,
transcriptomics, metabolomics with particular reference to medicinal &
aromatic plants; To organize short term training & workshop annually for the
benefits of researchers involved in biotechnological/bioinformatics research;
To develop teaching/training package in Bioinformatics with particular
reference to the course work for Ph.D. research scholars; To cater the
regional & national needs, the work on the specific databases development;
Construction of Bioinformatics resource server.

Additional details:
Name of the Coordinator : Dr. Ashok Sharma
Postal Address : Central Institute of Medicinal & Aromatic
Plants, P.O. CIMAP, Lucknow-226015
Phone Number : 0522-2357133 Mobile : 09839075970
98
Fax No. : 0522-2342666
Website : www.cimap.res.in
Name of Contact Person : Dr. Ashok Sharma
Email : ashoksharma@cimap.res.in
ashok_sh58@yahoo.com

99
Central Plantation Crops Research Institute, Kasaragod, Kerala
Coordinator : Dr. George V. Thomas

The center was initiated in 2001. During the last seven years the centre has
concentrated on development of databases on plantation crops viz. cocoa, coconut
and arecanut. The centre has developed eighteen databases covering different aspects
of mandate crops dealt by the institute. The centre has also contributed for human
resources development activities and conducted eleven training programs on various
topics related to bioinformatics and information technology with specific reference to
Plantation crops. Twelve students have completed their project work and four are
doing their project work under studentship program. Seven were trained on different
aspects of bioinformatics applications and at present three are getting training as part
of traineeship program. A brainstorming session was conducted on Databases for the
Management of Genetic Resource on Horticultural Crops. The Centre provides web-
based services at http: www.bioinfcpcri.org. The centre has also developed and
customized two softwares.
institution
Molecular markers based characterization of conserved coconut germplasm in
national gene bank and selected farmers varieties in the IPGRI/COGENT poverty
reduction site in India.
Development of Molecular markers to fingerprint coconut accessions.
Molecular studies for tagging root (wilt) resistance genes in coconut.
Tissue culture for rapid multiplication of elite genotypes and basic studies in coconut
Early sex determination and in vitro multiplication in palmyrah palm.
In vitro Multiplication of Coconut and Arecanut
Developing coconut molecular marker database.

Bioinformatics applications in plantation crops (coconut, arecanut and cocoa)
During the reporting period the center has developed three databases Palm database,
Copgene data base and Stress gene data base. Other databases were updated regularly.
These databases are IP restricted and limited accessibility is provided at the website
http:// www.bioinfcpcri.org. During this period the center has conducted a ten days
training programme on Applications of Bioinformatics and Biotechnology in
Plantation Crops Research. At present four bioinformatics students are doing their
studentship project and three trainees are getting training under traineeship
programme.
a. Computer & Communication facility
IBM web server, LAN server, Pentium 4 Computers, Nodes, UPS and
other accessories with 512 Kbps leased line connectivity from BSNL.
b. Scientific Software packages
100
Data mining and analysis tools
1. EMBOSS Jemboss 2. GDE Genetic Data Environment
(Blast, Fasta, NCBI Tools, Read seq, Primer3, Fast PCR,
SCPrimer, Phylip, Clustal W or X, Tree Tools etc.) 3. Staden
Package 4. Forage 5. Protein docking software Hex, Argus lab 6.
Phred, Phrap, cap3
Phylogenetic & Map making Softwares
1.NTSYS 2.Phylip 3. Total Lab 4. Arelequin 5. Mapmaker
6. QTL 7. Popgene
Bootable CDs with Bioinformatics software
1.Biolinux 2. Vigyann CD 3. DNA linux
c. Databases & other information resources:
1. NISC Discover 2. Agris 3. Agricola 4. HortCD 5. Soil CD 6.
CAB Pest CD 7. Tropag and Rural CD 8. Indian Science
Abstracts on CD 9. AgEcon CD
absorption status)
1. Ramesh Kumar.
Acting Information Officer
Information Science
Six years (Permanent)
2.P.Saritha.
Project Assistant
M.C.A
3 Months
(Temporary)
3. V.Sreesmitha
Project Assistant
Bitechnology
1 month
(Temporary )
4. Anoop Raj P
Computer
Operator
MCA
8months
(Temporary )
5. Nishad.K.P
Data Entry
Operator
DCE
3 months
(Temporary )

6. Types of services provided : Provides
facilities to analyze the protein structure
prediction and nucleotide / protein sequence
homology search and molecular docking using
bioinformatics softwares and tools.
Provides web based access to databases
This center provides internet services for data mining, literature survey
etc.
Conducts training programmes and workshops in the field of
Bioinformatics.
Under studentship program four students are doing their projects on following
topics.
a)Molecular marker database for coconut germplasm accessions.
b) Molecular phylogenetic studies in palms.
c) Database of coconut from root wilt endemic areas
d)Validation of EST-SSRs in coconut and Cocoa
e)Isolation and charecterisation of insect odorant binding proteins
f)Detection of phytoplasma in palms using molecular technique
101
Researchers of the institute are using the software and databases developed by the
centre.
The research community is utilizing all databases.
Software developed by the centre is being used for analyzing sequence data
and protein structure.
Collaborative activities are taken up with the other Bioinformatics
Centres working on similar crops.
During this period 2006 07 the centre has developed following databases.
a. Palm database
A database of Palm Resources. belonging to the family Arecaceae. The palms are
monocots and have 202 described genera with about 2779 species. Evaluation of
relationships among palms through molecular and morphological tools could provide
some interesting insights to their phylogeny and its classification. This database provide
genomical approaches and taxonomical details of Palms.
b. Copgene database:
Coconut and Oil palm putative gene annotated database provide the blast results and gene
information of EST & Contigs of above crops.
c.Stress gene database:
Many genes and proteins are playing an important role in plantation crops.
Dehydrin , DREB (Binding factors & transcription factor), Heat shock protein, LEA-Late
Embryogenesis abundant, LTP- Lipid transfer protein, MAPKINASE - Mitogen activated
protein kinase,SERK- Somatic Embryogenesis receptor kinase, SERK-Somatic
Embryogenesis receptor kinase, WRKY- Transcription factor and14-3-3 protein are
found an important proteins and genes in plants. These proteins & genes sequences can
be retrieved with navigation menus of respective genes and proteins from this database.
a)Anitha Karun, Rajesh, M.K., Sajini, K.K., Radha, E., Parthasarathy, V.A.
(2007) Regeneration systems in plantation crops. Proceedings of National
Seminar on Horticultural Biotechnology: Present Status and Future Action
Plan. Held at IIHR, Bangalore on 8
th
December 2007, pp. 50-56.
b)Jiji, G., Karun, A., Manimekalai, R., Rajesh, M.K. and Remya, P. (2007)
Identification of RAPD markers linked to sex determination in palmyrah
(Borassus flabellifer L.). Current Science, 93(8): 1075-1077.
c)Rajesh, M.K. and Anitha Karun (2007) Isolation and characterization of
stress responsive genes in coconut. Proceedings of National Seminar on
Horticultural Biotechnology: Present Status and Future Action Plan. Held
at IIHR, Bangalore on December 8
th
2007, pp. 9-11.
c)Rajesh, M.K., Anitha Karun, George V. Thomas, Parthasarathy, V.A.
(2007) Databases for coconut and cocoa. Proceedings of National
Seminar on Horticultural Biotechnology: Present Status and Future Action
Plan. Held at IIHR, Bangalore on 8
th
December 2007, pp. 272-273.
102
d)Rajesh, M.K., Niral, V., Manimekalai, R., Devakumar, K., Anitha Karun
and Parthasarathy, V.A. (2007) Molecular markers in coconut.
Proceedings of National Seminar on Horticultural Biotechnology: Present
Status and Future Action Plan. Held at IIHR, Bangalore on 8
th
December
2007, pp. 176-180.
e)Riju et al., Bioinformation 2(4): 128-131 (2007)

1. Gene expression studies and development of molecular databases on
palms and cocoa.
2. Molecular Docking of chemical constituents of areca.
3. Creation of coconut genomic databases.
1. Applications of Bioinformatics and biotechnology in plantation
crops research for the period of ten days with ten participants.
The centre extends facilities for the researchers and students
from Mangalore University, University of Kannur, University of
Calicut, University affiliated colleges, IISR, NRC Cashew, NRC Oil
Palm and all ICAR institutes
In the current year twenty-five research workers/ students were given
training on various aspects of bioinformatics.

Creation of database of stress responsive genes
Gene expression studies and updating molecular markers databases
on palms and cocoa.
Genomics and proteomics studies of coconut related genes.
Updating of existing databases.
Conducting training programmes.

Name of the Coordinator : Dr.George. V.Thomas
Postal Address :Central Plantation Crops Research Institute,
Kudlu P.O, Kasaragod 671124, Kerala, India.
Phone Number : 04994-232974, 04994-232894, (5)
Fax No. : 91-04994-232322
Email: bioinfocpcri@yahoo.com
Website : http://www.bioinfcpcri.org
Name of Contact Person(s) : Dr.George. V.Thomas, Coordinator
Email : bioinfocpcri@yahoo.com
103
Central Sericultural Research and Training Institute, Mysore
Coordinator : Dr. C. K. Kamble


The Bioinformatics Centre at CSRTI, Mysore was established in November, 1999
under the BTIS programme of the DBT, Govt. of India as a Sub-DIC. The center is
well equipped with the infrastructure facilities comprising of 11 computers, one
server, five printers, one digital video camera, one multimedia projector etc. The
internet is being accessed through leased line of BSNL with 512 kbps speed. The
website of the center is being hosted from the centres server with the URL
www.btismysore.in. The main focus of the center is to support biotechnology
research pertaining to Sericulture and so far seven databases related to the host plant,
mulberry and silkworm have been developed. The center has conducted 14
workshops in which 451 personnel were trained.

2. Major research activities in Biotechnology and its related fields
in your institution

Central Sericultural Research and Training Institute, Mysore is the premier
Institute par excellence with all modern facilities and infrastructure, which has
made a mark as leading R &D institution on Tropical Sericulture in country
and is well recognized as a centre for higher learning and advanced training
on International front. The research focus of the Institute is slowly but steadily
shifting to the molecular biological aspects of sericulture and biotechnological
investigations are likely to assume center-stage during the coming years. A
total of 12 research projects mostly funded by DBT are being carried out on
the areas like mulberry genome characterization, identification of QTLs for
root traits and water use efficiency, cloning and characterization of
epicuticular wax synthesizing genes, DNA markers associated with diseases
and pest resistance in mulberry, transformation for draught tolerant mulberry,
evaluation of transgenic mulberry for abiotic stress, cloning and
characterisation of antiviral gene in silkworm, DNA markers associated with
baculovirus resistance in silkworm, digital inventory of silkworm resources etc.
3. Area of Specialization of the center
The main thrust area of this center is Seri-biotechnology and
Seri-bioinformatics.

4. Major activities of the center during the year 2007-08

Seven Databases developed were updated and maintained. Infrastructure
facilities and support through bioinformatics tools and techniques were
provided for the scientists of the Institute for their projects and experiments.
The center is hosting the 19
th
Annual All India Coordinators meeting of
BTISnet during February 3-4 2008.

104
A. Computer & Communication Facility:
The center has 7 Pentium III, 3 Pentium IV desktop computers, 1 Lap
top computer, 1 HP Compaq ML 150 Server, 1 Epson Dot matrix, 2 HP
inkjet and 2 HP laser printers, 3 CD and 2 DVD writers, 1 Sony digital
Video camera, 1 5 KVA UPS and 1 Mitsubishi Multimedia DLP projector.
The internet access is through 512 kpbs leased line from BSNL.

PHYLIP, SPSS, Cn3D, Clustal W, PDB on five CDs, EMBOSS, Artimis
Genome analysis package, Pinnacle DV Studio.

Name of the staff Designation Specialization Period working
Dr. S. K. Ashwath Scientist C M.Sc., P.hd April 2007
2. Mr. Anis Ahmed Shariff Technical
Assistant
B.Sc., PGDCA, PGDSM,
Computer Applications;
Sericulture & Sericulture
Management
November 1999

8 years
3. Mrs. Gousia Kauser Technical
Assistant
B.Sc., STC in Sericulture,
Diploma in Computer Office
Automation

November 1999

8 years
4. Mr. K. Guruprasad Computer
Operator
Master of Computer
Application
December 2004

3 year
Computer
Operator
Under
Recruitment
Note : The recruitment of Information Officer is under progress
7. Type of Services provided
The center is equipped with 512 kbps BSNL Leased Line Internet
connectivity and internet facility is provided to all the research laboratories through
LAN. The centre extends the infrastructure facilities and software support to the
scientists working in the field of molecular biology and offers guidance to students
for their dissertation or project work.

The center does not offer any course in bioinformatics which can lead to placement.

The databases developed related to silkworm and mulberry biotechnology have been
made accessible through the website of the center for the use by scientists working in
seribiotechnology.

The training in Bioinformatics has been incorporated in to the Adhoc Practical
Training Course for M.Sc. Sericulture students from SPMVV Tirupati This centre is
imparting need based training programmes in various topics in bioinformatics and
also dissertation and projects works for students of both under graduate and Post
graduate level from the engineering colleges and university of Mysore, Tamil Nadu,
Andhra Pradesh and Kerala.
105

11. Databases/Software developed/maintained: The following Databases
have been developed & maintained.

1. An Annotated Protein database for Silkworm and Mulberry : SILKPROT
2. Growth indices in popular breeds/hybrids of silkworm Bombyx mori L. in
relation to nutritional conditions
3. Database of DNA sequences for important plant genes and mulberry.
4. Mulberry Genome database
5. The Silk e-Lab
6. Sample Web Application for Analysis of RAPD scores
7. Web Application for Mulberry varieties, diseases, products and byproducts
utilization in sericulture
8. Wikipedia for the Bioinformatics Centre

The centre is planning to host the databases from its own server. The present
databases are being updated and upgraded regularly.

1. Kaladishvarane K., Guruprasad K., Raveendra M., Dandin S. B., (2006).
Silkprot : a database of silkworm proteins. Paper presented at
International conference on Bioinformatics (InCoB) 2006.
2. Guruprasad K., Raveendra M., Girish Naik V., Dandin S. B., (2006).
Mulberry Genome database of silkworm proteins. Paper presented at
International conference on Bioinformatics (InCoB) 2006.

13. Initiation of R&D activities in Bioinformatics: The centre is involved in
developing algorithm, designing database structure and modifying the same
for the development of databases on silkworm proteins and ESTs.
106
So far, this centre has trained 451 personnel through the following workshops and
training programmes.
No. of Resource Persons SL.
NO
Titles of Training
Programme / Workshop
Date
From -To
No. of
Partici
pants
External
Faculty
Internal
Faculty
Chair
persons
1. Computer Basics and
Applications
June 14-15,2002 14 7 - -
2. Intensive Workshop on
Bioinformatics
February 3 -7, 2003 78 16 4 8
3. Career Planning in
Bioinformatics
June 20-21,2003 23 - 9 -
4. Intellectual Property Rights August 25-28, 2003 30 13 2 -
5. Training Programme on
Biotechnology And
Bioinformatics in
Sericulture
August 29-30, 2003 26 3 4 4
6. Workshop on
Biotechnology and
Bioinformatics In
Sericulture
Dec. 9-10, 2004 32 2 5 4
7. Computer Basics &
application in Modern
Audio Visual
Presentations
Mar.7-14 2005(BatchI)
Mar.28-Apr.7 2005 (Batch II)
May 30-Jun.9 2005(Batch
III)
30 - 3 -
8. Career Awareness
Programme
April 5,2005 15 - 3 -
9. Workshop on
Bioinformatics
September14 15, 2005 35 4 4 4
10. Workshop on
Bioinformatics
October 17-18,2005 47 7 2 4
11. Workshop on Information
Commu-nication
Technology initiative
February 23, 2006 30 -- -- --
12. Workshop on
Bioinformatics for BTech
Biotechnology students.
August
28-29, 2006
38 9 3 4
13. Workshop on
Bioinformatics for B.Sc. &
M.Sc. Biotechnology and
Life Science students.
December
28-29, 2006
32 04 3 4
14. Need Based training in
Bioinformatics

22.01.2007 to 01.02.2007

21 -- 3 --
Total 451

areas.
107
A total of 233 Research papers were published by the scientists of the
Institute & Nested units (International - 31; National 43; Books/Booklets
6; Published in proceedings 1; Presented in Conferences 109; and
Popular articles 49). The institute is publishing the Indian Journal of
Sericulture ( Biannual), Seridoc (Biannual) and Reshme Vahini ( Bimonthly).
CSRTI, Mysore is has made a mark as a leading R & D institute on tropical
sericulture in the country and is well recognized as centre for higher learning
and advanced training on international front. With its well developed
infrastructure and strong indigenously developed technological base, the
institute Its role in generation of trained human resources has been always on
high pedestals, both at domestic and international levels. As a major
component of the institute mandate, training was provided to a total of 3757
persons under different programmes. Major Sericulture states were covered
to impart training in different disciplines of sericulture.
Students of biotechnology from colleges under Mysore University and
engineering colleges in and around Mysore are being given training in
bioinformatics and also projects/dissertation works are being supervised..
Applications for the patents were submitted for the technologies, like Chetak
for controlling mulberry diseases and pests and Semi synthetic diet for rearing
young instar tropical tasar silkworm. Further, products/machines, namely,
Samrudhi (Juvenile Hormone Analogue), Spoorthi (Mulberry Health Drink),
Plastic rotary montages and frames, Hydrodynamic incubator, Single cocoon
pusher, Composite cocoon harvester, were licensed for commercial
production.

16. Future Activities
The existing databases will be enhanced to add further new feature. The
same will be hosted from the present server. New databases on mulberry
proteins, ESTs in silkworm will be developed and blast feature will be made
available locally. This centre will conduct workshops and training programmes
in Bioinformatics to suit to the needs of students and professionals.

Additional Details:
Name of the Coordinator : Dr. C. K. Kamble
Postal Address : Director and Coordinator,
Central Sericultural Research & Training Institute,
Manandavadi Road, Srirampura, Mysore 570008,
Karnataka.
Phone No.: (0821) 2362757, 2362406, 2363440
Fax No.: (0821) 2362845, 2362420
Email : drckkamble@yahoo.com, director@csrtimysres.in
btis_csrti@yahoo.com
Website : www.csrtimys.res.in
Name of Contact Person: Dr. S. K. Ashwath, Scientist C
Email : btis_csrti@yahoo.com
108
Centre for Cellular & Molecular Biology, Hyderabad
Coordinator : Dr. K. Guruprasad

The centre has transformed itself from primarily hosting public databases to
conducting research and development in bioinformatics. It has developed a number
of useful databases & software applications in bioinformatics. Various research
groups in the institute use & develop methods in bioinformatics for protein sequence-
structure analysis, analysis of non-coding regions in human genome, SNP analysis,
EST analysis, gene prediction, proteomics & micro-array data analysis, mathematical
modeling of biological systems, plant host-pathogen interactions, protein pathways,
comparative genomics, RNAi mechanism & structural biology. With state-of-the-art
experimental infrastructure in place at the CCMB, such as, sequencing, micro-array,
proteomics, confocal microscopy, AFM, crystallography & NMR, bioinformatics is
central to integrating data generated from these resources.

institution
Identification of DNA markers associated with disease and pest resistance in
Mulberry (Morus spp.). Development of microsatellite markers for mulberry,
beetlevine, Red Panda/olive ridleys. Molecular & prenatal diagnosis for
genetic disorders & chromosomal diagnostics. Molecular imaging. Cell and
tissue engineering of animal and human cells. Stem cells from murine bone
marrow and human fetal liver for use in hepatic regenerative medicine.
Evaluation of new ceramic-based biomaterials for use as osteogenic implants.
Nanomaterials and nanodevices in health and disease. Triglyceride sensor,
lipid and peptide-based gene delivery strategies. Plasma proteomics in health
and disease. Proteomics of mouse embryonic stem cells. Transgenics and
aquaculture. Use of AI techniques for producing spotted deer. Gene-
environment interaction to study drug response. Non-invasive detection of
hormonal steroids in scat samples of lions. Antibacterial activity by peptides
derived from human beta defensins. Gene silencing and RNA interference.

Sequence/structure analysis of nucleic acids/proteins, micro-array &
proteomics data analysis, comparative genome analysis, SNP analysis &
mathematical modeling and protein networks, biodiversity analysis, wild-life
identification, databases/software development.

1. We are identifying triplet repeat associated genes in the human genome
and studying their evolutionary conservation across different organisms.
We are carrying out molecular analysis of the genes associated with sex
determination/differentiation and using mitochondrial DNA analysis for
studying human population diversity and the origin of deep rooting
lineages of mitochondrial macrohaplogroup M in India. We are analyzing
non-coding regions in human genome. We have updated the following
databases: beta-propellers (version 2.0) in protein tertiary structure,
protein sequence-structure PSSARD (version 2.0), HETGRPANAL
(version 2.0) database/software that can identify all the known hetero-
groups in protein tertiary structure and their neighbouring atoms. We are
109
analyzing specific sequence patterns observed in protein tertiary structure
and the binding preferences for some of the metal ions in protein
structure. We have analyzed and generated database of disulphide bond
connectivity patterns (DBCP) and intra-chain disulphide bridged peptides
(ICDBP) in protein tertiary structure. A beta-version of the relational
Database of Structural Motifs in Proteins (DSMP-O) is developed. We are
analyzing the non-coding part of a genome in order to identify novel
elements that function by programming the genomic packaging and to
study genome organization and regulation of gene expression. We are
identifying SNPs and SNP haplotypes, developing de novo gene finding
methods and a database of signal transduction pathways. We used
sequence analysis to show that the non-coding RNA controls the
synthesis of cell division kinase protein in testis. We are modelling
spatiotemporal organization in biological systems. We are carrying out
genomewide analysis of Bkm sequences (GATA repeats): Human,
Mouse and Chimpanzee Genome. We are predicting the RDE-4
structure involved in RNA Interference pathway of C.elegans. We are
analyzing the molecular dynamics simulation of alpha and beta-defensins.

d. Computer & Communication facility
Dell Poweredge 2850 Servers: Used for Web and Email Services.
Compaq Alpha ES45 Server: Used for Scientific Softwares & Scientific
Databases.
Sun E420R Server: Used for Scientific Softwares.
SUN UltraSparcII 60.0 workstation: Used for Sequence Analysis Server
ONYX 2 Workstation: Molecular Modeling Server
Dell Poweredge 2800 Servers: Used for Databases (like SPINE (Stores and
Purchase Integrated Management Software, FBIS (Fine Biochemicals
software)
Dell Optiplex GX280 PCs: These PC are used for Intranet Server, DHCP
Server, Firewall (Check Point) Server, (Inter Web Scan and Internet Mail
Scan) IWSS and IMSS Server
Dell Optiplex GX280: It is configured for Scientific Softwares like sigma plot,
SPSS, Reference Manager.
Dell Optiplex GX280: PC is configured for Discovery Studio Modeling 1.1
Software
Dell Optiplex GX270: Oracle Database Server.
Number of PCs in Bioinformatics Division: 40 PCs. All the PCs are
connected to the Internet.
Telephone Instruments in BIC: 4 External , 5 Internally connected
Printers: 3 Nos (HP Laser Printers)

e. Scientific Software packages

1. Sigma Plot 9.0 : SigmaPlot 9.0 is specifically designed to aid in
documenting and publishing research, specializing in the graphical
presentation of results. It is used for data analysis.
110
2. Discovery Studio Modeling 1.5 from Accelrys: It is used for basic
functionality focused on protein characterization, X-ray analysis,
proteomics functional annotation and homology Modeling.
Discovery Studio Modeling 1.2 from Accelrys: It is used for structure
based drug design, including evaluation of ligand-protein interactions, de
novo design and virtual screening.
3. SPSS 11.0: It is a package used for statistical analysis.
4. Reference Manager 11.0.1 for Windows: It is an online search tool. It
provides a simple way to search online bibliographics databases and
retrieve the references directly into Reference Manager
5. Local versions on HPC server model HCL of Blast, Clustal, T-Coffee,
Phylip, EMBOSS, Repeat Masker, Phrap, SIFT, Polyphen, Mfold, MEME,
Phred, Grail.
6. Smart Draw Suite ver.7 a tool for creating flowcharts and technical
diagrams.
7. Solar Winds Engineers ver.8 Network Management
8. AVADIS for Affymetrix Gene Chip system

f. Databases & other information resources
Nt, Nr, SP, PDB, EST, human genome (chromosome-wise), chimp genome,
mouse genome, etc., for Blast.

Other Softwares and Databases installed at Bioinformatics are: Oracle 10g
Database, MySql Database, Red Hat Linux Enterprise ES ver 3.0, Red Hat
Linux Enterprise AS ver 3.0, MS Windows 2003 Advanced Server, MS Office
2003, Macromedia Web Design Studio, Adobe Acrobat 7.0, Adobe
PageMaker ver 7.0, Adobe Photoshop 7.0, Macromedia Dreamweaver,
Fireworks, Freehand, Homelite, Microsoft Windows XP, Microsoft Windows
98/2000, Microsoft Office 2000/XP

Local Area Network: CCMB has a Local Area Network (LAN) connecting all
buildings in the campus at 1 Gbps core backbone speed and switched 10/100
Mbps to desktops, Spectroscopy, Proteomics and DNA sequencing facilities.
Cisco 3825 series Router with 2 WICs, 2 NICs and 2 serial ports. One 48-port
and two 24-port HP Procurve switches with 1 Gbps uplink fiber modules have
been installed. The CCMB network is secured by Nortel Alteon Firewall with
Checkpoint software and centralized gateway-level Antivirus (including Web
and E-mail), SPAM prevention and Damage Cleanup Services (Trend Micro
Neat Suite, Enterprise Edition). The last mile connectivity for the Internet
leased line is connected with optical fibre cable from the nearest telephone
exchange to the CCMB campus. The Internet leased bandwidth from VSNL is
2 Mbps. Internet kiosks, wireless access points provided during all major
seminars and workshops. VPN connectivity between CCMB & IGIB, Delhi
established for collaborative SNP project aimed at sharing details of
populations as well as gene polymorphisms.

CCMB E-Mail Service: The Web Mail (Mithi Connect Server) including global
access has been deployed on Red Hat Enterprise Linux AS3.0 with X86_64
bit architecture to enhance the processing speed with 2GB RAM and about
1TB RAID storage devices for storing mail users data. The primary mail
server is supported with a redundant disaster recovery secondary server of
111
identical architecture mirroring the users data in real time along with an auto
fail over.

absorption status): N/A (The staff employed against the sanctioned
positions at the Bioinformatics centre have been absorbed).


The bioinformatics centre and infrastructure facilities are open round the clock for use
by CCMB staff and research students/post-docs, summer students, project
assistants/trainees, guest workers or collaborators. Periodic symposium/workshop are
organized.

8. Educational activities with details of placement N/A

9. Initiative to validate the outcome of bioinformatics resources N/A

CCMB Bioinformatics staff participated in the NMITLI SNP network project,
CSIR project with Proctor & Gamble, USA, and a number of internal
collaborations with other CCMB staff and other external collaborations.

1. PSSARD: http://203.200.217.185:8000/rdpssa/index.htm
2. HetGrpAnal:
http://203.200.217.185:8000/hetatm/index.htmDBCP:
http://203.200.217.185:8000/dsbcp/index.htm
4. ICDBP: http://203.200.217.185:8000/dsl/index.htm
5. BETA PROPELLERS:
http://203.200.217.185:8000/dsmpo/propellerversion2/home.htm
The above databases/software were developed in-house and are freely
accessible from our website. PSSARD is a database for the analysis of
protein sequence-structure. HetGrpAnal is a database of heteratom groups in
protein tertiary structure and an application to identify neighbours. DBCP is a
database of intra-chain disulphide bond connectivity patterns in protein
tertiary structure. ICDBP is a database of intra-chain disulphide bridged
peptides in protein tertiary structure. Beta-propeller is a database of all known
beta-propellers in the PDB. COMBITURNS is a database of combination of
turns in proteins. Beta-propeller.pl is a software for the automatic detection of
known beta-propellers in a given Protein Data Bank (PDB) file.

1. Settu Sridhar and Kunchur Guruprasad Conformational analysis corresponding to intra-
chain disulfide bridged peptides in proteins of known three-dimensional structure. Protein
and Peptide Letters (2007, in press).
2. Settu Sridhar, A. V. N. Babu and Kunchur Guruprasad PSSARD (2.0): A database server
for making flexible queries relating amino acid sequences to main-chain secondary
structure conformations for proteins of known three-dimensional structure and certain
useful applications. Int J Biol Macromol. 2007 Jun 1;41(1):109-113.
112
3. V.Jai Kartik, T.Lavanya and Kunchur Guruprasad Analysis of disulphide bond
connectivity patterns in protein tertiary structure. Int J Biol Macromol. 2006 May 30;38(3-
5):174-179.
4. Kunchur Guruprasad, V.Jai Kartik, T.Lavanya and Lalitha Guruprasad Juxtaposed half-
cystines as disulphide bridged partners in protein tertiary structure. Protein and Peptide
Letters 2006;13(6):577-579.
5. Aggarwal, R.K., Kivisild, T., Ramadevi, J., and Singh, L. Mitochondrial DNA coding region
sequences support the phylogenetic distinction of two Indian wolf species. Journal of
Zoological Systematics and Evolutionary Research 2007;45:163-172.
6. Bajpai, A. Settu, S., Reddy, H.M. and Rachel, A.J. BRM-Parser: A tool for comprehensive
analysis of BLAST and RepeatMasker results. In Silico Biology 2007;7:27.
7. Rajesh, S., Sinha, S. and Somdatta Sinha. Synchronization in coupled cells with
activator-inhibitor pathways. 2007, Physical Review E, 75:011906.

Poster presentations:
1. Bhardwaj, A. and Tiwari, S. Evaluating the association of mitochondrial
SNP haplotypes with disease phenotypes using a novel in silico tool E-
MIDAS. In: Proceedings of the 9
th
International Conference on Information
Technology (ICIT 2006), IEE Computer Society, 17-20.

We have initiated R & D activities in protein sequence-structure analysis,
comparative genome analysis, SNP analysis, drug-design, pathway modeling,
systems biology and human genetic diversity analysis.

14. Details of Training/ Workshop organized and total number of users trained:
11
th
ADNAT Convention A Three Day Symposium on Advances in
Structural Biology and Structure Prediction, Feb 23, 24 & 25, 2007.
11
th
ADNAT Convention Hands on Training Course on Protein Structure
Prediction and Structure Determination, Feb 26 March 8, 2007 [15
participants].
One-week DST sponsored Bioinformatics Training Programme for Senior
Scientists & Technologists (working with Government of India) titled
Perspectives and Current Trends in Bioinformatics, 12 18
th
September
2007 [42 participants].
There are a number of visiting scientists and guest workers apart from the regular
staff and research scholars who use the facilities. We provide summer training (6-8
students) and also provide long-term training to 10-12 graduates/post-graduates under
the DBT traineeship/studentship program every year. We also train our JRF batches.

Number of papers published: 7. The infrastructure facilities provided at the
centre is helping users of these facilities both within the laboratory and from
outside to add-value to their research. This is evident from some of the
publications and patents listed at (http://www.ccmb.res.in). A number of
project students and trainees have benefited by working at the centre. It has
helped them procure jobs in industry or in further developing their career by
113
seeking Ph.D positions abroad. Some trainees have contributed to research
publications and are therefore better qualified to seek Ph.D positions abroad.

We will develop databases/software tools relevant to bioinformatics. We will
continue to accept post-graduate students for short-term training programs
sponsored by the DBT and contribute to manpower development. We will
organize symposium/workshops periodically. We will recruit project
assistants & research associates funded by grant-in-aid programs to work on
bioinformatics projects.

Additional Details:
Name of the Coordinator: Dr. K. Guruprasad, Ph.D (Univ. of London, U.K.)
Postal Address:CCMB, Uppal Road, Hyderabad 500 007.
Phone Number: +91 40 2719 2779 Fax No.: +91 40 2716 0591/0311
Email:guru@ccmb.res.in Website:www.ccmb.res.in
Name of Contact Person(s): Dr. K. Guruprasad, Email:guru@ccmb.res.in
114
CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur
Coordinator : Dr. S. R. Thakur

1. Summary of the progress made by the Centre from its inception
Distributed Information Sub-Centre (DISC) at Advanced Centre of Hill
Bioresources and Biotechnology, CSK HPKV, Palampur (HP) came into
existence in October, 2002. The Centre has developed fairly good infrastructure
that comprises 28 Computers, two servers (one is used as web server and other
is internal server), Communication equipments and Printers, Photocopier, Fax
machine etc. All the computers are linked through Local Area Network (LAN) and
internet with 256 kbps lease line. The Centre has procured softwares like LINUX,
ORACLE, WINDOWS NET SERVER WINDOWS SERVER 2003, BIO-
SYSTEMATICA, SQL SERVER, ADOBE ACROBAT PROFESSIONAL,
VStudio.Net, DNA Star and Gen Check
TM
for day to day bioinformatics work and
for software development, database creation and management. The Centre has
also developed an e-Extension system for quick and efficient dissemination of
agricultural technologies to farming community. The Centre is engaged in
analysis of genome sequences of different crop species and plant pathogens.
The rice genome is being analyzed for NBS-LRR (nucleotides binding site-
leucine rich repeat) genes, which have been implicated in plant disease
resistance. The lentil and red clover genomes are being analyzed for identifying
genes associated with traits of agronomic importance and to identify markers
linked to QTLs responsible for important plant traits.
your institution
The Advanced Centre of Hill Bioresources and Biotechnology is engaged in
research on following areas in Agricultural Biotechnology:
i. Understanding molecular genetics of bacterial wilt resistance in pepper
with implications in solanaceae genomes
ii. Biofortification of maize for enhanced zinc and iron content in grains
iii. Molecular marker-assisted pyramiding of blast resistance genes in rice
iv. Development of DNA-based diagnostics for Fusarium species
v. Development of SSR markers in Trifolium pratense and identification of
QTLs associated with important plant traits
vi. Mapping of rust resistance locus in Lens using genomic resources from
related taxa
vii. Probing the molecular mechanisms governing cold tolerance during
reproductive growth in chickpea (Cicer aeritinum L.)
viii. Molecular marker-assisted pyramiding of powdery mildew resistance
genes in pea
Development of sex-specific markers in sea buckthorn
3. Area of specialization of the Centre
Bioinformatics & Agricultural Biotechnology
Following databases have been upgraded by the Centre during 2007-08:
1. Database on Biological Wealth of Himalayas
2. e-Extension network system
3. Library Management System

115
IBM servers (2), IBM Computers (13), HCL computer (Linux based), Thinkpad
(3), eMac G4(1), LCD(1), Deskjet Colour HP printer 840(1), Laser jet HP Printer
2200D(1), Print server(1), UPS 6KVA(1), Fax machine(1), Scanner(1),
Photocopier(1), Backup Device 250GB(1)
b. Scientific Software packages
Scientific Software: DNASTAR, Bio-Systematica , Bioedit, Mapmaker
System Software: LINUX 9.0, Microsoft 2000 server, Microsoft server 2003
Standard Edition, Window XP Home edition (IBM recovery)
Application Software: Adobe Acrobat Professional 7.0, Microsoft Vstudio.Net
2002, Open Office Org. 5.0, Win Zip 9.0, Win split
c. Databases &other information resources
ORACLE 9i and SQL Server 2000 Standard Edition
6. Details about staff members working in the Centre

*Not absorbed
1. Internet and email facility to users
2. User access to Bioinformatics resources available in the Centre
3. Trainings in the field of bioinformatics
4. Bioinformatics course at Masters level
The infrastructure of the Bioinformatics Centre has been used in teaching a
Bioinformatics course of 2 credit hours (1+1) to M.Sc. students of Agricultural
Biotechnology. The students are given theory lectures as well as practical
classes on various topics as prescribed by the Department of Biotechnology,
Govt. of India in the course contents. The students are given hands on training
on database development and the use of DNA sequence analysis software in
sequence assembly and annotation for gene finding. The students are also
taught about gene prediction, construction of restriction maps, drawing structures
of various recombinant molecules and other bioinformatics tools of current and
future importance.
The bioinformatics resources are being used by the students and scientists of the
biotechnology Centre of the university.
working
Dr. T.R. Sharma Bioinformatics In
Charge
Plant Genomics
& Bioinformatics
Since Aug.,
2006
Dr. Rajeev
Rathour
Bioinformatics Officer Plant Genomics
& Bioinformatics
Since April,
2004
Mr. Mukesh
Sharma
Technical Assistant* Computer Since Feb.,
2004
Mr. Ajay Kumar
Walia
Data Entry Operator* Computer Since April,
2003
Mr. Pardeep
Kumar
Traineeship Computer Since April,
2007
Mr. Ashish Rana Studentship Computer Since April,
2007
116
The Bioinformatics Center is also catering to other scientists for bioinformatics
analysis pertaining to R&D projects shown at S. No. 2
Following databases have been developed by the Centre:
1. Database on Biological Wealth of Himalayas
2. e-Extension network system
3. Library Management System (LMS)
4. DNA , RNA and Protein sequence alignment Tool
The Bioinformatics Centre has developed its own website. Home page of
website is www.hpbioinformatics.org
12. Papers published or presented
1. Chauhan RS. 2006. Bioinformatics approach toward identification of candidate genes for zinc and
iron transporters in maize. Current Science 91: 510-515.
2. Hong CP, Plaha P, Koo DH, Yang TJ, Choi SR, Lee YK, Um T, Bang JW, Edward D, Bankroft I,
Park BS, Lee JL and Lim YP. 2006. A survey of the Brassica rapa genome through BAC-End
sequence analysis and comparison with Arabidopsis thaliana. Mol Cell 22: 300-307.
3. Kapila, RK, Yadav, RS, Plaha, P, Rai, KN, Yadav, OP, Hash, CT and Howarth, CJ. 2007. Genetic
diversity among pearl millet maintainers using microsatellite markers.Plant Breeding: In press.
4. Lim YP, Plaha P, Choi SR, Uhm T, Hong CP, bang JW, Hur YK and Park BS 2006.
Towards unraveling the structure of Brassica rapa genome. Physiol. Plantarum 126: 585-
591.
5. Sharma P, Sharma KD, Sharma Rajan and Plaha P. 2006. Genetic variability in pea wilt pathogen
Fusarium oxysporum f. sp. pisi from north-western Himalayas. Indian Journal of Biotechnology 5:
298-302.
6. Sharma TR, Rana JC, Sharma Rajan, Rathour R, and Sharma PN 2006. Genetic diversity analysis
of exotic and Indian accessions of common bean (Phaseolus vulgaris L.) using RAPD markers.
Indian Journal of Genetics & Plant Breeding 66:275-278.
7. Sharma R, Singh S, Chahota K, Rathour R and Sharma SK 2005. Analysis of genetic
diversity in white clover (Trifolium repens) breeding populations using agro-morphological
and RAPD markers. Journal of Genetics & Breeding 59:297-302.
In Silico Development of simple sequence repeat (SSR) markers for
genetic mapping:
We have developed a set of 127 SSR markers by bioinformatics analysis of
publicly available sequence of chromosome 12 of the japonica cv. Nipponbare
(http://rgp.dna.affrc.go.jp). SSR motifs were identified among the BAC/PAC
clones spanning 27.1 to 72.2 cM on the integrated genetic and physical map
of chromosome 12 using simple sequence repeat identification tool (SSRIT)
(http://gramene.org) and primers were designed from the sequences flanking
the SSR loci using primer 3.0 software(http://frodo.wi.mit.edu/cgi-
bin/primer3/primer3_www.cgi). The uniqueness of each primer was confirmed
by BLAST analysis against the complete rice genome sequence database.
SSRs were typed by amplifying the DNA of an indica rice genotype, HPU 741
and a japonica genotype, Fukunishiki with flanking primers. PCR conditions
were optimized individually for each SSR using the gradient PCR. Majority of
these markers amplified single locus polymorphic amplicons among the rice
genotypes tested. These studies indicated that in silico analysis of rice
genomic sequences available in public domain offers a speedy and cheap
means to develop SSR markers for genetic mapping in rice, thus obviating the
tedious procedure of constructing SSR enriched genomic libraries and their
subsequent sequencing for developing SSR markers.
117
In addition, 100 SSR primers from BAC and EST databases of Medicago
truncatula have been developed for genetic mapping in lentil and red clover.
14. Details of Training/Workshop organized and total no. of user trained

allied areas.
C. No. of registered /regular/online users : 100
D. Research Publications (including biotechnology) : 10
E. Technical/Project proposals (including biotechnology) : 5
IV) Abstracts/ Brochures/Training manuals : -
for seminar/workshops/training (in bioinformatics)
During the coming year the Centre proposes to strengthen infrastructure in terms
of software tools for biological data analysis for providing better services to the
users. Besides this, the following activities will also be undertaken:
1. Using new bioinformatics tools for furthering biotechnology resaerch.
2. Developing software tools and writing algorithms for extracting information
from model genomes and utilizing in biotechnology interventions in
resource-poor crops.

Additional Details:
Name of the Coordinator: Dr. S.R.Thakur
Postal address: ACHBB, CSKHPKV, Palampur HP 176062
Phone No.: 01894-230314
Fax No.: 01894-230511
Email: sharmat88@yahoo.com, achbb@hillagric.ernet.in
Website: www.hillagric.ernet.in
Name of the Contact Person(s): Dr. T.R.Sharma
Email: trsharma@hillagric.ernet.in
Title Duration No. of
participants
Bioinformatics tools in genome
analysis
5
th
-7
th
July, 2006 20
Role of computers in
bioinformatics
17
th
-18
th
March, 2007 20
118
Devi Ahilya University, Indore
Coordinator : Dr. Anil Kumar

The Distributed Information Sub-Centre was established in the School of
Biotechnology of Devi Ahilya University, Indore in 1993 under the BTIS-Net
program of DBT. Since inception, we are engaged in Bioinformatics research
and education. Our center has got BSNL 512 Kbps internet lease line
connection and a user lab comprising of 40 desktop PCs and 24 hours
internet connectivity. This facility is being used in Bioinformatics research and
by the students and faculty of the department. We have also setup a web
server (http://www.davvbiotech.res.in) having all the software and database
developed/procured by the centre. The development of FTP server has been
initiated. The development of a server for the identification and
characterization of Genomic and Pathogenicity Islands has been completed
and a research paper has been communicated in In-Silico Biology.
PredictBias is available at http://www.davvbiotech.res.in/PredictBias. We
have designed primers for endo-1,4- Xylanase gene. We have also
designed primers for DREB2A gene. We have published full length papers in
primer designing of Xylanase as well as DREB2A genes. We have also
presented papers for the above works in various conferences specified in the
papers published section.

Since 1997, we are regularly organizing workshops on bioinformatics. As per
records, till now 17 workshops have been organized and nearly 880
registered participants have been trained in these workshops. Many students
do their research projects in the field of bioinformatics at our Centre (towards
partial fulfillment of their M. Sc. Biotechnology/ life science/ biochemistry or
BE/MCA or M. Pharma degree). During 2007-08, two students from
Banashthali University have taken two months summer training at our Centre.
Two students from BIT Jaipur will take six months training. We also offer
studentship and traineeship to eligible candidates. During 2007-08, one
studentship and traineeship is offered to a M. Sc. Biotechnology student and
a research scholar, respectively.

2. Major Research activities in Biotechnology & related fields at our
Institution: Our lab is mainly Enzyme technology lab, we also do research in the
field of Plant Tissue Culture and Molecular Biology etc. We have developed
following lab scale technologies:
1. Lab scale technology for production of glucose-1-phosphate using
immobilized enzyme bio-reactors.
2. Lab scale technology for production of low molecular weight polygalacturonic
acid and low methoxyl pectin.
3. Technology developed for fruit juice clarification using immobilized enzymes.
Many papers have been presented in various national and international
conferences. Our faculty members of biotechnology also authored
books/Chapters in edited books/Encyclopedia. Twenty students have been
awarded Ph.D. in Biotechnology.

3. Area of specialization of the Centre:
119
Sequence analysis, Biological software & database development related to
medical bioinformatics and human resource development.

4. Major activities of the Centre in the year 2007-08:
Database & Software Development:
S. No. Name of the
Software/Database
Functions Availability
1 PredictBias Web application for detection of
Pathogenicity Islands in pathogenic
bacteria.
http://www.davvbiot
ech.res.in/PredictBi
as/
2 QGenBank A comprehensive parser of
GenBank file format in Java.
The development is
currently in
progress.
3 PredictSecSys A prediction server for the
identification of Secretion systems in
bacteria based on SVM.
Data analysis has
been completed.

Human Resource Development: During 2007-08, We successfully organized
workshop (lecture cum hands on training) on Genome Data Analysis and
trained nearly thirty five participants. Centre offered one-studentship to a student,
Mr. Rustam Ali for doing his M.Sc. Biotechnology project in the field of
Bioinformatics.

Provision of Information resources: Database & abstract search and scientific
software are being provided to the staff & students of the University. Good
Internet facility has been provided to the staff & students of the Department.

5. Infrastructure facilities in the Bioinformatics Sub-Centre:
A. Computer & Communication facility:
(i) Servers
Web Server: HP Prolient ML 570 (Quad Processor with 4 GB RAM)
Proxy Server: HP Prolient ML 150 with 1 GB RAM
(ii) Desktops Pcs, Printers & Scanners
1GB (RAM) 512MB 256 MB Others
Desktop 15 6 13 11
Firewall System 1
Printer 4
Scanner 2
Photocopier 2
(iii) Communication Facility
Leased Line Router Fax Switch/Hub Projector
512 Kbps Cisco 1751 2 5 3
B. Scientific software packages: MATLAB, DNASIS, PROSIS, AMOS, SPSS,
MOE, Reference Manager 11.

C. Databases & other information resources: Derwent Biotechnology
Abstracts from 1982 -2004, Journals like Nature & Journal of Bioscience &
Bioengineering & Journals of Cell and Tissue Research.

6. Details about staff members working in the Centre:
S. Name of the staff Designation
Specializatio
Period of
120
No. member
n
working.
1. Mr. Sachin Pundhir Information
Officer.
Bioinformatics. Two year &
Ten months.
2. Mrs. Rachana
Tiwari
Technical
Assistant
Biotechnology Seven Months
3. Mr. Dhiraj Singh
Panwar
Computer
Operator.
Computer
Engineering.
Three years &
four months.
5. Mrs. Kavita Yadav Computer
Operator
Computer
Science
Seven months
6. Mr. Amey Kekre Data Entry
Operator.
Computer
Applications.
Seven years &
eight months.
Absorption Status: University has approved the absorption of Bioinformatics
Posts (as regular employees) in the meeting of Executive Council held on Dec.
01, 2007, subject to approval of State Govt.

We provide Internet services to the teaching & non-teaching staff, postgraduate
& research students of the School of Biotechnology. Database & abstract
search is facilitated to the research community of not only our department, but
also other departments of the University. We also provide our software for
scientific work to researchers of other institutes. We also provide guidance &
training to the students of Bioinformatics/ biological sciences of other Institutes /
Universities.

We impart bioinformatics training to the researchers, students & teachers through
workshops. At present, we do not offer any course. Our University plans to start
M. Sc. Bioinformatics program from 2008-09 Academic Session.

Our Centre is actively engaged in Bioinformatics education. With the help of
bioinformatics resources, we are training students who will fulfill the requirement
of industries engaged in the field of bioinformatics.

10. Collaborative works / initiatives:
We have Collaboration with NCCS, Pune and Jain Hi-Tech Industry, Jalgaon.
11. Databases / Software packages developed:
Name of the
Software/Database
Functions Availability
PredictBias Web application for detection of
Pathogenicity Islands in
pathogenic bacteria.
http://www.davvbiotech
.res.in/PredictBias/
MTGenomeDB A secondary database of
Mycobacterium Tuberculosis.
.res.in/MTGenomeDB/
OrchidDB A Taxonomical database of
Orchid species of Indian origin
.res.in/OrchidDB/
ResCut Program to find restriction
enzymes cutting site nucleotide
sequence.

AnaSeq Program to analyze the effect of
mutation on translation product

121
with BLAST facility

12. Papers published or presented in the conferences with reference:
1. Mishra, B.N., Singh S.P. and Kumar A. (1997) A biofilm model for fixed bed
anaerobic reactors: Performance analysis considering diffusional resistances
and axial dispersion. The Genetic Engineer and Biotechnologist 17 5-21.
(MATLAB USED).
2. Singh, V.K. and Kumar A. (2000) PCR Recipe: Software for setting up PCR
reactions, Biotechnology software and Internet Journal 1, 276-277.
3. Singh, V.K. and Kumar A. (2000) OLREA: A faster restriction enzyme
analysis using JAVA. Biotechnology software and Internet Journal, 1, 278-
279.
4. Singh, V.K., Govindrajan, R., Naik, S. and Kumar, A. (2000) The effect of
Hairpin structure on PCR amplification efficiency, Mol. Biol. Today 1 (3), 67-
69.
5. Samanta, J. and Kumar, A. (2001) TAXON: A software package for the
Management of Plant Database using Visual Basic. Biotechnology software
and Internet Journal, 2 (5), 201-203.
6. Singh, V.K., Mangalam, A.K., Kumar, A., Naik, S. (2001) Universal primers
can amplify tumor necrosis factor gene across species. Mol. Biol. Today 2,
11-12.
7. Singh, V.K. and Kumar, A. (2001) PCR Primer Design. Mol. Biol. Today 2, 27-
32.
8. Khan, I., Desai, D. V. and Kumar, A. (2004) Carbochips a New Energy for
old Biobuilders. Journal Biosciences & Bioengineering 98, 331-337.
9. Garg, N. and Kumar, A. (2006) Primer designing of DREB2A, a drought
resistant gene in soybean. 93
rd
Indian Science Congress Association meeting,
Hyderabad, January 3-7, 2006.
10. Garg, N. and Kumar, A. (2006) Primer designing of DREB2A, a drought
resistant gene in Glycine max. J. Cell Tissue Res. 6, 807-813.
11. Pundhir, S., Vijayvargiya, H. and Kumar, A. (2006) Poster presentation,
Predict Bias: Detection of Pathogenicity Islands in Pathogenic bacteria,
International Conference in Bioinformatics (InCoB2006), New Delhi, Dec. 18-
20, 2006.
12. Garg, S., Sohani, N., Pundhir, S. and Kumar, A. (2006) Primer Designing for
Endo-1, 4--xylanase gene, Oral Presentation, National Conference on
Biotechnology, Science & Environment, Indore, Dec. 28-29,2006.
13. Pundhir S. and Kumar, A. In Sillico Classification of Virulence factors,
National Conference on Biotechnology, Science & Environment, Indore, Dec.
28-29, 2006. (Best paper award).
14. Garg, S., Sohani, N., Pundhir, S. and Kumar, A. (2007) Primer designing of
for Endo-1, 4-b-18 Xylanase gene. J. Cell Tissue Res 7(3), 1147-1154.

Initiated the development of a parser for GenBank file format using Java.
Initiated the development of a comprehensive Database on Starch
Phosphorylase.
Initiated the development of a prediction tool for the identification of
secretion system in bacteria using support vector machine.

122
14. Details of Training/Workshop in 2007-08 organized and total
numbers of user trained:
S.
No.
Dates
Theme of the Workshop /
Training Program
No. of
Participants
1. Oct 29
th
- 02
nd
Nov. ,
2007
Genome Data Analysis 35
The workshop included lectures & demonstration sessions by speakers from our own
Bioinformatics Sub-centre as well as eminent scientists from other institutions.

15. Impact shown by our Centre on the growth of biotechnology and
allied areas:
The Bioinformatics sub Centre is contributing in research field of
biotechnology and enhancing the research activities. The research papers are
published in national and international journals of high repute. We have also
trained nearly 880 participants by successfully organizing 17 workshops since
1997. The Centre also provide information to the students and research
scholars of biotechnology as well as to other neighboring
departments/institute by the Internet facility, Scientific Software, Studentship,
Abstract Database CDs and office automation software.
Our University plans to start M.Sc. Bioinformatics program. We are also
doing research & development work related to the primer designing for -
Glucan Phosphorylase. We also plan to design processes for enzymes.

Additional Details:
Coordinator: Dr. Anil Kumar
Postal Address: Professor & Head, School of Biotechnology
Devi Ahilya University, Khandwa Road
INDORE - 452001, M.P., INDIA.
Phone Number: +91-731-2470372, 2470373; Fax No.: +91-731-2470372.
Email: ak_sbt@yahoo.com, bioinfo@sancharnet.in
Website: http://www.davvbiotech.res.in

Name of Contact Person(s): (i) Dr. Anil Kumar, Email: ak_sbt@yahoo.com.
(ii) Mr. Sachin Pundhir, Information Officer
Bioinformatics Sub Centre.
Email: sachbinfo@rediffmail.com.
123
Dr. Y S Parmar University of Horticulture and Forestry, H.P.
Coordinator : Dr S V Bhardwaj

The Distributed Information Sub Centre (Sub-DIC), at YSPUHF, funded by
DBT, New Delhi became operational during June, 1999 The major
achievements and progress made by the Centre since its inception are:
The Centre facilitates the research work of the department by providing
bioinformatics softwares (PRISM and EXOME) and databases (Biotechnology
Abstracts, Directory of Biotechnology Institutes) in addition to the online
bioinformatics tools, email and online literature search facility. (i) The three genes
of Tomato leaf curl virus Himachal strain ToLCHimV and a Bean yellow mosaic
virus isolate Solan coat protein (CP) gene sequenced, were submitted to the
NCBI and phylogeny of the genes was traced using bioinformatic tools. (ii)
Sequencing of coat protein gene of Bean yellow mosaic virus (BYMV) from
gladiolus (Gladiolus sp.) done.(iii) Phylogenetic analysis of Lily symptompless
virus done. (iv) Primer designing against Lily symptompless carlavirus (LSV)
infecting Lilium spp. using bioinformatics tools has been completed.(v) Studies
on Molecular characterization of a potyvirus infecting radish (Raphanus sativus
L.) in Himachal Pradesh have also been completed.
Research work being offered to Post graduate students in biotechnology using
bioinformatics tools and applications like primer designing,
phylogenetic/evolutionary studies, ligand receptor interactions and molecular
characterization of viruses using CLUSTALX (1.8), CLUSTAL W, GeneDoc,
EXOME, EXOME BLAST, EXOME HORIZON, AutoDock or DOCK or LUDI and
other public domain softwares.
Four patents on plant biotechnology work and another one (PCT) with help of the
Centre have been granted through the IPM Cell established in the Sub DIC.
Centre has organized 28 trainings/ workshops/ seminars till date and 741
persons have been trained/participated in them.
The Bioinformatics Centre has developed information systems viz, (i) Package of
Practices of Fruit Crops in Himachal Pradesh ,(ii) Alternative Methods of Plant
Disease Control (iii) Package of Practices of Vegetable Crops in Himachal
Pradesh (Hindi version)
The Centre has developed a database on Plant species Germplasm available
in the university. Further, the database on various crops i..e. HimCrop is under
preparation.
The Centre has developed 5 video CDs on Temperate Horticulture in
collaboration with the Directorate of Extension Education of the university.
The Bioinformatics Centre has also developed training manual on Computer
Basics for internal circulation.
The Centre has completed two adhoc research projects .
Website of the university was developed in Jan., 2000 and maintained till March
2004.

institution
The research mandate of the department of biotechnology of the university
pertains to micro-propagation of plants, cell mutagenesis and cell selection for
developing biotic and abiotic stress resistant plants, genetic transformation
with marker genes and genes of interest, retrieval of virus free plant material
from infected mother plants, development and production of bio-fertilizers,
124
molecular-characterization of plants by RAPD-PCR and application of
bioinformatics in research.

3. Area of Specialization of the centre : Crop Biotechnology/Horticulture
The Centre facilitates the research work of the department by providing
bioinformatics softwares (PRISM and EXOME) and databases (Biotechnology
Abstracts, Directory of Biotechnology Institutes) in addition to the online
bioinformatics tools, email and online literature search facility and conducting
workshops/trainings.
i) Research
Studies on Molecular characterization of a potyvirus infecting radish
(Raphanus sativus L.) in Himachal Pradesh were conducted while studies
to know the effect of Asparagus adscendens Roxb. on molecular
modelling of target-receptor interactions are continuing.
Comparative analysis of coat protein gene of Lily symptomless virus
infecting Lilium species with other carla viruses was done.
Primer designing against Lily symptomless carlavirus (LSV) infecting
Lilium species using bioinformatics tools.
Virus has been sequenced and primers for detection of the virus have
been designed using bioinformatics tools besides evolutionary of the same
virus.
ii) of Database Development
The database on various horticultural crops of HP viz, HimCrop is under
preparation.
iv) Trainings/workshops
The Centre has organized 4 trainings on, Computer Basics and 2
trainings on, Creation and Management of Database and a Regional
Seminar on Patenting in Biotechnology during 2007.
The Centre proposes to organize a 3 days training on, Bioinformatics
Basics - Application in Biological Sciences in Feb, 2008.
Computer & Communication facility: 1 Xeon server, 21 PCs, 2
Modems, 2 Dot Matrix Printers, 2 Laser Printers (Black), a Colored
Laser Printer, a 3KVA UPS, a 1KVA UPS, a 625VA UPS, a 8 Port Hub,
a Scanner, a CD-Writer, a 8 Port Switch, a Thinkpad (laptop),
Multimedia Projector and a Photocopier.
Scientific Software packages: Prism, Exome, Exome ED , Exome
BLAST, Hyperchem
Databases & other information resources: Biotechnology Abstracts on
CD ROM, Directory on Biotechnology Industries
absorption status)
S.NO. NAME OF THE
STAFF
DESIGNATION WORKING SINCE ABSORPTION
STATUS
1. Ms Anju Sharma Technical Assistant
Information Officer
June, 1999 to May 2000
May, 2000
Not absorbed
2. Mr Kailash Sharma Technical Assistant June, 2000 Not absorbed
125
3. Ms Kamlesh Nagar Data Entry Operator June, 1999 Not absorbed
4. Ms Taruna Sharma Data Entry Operator September, 2006 Not absorbed
5. Mr Neel Thakur Data Entry Operator March 2005 Not absorbed
6. Ms Aarti Thakur Traineeship Holder March, 2007 For one year
7. Ms Taruna Sharma Studentship Holder July, 2007 For one year

The Centre offers a high speed leased line internet connectivity to the host
university and facilitates online and offline literature search in field of
biotechnology, bioinformatics and other related areas that include
bibliographic and patent search. The Derwent Biotechnology Abstracts
(offline database) is being used for literature search.
The Intellectual Property Management Cell (IPM Cell) established in the
Centre facilitates patent search and patent filing.
The data generated is being analysed statistically using Prism software
and other public domain softwares. The Centre provides Nucleotide and
Protein Sequence Analysis using online public domain databases and
sequence analysis softwares viz Exome, Exome Blast, Exome Horizon
etc. While the recently purchased Hyperchem software will facilitate
chemical molecular modeling research.
The Centre offer trainings on basics as well as on advanced topics in
computer application/bioinformatics/IPR to scientists, technical/ministerial
staff and research scholars/students of the University.
The Centre has a collection of books (covering areas of biotechnology,
bioinformatics, computers and horticulture) which are being kept in the
University library for reference.
Besides above, some other services like creation of multimedia CDs, web
page designing, scanning, CD writing, report writing, printing, preparation
of presentations on powerpoint, conducting seminars and Xeroxing of
documents etc are being provided to the students/scientists of Department
of Biotechnology of the University. The Centre also provides complete
technical support to various National or International workshops and
seminars organized at the University. Minor hardware maintenance is also
being provided by the Centre.
8. Educational activities with details of placement : The Centre proposes
to start a one year diploma course in course in bioinformatics during
the next academic session.
9. Initiative to validate the outcome of bioinformatics resources : NIL
10. Collaborative works/ initiatives: Gene sequencing work is being carried
out in collaboration with the molecular biology laboratory of Central
Potato Research Institute, Shimla, and CSIR Palampur, Himachal
Pradesh.
11. Databases/ Software packages developed: The database on various
horticultural crops of HP viz, HimCrop is under preparation.
Bhardwaj SV and Gupta R. 2007. Novel eco-friendly approaches for
plant virus management. Paper presented in International Symposium
on Viruses of Ornamental and Temperate Fruit Crops held at IHBT,
Palampur (HP) on 17-18
th
December, 2007.
126
Huddone S, Bhardwaj S V, Malhotra B, Thakur P D and Kanwar K.
Comparative nucleotide sequence analysis of coat protein gene of lily
symptomless virus isolate LSV Oh with other carlaviruses. Paper
presented in Symposium on Eco-friendly Disease Management
Approaches for Organic Farming in Horticultural Crops held at Dr Y S
Parmar University of Horticulture and Forestry, Nauni-Solan, (HP) on
16-17
th
November, 2007. Abst. 61.
Bhardwaj S V, Sambyal P S, Thakur P D, Gupta R and Huddone S.
Sequence analysis of tomato leaf curl virus Himachal strain
(ToLCHimV). Paper presented in Symposium on Eco-friendly Disease
Management Approaches for Organic Farming in Horticultural Crops.
Dr Y S Parmar University of Horticulture and Forestry, Nauni-Solan,
(HP) on 16-17
th
Malhotra B, Bhardwaj S V, Huddone S, Handa A and Kanwar K.
Detection of lily symptomless carlavirus using specific primers. Paper
presented in Symposium on Eco-friendly Disease Management
Approaches for Organic Farming in Horticultural Crops. Dr Y S Parmar
University of Horticulture and Forestry, Nauni-Solan, (HP) on 16-17
th

Huddone S, Bhardwaj S V, Malhotra B, Handa A and Kanwar K.
Evolutionary pattern of lily symptomless virus isolate LSV-Oh using
phylogenetic analysis. Paper presented in International Symposium on
Viruses of Ornamental and Temperate Fruit Crops held at IHBT,
Palampur (HP) on 17-18
th
December, 2007. Abst. No. 11.
Malhotra B, Bhardwaj S V, Huddone S, Thakur P D and Kanwar K.
Designing specific primers for CP gene of lily symptomless carlavirus.
Paper presented in International Symposium on Viruses of Ornamental
and Temperate Fruit Crops held at IHBT, Palampur (HP) on 17-18
th

December, 2007. Abst. No. 14.

13. Initiation of R&D activities in Bioinformatics: Post graduate (MSc and
PhD) students of the department are being given bioinformatics
research problems.

Duration with Date (s) and year Topic
From To
No. of
participa
nts
Seminar on E-Commerce and latest
IT Trends
8th Feb, 2001 - 50
Training on Windows 98 and MS
Office 2000
14th Feb,2001 28th Feb, 2001 22
Workshop on Patent Awareness 5th March,2001 40
Office 2000
9th July, 2001 21st July 2001 16
Workshop on IPR Awareness
Programme with special reference to
Plant Varieties and Farmers Rights
Protection Act
8th Nov, 2001 - 33
Training on Troubleshooting in
Computer Software and Hardware
6th May, 2002 7th May, 2002 13
Office 2000
15th Jan., 2003 28th Jan., 2003 11
127
Office 2000
15th Jan., 2003 28th Jan., 2003 13
Training on Introduction to Computer
Networks and Internet
29th Jan, 2003 3rd Feb, 2003 15
Training on Introduction to Computer
Networks and Internet
29th Jan, 2003

3rd Feb, 2003

15

Office 2000
9th June,2003 21st June,2003 13
Workshop on Patent Awareness 18July, 2003 19 July,2003 58
National seminar on IPR in
horticultural crops
12 Oct, 2004 13 Oct., 2004 150
Workshop on IPR Awareness 23rd Sep, 2005 24th Sep, 2005 20
Training on Computer Basics 9th Jan., 2006 17th Jan., 2006 20
Training on Computer Basics 7 Mar, 2006 14 Mar, 2006 17
Training on Computer Basics 17 April, 2006 22 April, 2006 19
Training on Creation and
Management of Database
28 Aug, 2006 2 Sep, 2006 12
Training on Computer Basics 11 Sep, 2006 16 Sep, 2006 18
Training on Computer Basics 3 Oct, 2006 10 Oct, 2006 20
Training on Computer Basics 1 Nov, 2006 7 Nov, 2006 20
Training on Computer Basics 12 March, 2007 17 March, 2007 19
19 March, 2007 24 March, 2007 12
Training on Computer Basics 9 April, 2007 16 April, 2007 19
Training on Computer Basics 21 May,2007 26 May, 2007 20
Training on Computer Basics 16 July, 2007 21 July, 2007 9
Regional Seminar on Patenting in
Biotechnology
17 July, 2007 - 56
16 July, 2007 20 July, 2007 11
TOTAL 741

Patents granted
Patents filed
Papers published

Research work in different aspects of Bioinformatics including ligand
receptor interaction to Ph.D/ M. Sc students in the department.
Development of information systems and databases on horticultural
crops.
Atleast two short term trainings or workshops on Bioinformatics and /
or IPR and one refresher course/training of 21 days on Bioinformatics
Procurement of databases, specialized scientific softwares, books and
journals on computers/ Bioinformatics/ Biotechnology.
Establishment of database and web server.
Work on Crop databases, HimCrop will continue.
128
A separate website of the centre shall be hosted.

Additional Details:
Name of the Coordinator: Dr S V Bhardwaj
Postal Address: Senior Virologist cum Coordinator, Sub DIC, Department of
Biotechnology, Dr Y S Parmar University of Horticulture and Forestry, Nauni,
Solan . HP. 173 230
Phone Number: 01792 252310, Mobile:094180 61835 Fax No.:01792
252242
Email: satbhardwaj@yahoo.com Website: www.yspuniversity.ac.in
Name of Contact Person(s): Dr SVBhardwaj
Email: satbhardwaj@yahoo.com
129
G. B. Pant University of Agriculture & Technology, Pantnagar.
Dr. Soma S. Marla, MS (Comp., USA), Ph.D (Mol. Biol)

Bioinformatics sub-DIC was established in November 1998 in the College of
Basic sciences & humanities, G.B.Pant University of agriculture &
Technology, Pantnagar. This is one of the sub-DIC of Uttaranchal. Since
inception the centre is actively involved in teaching and conducting
research in Bioinformatics. The centre is also actively involved in
disseminating information in biotechnology and assisting on-going research
in the university aimed at improvement of crop & animal productivity. Two
Bioinformatics courses- Elements of Bioinformatics (offered every semester)
and Use of computers in molecular modeling are being offered by the
centre to students at the Post graduate level. The centre has initiated
electronic inventerization of plant biodiversity of Uttaranchal. A small green
File database Uttaranchal Plant Resource DB of 50 plants, A Nutritional
Plant Resource Database of Utttaranchal , enumerating nutritional and other
information about nearly 60 genotypes of small grains has been developed.
Another Database Cry gene Transgenic database providing
comprehensive information about transformed Cry genes in various crops
has been developed. Similarly a Prokaryotic pathogen genome
visualization tool have been developed and published in an international
journal. The centre is also actively involved in hands on skill training of
Bioinformatics skills by conducting workshops. So far ten training workshops
were conducted with active funding support from DBT. A web site was
launched on-line reflecting the various activities of the Bioinformatics centre,
Pantnagar
(http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/home.htm).

2. Major Research activities at G.B.Pant University
G.B.Pant University of Agriculture & Technology is the first agricultural
university in India. Since its inception, it has had very strong basic sciences
disciplines like microbiology, biochemistry, Genetics, etc; helping the
intensive efforts in plant breeding, plant pathology, horticulture, veterinary,
process engineering and food technology. The University has been working
on various projects in biotechnology in the areas of crop biotechnology,
biological pest & disease control, biofertilizers, process engineering, funded
by the Dept. of Biotechnology, besides its own efforts in the areas of vaccine
development, immunodiagnostics, embryo transfer technology and plant
tissue culture. Recently the University has been recognized by DBT as one
of the centre of excellence and with a funding of nearly Rs 6 crores
conducting active research in areas of plant abiotic stress, MAPKinase
signaling networks in Brassica juncea, aromatic rice and metabalonomics of
medicinal plants. Apart from disseminating and online accessing of relevant
research information the centre is also providing support in experimental data
analysis to the ongoing-research in the university. The bioinformatics centre is
presently executing a project (BTPR7849/AGR/02/374/2006) on Building
MAP Kinase protein signaling networks in Arabidopsis and Brassica species
with DBT funding. The centre joined International initiative for sequencing of
Brassica rapa genome and will be staring soon sequencing of part of Chr. 4 .
Work on comparative metabolonomics for improvement of rice crop is
130
actively being conducted. Three hene sequences (LOX genes) from
Octodecanoid pathway from Jasmonic acid biosynthesis ( regulating
resistance to Blast disease) have been identified in silico and PCR amplified
& sequenced gene sequences were submitted to GenBank.
3. Areas of specialization of the Centre
development of Bioinformatics anlysis software tools & databases
Metabolic pathway modeling & flux analysis.

1. Teaching: Every semester the introductory Bioinformatics course
Elements of Bioinformatics is being offered to PG students of
Biotechnology.
2. Research: The centre is also involved in conducting active research in
development of databases for enumerating plant resources of Uttaranchal
and two databases were developed. Also work on metabolic modeling
and flux analysis of glycol sis in human cancer cells. Also a Prokaryotic
genome visualization tool was developed . These research was findings
were published in two international conferences and published in
research journals.
3. Data analysis support: The centre has acquired state of the art
bioinformatics packages such as DNA STAR, GCG Package, MOE,
Hyperchem, and provides data analysis facility for the on-going
research in area of Biotechnology.
4. Training Workshops: The centre has conducted has successfully
conducted three DBT funded regional workshops - Fundamentals of
Protein Docking (December, 18
th
-20
th
2006) and Elements in Computer
Assisted Analysis of Protein Structure and Function (12-14, Dec. 2005),
Biological sequence analysis ( Nov, 16-18, 2007) and were attended by
87 participants respectively from all over the country.
A. Broadband internet connectivity was started, B. Windows (25
computers) and Linux (2 computers), 2 servers, 2 printers.
6. Details about staff members: 1. Dr. Soma S. Marla, Coordinator,
Since July 2006 to date , Two data wntry Operators on contractual basis hired,
since 1999).
Two bioinformatics courses- Elements of Bioinformatics and Use of computers in
molecular modeling are being offered by the centre to students at the Post
graduate level. Two Ph.D & two M.Sc students are being supervised in area
of Bioinformatics.
Two plant databases documenting the plant resources of Uttaranchal. The database
gave impetus to the currently executed project in GBPUAT on Bioprospecting of
Uttaranchal plant resources.
The centre is actively involved in knowledge mining from various online databases &
disseminating knowledge available on the web. Various Bioinformatics packages
available in the centre are very handy to the faculty in teaching & conducting, data
analysis and knowledge discovery from experimental data.
Bioinformatics approaches to metabolic pathway and flux analysis suggested by the
centre are aiding the ongoing- research in departments of Biochemistry and
Microbiology.Conducted metabolic modeling & flux analysis of Glycolasis in human
cancer cells was presented at the Asia Pacific International Conference on
131
Bioinformatics held in N.Delhi, Dec. 2007. The outcome of the research is in Press
for publication in a scientific journal.
Bioinformatics centre, Pantnagar is also actively involved in training hands on
experience in various Bioinformatics skills by conducting several workshops. These
workshops became popular especially with student community attracting huge
number of applicants, practically conducting the training programs hard due to
limited funds and material resources available with the centre.
Available Bioinformatics tools were placed in Centres web site:
http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/home.htm.
9. Collaborative works/ initiatives:
Bioinformatics centre from the very inception has been a good team player working
with researchers from other disciplines such as Computer science, electronics,
molecular biology and biochemistry. Bioinformatics centre is collaborating with
Rothamstead research station as part of international initiative to sequence genome
of Brassica rapa. For example the centre collaborated with the department of
Electronics, Jaypee University of Information Technology, Shimla and successfully
developed virtual electronic circuit that mimicked the Glycolasis occurring in human
cancer cells.
The centre is assisting the department of microbiology, GBPUAT in analysis the
microbial pathways in Rhizobacterium species and building Phylogenic trees. The
centre is also actively collaborating with Department of Environmental sciences in
developing databases for managing crop environmental resources.
10. Databases and Software developed
A Java based pathogen genome Visualization & annotation tool was developed at
the centre. Development of Biological databases for documenting the rich diversity of
Uttaranchal. Two databases were designed.A database of Cry genes present in
Transgenic plants developed.
11. Papers Published
Results of the work done at the centre was presented at two International
Conferences and is being communicated for publication in Scientific journals as
listed below:
1.Soma Marla and V. Singh (2007) Procaryotic Genome Visualization tool. In Silico Biol. 7,
0038 (2007)
http://www.bioinfo.de/isb/2007/07/0038/
1. Soma Marla et al, (2006), Comparative Structure and function analysis of
chorismate synthase genes in Prevotella rumnicola, Online Journal of
bioinformatics,Australia,7(1):35-45,2006
2. Harkewal Singh, Soma Marla and Manas Agarwal, (2006) Docking
studies of Tau Protein, Engg. Letters, Hong Kong Protein, Engg. Letters,
IMECS 2006: 154-159,http://www.informatik.uni-trier.de/~ley/db/indices/a-
tree/a/Agarwal:Manas.html, Hong Kong.
3. Singh H, Marla SS, Verma D, 2007, Comparative Analysis of MMFF94x and AMBER99
force fields using Aspartic Proteases, Serine Proteases, Metallo-Proteases and Sugar-
Binding Proteins asdifferent data sets. Online Journal of Bioinformatics, 8 (1) : 45-55,
200.
4. Rice DNA gene sequence submissions: LOX1, LOX2 & LOX3: GenBank Submission
numbers: EU032587, EU032588 and EU146294.
Research in metabalonomics in humans and micro organisms is initiated in
Initiation of R&D activities in Bioinformatics. Development of Biological databases for
documenting the rich diversity of Uttaranchal and a databases was designedo of Cry
genes present in Transgenic plants developed at the centre. Research in
metabalonomics in humans and micro organisms is initiated in the centre. The
bioinformatics centre is presently executing a project
132
(BTPR7849/AGR/02/374/2006) on Building MAP Kinase protein signaling
networks in Arabidopsis and Brassica species with DBT funding.
The center has conducted since its inception nine DBT sponsored
training workshops and another two day workshop sponsored by
Rural Bio complex for faculty of Plant Pathology was conducted.
14. Impact shown by the centre
The database on Cry genes in transgenic plants was presented in the
international conference on the Implications of the Cartogena Protocol on
Biosafety, Held in N.Delhi in Nov., 2006. Conducted research on metabolic
modeling & flux analysis of Glycolasis in human cancer cells was presented
at the Asia Pacific International Conference on Bioinformatics held in N.Delhi,
Dec. 2007.
Soma Marla, Srivatsav.R, Patel G.(2007) PGV- Prokaryotic Genome
visualization tool,
Bioinformatics (In silico Biology, 2007).Various resources/ analysis tools
available are available at Centres web site:
http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/home.htm
15. Future Activities:
Apart from continuing our initiated research efforts on development of
databases and data analysis tools, research in metabalonomics we intend to
strengthen this work in future. This we intend to do by employing comparative
analysis of genomes of model species and there by discovery of
agronomically useful orthologs in rice and Brassica. We are currently
executing a DBT funded project (BTPR7849/AGR/02/374/2006) on Building
MAP Kinase protein signaling networks in Arabidopsis and Brassica species
with DBT funding. The execution of initiated research is severely hampered
due to adequate infrastructure (hardware, furniture and equipment) and
required software packages due to paucity of funds. To successfully conduct
the current activities of teaching, training and research the Bioinformatics
centre requires support in terms of manpower, infrastructure, acquisition of
state of the art bioinformatics software packages.

Additional Information:
Name of the Coordinator : Dr. Soma Marla
ADDRESS : Coordinator, Bioinformatics sub-DIC
MBGE, CBSH, G.B.Pant University of Agriculture
& Technology, Pantnagar, USN.Dist.Uttaranchal.
Tel:05944-233287, EMAIL: ssmarl@yahoo.com , bioinfo.pantnagar@gmail.com
WEBSITE: http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/home.htm
Names of Contact persons: Dr. Soma Marla Coordinator, Bioinformatics centre
EMAIL: ssmarl@yahoo.com
133
Guru Nanak Dev University, Amritsar
Coordinator : Prof. Gurcharan Kaur

The Distributed Informatics Sub-Centre (DISC) at Department of
Biotechnology, Guru Nanak Dev University, Amritsar was established in the
1995. Since its inception, the DISC has procured various scientific softwares
like Microsoft Office 2000, SQL Server 2000, Borland Turbo c++ Suite, Visual
Studio, Sigma Stat, Sigma Plot 2001, (V-7.1), Grafit version 4, Minitab 13.3,
Lasergene-5 Sequence Analysis, Oracle 10g, Exome, Exome Blast and
Exome Horizon software. In addition, different databases like Medline,
Agricola, Agris, Life Science Collection, Food Science & Technology,
Biotechnology Abstracts are also being subscribed for facilitating literature
search by students and faculty members. So far about 22000 users
comprising of students and teachers of Guru Nanak Dev University and
neighbouring Institutes have availed the services of the Centre. The DISC is
having 512 kbps leased line connectivity for Internet. At present the hardware
installed includes Computers Systems (42) including three servers, two HP
Coloured Laserjet Printer 5500 DTN and HP 3550, HP Laserjet Printers (six),
Deskjet Printers (two), one Line Matrix Printer Wipro P500 LPM, one HP
Scanner 6100C, one HP Coloured Scanner 7450C, Xerox Machine,
Multimedia Projector and one laptop computer. In the last nine years the
DISC has organized eight workshops benefiting more than 124 candidates.

institution : The biotechnology related research at Guru Nanak Dev
University, Amritsar is being carried out in the Department of Biotechnology
as well as in other Departments under the Faculty of Life Sciences. A number
of research projects have been undertaken to study the molecular basis of
stress adaptation in crops like sorghum and wheat which have resulted in
cloning of many stress modulated gene fragments which are in the process of
being characterized. Tissue culture techniques are being employed for micro
propagation and production of secondary metabolites for different plants such
as citrus, petunia, withania, delburgia, rose, cacti and datura. Lectins from
different plant sources have been isolated and characterized for their possible
biotechnological applications.
Various enzymes of industrial importance have been purified from different
microbial sources and characterised for biotechnological applications. Some
of the enzymes included in the study are inulinases, xylanases, amylases,
cellulases, glucose, isomerases, phytases, lipases, lignin, peroxiadases, etc.
The potential of some of these enzymes is also being explored for
biotransformation. Studies are also going on for determining the potential of
selected microbial strains for bioremediation. Another potential area of
research is in vivo and in vitro studies directing neuroaxogenesis and
neurogenesis for rational therapy in neurodegenerative diseases and brain
injuries.

3. Area of Specialization of the Centre : Biotechnology
134
4. Major activities of the centre during the year 2007-08 : A two day workshop on
Bioinformatics : Conceptualizing Biology in terms of Molecules was organized on
February 22
rd
& 23
rd
, 2007 by the Distributed Informatics Sub-Centre, Department of
Biotechnology, Guru Nanak Dev University, Amritsar. Prof. S.I. Ahson, Head,
Department of Computer Science, Jamia Millia Islamia, New Delhi, Mr. Vivek Mahale,
Computational Biologist, Mascon Lifesciences, New Delhi and Mr. Y.M. Ragothaman,
J.N.U., New Delhi were invited to deliver the lectures & to impart hands-on training to
the participants The workshop was attended by sixteen participants from different
Universities. The Centre has also started M.Sc. in Bioinformatics from the session 2006.
Further, the Centre has purchased fifteen computers systems. DISC has also been updated
by acquiring the latest version of Databases and Softwares. More than fifty research
papers have been published in the last one year using the services of Centre.

A. Computer & Communication facility : There are forty two Computer
Systems (including three servers), one laptop computer, two coloured
Laserjet Printer, one Line Matrix Printer, six Laserjet Printers, two Deskjet
Printers, two Scanners, one Xerox machine. The center is also having one
Multimedia Projector.
Networking System : 512 kbps leased line connectivity
Communication Facilities : Phone : 0183-2258431
Fax : 0183-2258272 ; Email : bicamritsar@yahoo.com

B. Scientific Software packages : Microsoft Office 2000, Microsoft Windows
2000, Windows 2000 Advanced Server (25 Client), SQL Server 2000,
Borland Turbo c++ Suite, Visual Studio 6.0, Sigma plot 2001, Sigma stat,
Grafit Version 4, Adobe Page Maker, Adobe Illustrator, Adobe Photoshop,
Corel Draw, Minitab 13, Lasergene-5 Sequence Analysis software,
Macromedia Studio MX-2004, Exome, Exome Blast, Oracle 10g and Exome
Horizon.

Databases available are Medline, Agricola, Agris, Life Science Collection,
Food Science & Technology, Biotechnology Abstracts.

6. Details about staff members working in the centre :

NAME OF THE
STAFF
DESIGNA
TION
PERIOD OF
WORKING
ABSORPTION
STATUS

Mr. Md. Sufian Badar Lecturer Since July, 2006 Sanctioned by
the University in
2006
Mr. Manish Kumar Lecturer Since July, 2006
Mr. Harbhajan Singh Computer
Operator
Since 3.10.2006
(Worked as DEO
from 30.08.1995 -
2.10.2006)
DEO promoted to Computer Operator, Post advertised
and will be filled shortly.
These three
positions have
been taken over
by the
University w.e.f.
01.04.1998
Mr. Rajwinder Singh Computer Since 23.10.2007 Sanctioned by
135
Operator the DBT

7. Types of services provided : Every year about 3000-3500 students/research
fellows/faculty members of Guru Nanak Dev University and from neighbouring
Departments/Institutes are using CD-ROM based and online data, internet
and computer facility of DISC. A 512 kbps leased line connectivity has been
established in DISC Email, fax, Xerox, software analysis and data search
facilities are also provided to other Life Science Departments.

Department has introduced M.Sc Bioinformatics degree course from this
session 2006-07 and DISC staff is imparting theoretical and practical training to
the students of M.Sc Bioinformatics in Computational Methods for Sequence
Analysis, Structural Biology and Bioinformatics, Genomics and Proteomics,
Advanced Algorithms for Computational Biology, System Biology and Metabolic
Pathway Engineering, Molecular Modeling and Computer aided Drug Design
etc. Staff is also imparting theoretical as well as practical training to the students
of M.Sc Biotechnology in Computer Applications & Bioinformatics.

9. Initiative to validate the outcome of bioinformatics resources :
We are in the process to develop database which will be connected to
NCBI server through the server of Indian Institute of Science, Bangalore. Then It
will be easy for us to access online database of NCBI thru IISc Bangalores
server.

10. Collaborative works/ initiatives :
Biotechnology faculty collaborating with IHBT, Palampur, Delhi University,
South Campus, Delhi, Jawahar Lal Nehru University, New Delhi, INSERM
France, AIST, Japan.
Bioinformatics faculty from various DBT sponsored Bioinformatics Centres is
regularly invited for delivering lectures to students of the department and
training of research scholars & faculty during DISC workshops.

11. Databases/ Software packages developed : Database development :
Global analysis of functional surfaces of core histones with comprehensive
point mutants, Database of stress tolerant proteins of microbial, plant and
animal system, Promoter prediction in E.coli.

More than fifty research papers have been published in the last one year
using the services of Centre.

13. Initiation of R&D activities in Bioinformatics :
136
We are doing global analysis of functional surfaces of core histones with
comprehensive point mutants.

14. Details of Training/ Workshop organized and total no. of user
trained : In the last nine years DISC has organized eight workshops
as per the details given below :

S.No. Title of Workshop /Year No. of
Participants
1. Workshop on Latest Trends in Bioinformatics
March 4-6, 1998
16
2. Workshop on Use of Internet & Patenting in
Biosciences Research March 23-24, 1999
14
3.

Workshop on Role of Networking in Scientific
Information Processing October 27- 28, 1999.
10
4.

Workshop on Internet and Web Designing
October 5-6, 2000
15
5. Workshop on Tools for Data Mining
October 7- 8, 2003.
17
6. Workshop on Tools of Bioinformatics
March 3-4, 2005
21
7. Workshop on Advances in Bioinformatics
February 23
rd
& 24
th
, 2006
18
8. Workshop on Bioinformatics: Conceptualizing
Biology in terms of Molecules February 22
nd
&
23
rd
, 2007.
16

areas : The DISC is assisting students and faculty from neighbouring
Departments and Colleges/Institutes to acquire scientific information through
different databases/softwares available in the Centre. The Centre is also
providing practical training in computer based application, software analysis,
computational methods, etc. to M.Sc. Biotechnology & M.Sc. Bioinformatics
and Doctoral students. Training workshops at regular intervals are also
organized to apprise faculty and students of the latest developments in
Bioinformatics. Sixteen thesis of M.Sc. students of the Department have been
submitted last year taking assistance from DISC facilities. Introduced M.Sc.
Bioinformatics programme from 2006 onwards with the help of facilities
available in the Centre. Services of staff are being utilized for teaching of
M.Sc Bioinformatics and M.Sc Biotechnology students.

16. Future activities :
1. Strengthening of M.Sc. Bioinformatics course.
2. To organize Workshop(s) for training of faculty and Ph.D. stdents.
3. Six months research project of M.Sc. Bioinformatics students.
4. Database development : Global analysis of functional surfaces of
core histones with comprehensive point mutants, Database of
stress tolerant proteins of microbial, plant and animal system,
Promoter prediction in E.coli.
137

Additional Details :
Name of the Coordinator : Prof. Gurcharan Kaur
Postal Address : Distributed Informatics Sub-Centre (DISC)
Department of Biotechnology
Guru Nanak Dev University
Amritsar 143 005
Phone Number : 0183-2258431 Mobile : 09815450737
Email : bicamritsar@yahoo.com
Website : http://department.gndu.ac.in/department/biotech.asp
Name of Contact Person(s) : Prof. Gurcharan Kaur
Email : gurcharank@yahoo.com

138
Himachal Pradesh University, Summer Hill, Shimla
Coordinator : Professor T. C. Bhalla

1. SUMMARY OF THE PROGRESS MADE BY THE CENTRE FROM
ITS INCEPTION
The Bioinformatics Centre of Himachal Pradesh University was established in
1999 with the approval and financial support of Government of India, Ministry of
Science and Technology, Department of Biotechnology (DBT), New Delhi. The Centre
is housed in the Netaji Subhash Chandra Bose Bhawan of Himachal Pradesh University
This Centre has a DELL Make server (Xenon 2.8 GHz) running on
Windows sever 2000/2003, 4 Intel Celeron 366 MHz and 3 HCL PIII 750 MHz
machines running on Win 98 operating system and 10 Acer PIV 1.7 GHz
machines running on WinXP operating systems. These entire machines are
connected to server through LAN connectivity using CAT5 UTP cables. Internet
connection is available through BSNL (ISP) and it can be accessed through all
nodes. The Centre also has a Laser printer, Dot Matrix printer, 1200dpi Scanner,
Inkjet printer, Xerox machine, Multifunctional printer, Laptop and a Multimedia
projector, P-III 550 MHz server running on Windows 2000, ELNOVA; 1 KVA Off-
Line UPS, Window XP Professional OEM Pack. The softwares available at the
Bioinformatics Centre includes; Offline Derwent Biotechnology Abstracts CD-
ROM database, Exome software for protein & gene sequence analysis and
pDRAW32
Two databases were developed i.e. Traditional Fermented Foods and
Beverages of Himachal Pradesh and Microbial and Mushroom Resources of
Himachal Pradesh. The Centre has successfully organized thirteen
training/workshops covering various aspects of the Bioinformatics and has
trained around 202 participants during these trainings/workshops

2. MAJOR RESEARCH ACTIVITIES IN BIOTECHNOLOGY AND
ITS RELATED FIELDS AT THE UNIVERSITY
The research activities of the University in the area of biotechnology have major
focus on following themes:
i) Microbial enzymes: Purification, application in organic synthesis,
medicine and food processing
ii) Microbial diversity
iii) Mycorrihzae
iv) Traditional fermented food
v) Nutraceutical aspects of mushroom

3. AREA OF SPECIALIZATION OF THE CENTRE
i) Microbial diversity and resources
ii) Enzymes: sequence, structure and functional relationship
iii) Nucleotide and protein sequence analysis

4. MAJOR ACTIVITIES OF THE CENTRE DURING THE YEAR
2006-07
A Workshop training organized
i) Two workshops were organized from May 4-6, 2006; Sep. 6-8,
2006
B Improvement expansion of databases
139
i) Traditional Fermented Foods and Beverages of Himachal
Pradesh
ii) Microbial and Mushroom resources of Himachal Pradesh
C Research Project
i) In silico study of cobalt binding proteins were initiated
ii) Comparative genomics of fatty/lipid metabolism
iii) Nucleotide and amino acid sequence analysis of Cholesterol
Oxidase
D Academic support activities
i) Organized practical classes in Computer Applications and
Bioinformatics course for M.Sc. Biotechnology students.
ii) Provided online/offline database access and internet facility to
researchers and the faculty members of the various departments
of the university
E Following Infrastructure was added during the year
1. Ten Computer system Acer / HCL make (E-4300 processor,
Intel Q965 chipset)/
2. HP Color Laserjet-2605DTN Network Printer
3. HP Scanjet-4370/G3010 Photo Scanner

5. INFRASTRUCTURE FACILITIES IN THE BIOINFORMATICS CENTRE
A. Computer and Communication
i) Computer Hardware
Server (Xenon 2.8 GHz, DELL Make) : One
PC nodes (Acer 1.7 GH) : Ten
Multi Media Projector (PLC-SU 30) : One
Laser Printer (HP 2100 M, 1200dpi) : One
Dot Matrix Printer (Wipro HQ 1040+) : One
UPS (Pyramid, 3KVA, 30 min backup) : One
Multifunctional printer (Modi XD-100) : One
Xerox Machine (Modi 5821 IV) : One
ELNOVA;UPS 1 KVA Off-Line UPS : One
ii) Communication: Two Telephone lines: 0177-2832153
0177-2832154
Internet Facility, Email: bhallatc@rediffmail.com
B. Scientific Software Packages
i) Exome software for protein and gene sequence analysis
ii) pDRAW32 for DNA cloning and sequencing
C. Database and other Information Resources
i) Offline Derwent Biotechnology Abstracts CD-ROM database

6. DETAILS ABOUT STAFF MEMBERS WORKING IN THE
CENTRE

Name Designation Area of
Specialization
Period of working Absorption
Status
Prof. T.C.
Bhalla

Coordinator
Enzyme and
Fermentation
Technology
From the start of
Centre (1999) till date

Mrs. Leena
Mishra

Data Entry
Operator

Computer
Applications

9th July, 2001 till date
Matter pending
with state Govt.
for approval

140
7. TYPES OF SERVICES PROVIDED
The Centre provided the following services to the students, research
fellows, and faculty members of the University
i) Derwent Biotechnology Abstracts Offline Database
ii) Nucleotide and Protein Sequence Analysis
iii) Bibliographic and Patents Search, E-Mail and Internet Access,
Training in Bioinformatics
iv) Bioinformatics library facility: Books 92, Journals 2

8. EDUCATIONAL ACTIVITIES WITH DETAILS OF PLACEMENT
The Centre does not offer any Diploma/Degree course in bioinformatics

9. INITIATIVE TO VALIDATE THE OUTCOME OF
BIOINFORMATICS RESOURCES: (N/A)

10. COLLABORATIVE WORKS/INITIATIVES
i) The Centre has collaboration with the Department Biotechnology &
Biosciences for development of databases.
ii) Work related to structure, function relationship of enzyme has been
undertaken in collaboration with Department of Biotechnology, Himachal
Pradesh University, Shimla-5

11. DATABASES/SOFTWARE PACKAGES DEVELOPED
Two databases were developed and validated
i) Traditional Fermented Foods and Beverages of Himachal Pradesh
ii) Microbial and Mushroom Resources of Himachal Pradesh

12. PAPERS PUBLISHED OR PRESENTED IN THE CONFERENCES WITH
REFERENCES
The Centre has not published papers in the area of bioinformatics
However, the researchers from the Departments of Biotechnology and
Biosciences have availed the facility of the Centre for publications

13. INITIATION OF R&D ACTIVITIES IN BIOINFORMATICS
i) Structural, biophysical and biochemical aspects of various enzymatic
proteins
ii) Nucleotide and protein sequence studies of nitrile hydratase

14. DETAILS OF TRAINING/WORKSHOPS ORGANIZED AND TOTAL
NUMBER OF USERS TRAINED
This Centre has organized thirteen workshops/ training programs

1. Modern trends in retrieval of bioinformation (Oct 10-12, 2000)
2. Nucleic acid and protein sequence analysis (Sep 28-30, 2001)
3. Tools and techniques to access biological database (Jun 20-22,2005)
4. Recent trends in genomics and proteomics (Oct 24-26,2002)
5. Tools and techniques to access biological database-II (June22-23, 2005)
6. Trends in genomics and proteomics II (Oct 20-22,2003)
7. Prelude to Bioinformatics (June14-16, 2004)
8. Internet Resources and Bioinformatics (Oct 11-13, 2004)
9. Tools and Techniques for Protein Structure & Drug Designing
141
10. (May16-18, 2005)
11. Application of Linux in Bioinformatics & Biocomputing (Sep.26-28.2005)
12. System Biology: A New Era in Bioinformatics (May 4-6, 2006)
13. Computational Biochemistry: Approaches and Applications(Sep.6-8,2006)
14. Tools and Techniques for Nucleic Acid & Protein Sequence
(Sep.17-21, 2007)
About 202 professionals from various institutions/ organizations have been trained
through these training/workshops

15. IMPACT OF THE CENTRE ON THE GROWTH OF BIOTECHNOLOGY
i) The facility of the on-line and offline database search related to
literature in biotechnology has improved the quality of project
reports, dissertations and publications
ii) Exposure of M.Sc. Biotechnology students of the university to
bioinformatics has helped students to join very good national R&D
laboratories
iii) The training of college teachers in bioinformatics at the Centre has proved
beneficial in sensitizing undergraduate students to the domain of
bioinformatics
iv) 11 papers were published with the help our centre

16. FUTURE ACTIVITIES
i) Sequence, structure and functional correlation of nitrile
metabolizing enzymes
ii) Development of simple softwares for enzymes and microbial
growth kinetics
iii) Development of a local database for some industrial enzymes

NAME OF THE COORDINATOR: Professor T. C. Bhalla
POSTAL ADDRESS: Bioinformatics Centre (Sub-DIC),
Himachal Pradesh University,
Summer Hill, Shimla-171005.
PHONE & FAX NUMBER: 0177 2832153, 0177 2832154
E-MAIL: bhallatc@rediffmail.com,
bhallatc@gmail.com
NAME OF CONTACT PERSON: Professor T. C. Bhalla
142
Indian Agricultural Research Institute, New Delhi
Coordinator : Dr. H. Chandrasekharan

1. Summary of the progress made by the centre from its inception Bioinformatics
Centre at IARI, New Delhi was established in 1989 under Biotechnology Information
System (BTIS) Network to function as a computerized information base in fields
related to Agricultural Biotechnology in particular and fields allied to agriculture in
general. Since its inception, the Centre has provided various services, such as on-
line bibliographic search through network, off-line bibliographic search through CD-
ROM server, electronic mail, internet, creation and update of database, Statistical
analysis of research data, protein sequence analysis, training programmes,
workshops on bioinformatics and current awareness services etc., to the
researchers, students and farmers. Biotechnological Abstract Information retrieval
System (BAIRS) was developed by the Centre and extensively used by students and
researchers. The Centre became a part of Unit of Simulation and Informatics (USI)
in November 2003. The USI is entrusted with the additional responsibility of
maintaining the Institutes campus network, the website and the web server
administration. While initiating the work on e-agro-advisory in 2005, the Centre has
developed the IARI Centenary Year documentary film on IARI-A Catalyst of
Change that was widely circulated to visiting dignitaries since 2006. During the year
under report, apart from Bioinformatics Studies, a teleconference facility has been
developed and made operational at IARI.

institution
Structural and functional predictions of hypothetical proteins
Development of specific software in Bioinformatics,
Novel Gene Identification in Medicago trucatula using In silico approaches.
Analyses of database on pedigree management of wheat, maize, rice, chickpea
and mung

3. Area of Specialization of the centre: Agri-Informatics
(Comprising Computerized Information Systems in various branches of agricultural sciences
with special reference to Agricultural biotechnology/Bioinformatics)

4. Major acti vities of the centre during the year 2007-08 (15 lines)
Insilco prediction of structure and function of hypothetical proteins: In our study
we have tried to predict the structure and function of the protein (acc, no AAG
52239) of Arabidopsis thaliana which is hypothetical in nature. Arabidopsis
thaliana is a mustard weed which contains 27,029 protein coding genes (TAIR7).
Majority of proteins are still unannotated and have been termed as unknown or
putative or hypothetical. The difficulty in the prediction of structure and function
of hypothetical protein is due to its low similarity with other known proteins.
Therefore, more emphasis was given on fold recognition and domain
identification. In this study we used number of online as well as offline tools. We
have found that our query sequence is quite similar to 2bw3A sequence and this
template have the same domain i.e. hATC dimerisation domain.

Novel gene identification in Medicago truncatual using in silico approaches:
Present work was carried on completed sequences of Medicago truncatula
which is a forage legume. Genes from M.truncatula share identity to legumes and
established symbiotic relationships with nitrogen fixing Rhizobia and is colonized
143
by mycorrhizal fungi. In this study several gene finding programs were used to
find genes in the sequences, which utilized one or the other gene-fining
algorithmic strategies. For increasing gene prediction accuracy we included both
instrinsic and extrinsic approaches by using ab-initio programs and blast search.
We also used TWINSCAN which uses a combination of both approaches for
prediction enhancement. The novel genes as predicted by most of the softwares
was composed of single exons, hence there was no splice results when
NNSplice and NetPlantGene were used on this gene which again validates our
results. Some of the gene finding programs used were GENSCAN, GeneID,
GrailEXP, GenMark.hmm and Augustus. BLAST analysis was performed on the
genes predicted by these programs to infer homology. WU-BLAST was also
executed against the EST sequences of M.Truncatula to enhance the validity of
the gene. Further confirmation of the result was done through splice-site
detection programs and gene prediction program well trained on dicotyledons
databasets (Diogenes, TWIMSCAN). From the study, nineteen new genes were
predicted from the seven sequences. Out of 19 sequences, 10 had a function, 8
were of unknown function and 1 sequence was novel gene.

5. Infrastructure facilities in the Bioinformatics Centre (25 lines)

A. Computer & Communication facility : Sun Enterprise 420R Server, SGI 02+ computer
system, Alpha 200, 4/233 computer system, Axis online CD-net DVD Rom Server, Pentium
IV Multimedia Systems, ILL from both VSNL and ERNET are available for various web
related activities.

B. Scientific Software packages: Centre is in possession of certain scientific software
packages, which have been procured / developed over the years. These include Advanced
Sequence Analysis Software EXOME; EASI/PACE image processing; SPANSGIS,
simulation models such as WTGROWS, INFOCROP, ORYZA, CERES; user-friendly
information system software for rice, maize, wheat pedigree, chickpea, rice IPM, Indian soils,
pesticides; Biotechnological Abstract Information retrieval System (BAIRS).

C. Databases & other information resources:
Database of Crop Production & Productivity
Database of Area under High Yielding Varieties
Land Use Database

absorption status)
Dr.H.Chandrasekharan, Head & Principal Scientist (Agricultural Physics-
hydroinformatics and DSS for Natural Resource Managent) - Permanent
Dr. S. K. Bandhyopadhyay, Sr.Scientist (Agronomy-Crop informatics and crop
growth simulation modeling) Permanent.
Mr. A. K. Mishra, Scientist (Computer Applications) Permanent now on study
leave.
Mr. M. S. Pillai, Technical Officer Permanent
Mr. Naresh Katoch, Technical Officer Permanent
Mr. Rajender Sharma, Technical Officer Permanent
Mr. Kamal Batra, Technical Assistant Permanent
Mr. Sanjiv Kapur, Technical Assistant Permanent

Software and Simulation Models development
144
Creation and update of databases (agri and bioinformatics)
Statistical analysis of research data (students and staff of the institute)
Human resources development

Several M.Sc. and Ph.D students of IARI are being guided in their research by
scientists of this Centre. A relatively new discipline of Simulation and
Informatics with four PG courses has been functioning at this Unit since the
academic session 2005-06. This serves as a minor discipline for M.Sc. and
Ph.D. students of IARI. Of these, the course titled, Foundation Course on
Informatics is one of the compulsory courses for all M.Sc. and Ph.D. students of
IARI.
The Centre provides facilities for attachment training for a limited number of the
final year students of M.Sc Bioinformatics for completing their short-term
projects. Many students from outside universities and institutes avail this
opportunity. More than five such trainee of the Centre got placement after
completing their tenure at the Centre.
Work has been initiated for application and validation of various bioinformatics
resources for nucleotide and protein sequence alignment, gene prediction, genetic
markers establishment and protein structure prediction and modeling.

Our Centre has collaboration with Department of Science and Technology (DST),
National Informatics Centre (NIC) and a score of other research and development
organizations.

Databases
Crop Production & Productivity
Area under High Yielding Varieties
Land Use
Fertilizer Consumption
Indian literature on Tissue Culture, Photosynthesis & Plant Molecular Biology

Crop growth simulation models
INFOCROP- a generic crop growth simulation model
INFOSOIL
INFOCANE
Simple models for tea and coconut

User-friendly information system software
Rice
Wheat Pedigree
Maize
Chickpea
Rice IPM
Indian Soils
Pesticides

145
1. Rajendra Sharma, Garima Khandelwal and Chandrasekharan H. 2007. Novel
Gene Identification in Medicago truncatula using In silico approaches INCOB-
2007, Hong Kong
2. Rajendra Sharma, Abhiranjan Prasad and Chandrasekharan H. 2007. Micro
Designer~a standalone tool for designing micro-RNA INCOB-2007, Hong Kong
3. Sharma, Sasmita Joshi and H. Chandrasedharan 2007. In-silco prediction
Rajendra of Structure and Function of hypothetical protein of Arabidopsis
thaliana. (Communicated).

13. Initiation of R&D acti vities in Bioinformatics
Application of bioinformatics tools is being initiated for nucleotide and protein
sequence alignment, gene prediction, genetic markers establishment and protein
structure prediction and modeling. We aim to identify sequence genes and their
products, which are responsible for quality traits, pest and disease resistance,
drought resistance, salinity resistance in different crops and genes responsible for
pesticide resistance in important pest species of crops. Besides, ICT tools are being
used for designing user-friendly application software on agri-informatics which will
ultimately be made online.

PG Education and Placement
Scientists of this Centre are guiding M.Sc. and Ph.D. students of IARI as part of
their research activities. Since last year (2005) the Unit is offering four PG
Courses in the areas of Simulation and Informatics at IARI. This discipline
serves as a minor discipline for M.Sc. and Ph.D. students of IARI. Of these, the
course titled, Foundation Course on Informatics is compulsory for all PG
students of IARI.

The Centre provides facilities for attachment training for select final year students
of M.Sc. Bioinformatics for completing their short-term projects. Many students
from recognized universities and institutes avail this opportunity. During the year
under report, two traineeship students of the Centre got placement after
completing their tenure at the Centre.

o Details of Training organized

SNo. Name of the training Duration
From To
No. of
Participants

1

2

Emerging trends in Agri-
informatics
*

(scheduled in February-
March 2007)

Internet training
programme

13-2-07 05-3-07

03-7-07 04-7-07

20

12

15. Impact shown by your centre on the growth of biotechnology and allied areas.
In this you may highlight the details like number of paper published/ number of
various acti vities of your organization and neighboring institutions, manpower
offered etc.
146
Centre is entrusted with developing the discipline of Bioinformatics as a component
of Agri-informatics under the Unit of Simulation and Informatics at IARI. The Centre
has taken active role in developing crop related databases, simulation models, user
friendly information software in agriculture and imparting bioinformatics related
training to the stake holders from time to time. Efforts are on to upgrade the present
set up to a Division having M.Sc. / Ph.D. degree programme in the field of Agri-
Informatics during the XI Plan period.

14. Strengthening research on bio- and agri-informatics aspects as related to crops
15. To make IARI website as state of art for knowledge dissemination of Agri-
Bioinformatics to various stakeholders.

Additional Details:

Name of the Co-ordinator Dr. H. Chandrasekharan,
Head, Unit of Simulation & Informatics,
Address A-0 Block, LBS Building, IARI,
New Delhi-110012
Phone 011-25841255, 011-25842490,
Fax: 011-25843719
Email head_usi@iari.res.in, chandrasekharanh@hotmail.com

Name of Contact persons

Dr.H.Chandrasekhran, <hcsekaran@iari.res.in >
Mr.M.S.Pillai, <mspillai@iari.res.in>
Mr Rajendra Sharma < rajendra621@iari.res.in >
Indian Institute of Science, Bangalore
Coordinator : Professor M. Vijayan

1. Summary of the Progress made by the Centre from its inception
The Centre has been recognized as a Centre of Excellence in structural Biology
and Biocomputing by the Department of Biotechnology, Government of India.
The Centre created in 1985 was one of the earliest in the country to establish
information dissemination and formal teaching in bioinformatics. In tune with the
evolving nature of this discipline, there has been a paradigm shift in the focus of
the Centres activities, which are now directed towards strengthening integrated
research programmes in several areas of bioinformatics with a long-term goal of
developing computational models of biological macromolecules, metabolic
pathways and cellular processes at different levels of abstraction, to aid in new
hypotheses generation, new ways of research in biology and in generating
application opportunities in drug and vaccine discovery.

2. Major Research Activities
Genome Analysis, De-novo Design of Bio-molecules, Protein Structure
Prediction, Structural Biology and Structural Bioinformatics, Systems Biology,
Pathway Modeling and Application in Drug Discovery, Computational
Immunology, Biological Networks, Protein Function Prediction, Drug-DNA
interactions, Creation of Value-added Knowledge-bases, Algorithm Development
and Software Engineering

147
Significant leads & achievements Possible Applications
Systems biology
M.tuberculosis system level models

Pharmacodynamic modeling

Integrated Databases-
LectinDB
CancerlectinDB
CADB-2.0

Algorithm development
PocketDepth
FAIR (Finding All Internal Repeats)

Data mining
Non-canonical interactions in protein
structures
Determinants of ligand recognition

Software engineering
PSAP
RPMS
RP-2.0

Structural bioinformatics
Protein Interaction Finger Printing,
Anion recognition modules and
Phospholipase-A
2
complexes
System design, Pathway modeling, Drug target
identification, Gene essentiality prediction

Predicting adverse effects of drugs- useful in
every stage of drug discovery

Integrated knowledge-bases of lectins

Analysis of backbone conformation angles

Genome Sequence Analysis

A novel algorithm for cavity detection in proteins
Efficient data retrieval from massive databases,
Protein classification and similarity estimation

Drug-receptor interactions, Derivation of
fundamental parameters for protein structural
analysis,

Protein structure visualization and knowledge
extraction

Structural and interactions modules
Building macromolecular assemblies

Mirror sites
PDB, SCOP, GDB
Fast access to latest information that enables
large scale data mining research

Human Resource development
Training several students in bioinformatics for
academic institutions and industries

3. Areas of Specialization of the centre
Structural Biology, Structural Bioinformatics, Genome Analysis, Structural and
Functional Genomics, Systems Biology, Fundamental aspects of Drug and
Vaccine Discovery (including Structural Pharmacology and Computational
Immunology), Development of highly specialized and versatile Databases,
Development of software tools and software engineering.

4. Major research activities during the year 2007-2008
The major research activities at the Bioinformatics Centre can be classified into
the following areas: (a) Genome sequence and structural analysis, (b)
Development of new algorithms in bioinformatics, (c) Internet computing, (d)
Integrated Database development, (e) Structural analysis of biological
macromolecules, (f) Structural pharmacology, including in-silico drug discovery,
(g) computational immunology and (h) Systems biology. While the first four
pertain to development of new concepts and resources that often goes back into
the public domain resource bank in bioinformatics, the other areas pertain to
application of the existing information to generate new kinds of knowledge that
may ultimately lead to useful applications not only in the understanding of basic
science but also as useful therapeutic pointers. Examples of specific projects are
de novo design of biologically active and conformationally important peptides,
148
structural biology and bioinformatics of phospholipase and thermophilic enzymes,
deriving determinants of carbohydrate recognition, creation of an integrated
plant lectin knowledge-base, metabolic- flux balance analysis and modeling of
pathways relevant to Mycobacterium tuberculosis, development of a virtual
mycobacterial cell, development of algorithms for predicting T-cell receptor
antigens and analysis of protein-protein interaction networks.

5. Infrastructure facilities at the Bioinformatics Centre
The Bioinformatics Centre, which is funded by the Department of Biotechnology
(DBT), has been successful in providing continuous and up-to-date information
and access to databases and software. Databases include nucleic acid and
protein sequences and their 3-dimensional structures. Software available at the
centre enables sophisticated analysis of sequences, manipulation, visualization
and study of the three-dimensional structures of biomolecules as well as a wide
range of genome analysis. The centre has SYBYL and INSIGHT modelling
packages. In addition, the centre has several computing machines, graphics
workstations and several Intel based Linux and Solaris workstations.

6. Details of faculty members working in the centre
Dr. S. Ramakumar Professor Structural Bioinformatics, Machine
learning methods in life sciences,
Sequence Analysis, Genome
Analysis

Dr. K. Sekar Principal Research Structural Biology, Internet
Scientist computing, Datamining, Algorithm
Development and Creation of
Integrated knowledgebases

Dr. Nagasuma Chandra Principal Research Systems biology and its
Scientist application
in drug and vaccine discovery
Sequence and Structural
bioinformatics

Dr. Debnath Pal Asst. Professor Structural bioinformatics
Comparative genomics, Systems
Biology

The centre plays an active role in disseminating various types of information in biological
sciences. Some examples are, the three-dimensional Protein Structures, and the gene
sequences of all the genomes available in the Genome database. In addition, the centre
hosts a major mirror server for Structural Classification of Protein structures. The
recently available genome databases as well as derived specialized knowledge bases are
also made available at the centre. Further, the centre also has Cambridge Structural
Database (CSD), which contains more than 4233,752 small molecule structures. The
faculty at the centre also provide advice to various research groups about bioinformatics
methods relevant to their research problems as well as in their interpretation.

Hundreds of research associates and other personnel have been trained at our
institution under several DBT programmes. 64 project assistants, 22 project
trainees and 80 summer trainees have been trained at the Bioinformatics centre
149
and the Interactive Graphics Facility. The faculty members of the centre have
participated in the training of scores of Ph.D. students at the institute. Most of
them are well placed in IT and Biotech companies and in reputed academic
institutions in India and abroad. In addition, the faculty members of the centre
are offering the following three courses to the Ph.D. students of the institute.

SE 301: Bioinformatics
SE 302: Computational approaches to Drug Discovery
SE 303: Chemoinformatics
Further, training programmes and workshops are a regular feature of the activity of the
centre to introduce the available facilities and their application to users.

The faculty at the Centre has been publishing scientific papers and articles in
well recognized international journals. This is a pointer to describe the outcome
of the usage of the bioinformatics resources available at the Centre. In addition
several other research groups, both within and outside IISc have also
acknowledged the usage of the facilities in their publications and research thesis.
Another major outcome of the usage of the resources is the large number of
databases and software tools that are made available through the world-wide-
web, accessible from anywhere in the world.

The faculty members of this centre are actively engaged in several collaborative projects
such as (a) the International structural genomics program on Mycobacterium
Tuberculosis funded by National Institutes of Health, USA, (b) Institute wide
Computational Genomics project funded by Department of Biotechnology, Govt. of India
(c) The faculty members of the centre are involved in the Institute wide Structural
Genomics funded by Department of Biotechnology, Govt. of India, (d) a collaborative
project with Satyam computers for profiling in drug discovery, (e) joint project using
genetics aided systems biology for identifying interactions between genes involved in
E.Coli protein biosynthesis funded by DBT and (f) participant in centre of excellence on
molecular strains of mycobacteria funded by DBT.

11. Database/software packages developed
The centre is actively involved in creating softwares and databases for those who
are working in the area of structural Bioinformatics. Some of the softwares
developed at the centre are PSAP, RPMS and RP-2.0. The faculty members of
the centre are involved in creating web-based databases like CADB-2.0 etc.

The faculty members of the centre have published several papers (about 30 in
the year 2007) in the international journals, which have a high impact factor. In
addition, the members of the centre are involved in guiding/co-guiding several
Ph.D. and M.Sc (Engg) students.

In the last few years, the faculty members of the centre have provided consultancy,
advice or training to the biotechnology institutions/ industries
150

14. Details of Training/workshop organised
Every year, the centre conducts workshops and training programmes in areas related to
Bioinformatics. The workshop and hands-on experience sessions were well appreciated
by participants from all over the country. This provided an opportunity for useful
interactions among people from various fields, which is particularly important in the area
of bioinformatics, a purely multidisciplinary subject. The following seminars were
conducted.

Course Sponsoring agency Duration Target group
Drug Design Workshop DBT & IISc 5 days,
July 2007
Biology , Pharmacology &
Medicinal chemistry Faculty,
Post-docs, graduate students,
Pharma R & D
Structure and Ligand
based drug design
Open Eye Software 1 day, Dec
2007
Bioinformatics & biophysics
Students & Faculty

The range of projects being carried out, reflect the long-term goals of the centre
towards genomic-scale studies of hypotheses generation, new ways of research
and in generating application opportunities. The following are the main thrust
areas: Systems Biology, Structural Biology and Bioinformatics, Molecular Design,
Molecular Modelling, Structural Pharmacology and Computational Immunology
and Human Resource development. The centre will continue to emphasize the
activities of structural bioinformatics. In the future, newer databases and
software will be developed. The centre will continue to contribute significantly in
the field of Systems biology, computational approaches to inhibitor design, drug
and vaccine discovery.

Name of the Coordinators:
Professor M. Vijayan, Coordinator, Interactive Graphics Based Molecular
Modelling, Professor, Molecular Biophysics Unit and Distinguished Biotechnologist,
Indian Institute of Science, Bangalore 560 012, India (Phone: 080-23600765; Fax No.
080-23600683; E-mail: mv@mbu.iisc.ernet.in)
Professor S. Ramakumar, Coordinator, Bioinformatics Centre, Indian Institute of
Science, Bangalore 560 012, India. (Phone: 080-23601409; Fax No. 080-23600683;
E-mail: ramak@physics.iisc.ernet.in)

Name of Contact person for both facilities
Dr. K. Sekar, Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012,
India. (Phone: 080-23601409 and 080-22933059; Fax No. 080-23600683; E-mail:
sekar@physics.iisc.ernet.in and sekar@serc.iisc.ernet.in).
151
Indian Institute of Spices Research, Calicut, Kerala
Coordinator : Dr. Santhosh J. Eapen

The Bioinformatics Centre was established at the Institute as a sub-centre under the
BTIS network during 2000. It has a mandate to provide computational support and
training to students and scientists. The centre, since its inception, has organized over a
dozen training programmes, some of them of 21 days duration. The Centre has a
dedicated Internet connectivity (1 mbps), necessary hardware and software resources to
initiate and support the Spice Bioinformatics/Biotechnology programmes. A
Bioinformatics Library with more than 100 reference books, journals, databases etc. was
also set up. A round the clock browsing facility, SpicE-Lab, is also made available for the
benefit of students and research fellows. Development of integrated databases on
various aspects of spices viz. genetic resources, their chemical constituents, pathogens
of spices etc. was one of the key activities of this centre. As on today, there are 14
databases to its credit and many of them are available online.
Biodiversity informatics: Information management has central place in the conservation
of plant and microbial genetic resources. Realizing this, the Centre has launched several
databases under the series Spice Genes.
a. Spice Genes Part 1: Black Pepper: A database of black pepper germplasm
resources available at IISR. Available online as well as CDs (http://www.iisr.org
/germplasm/index.htm).
b. Spices Genes-Part 2: Curcuma Species: An offline database on various
Curcuma species.
c. Spices Genes-Part 3: Myristica Species: A database of different Myristica
species and nutmeg germplasm.
d. Piperbase a database of Piper species of India that includes botany,
taxonomy, agronomy, biochemistry and medicinal properties of various Piper
species.
e. PLASBID: A database on plant associated bacteria integrated with several tools
like sequence editing, primer analysis etc.
f. PhyDisH: A database on Phytophthora diseases also includes searchable
information on Phytophthora cultures maintained in the Institute repository.
Chemoinformatics: Integrated databases pertaining to chemical compounds
available in various spices are also developed. A library of chemical compounds of
spices is under preparation.
a. Chitinase database: An online database (http://www.iisr.org/bioinformatics
/project/index.htm) on plant chitinases.
b. PAL database: An enzyme database of Phenylalanine Ammonia Lyases (http://
http://www.iisr.org/bioinformatics/project/index.htm)
c. CardCC&Mpbase: A cheminformatics database on chemical compounds in
cardamom.
Other databases: Several other databases dealing with patents, tissue culture
protocols, spice literature are also developed by the Centre.

institution
The major areas of Biotechnology work at IISR are:
Molecular characterization of spice germplasm accessions, pathogens and
biocontrol agents.
Diagnostics for major pests and pathogens in spices.
152
Gene expression and genetic transformation in spices for desirable agronomic
traits.
Marker assisted selection in major spices and efficient biocontrol agents.
Cloning and sequence analysis of genes of economic importance from spices
and related genera, OUT in plant viruses, bacteria, fungi and nematodes etc.
Biosynthesis of secondary metabolites and characterization of bioactive
principles in spices.
Biodiversity and Biotechnology of Spices
4. Major acti vi ties of the centre during the year 2007- 08
The Centre has developed two databases viz. PLASBID - a bioinformatics based bacterial
identification database and PASSCOM, on predicted activity spectra of spice compounds.
During the reporting period only one bioinformatics training programme of one month duration
was conducted for the M.Sc. students. The centre has provided traineeship to two candidates
and three students were selected for doing their M.Sc. project work. The Centre has sustained
the Bioinformatics lab with a dedicated leased line connectivity, hardware and software tools
which is an excellent asset to the research community of the region. The centre also
maintained the Institute website (www.spices.res.in) and continued to provide intranet
(SpiceNet) and web mail (Spicemail) services to the institute. Support on website development
was extended to other organizations under ICAR too.
iv. Computer & Communication facility
Item No. Remarks
Internet connectivity
Servers
Work station
PCs
Laser printers
Scanners
Dot matrix printer
UPS
LCD projector
Photocopier
Router, switches &
modem
-
3
1
16
2
2
1
2
1
1
-
Reliance Leased line 1 mbps
HP & HCL
-
-
-
-
-
5 KVA & 4 KVA
-
-
For leased line connectivity
Discovery Studio of GENE- DS GENE, JEMBOSS, EMBOSS, Modeller, Autodock,
BLAST and FASTA, ClustalW,X, Phylip, Chime, Rasmol, Cn3D viewer and Swiss
PDB viewer, Fast PCR. CAP3, PHRAP and SEAN.
Crop Pest CD, Derwent Biotechnology Abstracts, Ekaswa Patent Database,
Dspice Literature database on spices, Functional Plant Biology, Mycological
research
absorption status)
working
Absorption
status
K. Jayarajan Technical
Officer
Computer
Science
Permanent staff Permanent staff
153
A. Chandrasekar Research
Associate
Msc.Biotech. 17-10-2007
onwards
NIL
V. Sathyanath JRF MCA 20-03-2006
onwards
NIL
A. Riju JRF Msc.
Bioinformatics
22-10-2007
onwards
NIL
a. Computational and Information support to various R&D projects of the institute.
b. Maintenance and updating of the institute website (www.iisr.org), intranet
(SPICENET) and the email facility (Spicemail).
c. Designing and developing customized databases, web portals and software for
scientists, administration etc.
d. Providing round the clock access to Internet and Bioinformatics tools through the
facility called E-Lab.
e. Organizing in-house training for institute staff in computers and other IT areas.
Bioinformatics Centre collaborates with NIT, Calicut and offers Bionformatics as an informatics
subject for M.Tech (Computer Science) students. The Centre provides opportunity to MSc
Bioinformatics students from other institutes and universities to carry out their project work.
The above mentioned databases developed by the Centre are utilized by the other
departments and nearby institutes. Software programmes like SpicePat and SignO-Bacteria
are also validated in wet lab studies. In silico designed primers are routinely used in wet lab
studies.
Active collaboration with nearby BTISNet centres, especially with the centres at CPCRI,
Kasaragod and Calicut University in organizing Bioinformatics trainings and sharing of
resources. The Centre also collaborates with NIT, Calicut for conducting a Bioinformatics
course for M.Tech students.
PLASBID: A database on plant associated bacteria integrated with several tools
like sequence editing, primer analysis etc.
PASSCOM: A database on predicted activities of spice compounds is being
developed. The module on black pepper has been completed.
Integrated database on Phytophthora spp.: The databases PIR and PHYDISH
are integrated to serve as a National Repository of Phytophthora.
Eapen, S.J and Chandrasekar, A, 2007. Primer designing and molecular
visualization. Paper Presented at Workshop on Applications of Bioinformatics
and Biotechnology at Bioinformatics Centre, Calicut University.

R&D activities have been initiated on EST analysis of various spices. The outcome of
this study will be used for developing an exclusive database on Spice Genomics.
Work on an integrated database on spices with different modules has also been
initiated.
Summer training 2007 in Biotechnology and Bioinformatics, 05
th
May to 05
th
June
2007, 20 trainees.
154
offered etc.
Several students are availing the facilities of the Centre for carrying out their M.Sc. and Ph.D.
research projects. Currently out of the 22 M.Sc. students, 12 are from the Biotechnology
stream while three are Bioinformatics students. The Centre has submitted two research
papers for publishing in reputed scientific journals. Two molecular biology papers published
from the Institute had significant support of the Centre.
As in the previous years, the Centre played a crucial role in the HRD activities of the Institute.
The Summer School in Bioinformatics organized at the Institute during May-June 2007 was
well attended. The faculty has extended support to the Bioinformatics training programmes
organized at CPCRI, Kasaragod and Calicut University.
R&D activities in comparative genomics, chemoinformatics, EST analysis and QSAR studies
on bioactive compounds in spices will be strengthened. Bioinformatics support will be
extended for gene/QTL mapping, expression studies etc. The existing databases and
institutional repositories will be updated and maintained. Development of a holistic database
on spices is also envisaged. HRD and educational activities will be continued in collaboration
with nearby institutions like NIT, Calicut and DOEACC, Calicut.
Name of the Coordinator : Dr. Santhosh J. Eapen
Postal Address : Bioinformatics Centre
Indian Institute of Spices Research,
P.B. No. 1701, Calicut 673012, Kerala
Phone Number : 0495-2731410, 0495-2731566
FAX : 0495 2731187
E.Mail : disc@spices.res.in
Website : www.spices.res.in
Name of Contact Person(s) : Dr. Santhosh J. Eapen
E.Mail : sjeapen@spices.res.in,
sjeapen@gmail.com
155
Indian Institute of Technology, New Delhi
Coordinator : Dr. A. K. Srivastava

1. SUMMARY OF THE PROGRESS MADE BY THE CENTRE FROM ITS INCEPTION.
The Biochemical Engineering & Biotechnology department was established in
1969 at IIT Delhi to generate quality human resource & undertake research
work particularly in the area of Biochemical Engineering & Industrial Bio-
technology. The department is presently offering a unique five-year dual
degree (B.Tech and M.Tech) program in Biochemical Engineering and
Biotechnology. The department also has a two-year M.S. (By research) and
very interdisciplinary Ph.D. program in the area of Biochemical Engineering
and Biotechnology.

The BTIS sub-centre at IIT Delhi was established in 1989 (equipped in 1991)
by the support of the DBT, GOI, New Delhi, as a part of the nation wide
networking of Biotechnology Institutions of National importance.
2. MAJOR RESEARCH ACTIVITIES IN BIOTECHNOLOGY AND ITS RELATED FIELD AT YOUR
INSTITUTION.
The department is very actively engaged in almost all emerging areas of
Biotechnological research e.g., Bioprocess Engineering, Down Stream
Processing, Bioprocess control, Modeling and Simulation of Bioprocesses,
Plant Cell technology, Animal cell Technology, Genetic Engineering,
Environmental Engineering, Bioinformatics, Molecular Machines and
Nanotechnology etc.

The BTIS-sub centre acts as an integrated information resource centre in the
teaching and research in all the above areas of Biochemical Engineering and
Biotechnology. The centre provides total computer support for extensive
computations, information retrieval and dissemination for all the departmental
courses and to the ongoing research projects (M.Tech., Ph.D. and sponsored
projects) of the department and also to the neighboring educational centers.
Recently the sub-centre has graduated from an Information Resource Centre
to an Instruction facility for quality teaching and research particularly in
Mathematical Modeling of bioprocesses, Artificial Neural Network based
bioprocess control and Bioinformatics.
3. AREA OF SPECIALIZATION OF THE CENTRE.
The main research areas of the department are Biochemical Engineering /
Industrial Microbiology / Fermentation / Bio-informatics
4. MAJOR ACTIVITIES OF THE CENTRE DURING THE YEAR 2007 - 08
The Department organized an International Symposium Biohorizon
2007 , A Joint Indo-Korean Symposium on Biotechnology during 22-24
Feb - 2007.
Fifth Practical Summer Training in Biochemical Engineering &
Biotechnology during June 20 July 21 2007.
Proposed workshop on Bioinformatics Fundamentals and Whole Genome
Analysis during February 2008
5. INFRASTRUCTURE FACILITIES IN THE BIOINFORMATICS CENTRE
A. COMPUTER & COMMUNICATION FACILITIES
156
IBM Netfinity 5000 Server : 1, Dell Server with dual Processor : 1, Intel Xeon
Server : 1,Desktops (Pentium IV/III/II) : 4/2/1, Workstations (Intel Core 2 duo/
Dual core): 5/10, Silicon Graphics Workstation : 1(From Institute grant), Color
LaserJet Printer: 1(From Institute grant)LaserJet Printer: 3, DeskJet Printer : 2,
Scanner : 2, Fax Machine: 1, Xerox Machine: 1, Networking speed through
IIT, Delhi network : 2X5 Mbps.
B. MAJOR DATABASES /SOFTWARE PACKAGES:
DNA Star, Chem Draw, Design Expert (Statistical Optimization Software), Matlab
2007 with Bioinformatics Tool Box (Access through Institute LAN), Windows
Operating Systems (Windows XP, Windows Server), Microsoft Office, Derwent
Biotechnology Abstract (1982-Till date) (on CD), Medline(1982-1998) (on CD),
Science Direct by Elsevier Science (On-line Access), Institute is the member of
INDEST consortium initiated by MHRD, Institute has the provision for
procurement of printed as well as electronics version of selected journals.(Details
on www.iitd.ac.in).
C. DATABASES & OTHER INFORMATION RESOURCES:
Bibliographic Database of research publications of the Department, Catalogue of
Departmental Library, Bibliographic Database of Departmental Theses, Full Text
Database of Departmental Theses
6. DETAILS OF STAFF MEMBERS WORKING IN THE CENTRE:
*Resigned w.e.f September 2007, Two posts advertised, One full fledged faculty
member with Ph.D. in Bioinformatics short-listed, interview 18.1.08
7. TYPES OF SERVICES PROVIDED:
Literature Search: Information retrieval and storage facility from its rich In-
house / On-line database(s) & Journals to the faculty, student and researchers of
IIT Delhi/ Neighboring Institutions.
Bioinformatics Courses & Project work: Students taking elective course on
Bioinformatics, Genomics & Proteomics for the dual degree (B.Tech & M.Tech)
students heavily use the infrastructure facilities of the center. Beside final year
M.Tech students of the department / students form the other universities also do
their dedicated 6-12 months Major Project work using the centers facility.
8. EDUCATIONAL ACTIVITIES WITH DETAILS OF PLACEMENT
Elective course on Bioinformatics (2-0-2, 3credits) for M.Tech students of the
department, Elective course on Genomics and Proteomics (3-0-0, 3credits) for
M.Tech students of the department, Elective course on Data Analysis for DNA
Microarrays (3-0-2, 4 cedits) for the M.Tech students of the Department. All the
students get excellent placement from the Institute.
Ongoing projects in Bioinformatics
>To study phylogeny of eukaryotic single cell organisms whose shole genome is
sequenced and annotated. (Vikas Balhara Supervisors G.P.Agarwal, DBEB &
Jayashree Santosh, Computer Service Center), 2007-2008.
Completed Projects in Bioinformatics
>To formulate Intelligent methodology to remove redundancy of genes from a
large set of microbial genomes. (Abhishek Dubey Supervisors G.P.Agarwal,
DBEB & Jayashree Santosh, Computer Service Center), 2007.
S.NO. NAME OF THE
STAFF
DESIGNATION WORKING
SINCE
ABSORPTION
STATUS
1. Nibedita Mishra Project Assistant May 2007 contractual
2. S. K Patra
*
Project Assistant Jan 2007 contractual
157
>Chromosomal grouping of Saccharomyces cerevisiae and Ashbya gossypii and
its implications on their evolution. (Vamshi Krishna, T Supervisor G.P. Agarwal),
2007.
>Development of an ab-initio Eukaryotic gene predictor. (Sahil Sethi Supervisors
B. Jayaram. Chemistry Department & J.K.Deb, DBEB), 2007.
>Identifying Early Nuclei in folding Kinetics: novel methods in Protein structure
prediction. (Deepak Suri, Supervisors Nalin Pant, Chemistry Department & Saroj
Mishra DBEB), 2007.
>Development of new tools for comparing large segment of nucleotide
sequences (Nitin Chanduka Supervisors G.P.Agarwal, DBEB & Jayashree
Santosh, Computer Service Center), IIT Delhi, 2007.
>Studies on protein based Nano drug delivery system (Shipra Jain, Supervisor
Prashant Mishra DBEB), 2007
>Expression of recombinant chaperones in Escherichia coli and studying their
role in the folding of recombinant proteins like maltodextrin glucosidase / malate
synthase G or single chain antibody (Vatsala Dutta Supervisor Tapan K.
Chaudhury, DBEB), 2007.
>Designing of circular ribozyme targeted to Gemini Virus (Punita Mittal
Supervisor J.K.Deb, DBEB) 2007.
9. IINITIATIVE TO VALIDATE THE OUTCOME OF BIOINFORMATICS RESOURCES
The Sub-centre is publishing the papers in the area of Bioinformatics.
10. COLLABORATIVE WORKS / INITIATIVES:
The center has active collaboration with various departments within the Institute
e.g Mathematics, Chemistry and Computer Science & Engineering (CSE) of IIT
Delhi. The department has also strong collaboration with Institute of Genomics
and Integrated Biology (IGIB) New Delhi, All India Institute of Medical Sciences,
(AIIMS), New Delhi and Jawaharlal Nehru University (JNU), New Delhi.
11. DATABASES/SOFTWARE PACKAGES DEVELOPED:
Catalogue of Departmental Library about 2,000 records, searchable by author,
title and keywords, Bibliographic database of Ph. D and M.Tech theses of the
department about 522 records, About 150 Full-Text versions of the Ph.D. and M.
Tech. Thesis of the department using Greenstone Digital Library Software,
Institutional Repositories of thesis, Dissertation and other biological information,
Other In-house developed specialized databases like Plant Cell Culture (PCC)
Animal Cell Culture (ACC) etc., Different custom made soft wares for Bioprocess
Modeling & Simulation.
12. PAPERS PUBLISHED OR PRESENTED IN THE CONFERECE WITH REFERENCE: PLEASE
SEE www.iitd.ac.in
13. INITIATION OF R & D ACTIVITIES IN BIOINFORMATICS
The department is involved in Teaching & Research (one semester research
projects) in the area of Bio-informatics for dual degree students.
14.DETAILS OF THE TRAINING/WORKSHOP ORGANIZED AND TOTAL NO. OF USER
TRAINED.
Following Short-Term Courses & Workshops were organized
1. An International Symposium Biohorizon 2007 , A Joint Indo-Korean
Symposium on Biotechnology during 22-24 Feb- 2007.
2. Fifth Practical Summer Training in Biochemical Engineering &
Biotechnology during June 20 July 21 2007.
158
3. Proposed workshop on Bioinformatics Fundamentals and Whole Genome
Anal ysis during February 2008
15.IMPACT SHOWN BY YOUR CENTRE ON THE GROWTH OF BIOECHNOLOGY.
Patents & Technology Transfer
Bisaria V.S., Srivastava A.K., Baldi A, Jain A., Gupta N. (2007) A process for
enhanced production of bio-active compounds, Indian Institute of Technology
Delhi , India. Patent Application No. 1266/Del/2007.
i. Research Papers published in peer reviewed journals by using BTIS
Sub Centres Support.
The Department has published more than 425 journal papers, 30 Books / Book
Chapters, More than 100 conference publications since 1990 in different peer
reviewed journals with the help of BTIS facilities of the centre. Details of the
publication are available Faculty / Area wise on our website www.iitd.ac.in.
ii. Bioinformatics Research Papers Published, in peer Reviewed journal
by the centre.
1. Alok Malviya, James Gomes In-Silico methods for rapid screening and
isolation of industrially important Micro organisms (2007), Bioinformatics
(Submitted).
2. Gupta, Shwetank; Bansal, Saurabh; Deb, Jahar K; Kundu, Biswajit (2007)
Interplay between DtxR and nitric oxide reductase activities: a functional
genomics approach indicating involvement of homologous protein domains in
bacterial pathogenesis. Int.J. Exptl..Pathol., 88,377-85.88 377-385.
3. Salony, N. Garg, R.Baranwal, M. Chhabra, S.Mishra, T.K.Chaudhuri and
V.S.Bisaria. Laccase of cyathus bulleri; structural, catalytic characterization and
expression in Escherichia coli. Biochem. Biophys. Acta Proteins and
Proteomics (2007), doi:10.10.1016/j.bbapap,2007.11.006
4. Patra, S.K. HIV/AIDS Research in India: A bibliometric study Library and
Information Science Research 29, 2007, 124-134.
5. B. Chandra, S. Shankar, Saroj Mishra, A new Approach: Interrelated two way
clustering of gene expression data Statistical Methodology 2006, 3 (1) 93-102.
6. Chaudhuri T.K and Paul S. Protein misfolding diseases and chaperone based
therapeutic approaches. FEBS Journal (2006) Vol 273, pp 1331-1349.
7. Eli Chapman, George W. Farr, Renata Usaite, Krystyna Furtak,Wayne A.
Fenton, Tapan K. Chaudhuri, Elise R. Hondorp,Rowena G. Matthews,Sharon G.
Wolf, John R. Yates, Marc Pypaert, and Arthur L. Horwich. Global Aggregation
of Newly-Translated Proteins in an E.Coli Strain Deficient of the Chaperonin
GroEL. Proceedings of National Academy of Science (PNAS, USA) Vol.103,
No.43, pp15800-15805 (2006).
8. Jana S, Chaudhuri TK and Deb JK. The effects of guanidine hydrochloride on
the conformation and enzyme activity of streptomycin adenyltransferase
monitored by circular dichroism and fluorescence spectroscopy. Biochemistry
(Moscow), 71 (11) 2006.
9. Parul Gupta, Nishtha Aggarwal, Pragya Batra, Saroj Mishra and Tapan K.
Chaudhuri*. Co-expression of chaperonin GroEL/GroES enhances in vivo
folding of yeast mitochondrial aconitase and alters the growth characteristics of
Escherichia coli. The International Journal of Biochemistry and cell Biology, Vol.
38 (11), 2006, 1975-1985.
10.Patra, S.K. and Mishra, S., Bibliometric study of Bioinformatics Literature.
Scientometrics Vol 67 No-3, 2006, 477-489.
159
11. Tapan K. Chaudhury and Subhankar Paul, Protein Misfolding diseases and
chaperone-based therapeutic approaches FEBS Journal 273, 2006, 1331-1349.
16. FUTURE ACTIVITIES
1. An interdisciplinary 4 Semester M.Tech (Bioinformatics) program in
collaboration with Biochemical Engineering & Biotechnology, Mathematics,
Chemistry and Computer Science & Engineering Departments is being proposed
at IIT Delhi
2. Attempts will be made to train more students for Bioinformatics related
projects. The centre will focus on the development of user-friendly interactive
software tools for Modelling & Simulation of Bioprocessing, Bioprocess control
etc.
3. Attempts will be made to develop Multimedia Course Materials for different key
areas of Biochemical Engineering & Biotechnology and these can be eventually
put on the BTIS centre Web Server for access by other BTIS centers and sub
centers of the country.

ADDITIONAL DETAILS: NIL

NAME OF THE COORDINATOR: PROF. A. K. SRIVASTAVA
POSTAL ADDRESS: DEPARTMENT OF BIOCHEMICAL ENGINEERING AND
BIOTECHNOLOGY, IIT DELHI, HAUZ KHAS, NEW DELHI 110016
PHONE NUMBER: 26596109 MOBILE: 9868551429
EMAIL: ashokiitd@hotmail.com WEBSITE: www.iitd.ac.in

Name of Contact Person(s): Prof. A. K. Srivastava

160
Indian Institute of Technology, Kharagpur
Coordinator : Professor S. C. Kundu

Bioinformatics activities have been initiated in January 1999 with the aim to
provide Bioinformatics facilities to students as well as the research community
not only to the Institute but also to the surrounding region. The Centre is
having its own space in the Department of Biotechnology. The centre
provides facilities to the B.Tech and M. Tech and Ph. D students to carryout
their project work and summer trainings in the field of Bioinformatics. A
number of research students in and around the region have been using the
centre for the bibliographic searches using the Bioinformatics tools available
in the centre and Internet searches for their research work. The Institute has
introduced two separate 3- credit courses in Bioinformatics and Algorithms for
Bioinformatics for the students. A number of thesis, publications in journals,
oral and posters presentations are being made in national and international
conferences.

2. Major research activities in Biotechnology and its related fields in the
Institution
Scale up of recombinant proteins, molecular farming of therapeutic and
diagnostic proteins, Immunodiagnostics studies and bio-hydrogen
production in different bioreactors
Evolution genomics, Indian non-mulberry silkworm and its medical
applications as biomaterials.
Cloning, expression and purification of response regulator domains from
Mycobacterium tuberculosis and Cloning and expression chitinases of
Entamoeba invadens

Comparative genomics, protein modeling and Database development

4. Major activities of the centre during the year 2007 - 08
A two-day (Sep 21
st
and 22
nd
) workshop on Bioinformatics in Genomics and
Proteomics was conducted to train the participants (M. Sc. / Ph. D students /
teachers) to get them acquainted with the frontier areas of Biological Data Banks,
Molecular Modeling, Genomics and Proteomics, Analysis of Nucleic acid and
Proteins.

5. Infrastructure facilities
Computer hardware: Several Pentium Core2 Duo PCs, Silicon Graphics
O2, Workstation, Sun Server with 10 numbers Thin Client. HP Color Laser
Printer, HP Scanner, Fax, Digital Xerox machine.
Operating systems: MS Windows Vista, Redhat Linux 9.0, Mandrake
Linux 10.2, and Sun Solaris 9.
Internet facility: 10 mbps direct satellite link from ThaiNET.
b. Scientific software packages
161
Sequence analysis: OMIGA 2.0, Sequencer 4.1.4, EMBOSS.
Molecular modeling: GCG Wisconsin Package, MSI Insight II (Perpetual
licensed), Modeler, DS Modeling, Swiss PDB viewer

c. Databases & other information resources
SciFinder, ISI Web of Knowledge, Springer Verlag, Elsevier Science
Direct, Biomednet and PNAS etc. (Access through the INDEST
Consortium. Central Library receives hard copies of several journals like
Bioinformatics, EMBO J, Nature Biotechnology, Nature genetics, Cell,
Nature Medicine and other CD-ROMs and Current Protocols related to
Biological Sciences; Derwent Biotechnology Abstracts; Dialog on Disc
Biotechnology and Bioengineering; CAB Abstracts (Commonwealth
Agricultural Bureau Abstracts); CURRENT CONTENTS (CC) Agriculture,
Biology, Environmental Sciences and Life Sciences.

work
Absorption
status
Mr. Baghirathi
Nayak
Technical Assistant System
administration
8 years Not absorbed
IO, SPA &
Data Entry Operator
Re advertised

The centre offers a, good collection of the electronic resources of large number of
journals full text and several abstracts through INDEST consortium. High-speed
broadband Internet facility (10 mbps leased line) and access to GCG Wisconsin
Package, INSIGHT II software on SGI machine and other computational facilities.

8. Educational activities with the placement details
Institute offers two separate 3-credit courses to the students (UG/PG and
research scholars). The Bioinformatics related companies through campus
interview select B. Tech and M. Tech students and others opt for pursuing
further studies in the areas of Bioinformatics abroad.

9. Initiative to validate the outcome of Bioinformatics resources
Publications were made in peer reviewed journals; every year and average of
75 students are being trained in the Centre; creation of database Wild
silkworms; a committee headed by the Director to monitor the progress and
assets maintained as per the Institute rules.

10. Collaborative work/ initiatives
Linkages have been established with some Institutes/ organizations like Indo -
Norwegian Institutional Cooperation Programme on structural and functional studies
of the major pathogenic proteins of Tuberculosis, Clean Energy Research Institute,
College of Engineering, University of Miami, and University of Ruhr-Bochum,
Germany for improvement of hydrogen production, Institute of zoology, Dresden
University, Germany on Biotransformation, biomaterials and Tissue Engineering at
NSW University, Sydney and UCSD, San Diego and Institutions like IICB, Bose
Institute and Jadavpur University, Kolkata.

162
11. Databases/ software packages developed
Development of integrated search tools to decipher sequence alignments,
gene mapping/manipulation and enhancing polymerase chain reaction and
Development of versatile portable software for bioinformatics) are being
initiated by this Institute. A database called WildSilkBase is being developed
using MySQL and PHP.
12. Papers published or presented in the conferences with reference (2007-
2008)
Functional insights from the molecular modeling of a novel two-
component system,
Biochem.Biophys.Res. Commun. 344, 1327 1333, (2006)
Molecular phylogeny of silk producing insects (Saturniidae family,
Genus, Antheraea) based on 16S ribosomal RNA and cytochrome
oxidase genes, Journal of Genetics, 85, 31-38. (2006)
Molecular identification of tropical tasar silkworm (Antheraea mylitta)
ecoraces with RAPD and SCAR markers. Biochemical Genetics.44, 72-
85. (2006)
Repetitive DNA in topical tasar silk worm Antheraea mylitta.Gene.370,
51-57. (2006)
Genetic variation in ecoraces of tropical tasar silkworm, Antheraea
mylitta using RFLP technique. Curr. Sci, 90, 100-103. (2006)
Exploration of the secondary structure specific differential solvation
dynamics between the native and molten globule states of the protein
HP-36. J. Phys. Chem. B 110, 20629-20634. (2006)
Entamoeba histolytica: Computational identification of putative
microRNA candidates, Experimental Parasitology, 113, 239-243.
(2006)
Simulation and modeling of continuous H
2
production process by
Enterobacter cloacae IIT-BT 08 using different bioreactor configuration,
Enzyme. Microb. Technol. 31, 867-875. (2006)
Crystallization and preliminary X-Ray diffraction analysis of protease
inhibitor from the hemolymph of the Indian Tasar silk worm Antheraea
mylitta, Acat Cryst. F, F62, 669-671. (2006)
Molecular phylogeny of silk producing insects based on internal
transcribed spacer DNA1. Journal of Biochemistry and Molecular
Biology 39, 522-529, (2006)
Cyclosporin Abinding to Mycobacterium tuberculosis peptidyl-prolyl cis-
trans isomerase A Investigation by CD, FTIR and fluorescence
spectroscopy. FEBS Letters, 580, 6846-6860. (2006)
Crystallization and preliminary X-ray diffraction analysis of a protease
inhibitor from the haemolymph of the Indian tasar silkworm Antheraea
mylitta. Acta Cryst, F62, 669-671. (2006)
Copper complexes of (-)-Epicatechin gallate and (-)-Epigallocatechin
gallate act as inhibitors of Ribonuclease A. FEBS Lett. 580, 4703-4708.
(2006)
The binding of 3-N-piperidine-4-carboxyl-3-deoxyara- uridine to
Ribonuclease A in the crystal. Bioorg. Med. Chem. 14, 6055-6064.
(2006)
Interaction of (-)-Epigallocatechin-3-Gallate With Human Serum
Albumin: Fluorescence, Fourier Transform Infrared, Circular Dichroism,
163
and Docking Studies. Proteins 64, 355-362. (2006)
3-N-Alkylamino-3-deoxy-ara-uridines: A new class of potential inhibitors
of ribonuclease A and angiogenin. Bioorg. Med. Chem. 14, 1221
1228. (2006)
Comparison of metalamino acid interaction in PheAg and TyrAg
complexes by spectroscopic measurements. Biophysical Chemistry
120, 215 224. (2006)
Correlation between the dynamics of hydrogen bonds and the local
density reorganization in the protein hydration layer.J. Phys. Chem. B
111, 7626-7630 (2007).
Influence of experimental parameters on identification of whole cell
Rhizobium by matrix-assisted laser desorption / ionization time of fight
mass spectrometry. Eur. J. Mass Spectrom., 13(2), 165-171. (2007)
Probing the nucleotide binding and phosphorylation by the histidine
kinase of a novel three-protein two-component system from
Mycobacterium tuberculosis. FEBS Letters, 581, 1903-1909. (2007)
Temperature and urea induced conformational changes of the histidine
kinase from Mycobacterium tuberculosis. Int. J. Biol. Macromol, 41,
154-161, (2007)
Molecular Cloning, expression and Analysis of Antheraea mylitta
Cypovirus Genome Segments 8 and 11. International Journal of
Virology, 3(2): 60-72. (2007)
Molecular cloning, sequence analysis and expression of genome
segment 7 (S7) of Antheraea mylitta cypovirus (AmCPV) that encodes a
viral structural protein. Virus Genes. 35(2):433-41, (2007)
Transient expression, purification and characterization of bioactive
Human fibroblast growth factor 8b in tobacco plants, Transgenic
Research 17(1) 19-32 2008.

Bioinformatics research activities are being carried out at the UG/PG /
research student level by providing different Bioinformatics projects for
their academic / project work. Database and software developments -
Developing a few specialized databases.
Molecular modeling - Structure solving, dynamics and interaction study of
the some virulence protein of Mycobacterium tuberculosis
Specific gene analysis Analysis of virulence genes of Entamoeba
histolytica and Mycobacterium tuberculosis, hydrogenase gene of
Enterobacter cloacae and fibroin, sericin and seroin genes of
economically important tasar silkworm, Antheraea mylitta.
Comparative Genomics Molecular phylogeny and molecular clock
analysis based on the mitochondrial genes, RAPD-PCR, ISSR profiling
and retrotransposons of different ecoraces of Antheraea mylitta and
inter-species

14. Details of training/ workshop organized and total number of user
trained
The Center conducts workshop on Bioinformatics and its applications,
and Bioinformatics in Genomics and Proteomics in the fourth week
164
of September every year for research students, scientists, doctors,
university and college faculties to cater them hands-on training on
different aspects of Bioinformatics (trained 75 persons every year)

Molecular genetics of silkworm species; characterization of DNA
markers; cloning of silk protein genes fibroin and sericin; identification
and analysis of retrotransposons. Genome analysis of Entamoeba
histolytica production analysis and creation of database for Antheraea
mylitta ESTs. Molecular modeling of proteins and structure-function
relationships of tuberculosis organism; Database on Biomaterials and
Tissue Engineering.

Coordinator : Professor S. C. Kundu, Department of Biotechnology,
IIT- Kharagpur, 72 13 02. Phone: 03222 283764,
Mobile: 09434012848, iitkgp.ernet.in
Co-coordinator : Professor S. Dey
Contact person:Professor S. C. Kundu
(email. kundu@hijli.iitkgp.ernet.in)

Indian Veterinary Research Institute, Izatnagar
Coordinator: Dr. Rajendra Singh

The Bioinformatics Centre, actually started functioning in 1992, is ready to get
online /offline information from DICs, sub-DICs and other centers to meet
users specific requirements and also to provide online/offline information to
DIC, DISC, etc. The Centre has following credentials at his credit
a) Centre developed nine bibliographic, one livestock related database and
one wild life disease database.
b) Seven softwares using FoxPro/Clipper/Visual Basic with Microsoft and
Perl were developed.
c) More than sixteen softwares were downloaded.
d) Sites of many databases were listed for utilization in research work.
e) More than sixteen sites of bibliographical databases were listed in the
year.
f) Centre in collaboration with NLVS produces more than eight Databases.

2. Major research activities in Biotechnology and its related fields in the
institution
i) Number of divisions/Centers doing research in the area of Biotechnology
are involved in developing improved diagnostics/vaccines for differential
diagnosis and recombinant vaccines using RFLP, SSCP and synthetic
peptides etc with the help of bioinformatics data bases and softwares.
ii) Molecular modelling, gene analysis, sequencing, genetic identity index
and genetic distances were used to analyse information obtained from
different research projects persude in different divisions of the intiitute and
165
these data were also used for developing and updating related
databases.
iii) A large number of new sequence information was submitted to EMBL
GenBank.

3. Area of Specialization of the centre : Veterinary Bioinformatics.

i. Wild life disease database software was completed and database was
updated.
ii. Different databases and softwares were updated and improved
respectively.
iii. Online/Off-line information was collected and disseminated.
iv. Different primers and probes were developed to improve upon diagnostic
techniques, vaccines, etc.
v. Efficiency of different softwares were examined for analysis of nucleotide
and protein data.
vi. Different techniques were evaluated for removing the noise in microarray
data.
vii. Students and Scientists of IVRI and other research workers in the field of
Biotechnology and Bioinformatics from other organizations are trained in
handling Bioinformatics databases for sequence analysis, primer
designing, Probe searching and microarray analysis.
viii. We are in the process of offering 3 credit course in the fields of
Bioinformatics, Biostatistics and Information technology to Ph. D. and M. V.
Sc. Students of the Institute.
ix. Scientists and students of this institute used different databases for
sequence analysis, probe search, etc.

A. Computer & Communication Facility : The following are the new
development/augmentation of Bioinformatics:
512 kbps VSAT from EARNET. Up-gradation of V-SAT. Addition of 2
server. Faster E-mail and Internet facilities. A Bioinformatics Lab
containing almost all the facilities available at any center of bioinformatics
in the country. The Centre is connected with all divisions/sections of the
Institute by LAN and EPABX.
B. Scientific Software Packages : i) DNA Star ii) Genocluster Software.
In-house developed Softwares:
1. PhDTHESPACK 2. WILDLIFEPACK.
C. Databases and other information Resources
IVRI Ph.D. Thesis Abstract Database, Wildlife Disease Database and
Livestock Database.
SL.
NO
NAME OF THE
STAFF
DESIGNATIO
N
SPECIALIZATION WORKIN
G
1.
Dr.Rajendra
Singh
Project
Coordinator
Data Management &
Sampling
2001
2.
Sh. K.N. Tech. Officer Information & Com. 1992
166
Kandpal programming
3.
Sh.J.P.Yadav T-3 (Rep.) Reprography 2007
i. Online/Off-line collection and dissemination of information.
ii. Search and alignment of sequences and microarray analyses.
iii. Training, Workshop, etc.
iv. Internet, E-mail facilities, use of Libsys and other database.

8. Educational activities with details of placement : Not applicable

A number of diagnostics, differential diagnostics, identifications of marker
genes for improving productive and reproductive efficiency, characterization
of species and breeds, estimation of genetic diversity, vaccines, etc. were
achieved due to efficient use of facilities available at Bioinformatics
Information Sub-center, IVRI, Izatnagar. These technologies are in the
process of patenting.

10. Collaborative works/initiative
Institute has more than ten National/International projects and Bioinformatics
centre is providing all possible support in these research projects.

1. Wildlife Disease, 2. Livestock Databases
3. Bibliographic Databases 4. Softwares: i. THESPACK, ii. PUBPACK, iii.
RUMPACK, iv. LIGPACK, v. FMDPACK.

One Manual and Nine research papers have been published in National and
Inter-National Journals.

A number of divisions/centres like Bacteriology and Mycology, Veterinary
Public Health, Avian Disease, Pathology, Parasitology, Biochemistry, Animal
Genetics, National Biotechnology Centre, and Centre for Advance Disease
Research and diagnosis are involved in developing improved
diagnostics/vaccines and genome analysis work. In order to get inside into
the structural genomics, genome analysis of different species were carried.

14. Details of Training Workshop organized and total no. of user trained
During the year about 230 scientists, students and other research workers
have been trained in Bioinformatics and Information Technology.
National Workshop : National Workshop cum Training Programme on Bio-
computing was organised from March 24 to 27, 2007 at Bioinformatics
Centre, IVRI, Izatnagar. We declare only 10 seats for participants but
pressure from different corners compelled us to admit more then 52 students
in this workshop.
167
Students Trained: One student of M.Sc. (Bioinformatics) from Bioinformatics
Centre, Jamia Millia University, New Delhi was trained under Summer
Training from 5.6.2007 to 4.7.2007 in Evaluation of Bioinformatics Tools for
Sequence Alignments at Bioinformatics Centre,IVRI, Izatnagar.
Students Trainees: i) Two student trainees from J.N.U. were trained in
Bioinformatics on Cancer patients database and Sequence Alignment
Analysis. ii) Two trainees who have already completed their degrees have
been trained in Bioinformatics on Microarrays and development of information
databases.

15. Impact shown by the centre on the growth of biotechnology and allied
areas:
The information provided by Bioinformatics Centre helped in developing
diagnosis of diseases, development of vaccines and epidemiological studies
in different disciplines of veterinary and animal science. Polymerase chain
reaction amplified nucleic acids for epidemiological studies of diseases like
Infectious Bursal Disease, New castle disease, Orthopox viral diseases etc.
Full-length genes are also amplified by self-designed primers based on
sequence information available in various sequence databanks. The
Bioinformatics Centre extended all possible support on its command for all
round development, education and training in Biotechnology and related
subjects.

16. Future Activities:
The future plan can be delineated into following three major activities:
a) Scientific Support: The centre will cater the support to different National,
International and Post Graduate Research Projects of the Institute where use
of Biostatistics is required. The exchange of information in the field of
Bioinformatics will be continued.
b) Training and P.G. Education: The centre will organize short term and
long term training programmes for the students and research workers in the
fields of Biotechnology and Bioinformatics. Workshops will also be organized
for hands on training and better interaction among the people working in the
field of Bioinformatics. The Bioinformatics is in the process to be introduced
into course curricula of Ph.D. and Masters degree programmes of Deemed
University, IVRI, Izatnagar. During the present five year plan our endeavor
will be to open Masters Degree Programme in Bioinformatics.
c) Research and Development:
a. Major tools used in Bioinformatics will be assessed for sequence
alignment, using nucleotide and protein sequences of different
organisms, breeds, species, with varying origin, time and space.
b. Statistical and computational tools will be adapted and developed to reach
the conclusion with efficiency.
c. Univariate and multivariate statistical and computation tools will be
adapted and developed for better comparison of different tools for
sequence alignment.
d. To develop tools for Correction of noise in microarray data under finite
population.
e. To estimate effect of different factors causing variability in microarray data.
f. To adopt and develop statistical techniques for arresting the outliers in
finite population.
168
g. To adopt and develop statistical tools and softwares for efficient analysis
of microarray data .
h. To develop databases of different zoonotic diseases to safe guard
human and livestock population from hazard .
i. To develop databases of livestock diseases to make livestock sector
economically viable.
j. To develop softwares for experimentation to assess efficacy of different
diagnostic and profilectics at the place of livestock .

Additional Details:

Name of the Coordinator: Dr. RAJENDRA SINGH, Principal Scientist

Postal Address: D Di is st tr ri ib bu ut te ed d I In nf fo or rm ma at ti io on n s su ub b- -c ce en nt tr re e, , N NL LV VS S, ,
Indian Veterinary Research Institute,Izatnagar
(U.P.) - 243 122
Phone No. 0091-581-2300207/ 2300305
FAX No. : 0091-581-2303284
E-Mail : codisc@ivri.up.nic.in
Website : www.ivri.nic.in

Name of Contact Person: K.N.KANDPAL, Technical Officer
E- Mail: knkandpal@ivri.up.nic.in
169
Indian Institute of Advanced Research, Gandhinagar, Gujarat
Coordinator : Dr. Desh Deepak Singh

Indian Institute of Advanced Research at Gandhinagar, Gujarat is engaged in
research in the areas of biotechnology and biosciences. The bioinformatics
centre sanctioned by DBT is engaged in the training of scientists in the field of
bioinformatics, database and software tool creation, etc. The centre has
organized a training program for fifty five participants (Faculty, students,
scientists) from all over Gujarat, developed a database on adhesins and
extracellular matrix proteins, a database on plant pathogens and their
virulence factors, software tools like auto-PSIBLAST, motif search and
annotation of adhesin-like proteins. Two students from neighboring institutes
have completed their Masters projects of six months duration.

2. Major research activities in Biotechnology and its related fields:
(a) To compile the information on plants and their pathogens in a user friendly
database in conjunction with useful tools. This will help to forecast a plant
diseases in advance based on weather conditions.
(b) Identification of pathogens based on their characteristics and information
on support measures available for the control of diseases.
(c) To collect and compile data which will help us understand the tropical
pathogens more comprehensively.

(a) Database and software tool development.
(b) Identification and analysis of virulence factors from tropical pathogens.
(c) Extension of bioinformatics work to cloning and 3-D structure solution.

(a) Training Program: A three days bioinformatics training program was held
at IIAR from May 16-18, 2007 and fifty five participants (Faculty, students,
scientists) from all over Gujarat participated in it. The participants were
imparted lectures by eminent faculty Like Dr. AS Kolaskar, Dr. T Madhan
Mohan. Dr. GPS Raghava, and practical hands on training was also given.
(b) Development of software tools: Various software tools are developed,
being developed in the centre for data analysis. A motif search tool for
detection of particular motifs in sequence database has been developed and
is available online at our website. Auto PSI-BLAST tool for automatic analysis
of multi sequence, multi iteration queries against various databases has been
developed and is also available online.
A tool for gene annotation utilizing BLAST, HMMER, Threader is at advanced
stage of development and will also be made available online for free use by
the community.
(c) Development of Adhesin database: A database on Adhesins has
been developed using MySql and is currently being updated to make it
dynamic. Adhesins are an important category of proteins in host-pathogen
interactions and this database will help us understand this process more
efficiently. Also it will be made available to user community freely for use.
(d) Database on plant-pathogen interaction: A database on Plant
Pathogen interactions on Oracle 10g is being developed currently and it will
170
be made available with useful analysis and predictive tools and at a later
stage it will become a useful tool for the farmers for disease forecast and
preventive measures.
(e) Students training: Two students: one from SP University, Vallabh
Vidyanagar and one form DAIICT, Gandhinagar have done their six months
project work as part of their Masters curriculum with us and benefited from the
centre. Two other students are currently working as trainees in the centre.

A. Computer & Communications facility:
SGI Fuel One number
IBM Z pro Xeon 3.0GHz Six number
Dell Precision Quad core Four Number
Dell Desktops core 2 duo Ten number
HP Desktops PIV Five number
IBM e servers 2X Xeon 3.0GHz Three number
HP laserjet printers Two number
B. Scientific Software packages:
MOE, Rasmol Pymol, BLAST standalone,
Autodock, Oracle 10g, FUGUE, etc.
Refsequence, genome sequences of pathogen


Sl.
No.
NAME OF THE
STAFF
DESIGNATION WORKING
SINCE
ABSORPTION
STATUS
(YES/NO)
1. Mr. Vijay Singh Project
Assistant
March, 2006 With IIAR
2. Ms Divya Nair Project
Assistant
March, 2006 With IIAR
3. Mr. Bhavesh
Kataria
Programmer July, 2007 With IIAR
4. Mr. Ved Prakash
Tiwari
Trainee May, 2007 In DISC
project
5. Ms. Shivani
Viradia
Trainee July, 2007 In DISC
project

(a) Training
(b) Genome analysis
(c) In-silico anlaysis of protein-ligand interactions.

We are shortly starting PhD program and shall be enrolling students.

Since we are relatively newly established the databases and softwares
developed by us are being extensively validated right now.
171

We are developing linkages with Labs. having relevant expertise to extend
the bioinformatics analysis work to actual wet Lab. experiments.

11. Databases/ Software packages developed:
Same as 4(b), (c), (d) above.

Singh, V., Singh D. D., (2008). Leishmania major: Genome analysis for
identification of putative adhesin-like and other surface proteins. Exp Parastol
188, 139-145 (available online August 3, 2007).

(a) Genome analysis of tropical pathogens like tritryps etc. is in progress to
find out virulence factors in these pathogenic organisms.
(b) Work is in progress to identify the virulence factors in M. grisea which
causes rice blast disease.
(c) In-silico analysis and docking studies are being conducted to identify
pharmacophores modulating virulence factor expression in pathogens.

14. Details of Training/ Workshop organized and total no. of users trained:
A three days bioinformatics training program was held at IIAR from May 16-
18, 2007 and fifty five participants (Faculty, students, and scientists) from all
over Gujarat participated in it. The participants were imparted lectures by
eminent faculty Like Dr. AS Kolaskar, Dr. T Madhan Mohan. Dr. GPS
Raghava, and practical hands on training was also given.

areas:
(a) Research work undertaken in the centre published in peer review journal.
(b) Training of students, faculty, staff and scientists from all over Gujarat.
(c) Bioinformatics resource centre for the Institute.
(d) Maintaining institutional computational activities.

16. Future activites:
The current activities undertaken at the centre will be further augmented in
the coming time. More training programs will be organized, databases and
software tools will be developed and we hope to publish a lot more of the
work we do. We ultimately hope to be a nodal centre for Bioinformatics in
western India.
Name of the coordinator: Dr. Desh Deepak Singh

Postal Address: Indian Institute of Advanced Research,
Puri Foundation, Block-2, First Floor,
Udyog Bhawan, Sector-11,
Gandhinagar-3820017, Gujarat

Phone number: 079-30514150

Email: ddsingh@iiar.res.in
172

Website: www.iiar.res.in

173
Indian Institute of Integrative Medicine, Canal Road, Jammu
Coordinator : Dr. G.N.Qazi

Establishment of Molecular Modeling factility
The centre is now equipped with complete molecular modeling facility with
relevant software and hardware and qualified manpower to process the same.
R&D activities started
Based on the above said facilities, a lot of Research & Development activities
have been started by the centre, with a focus on molecular docking and QSAR
studies.
Official website of RRL (now IIIM) Jammu Launched
Official website of Regional Research Laboratory Jammu (now Indian Institute of
Integrative Medicine) is completely designed and hosted which is available at
http://www.iiim.res.in and http://www.rrljammu.org.
Complete Networking of RRL-J and also branch lab Srinagar
Complete networking of RRL was done with Fiber Optics back bone and
managed switches for better interconnectivity within the lab.
Up gradation of Infrastructure & Internet connectivity
2 Mbps Leased line connection is now functional for faster access to Internet in
addition to the Microwave Radio Frequency link with a maximum speed of 128
Kbps and CSIR-Net through the VSAT.

institution
In the Division of Biotechnology there are a number of projects being actively
pursued. The highlights of some of these:

Exploration and exploitation of microbial wealth of India for novel compounds and
biotransformation process.
Bioprospective of microbial wealth of North Western Himalayas
Development of Technologies for Pathway Engineering of Withania somnifera
an important plant component of Ayurvedic drugs.
Exploration and exploitation of microorganisms from North-Western Himalayas
for the present of Industrially important enzymes.

Medical, Drug discovery by Molecular Modeling & QSAR.

- QSAR analysis of aryl, alkyl, imine/amide based efflux pump inhibitors
QSAR studies of several amide molecules (from IIIMJ repository) have been
done for their inhibitory activity against NorA and a final QSAR model with r2 =
0.866 has been arrived at. For further refinement and validation of the QSAR
174
model developed, two external validation tests were performed and the results
obtained were in accordance with the validation criteria known for QSAR studies.
In order to further validate the statistical quality of the model developed, Leave-
25%-out experiment was also carried out, which further validated the derived
model. The results are incorporated in the manuscript, which is submitted to the
European Journal of Medicinal Chemistry.
- Molecular Docking of Ovalbumin
3-D structure of the protein ovalbumin (1OVA) was downloaded and ligands
(chiral) prepared at RRLJ were docked on to the protein to arrive at the
mechanism of the bioreduction reaction. The computational analysis revealed
intra-molecular hydrogen bonding to be the major factor for low-
diastereoselectivty of the hydroxyl-ketones when subjected to chemical reduction
in presence 1OVA for the preparation of diol. Manuscript to be communicated
to the Journal of Chemical Informatics and Modeling
- QSAR studies of parthenin derivatives
A library of parthenin derivatives has been created at IIIMJ and several
molecules from it have been identified to possess potent anti-cancer activity. In
order to arrive at more potent molecules, with less toxicity, QSAR studies of
these compounds have been done. Based on the IC50 values of the compounds,
the QSAR equation was derived wherein five descriptors were found to have
bearing on the overall activity of the molecules. Further studies for the refinement
of model are in progress
- Database on venom PLA2 and its inhibitors
Earlier, we have created a library of compounds possessing anti-snake venom
(precisely anti-PLA2) activity of the viper venom species. Through molecular
docking, we could also arrive at a novel PLA2 inhibitor. Based on the research
activities carried out on venom phospholipaseA2, a lot of data is generated. We
have also downloaded a lot of information on PLA2 from other venom species
including bee, scorpio etc. This information will be combined with the earlier data
in order to form a comprehensive source of information on PLA2 and its
inhibitors.
- Human Resource Development.
Regular training sessions on Bioinformatics were organized in order to train the
students within and around J&K state in the field of Bioinformatics. (Also see
point 14)
- Centre is participating in the mega Vaccine Adjuvants project which
is submitted in collaboration with Synthetic Chemistry Dept., RRL-J
and Institutes in Norway.
- The Centre is also a part of the recently proposed Cheminformatics
networked project by URDIP, Pune
- Bioinformatics related Database development undertaken.

175
Silicon Graphics Fuel, PCs & Server; HP laser printer. All computers are
on LAN with fiber optics back bone connected with 2Mbps leased line
supported with an alternate RF link , CSIRnet &VSAT link.
- Insight II & Cerius2 - Hyper Chem 7 - NTsys 2.1
- DNA Star, Laser gene - Phylip 3.
- Apart from ChemDraw, ISIS etc. and other public domain software.
MDL Crossfire, Biotechnology Abstract, Medline, Medicinal Plant
Database, Dictionary of Natural Products, J-Gate Access.

Sh. Abdul Rahim Scientist Computer Engineer 01.03.1999 till date
Sh. Amit Nargotra Scientist Engg & Bioinformatics 05.07.2001 till date
Ms. Monica Gupta Data Entry Operator MCA 17.10.2007 till date

i. Assistance to scientists, Research fellows, M.Sc Biotechnology students
in accessing, searching and retrieval of biological information.
ii. Software installation & demonstration.
iii. Human Resource development.
iv. Project Guidance to the students from various institutes across the country
to complete their bioinformatics and IT related project work.
v. Seminars and demonstration of bioinformatics and other software to
students of various universities within the state.
vi. Maintenance of the computers installed with Gene sequencer, HPLC,
Quality Control etc., and peripherals in various departments in the lab.
vii. Scientists, Staff and scholars from the following institutes besides RRL
Jammu are extensively using the facilities at the Bioinformatics Centre:
1. University of Jammu
2. Sher-i-Kashmir University of Agricultural Science & Technology.
3. Acharya Shri Chander College of Medical Science.
4. State Council of Science & Technology.
5. University of Kashmir
6. GNDU, Amritsar
7. IIIM Srinagar Br. lab
8. Educational activities with details of placement : NA
The centre works in accordance with various departments in this institute viz.,
Biotechnology, Pharmacology, Natural Product Chemistry etc. Hence all the
outcomes of the Bioinformatics research are validated with the wet lab
experiments in the concerned department. Besides this, the wet lab results are
also validated theoretically in order to establish a protocol in any new area of
study
176
a. The project Drug Target Development using Insilico Biology under
the Tenth Five Year Plan program with the following Labs : IGIB, Delhi;
IMTECH, Chandigarh; IICB, Kolkata; CDRI, Lucknow. (The project is
extended for two years [from 2007-2009])
Database on venom PLA2 initiated
Revised manuscript on QSAR studies of aryl, alky, imine/amide based
efflux pump inhibitor has been sent to the European Journal of Medicinal
chemistry. (MS. NO.: EJMECH-D-07-00615R1)
A paper comprising the work on molecular docking on Ovalbumin and its
molecular interaction analysis is ready for communication.

A lot of research activities on molecular docking, QSAR studies and
homology modeling are now going on in the Bioinfomratics Centre IIIM,
Jammu. The centre is now participating in other mega research projects of
the institute as well as in collaborative projects within and out side the
country. The experimental results from various departments of IIIM-J are
being validated theoretically at the bioinformatics centre in order to develop
a new protocol for any specific area of research involving biomolecular
targets of anti-cancer, efflux pump etc.

Mar-August 2007: Training programme on Bioinfomratics & its
Application for Engineering students from several colleges across India (4
students)
Apr- June 2007 : Training programme for three months on Database
development for B.Tech students (15 students)
September 2007: Demonstration of Bioinfomratics work at IIIM Jammu for
merit students under CSIR Open Day scheme. (about 105 students in 5
batches)
April-October 2007: Training programme on Molecular Modeling and
Algorithm development for MSc Bioinfomratics Students for 6 months. (3
students)
December 2007: Demonstration of Bioinformatics work at IIIM Jammu for
meritorious students under CPYLS scheme. (about 100 students in 5
batches)

allied areas
The centre is now equipped with all the major scientific software packages and hardware
and qualified manpower for carrying out the molecular modeling activities. Under this
area the major activities taken up were docking studies, homology modeling and QSAR
177
studies. Two papers on homology modeling have already been published, One paper on
QSAR is under revision and one paper on molecular docking is ready to be
communicated. One patent is also filed (NF0236/2006 dt. 12.10.2006). The centre is also
imparting training on various areas of Bioinformatics to the students of Bioinformatics at
the DOEACC centre and some of them have been placed in reputed organizations like
IGIB, Delhi. The centre is also giving introductory training course to several neighboring
institutes like University of Jammu, Sher-I-Kashmir University of Agricultural Sciences
and Shri Mata Vaishno Devi University. The centre is constantly in touch with the BIFs
created within the state and has always extended a helping hand for any teething troubles
faced by those centres.

QSAR studies on several bioactive compounds on different targets from
IIIMJ repository.
Database development on venom PLA2 to be completed.
Refinement of the QSAR model developed for parthenin derivatives.
Docking of selected compounds on PLA2 from different venom species
Threading exercise to determine the 3-D structure of proteins and hence
virtual screening of the compounds available in IIIMJ repository.
Algorithm development activities to be carried out as major activity with
the collaboration and support of Dr. G.P.S.Raghava, IMT, Chandigarh.
Location-specific databases based on Microbial Biodiversity of North
Western Himalayas is to be linked with IIIMJ website.
Frequent workshop and training programmes to expose the latest
techniques in Bioinformatics to the scientists as well as students.

Additional Details:
Name of the Coordinator: Dr. G.N.Qazi
Postal Address: Director, Indian Institute of Integrative
Medicine
Canal Road, Jammu
Phone Number: 2569111/222 Fax No.: 2569333
Email: qazi_gn@yahoo.com Website: www.iiim.res.in
www.rrljammu.org
Mr. Abdul Rahim, Scientist Mr. Amit Nargotra, Scientist
Email: arahim@iiim.res.in Email: amitnargotra@yahoo.com
anargotra@iiim.res.in

178
Indian Institute of Chemical Biology, Kolkata
Coordinator: Dr. Chitra Dutta

Since its inception in 2002, various scientific projects on microbial and
mammalian genome/proteome analysis have been carried out by the members of
the Centre. Among the problems addressed so far are studies on intra- and inter-
genomic compositional variations in pathogenic microbes, delineation of
molecular mechanisms of adaptation of extremophiles to their specialized niches
and analysis of trends in amino acid substitutions between human and mouse
orthologs. A number of novel genome data mining software tools have also been
developed in course of these studies.

institution
IICB is a constituent national laboratory of the Council of Scientific and
Industrial Research (CSIR), the premier multidisciplinary Research and
Development organization of the Government of India. IICB is engaged in
interfacial research on chemical and biological sciences addressing biomedical
problems of national importance as well as of global interest. There are six major
research groups working in the areas of Cell Biology & Physiology, Chemistry,
Molecular and Human Genetics, Structural Biology & Bioinformatics, Drug
Development/Diagnostics, Infectious Diseases & Immunology, and
Biotechnology. Major objectives of the research activities are to understand the
genetic basis and molecular mechanism of the inherited genetic disorders, to
have an insight into the pathophysiological basis of metabolic diseases, to
develop therapeutics, preventives and diagnostics for diseases
intimately associated with impairment of the host immunity, development of
herbal medicines, search for effective lead molecules from natural sources etc.
Various software are being developed for analysis of macromolecular structures
and elucidation of their interactions with bioactive molecules, which will facilitate
lead optimization for rational drug design.

3. Area of Specialization of the centre : Genome and Proteome Analysis

4. Major activities of the centre during the year 2007 - 08 :

(A) Polarized trends in nucleotide/amino acid substitution patterns in
human and mouse orthologs of two compositional extrema:

A genome-wide analysis of sequence divergence patterns of 12198 human-
mouse orthologous pairs revealed that the trends in nucleotide and amino acid
substitution patterns in orthologs of high and low GC-composition are highly
asymmetric and polarized to opposite directions. As the GC
3
contents of human
and mouse orthologous pairs exhibit a strong positive correlation (r= 0.86, p<10
-
7
), the entire dataset was divided into three broad groups on the basis of the
GC
3
content of human genes: (i) High-GC (GC
3
>70%), (ii) Medium-GC
(70%GC
3
50%) and (iii) Low-GC (GC
3
<50%). The analysis showed that at
nucleotide level, the high-GC orthologs have undergone a large excess of
ATGC substitutions over GCAT substitutions from mouse to human
individually in all three codon positions, while for low-GC orthologs, the reverse is
179
true. Consistent with these trends, the amino acid substitution also exhibit
definite, but opposite patterns in high-GC and low-GC orthologs. High GC-
orthologs exhibit significant bias in favor of ThrAla , SerAla, SerPro,
ValAla, LysArg, AsnSer, IleVal etc from mouse to human,, while in low
Gc-orthologs, the reverse trends prevail. The members of the GC-even group
share some trends with the high-GC group and some with the low-GC group.
These observations imply that there is a definite directionality in substitution
patterns towards increasing compositional divergence in human protein-coding
regions as compared to mouse. Surprisingly enough, the trend AspGlu from
mouse to human is shared by the members of all three groups of orthologs
irrespective of their GC-bias, the structural/functional implication of which is not
very clear.

(B) Anal ysis of Gene and Protein Architectures of Extremel y Halophilic
Microorganisms - Molecular Signature of Hypersaline Adaptation :

A large scale comparative study of the compositional characteristics of
genomes and proteomes of the extreme halophilic and non-halophilic
microorganisms has revealed the conspicuous characteristics relevant to life in
an extreme environment distinguished by hypersalinity. These are (i) distinct
synonymous codon usage, (ii) enhanced usage of negatively charged residues
on protein surface, (iii) decreased frequencies of hydrophobic residues, and (iv)
higher propensities for formation of random coil region in proteins, as compared
to their orthologs in non-halophilic organisms.
Comparison of 124 orthologous protein sequences from

halophilic and non-
halophilic species of comparable genomic

G+C contents has shown a strong bias
towards replacement of positively charged and hydrophobic residues of non-
halophilic proteins by Asp and Glu in halophiles. Higher propensity of formation
of random coil region and surface negative charge distribution are evident from
the previously reported experimentally determined three dimensional orthologous
structures of halophiles and non-halophiles. The analysis not only demonstrates
that genes/proteins of the extreme halophilic organisms are magnificently
engineered in order to survive in the high salt condition, but also offers an insight
into the nitty-gritty of the molecular strategies adopted by the microbial world to
optimize between their functional activities and structural stability in such a
specialized niche.

(C) Other activities:
Members of the Centre regularly take classes in Calcutta University, Jadavpur University
& Visva-Bharati and also in the pre-Ph.D. course at IICB. Hands-on training is provided
to the students and scholars of local Universities/Institutes. Students from various
Universities /Institutes perform short-term projects at the Centre.

SGI Octane Workstations
High End Server (Itenium II Hp Integrity Server 4640), Linux OS
Mail Server (Xeon server), Ftp Server (Xeon server)
180
P4 PCs, Laser Printers, DeskJet Printers
High speed Network Printer with Copier and Scanner function
High Resolution Scanners
4 mbps uncompressed leased line Internet connection from VSNL
B. Scientific Software packages :
Insight II Platform in Silicon, Graphics Octane (Version 2000.1)
GCG Wisconsin Package (Version 10.3) & SeqWeb (Version 2.1)
DNA Star Laser gene, DS Gene (Version 1.5)
Statistica (Version 6), Corel Draw
Visual Studio .NET, End Note (Version 8.0.2)
Adobe Creative Suite Sigma plot (Version 9.0)

Mr. S. Chatterjee Senior Tech. Asst. Bioinformatics
Mr. S. K. Bag Junior Tech. Asst. Comp. science
Mr. S. Paul Junior Tech. Asst. Bioinformatics

The sequence analysis using different software available in the centre,
bibliography search facility and web-based services from our local server are
provided to scientists and students of IICB and of other local Research
Organizations/Universities. The members of the Centre also actively take part in
organizing major events in IICB such as Open house or exhibitions.

Members of the Centre regularly take classes in Calcutta University, Jadavpur
University & Visva-Bharati, NIPER-Kolkata and in the pre-Ph.D. course at IICB.
Students from different Institutes/Universities of our country carry out short-term
projects at the centre.

Research papers have been published in International Journals, Novel genome
data mining software tools like SPAST, Gensyn have been posted in the web.

A database on Genetic Diseases among Indian Population is being developed
with the collaboration of Dr. Kunal Ray, Human Genetics & Genomics Group of
this Institute. Analyses of microbial genomes are being carried out in
collaboration with Prof. J. Chakrabarti, Indian Association for Cultivation of
Sciences, Kolkata.

11. Databases/ Software packages developed :
Among the novel algorithms and programs currently being developed by the
members of the centre for macromolecular sequence analysis are SPAST
(Substitution Pattern Analysis Software Tool), GeneSyn A program for analysis
of gene synteny in genomes of two or more related species and an integrated
software tool for prediction of cases of horizontal transfer.

12. Papers published :

181
(i) Bag SK, Paul S, Ghosh S, Dutta C.(2007) Reverse polarization in amino acid
and nucleotide substitution patterns between human-mouse orthologs of two
compositional extrema. DNA Res., 14:141-54.


During the reporting period, the following initiatives have been taken on :
(i) Development of novel software tools on Gene Synteny, HGT etc.
(ii) New collaborative projects on structural analysis of transcription factors of
hyperthermophiles (with Prof, S. Roy & Dr. T. Chakraborty, IICB)

14. Details of Training/ Workshop organized and total no. of user trained:
No. of Short-term (3-6 months) trainees : 12

areas:
No. of papers published by the Centre : 1
No. of papers published with the help of the Centre : 4
No. of Ph. D. thesis completed with the help of the Centre : 4
No. of Software tools developed/under development : 3
No. of database under construction : 1
No. of persons trained in the Centre (short-term projects) : 12
No. of collaborative research projects being carried out : 3

(i) Development of the database on Genetic diseases among Indian
Population.
(ii) Development of novel genome analysis tools
(iii) Comparative genome/.proteome analysis of microbial (especially
extremophiles and pathogens), fungal and mammalian organisms.

Additional Details
Name of the Coordinator: Dr. Chitra Dutta
Postal Address: Bioinformatics Centre,
Indian Institute of Chemical Biology
4, Raja S.C. Mullick Road, Kolkata 700 032
Phone Number: 91 33 2473 3491 (ext. 212)
Fax Number: 91 33 2473 0284 / 5197
Email: cdutta@iicb.res.in;
182
Institute of Bioresources and Sustainable Development, Imphal
Coordinator : Shri. Sunil. S. Thorat

The Distributed Information Sub-centre (DISC), Imphal has constituted an
Executive Committee for the proper functioning of the Bioinformatics
centre, The First Executive Committee meeting consisting five members
was held on 4
th
December 2006 at Conference Hall of the Institute of
Bioresources and Sustainable Development (IBSD). The Centre has
started functioning with the recruitment of one Information Officer, one
Technical Assistant, and one Data Entry Operator. For the establishment
of the Centre, necessary infrastructure development was made by
procuring two servers (Mail/Web and Power Database Solution), scanner,
color laser printer, 5 KVa UPS, Mac Book, 4 PCs, Plasma TV Screen for
presentation a Digital camera and Handycam for Documentation. In
addition to this the centre has few scientific software like Genocluster and
other softwares like Linux AS4, NOD 32 Antivirus, Microsoft Windows and
Office Professional edition along with paper license and a Microsoft Visual
Studio 2005 Standard version. The centre has subscribed three e-journals
namely Conservation Genetics, Plant Genetics Research and
Conservation biology and two databases namely AGRIS and AGRICOLA
for the students and researchers of the Institute. The centre has organized
3 (three) training programmes for the Teachers/Lecturers,
Researchers/students on 24-25 January, 2007, 29th - 30th March, 2007
and 17- 18th August 2007.Altogether 48 participants were benefited from
the trainings. Under Database development programme three Databases,
namely Birds database of Sikkim, Zingiberaceae database of NE with
special reference to Manipur and Cyanobacteria database have been
developed. Currently more than 400 records have been added to these
databases and database updating is in progress.

2. Major Research Activities in Biotechnology and its related fields at
your institution:
Invitro propagation and mass multiplication of plant resources of
selected medicinal, aromatic and horticultural plants for
conservation and sustainable development.
Isolation, identification and characterization of medicinal and
aromatic oils and bioactive principles from the plants used in
traditional/folklore medicines and their value added products.
Isolation, physiological and biochemical characterization isolates of
North-Eastern region of India for sustainable utilization and
development of cyanobacterial value added products.
Standardization of microbial fermentation for fermented food
products of North East Region and value addition for commercial
exploitation.

3. Area of Specialization of the centre: Environment & Biodiversity

An Executive Committee of the DISC was constituted.
183
Training is provided to the Teachers, Researchers & Students from
time to time.
Three Databases namely Birds database of Sikkim, Zingiberaceae
database of NE with special reference to Manipur and
Cyanobacteria database have been developed. Currently more
than 400 records have been added to these databases and
database updating is in progress.
One poster presentation on Ethnobotanical plant database of NE
India was presented in the International Conference on
Bioinformatics, 2007, HKUST, Hong Kong.

A. Computer and communication facility:
Two Servers (Mail/Web and Power Database Solution) , Scanner,
Color laser printer, 5 KVa UPS, Mac Book, 4 PCs, Plasma TV Screen
for presentation a Digital camera and Handycam for Documentation.

The Center has scientific softwares like Genocluster and other
softwares like Linux AS4, NOD32 Antivirus, Microsoft Windows and
Office Professional edition along with paper license and a Microsoft
Visual Studio 2005 Standard version.

C. Database & other information resources:
Three Databases, namely Birds database of Sikkim, Zingiberaceae
database of NE with special reference to Manipur and Cyanobacteria
database have been developed. Currently more than 400 records have
been added to these databases and database updating is in progress.

(Name of the staff, Designation, Specialization and period of working.
Please indicate their absorption status)
Sl.
No
Name Designation Working
Since
Absorption
status
1. Shri. Sunil S. Thorat Coordinator Core staff
2. Dr. S. Subharani Devi Information
Officer
December
2006
Not
absorbed
3. Ms. N. Abem Devi Technical
Assistant
December
2006
Not
absorbed
4. Shri. L. Amitkumar Data Entry
Operator
December
2006
Not
absorbed

E-Journals subscribed by DISC are open accessed to users.
Internet facilities to the Scientists and Researchers.
Printing, Scanning and Photocopying facilities are provided.
Technical assistance is provided for search & troubleshooting.

8. Educational activities with details of placement: Not applicable
184

9. Initiative to validate the outcome of bioinformatics resources: Not yet
initiated

10. Collaborative works/initiatives:
Manipur University and Colleges affiliated to MU are in touch for
necessary support and help from DISC, Imphal.

11. Databases/Software packages developed: Three Databases, namely
Birds database of Sikkim, Zingiberaceae database of NE with special
reference to Manipur and Cyanobacteria database have been developed.
Currently more than 400 records have been added to these databases
and database updating is in progress.

Title of the Paper: Ethnobotanical plant database of NE India.,
Proceedings of Incob2007, HKUST, Hong Kong.
Authors: Sunil. S. Thorat, Nilima Huidrom and Rajiv Das Kangabam

13. Initiation of R&D activities in Bioinformatics: Yet to begin

14. Details of Training/Workshop organized and total no. of user trained
Workshop/Trainings:
Application of Computer for Bioresources Conservation for Teachers:
24-25 January, 2007
Application of Computers for Bioresources Conservation for
Researchers:
29th - 30th March, 2007
Application of Bioinformatics for biodiversity conservation: 17- 18th
August 2007.
No. of Personnel Trained/Educated: 48

allied areas (In this you may highlight the details like number of
paper published/number of papers published with the help of your
centre, how your centre is promoting various activities of your
organization and neighbouring institutions, manpower trained, tools
developed, patents & copyrights acquired and other services offered
etc).
One poster presentation on Ethnobotanical plant database of NE
India was presented in the International Conference on Bioinformatics,
2007, HKUST, Hong Kong.
Three trainings were conducted on different topics for the teachers,
Researchers and students. Altogether 48 participants were benefited.
Three databases are developed and updation is in process.
Collaboration with Government Institutes and Universities are initiated.

Providing access to scientific information in the area of specialisation
of the centre to the scientific community.
185
Programme for the Development of Database and Software on
Biodiversity Conservation and Documentation.
To conduct certain awareness programme on biodiversity and
bioresources conservation for school children of the entire north east.
To organize suitable workshops/training programmes in bioinformatics
Plant biodiversity database: Separate database will be developed on
certain important plant families covering most of the important
characteristics available through the primary and secondary data from
the region.
Fauna Biodiversity database: Database will be developed on the
Insects and Fishes of Manipur followed by the data from the entire
north east.
Microbial biodiversity database: In addition to the existing database of
Cyanobacteria, more databases will be developed following the
authentic database format followed by the other Institutes.

Additional Details:
Name of the Coordinator: Shri. Sunil. S. Thorat
Postal Address: Distributed Information Sub centre, Institute of Bioresources
and Sustainable Development (IBSD), Takyelpat, Imphal.
Phone Number :( 0385) 2446122 Mobile: 09436065265
E-mail: sunilsthorat@yahoo.com Website: ibsd.gov.in

Name of Contact Person(s): As above
E-mail: As above
186
Institute of Microbial Technology, Chandigarh
Coordinator: Dr G P S Raghava


Over a period of time since its establishment in 1987, Bioinformatics centre at IMTECH
has shown consistent growth in the different areas of bioinformatics whether in carrying
out peer reviewed research or providing services to the world wide. Centre has
developed databases and softwares both for in house use and for scientists world over.
BIC has developed a number of web servers based on peer reviewed research carried out
at the bioinformatics centre. BIC staff has published more than 70 research papers in
reputed international journals and more than 30 abstract/poster/papers presented in
national and international conferences (http://imtech.res.in/raghava/pub.html). Our
servers are getting more than 15000 hits per day.

We have developed a number of programs/web servers for predicting secondary
structure of proteins. Our regular secondary structure (Helix & Sheet)
prediction method has been classified in category of highly accurate methods in
the world (CASP5, CAFASP3 & EVA). Centre has established the Genome
Wide BLAST and FASTA searching facility with integrated sequence analysing
tools. It is a world-wide facility for sequence similarity search over large number
of databases including genome and proteome. As of today we have genomes
and annotated proteomes of all prokaryote and Eukaryote (including human
genome) sequenced so far. Centre has developed following databases in biology
i) MHCBN: A curated database of MHC binders/non-binders & T-Cell epitopes
(~23000 entries); ii) Public Domain Software in biology (more than 500
software); iii) Free software for general purpose (more than 1500 entries); iv)
BCIPEP: A curated database of antigenic, immunogenic and non-immunogenic
peptides including B cell epitopes (more than 2300 entries); and v) HaptendB: A
database of small molecule which are antigenic but not immunogenic.

institution
Fermentation Technology & Applied Microbiology: Scale-up processes
which requires the specific skills of a fermentation technologist are also
involved in tackling problems related to stability of recombinant plasmids,
when cultivated at high density.
Cell Biology & Immunology: Development of monoclonal antibodies
(MAbs) in order to identify disease specific antigenic and molecular targets
for malaria, leishmaniasis and tuberculosis and to selectively eliminate
infected cells.
Molecular Biology and Microbial Genetics: Molecular Biology &
Microbial Genetics with special reference to infectious diseases &
bioremediation of environmental pollutants: In this area several different
projects are being pursued, aimed directly to address some of the
problems alluded to above, there are others which focus on problems
related to basic molecular biology. tc.
Protein Science & Engineering: The protein science and engineering
group at IMTECH combines on overt set of interests of a fundamental
187
nature with an equally overt leaning towards the finding of
applications.

3. Area of Specialization of the centre: Protein Modeling and Protein
Engineering

This year our centre developed methods for - i) Analyzung and predicting
antibacterial peptides ii) Subcellular localization of Mycobacterial proteins iii)
Identification of RNA interacting residues in a protein iv) Prediction of DNA
binding domain and proteins and v) Tertiary structure of bioactive peptides.
Computer facility
1. BioCluster from Apple Computers
2. Apple X-server with 10.5TB storgae
3. SUN Fire v240 Server.
4. SUN Enterprise 420R & 420E Server.
5. SGI ORIGIN 350 Server and Workstation SGI O2 R12000
6. Apple G5 Servers with 3TB RAID
7. DEC ALPHA Servers and worstations
8. Personal Computers; Printers; DVD Server
Communication Facilities:

1. Electronic Mail; Local Area Network
2. Two internet Connections (1MBPS [1:1] and 2MBPS[1:1] bandwidth)
3. Virtual Private Network (VPN)
4. Domain/Proxy Servers/ FireWalls.

BIC have a number of software packages for protein Modeling like
AMBER, CHARMm, GROMOS, X-PLOR, BOSS, Modeller, INSIGHTII,
RasMol, WHATIF, Midasplus, Pymol, GROMOS, GAMESS, DSSP,
MICROGenie etc. We have recently added sequence analysis
software such as, CLUSTALW for multiple sequence alignments,
ALSCRIPT for analysis of multiple sequences, PHYLIP for evolutionary
analysis etc. In addition, we have also procured software MOLSCRIPT
and RASTER 3D for presentation of protein structures.

Mirror sites of following databases/information resources i) Biological
Databases (e.g. genomes, proteomes, PDB, SWISSPROT); ii)
Biological software (EBI & Indian Univ.); and iii) General software
(GNU, PostgreSQL & SUN Freeware). We are the only official mirror
sites in India, for a number of sites.
188


S.
No.
Name of staff
Designation Specialization
1. Dr. GPS Raghava
Scientist
Bioinformatics
2. Dr. Balvinder Singh
Scientist
Bioinformatics
3. Dr. Manoj Kumar
Scientist
Bioinformatics
4. Sh. Harvinder
J. Tech. Asstt.
Computers


Biocomputing: Centre has expertise in the field of biocomputing, Protein
Modeling and Protein Engineering. The softwares are being developed in
the above areas on users request.
Consultation Services: Centre also provides consultation services in the
field of Protein Modeling, Protein Engineering, Biocomputing and
Networking (LAN, WAN, INTERNET, E-MAIL).
Thesis: 5 student completed and 10 students are doing PhD in bioinformatics. A
number of trainees has completed their projects as a partial fulfillment of their
degrees.
Collaborative Research: BIC staff has solved a number of biological problems
in collaboration with biologist.
Other Facilities:
Installing, implementing and maintaining software packages on
computers.
Preventive maintenance of computers.
Updates the user with recent advances in computers/Internet.


Regular workshops and training programmes in Bioinformatics at the
centre.
BIC staff is regularly taking classes in universities, delivers lectures in
workshops, conferences and training programmes.
Ph.D. students (More than 80 per year) and others are heavily using
facilities at BIC.
BIC staff participates in the pre Ph.D. course in Bioinformatics at IMTECH.


The research work is published in peer-reviewed journals and is available on
world-wide-web. Servers developed at the centre are receiving more than
15,000 hits per day. The research work has been initiated in collaboration
with wet lab scientists so as to test and validate predictions and results
obtained using computational tools.
189

10. Collaborative works / initiatives

Under NMITLI, centre has provided technological information/
know how about various software in the development of BIOSUITE
to TCS Ltd., New Delhi.
BIGTECH, a US based company has also signed MOU with
IMTECH in the area of bioinformatics.
Centre has also signed MOU for providing consultancy to
Opportunia, New Delhi in Bioinformatics. As part of this, centre has
provided two weeks training to a few personnel of Asia Privacy,
Korea.

11. Databases / Software packages developed
Databases Developed
This centre have developed more than 70 webserver and a number of curated
databases (http://www.imtech.res.in/bic/). Following is the list of web
databases.
PRRDB: A database of pattern recognition receptors and pathogen
associated molecular patterns. This is important database for innate
immunity.
MHCBN: A comprehensive database of MHC binding and non-binding
peptides. This is a curated database compiled from literature.
BCIPep: A database of immunodominant B cell epitopes or peptides that
can activate the B cell response. This is a curated database compiled from
literature.
HaptenDB: A database of haptens which are antigenic non-immunogenic
small molecules that can activate immune system with carrier proteins.
This is only database of its kind.
PDRB (Public Domain Resources in Biology): It is database of public
domain biological resources.
RFSB (Repository of Free Software in Biology): It is a database of
public domain software in biology and is available for distribution via on-
line as well as off-line modes.
PDWPB (Public Domain Web Pages in Biology): PDWPB consists of
the information about web pages in biology.
FSGP (Free Software for General Purpose): The database contains
software which is freely available for non-commercial users.

The BIC staff of this centre has published more than 70 research papers in
reputed international journals. Following is list of papers published/accepted
in year 2007.
1. Vivona, S., Gardy J.L., Ramachandran, S., Brinkman, F.S.L., Raghava, G.
P. S., Flower, D.R. and Filippini, F. (2007) Computer aided biotechnology:
190
from immunoinformatics to reverse vaccinology Trends in Biotechnology
(In Press)
2. Muthukrishnan S., Garg A. and Raghava, G. P. S. (2007) OxyPred:
Prediction and Classification of Oxygen-Binding Proteins Genomics,
Proteomics & Bioinformatics (In Press)
3. Kumar, M., Gromiha, M.M. and Raghava, G. P. S. (2007) Prediction of
RNA binding sites in a protein using SVM and PSSM profile. Proteins:
Structure, Function and Bioinformatics. (In Press)
4. Pashov A., Monzavi-Karbassi B., Raghava, G. P. S. and Kieber-Emmons,
T. (2007) Peptide mimotopes as prototypic templates of broad-spectrum
surrogates of carbohydrate antigens for cancer vaccination CRITICAL
REVIEWS IN IMMUNOLOGY 27 (3): 247-270
5. Saha, S. and Raghava, G. P. S. (2007) Prediction of allergenic proteins
and mapping of IgE epitopes in allergens Nature Protocols
10.1038/nprot.2007.505 (Online)
6. Singh, H. and Raghava, G. P. S. (2007) Prediction and mapping of
promiscuous MHC class II binders in an antigen sequence Nature
Protocols 10.1038/nprot.2007.502 (Online)
7. Lata, S., Sharma, B.K. and Raghava, G. P. S. (2007) Analysis and
prediction of antibacterial peptides Nature Protocols
10.1038/nprot.2007.503 (Online)
8. Kumar, M. , Verma, R. and Raghava, G. P. S. (2007) Mitpred2: An
improved method for predicting mitochondrial proteins using SVM and
HMM Nature Protocols 10.1038/nprot.2007.488 (Online)
9. Kumar M., Gromiha M.M. and Raghava, G. P. S. (2007) Identification of
DNA-binding proteins using support vector machines and evolutionary
profiles BMC Bioinformatics 8:463
10. Kaur, H., Garg, A. and Raghava, G. P. S. (2007) PEPstr: A de novo
method for tertiary structure prediction of small bioactive peptides. Protein
Pept Lett. 14:626-30
11. Rashid M., Saha S. and Raghava, G. P. S. (2007) Support Vector
Machine-based Method for Predicting Subcellular Localization of
Mycobacterial Proteins Using Evolutionary Information and Motifs BMC
Bioinformatics 8: 337
12. Raghava, G. P. S. (2007) Prediction of subcellular localization of proteins
using machine learning techniques and evolutionary information Amino
Acids 33(3): X-XI
13. Lata, S., Sharma, B.K. and Raghava, G. P. S. (2007) Analysis and
prediction of antibacterial peptides BMC Bioinformatics 2007, 8:263
14. Mishra, N., Kumar, M. and Raghava, G. P. S. (2007) Support vector
machine based method for predicting Glutathione S-transferases proteins.
Protein Pept Lett. 6:575-80
15. Vidyasagar et al. ...... Raghava, G. P. S. ........ (2007) BioSuite: A
comprehensive bioinformatics software package (A unique industry-
academia collaboration). CURRENT SCIENCE 92 (1): 29-38
16. Saha, S. and Raghava, G. P. S. (2007) Prediction of bacterial proteins. In
Silico Biology 7: 0028
17. Saha, S. and Raghava, G. P. S. (2007) Prediction of neurotoxins based on
their function and source. In Silico Biology 7: 0025
191
18. Saha, S., Zack, J., Singh, B. and Raghava, G. P. S. (2007) VGIchan:
Prediction and classification of voltage-gated ion channels. Genomics
Proteomics & Bioinformatics 4:253-8
19. Greenbaum et al. ...... Raghava, G. P. S. ...... (2007) Towards a
consensus on datasets and evaluation metrics for developing B cell
epitope prediction tools. Journal Molecular Recognition 20:75-82
20. Bhasin, M. and Raghava, G. P. S. (2007) A hybrid approach for predicting
promiscuous MHC class I restricted T cell epitopes. J. Biosci. 32:31-42
[PDF]

Same as in 4


BIC organize minimum one workshop every year with average 30
participants per workshop. Every year we have different theme, following is
detail of workshops organized in last five years.
1. National Workshop on Subunit Vaccine design, April, 2003
2. Training to the trainers of DOEACC centre in the northern region, July,
2003
3. Database management and Analysis of Microarray, Oct., 2003
4. Protein simulations and docking, Oct., 2004
5. Machine Learning Techniques in Bioinformatics, Oct., 2005
6. Training Programme on GCG, sequence analysis software in Dec., 2005
7. Training Programme on InsightII, by Accelrys. Inc., in March, 9
th
& 10
th
,
2006
8. Bioinformatics resources on miRNA and siRNA, Nov. 14-17, 2006
9. Computational approaches for predicting molecular interactions. Oct. 9-12,
2007
In this you may highlight the details like number of papers published/number
of papers published with help of your centre, how your centre is promoting
trained, tools developed, patents and copyrights acquired and other services
offered etc.

Number of papers published/Number of papers published with help of your
centre: Solely based upon Bioinformatics approach, the number of publication
from the centre are more than 70. Papers published by BIC got high citations
more than 700 citations. Dr Raghavas name appear in hot 100 authors in
Biomed journals. This shows that BIC at IMTECH is making big impact on
society. It is difficult to calculate the number of papers published with help of
bioinformatics from the staff of institute. However, this number is increasing as
publishing in good journal/high impact factor journals requires the application of
bioinformatics tools.

192
Promotion of various activities of our organization and neighboring
organizations: As in 14 and 10.

Manpower Trained: Manpower is being trained by
a. Organizing workshops/training programmes by the centre;
b. Recruiting project assistants and sharpening their skills in
Bioinformatics

Tools Developed: As in 11.

Patents/ Copyright obtained/ filed by your centre:
1. Raghava, G.P.S. (1996) ASSP: A computer program for comparision of
observed and predicted protein secondary structure. L-15582/96.
2. Raghava, G.P.S. (1996) A computer program for analysing and creating
protein secondary structure database. L-15658/96.
3. Raghava, G.P.S and Agrawal, P. A (1997) Software for phylogcncitic
identification of microorganisms. C R. 1/97, date 11.3.97
4. Raghava, G.P.S (2001) A computer program for assisting the user in
using protein modelling software package (PMOD 1.0) . SW-393/2001,
date 08/02/2001
5. Kaur, H. and Raghava, G.P.S. (2002) BETATPRED: Software for
predicting b -turns using statistical algorithm. SW-1162/2003.
6. Raghava, G.P.S. (2002) DNASIZE: A software package for computing
DNA/Protein fragments. SW-1156/2003.
7. Issac, B., Singh, H., Kaur, H. and Raghava, G.P.S. (2002) FTG: Software
Package for Predicting Gene in DNA using Fast Fourier Transform. SW-
1154/2003.
8. Issac, B. and Raghava, G.P.S. (2002) GWBLAST: Software Package for
Genome Wide Similarity Search using BLAST. SW-1149/2003.
9. Issac, B. and Raghava, G.P.S. (2002) GWFASTA: Computer program for
genome wide FASTA search. SW-1143/2003.
10. Raghava, G.P.S. (2002) LibInet: Software Package for Managing Library
Resources and Accessing via Internet. SW-1155/2003.
11. Singh, H. and Raghava, G.P.S. (2002) MHCBench: Evaluation of MHC
Binding Peptide Prediction Algorithms. SW-1160/2003.
12. Singh, H. and Raghava, G.P.S. (2002) MOT: Matrix Optimization
Technique for identifying the MHC binding core. SW-1159/2003.
13. Raghava, G.P.S. (2002) PCLASS: Computer Program for predicting
structural class of protein via Internet. SW-1157/2003.
14. Raghava, G.P.S. (2002) PDSB: Software Package for Managing Public
Domain Software in Biology. SW-1148/2003.
15. Raghava, G.P.S. (2002) PDWSB: Software Package for creating and
managing Biological Web Servers. SW-1152/2003.
16. Singh, H. and Raghava, G.P.S. (2002) ProPred: Software package for
predicting promiscuous MHC class-II binding peptides. SW-1163/2003.
17. Singh, H. and Raghava, G.P.S. (2002) ProPred-I: Software package for
predicting promiscuous MHC Class-I binding peptides. SW-1161/2003.
18. Raghava, G.P.S. (2002) PSAweb: Software package for Analyzing of
Protein Sequence and Multiple Alignment. SW-1158/2003.
193
19. Bhasin, M. and Raghava, G. P.S. (2003) MHCBN: A software package for
managing data of Immunologically related peptides. SW-1151/2003.
Services Offered: As in 7.

Technologies Developed/Transferred:

Vaxiprep: A software package for predicting potential vaccine
candidates has been developed. This package integrates 14 web
servers developed at IMTECH in the field of immunoinformatics. The
integration and user interface was developed by Biomantra a
informatics company. This has been inaugurated by Dr R. A.
Mashlekar, Ddirector General, CSIR on 15
th
December 2004.
Under NMITLI, centre has provided technological information/ know
how about various software in bioinformatics to TCS Ltd., Hyderabad.
The software BIOSUITE has been launched by honourable president
of India in July 2004.


The future activities will focus on research as mentioned in 4.
Additional Details:
Name of the Coordinator: Dr G P S Raghava, Scientist
Postal Address: Bioinformatics Centre, Institute of Microbial Technology, Sector 39A,
Chandigarh-160 036, INDIA
Phone Number: +91-172-2690557 & +91-172-2695225
Fax No.: +91-172-2690632 & +91-172-2690585
Email: ragahva@imtech.res.in
Website: http://www.imtech.res.in/bic/ ; http://www.imtech.res.in/raghava/
Name of Contact person: Dr G P S Raghava, Scientist
Email: raghava@imtech.res.in
194
Karnataka Veterinary, Animal & Fisheries Sciences University, Mangalore
Coordinator : Dr. Indrani Karunasagar

1. Summary of the progress made by the center from its inception:
The Bioinformatics Centre (Sub-DIC) at the College of Fisheries, Mangalore since its
inception in 2000, is actively involved in carrying out research, preparing databases
and conducting training programmes in bioinformatics applied to aquatic marine
biotechnology
The Centre initiated research pertaining to a major shrimp pathogen, the White spot
syndrome virus (WSSV), a scourge to aquaculture. Based on a bioinformatics study,
a comparative analysis of the three complete genome sequences for WSSV
available in GenBank was made wherein we identified a number of repeats of
different sizes and composition. Our study showed that three of the minisatellite
repeats could be used for genotyping WSSV strains. This was further assessed by
experimental studies and our laboratory has been the first to show the use of the all
the three minisatellites as epidemiological markers in distinguishing isolates from
different geographical regions. This study is particularly useful in monitoring of
WSSV infections for shrimp health certification and in forensics and also in
epidemiological and ecological studies for tracing the movement and route of
infection.
We are also the first to characterize the evolutionary lineage of Indian WSSV strains
based on regions prone to deletion and recombination and the presence /absence of
transposase sequence which has led to the identification of a novel putative
ancestral strain of WSSV. The outcome of this research has resulted in three
publications. Several new sequences deposited have been assigned Genbank
accession numbers.
We have been studying the outer membrane proteins of the bacteria, Aeromonas
hydrophila, which is the most common warm water fish pathogen. Based on in silico
analysis we could identify two outer membrane proteins Omp48 and OmpTS, which
could be used as potential vaccine candidates. Our lab based experiments further
confirmed the above study, wherein the cloned and expressed recombinant protein
proved to be highly immunogenic to fish and resulted in high relative percent survival
on experimental challenge.
Our work also involves the study of virulence genes in human pathogens such as
Vibrio parahaemolyticus and Vibrio vulnificus associated with the aquatic
environment. A number of sequences pertaining to the virulence genes of these
organisms have been generated. Further, the sequences corresponding to the
genomic regions of the fish borne trematodes, Opisthorchis viverrini and Clonorchis
sinesis associated with cholangiocarcinoma have been deposited in GenBank and
accession numbers assigned. These sequences have helped in the development of
PCR based diagnostics for the above parasitic trematodes.
Another major work is in the study of the phylogenetic relationship of bacterial groups
associated with the marine sponge Halichondria nigricans. 35 unidentified bacterial
groups based on the 16S rRNA sequences have been assigned GenBank
accession numbers.
195
Antimicrobial peptide molecules such as lysozyme and ferritin from shrimps were
identified using bioinformatics based tools. They have since been cloned, expressed
and their activity studied. Studies on more molecules are in progress. In a major
project on Functioinal genomics of shrimp, several hundred ESTs have been
generated and submitted to GenBank.

institution
The major research activities include:
Development of rapid DNA based methods for the detection of pathogens
and application of these methods for diagnosis of diseases
Development of molecular diagnostics for fishborne trematodes
Development of vaccines, immunostimulants, probiotics for use in aquaculture
systems.
Study of marine toxins, harmful algal blooms and public health aspects of
fish and fishery products.
Development of DNA based methods for rapid detection of harmful algae
and cysts, blooms and their toxicity
Development of monoclonal antibodies to shrimp and fish pathogens
Development of microsatellites as molecular markers to study disease resistance
in Penaeus monodon (tiger prawn) and Macrobrachium rosenbergii (freshwater
prawn)
Genotyping white spot syndrome virus
Development of subtraction libraries to study differential gene expression with
respect of infection with viral and bacterial pathogens and salinity in larval and
adult stages of development.
Studying and characterizing antimicrobial compounds from marine bacteria
Studying the expression of genes involved in immune function of shrimp

Aquatic Biotechnology

The centre conducted successfully a National Symposium on Bioinformatics
during February 1-2, 2006. The Symposium was well attended with over 200
participants.
The Centre also took initiative in training rural women in the operation of
computers. Women were taught computer fundamentals and the basic softwares
such as MS-Word, MS-Excel, and word processing software in local language.

a. Computer and Communication facility
NT Server - 1 no.
Computers(Desktop) - 16 nos.
196
Laser printers (B/W) - 1 no.
Laser printer (colour) - 3 nos.
Inkjet printers - 2 nos.
Epson Dot Matrix Printer - 1 no
U.P.S. - 2 nos (3 KVA)
Photocopier - 1 no.
Internet - Lease line connectivity of 512 kbps
Software Application
Gel Compare II software - Comparision of DNA/Protein gels and
cluster analysis of RAPD and RFLPs,
Phylogenetic analysis
Discover Studio Gene ver 1.5 - DNA and Protein sequence analysis
Systat Version 10.2 - Statistical analysis
Exhome BLAST - Sequence alignments and analysis
GenoCluster - A suite of programs for comparative
proteomics
c. Databases and other information resources : Nil

Name of the Staff* Designation Specialization Period of working
Dr.Malathi Shekar Information Officer Ph.D in Microbiology and
Advanced Diploma in
Computer Applications
from Aug. 2001
Mr. Madhukrishna Technical Assistant Diploma in Computer
hardware and software
from Jan. 2007
Ms. Mohini M Data Entry Operator Advanced Diploma in
Computer Applications
from Dec. 2006
Mrs. Prathiba H. Data Entry Operator Certificate course in Microsoft
Office
from Dec. 2006
Ms. Aparna
Sharma
Data Entry Operator Bachelor in Computer
Application
from May 2007
*All Not absorbed

a. Use of computational softwares both online and stand alone - BLAST, FASTA,
CLUSTAL W, EMBOSS, DS-Gene, SYSTAT, GELCOMPARE II, Exhome Blast,
GenoCluster, SEQUENCE QUICKIE, Rasmol, TRF software etc. in routine
research
b. Web based data mining and prediction studies on available sequences in
Genbank.
c. Primer designing, uploading sequences to GenBank, e-submission of journal
articles for publication etc.
d. Providing e-journals such as Aquaculture journal to the university library for
benefit of students and staff.
197
e. Maintaining e-manuals such as FDA manual, FAO risk assessment documents,
AAPQIS etc.
f. Designing, updating and maintaining of website for university involving teaching
campuses and research stations of Mangalore, Bangalore, Bidar, Shimoga and
Hassan. Assisting researchers from neighbouring medical colleges in analysis of
data

We have been conducting only short term training courses. However, our graduates,
who worked in the Centre as data entry operators/technical officers have found
placement in Bioinformatics/ Biotechnology related areas abroad eg. USA, Germany
and Japan.

There is a close interaction between Bioinformatics Centre and various
biotechnology related project in our University and other neighboring
Universities like Manipal Academy of Higher Education, Rajiv Gandhi
University of Health Sciences, Mangalore University. Predictions made using
bioinformatic tools are validated by lab experiments carried out in various
projects. The centre has been successful in depositing a total of 76 sequences in
GenBank and obtaining accession numbers.

The Centre is collaborating with the following Centres and Universities
UNESCO Microbial Resources Centres
Wurzburg University, Germany
University of Goteborg, Sweden
Centre for Tropical Marine Ecology, Bremen, Germany
University of Kristianstad, Sweden
James Cook University, Townsville, Australia
Ghent University, Belgium

11. Databases/software packages developed
Database on:
a. Complete genome & protein sequence of whitespot syndrome virus
b. Genomics of Vibrio parahaemolyticus
c. Genomics of Aeromonas hydrophila
d. Genomics of Vibrio vulnificus
e. India Tiger shrimp Penaeus monodon
f. SOP for Antibiotic residues in shrimp
g. Bibliography of human food pathogens

Using bioinformatics facility the following papers were published
198
1. Divu, D., Khushiramani, R., Malathi, S., Karunasagar, I. and Karunasagar, I. (2007). Isolation,
haracterization and evaluation of microsatellite DNA markers in giant freshwater prawn
Macrobrachium rosenbergii, from South India. Aquaculture (in press).

2. Pradeep, B., Malathi S., Karunasagar, I. and Karunasagar, I. (2007). Genotyping of white spot
syndrome virus prevalent in shrimp farms of India. DAO. (in press).

3. Maiti, B., Rekha, K., Karunasagar, I. and Karunasagar, I. (2007). Cloning and expression of
ferritin from Penaeus monodon with a potential for application in aquaculture. Prot. Exp. Pur.
(submitted).

4. Bhowmick, P.P., Rekha, K., Raghunath, P., Karunasagar, I. and Karunasagar, I. (2007).
Molecular typing of Vibrio parahaemolyticus isolated from seafood harvested along the
southwest coast of India. Lett. Appl. Microbiol. (submitted).

5. Anuj, T., Rekha, K., Karunasagar, I. and Karunasagar, I. (2007). Antivibrio activity of
recombinant lysozyme expressed from black tiger shrimp, Penaeus monodon. Aquaculture,
272:246-249.

6. Rekha,,K., Girisha, S.K., Karunasagar, I. and Karunasagar, I. (2007). Cloning and
expression of an outer membrane protein ompTS of Aeromonas hydrophila and study of
immunogenicity in fish. Prot. Exp. Pur. 51, 303-307.

7. Rekha, K., Girisha, S.K., Karunasagar, I. and Karunasagar, I. (2006). Protective efficacy of
recombinant OmpTS protein of Aeromonas hydrophila in Indian major carp. Vaccine 25, 1157-
1158.

8. Godhe, A., McQuoid, M.R., Karunasagar, I., Karunasagar, I. and Rehnstam Holm Ann S.
(2006). Comparison of three common molecular tools for distinguishing among geographically
separated clones of the diatom Skeletonema marinoi sarno et zingone (Bacillariophyceae). J.
Phycol. 42, 280-291.

9. Parvathi, A., Sanath K. H., Bhanumathi, A., Ishibashi, M., Nishibuchi, M., Karunasagar, I. and
Karunasagar, I. (2006). Molecular characterization of thermostable direct hemolysin-related
hemolysin (TRH) positive Vibrio parahaemolyticus from oysters in Mangalore, India. Environ.
Microbiol. 8, 9971004.

10. Parvathi, A., Sanath K. H., Karunasagar, I. and Karunasagar,I.(2005). Study of occurrence
of V.vulnificus by RAPD and gyrB sequence analysis. Environ. Microbiol 7, 995-1002.

11. Manjanaik, B., Umesha, K.R., Karunasagar, I. and Karunasagar, I. (2005). Detection of
hepatopancreatic parvovirus (HPV) in wild shrimps in India by nested polymerase chain
reaction (PCR). DAO. 63, 255-259.

12. Parvathi, A., Sanath, K.H., Karunasagar, I. and Karunasagar, I.. (2004). Detection and
enumeration of Vibrio vulnificus in oysters from two estuaries along the south west coast of
India using molecular methods. Appl. Environ. Microbiol. 70, 6909-6913.
13. Shahadat, H. Md., Otta, S.K., Chakraborty, A., Sanath, K.H., Karunasagar, I. and
Karunasagar, I. (2004). Detection of WSSV in cultured shrimps, captured brooders, shrimp
postlarvae and water samples in Bangladesh by PCR using different primers.Aquaculture,
237, 59-71.

14. Sanath, K.H., Karunasagar, I., Karunasagar, I., Teizou, T., Shima, K. and Yamasaki, S.
(2004). Characterisation of Shiga toxin-producing Escherichia coli (STEC) isolated from
seafood and beef. FEMS Microbiol. Lett. 233, 173-178.
199

15. Manivannan, S., Bob, K.M.D., Karunasagar, I. and Karunasagar, I. (2004). Prevalence of
monodon baculovirus (MBV) in wild Metapenaeus species along the south west coast of
India. Aquaculture, 232, 63-67.

16. Umesha, R.K, Uma, A., Otta, S.K., Karunasagar, I and Karunasagar, I. (2003). Detection by
PCR of hepatopancreatic parvovirus (HPV) and other viruses in hatchery reared Penaeus
monodon postlarvae. DAO. 57, 141-146.

17. Sanath, K.H., Sunil, R. Venugopal, M.N., Karunasagar, I. and Karunasagar I. (2003).
Detection of Salmonella spp. in tropical seafood by Polymerase chain reaction (PCR). Int. J.
Food Microbiol. 88, 91-95.

18. Dhanashree, B, Otta,S.K., Karunasagar, I. and Karunasagar, I.(2003). Typing of Listeria
monocytogenes isolates by random amplification of polymorphic DNA. Ind. J. Med. Res. 117,
19-24.

19. Dhanashree, B., Otta, S.K., Karunasagar, I., Goebel, W. and Karunasagar, I. (2003).
Incidence of Listeria spp. in clinical and food samples in Mangalore, India. Food Microbiol. 20,
447-453.

20. Karunasagar, I., Karunasagar, I. and Otta, S.K. (2003). Disease problems affecting fish in
tropical environments. J. Appl. Aqua. 13, 231-249.

21. Dhanashree, B., Otta, S.K., Karunasagar, I. and Karunasagar, I. (2003). Protein profile
analysis of Listeria monocytogenes strains from tropics. Curr. Sci. 84, 628-630.

22.Karunasagar, I., Rivera, B., Joseph, B., Kennedy, V.R., Shetty, A., Huq, I., Karunasagar, I.
and Colwell R.R. (2003). OmpU genes in nontoxigenic V. cholerae associated with
aquaculture. J. Appl. Microbiol. 95, 338-343.

23. Dilip, H., Sanath, K.H., Kumar, Y., Karunasagar, I., Nishibuchi, M. and Karunasagar, I.
(2003). Application of polymerase chain reaction for detection of Vibrio parahaemolyticus
associated with tropical seafoods and coastal environment. Lett. Appl. Microbiol. 36, 423-427.

24. Otta, S.K., Karunasagar, I. and Karunasagar, I.. (2003). Detection of Monodon Baculovirus
(MBV) and whitespot syndrome virus (WSSV) in apparently healthy Penaeus monodon
postlarvae from India by polymerase chain reaction. Aquaculture. 220, 59-67.

25. Godhe, A., Rehnstam Holm, A., Karunasagar, I. and I. Karunasagar I. (2002). PCR detection
of dinoflagellate cysts in field sediment samples from tropic and temperate environments.
Harmful Algae (Elsevier), pp. 361-373.

26. Chakraborty, A., Otta, S.K., Joseph, B., Sanath, K.H., Shahadat, H. Md.., Karunasagar I.,
Venugopal, M.N. and Karunasagar I. (2002). Prevalence of white spot syndrome virus
(WSSV) in wild crustaceans along the coast of India. Curr. Sci., 82, 1392-1397.

27. Manivannan, S., Otta, S.K., Karunasagar, I. and Karunasagar, I. (2002). Multiple viral
infection in Penaeus monodon shrimp postlarvae in an Indian hatchery.DAO. 48, 233-236.
Papers presented at conferences:
1. Malathi, S., Pradeep, B., Karunasagar, I. and Karunasagar, I. Genotyping of White spot
syndrome virus of shrimps and its significance. Lecture presentation at the 48
th
Annual
Conference of the Association of Microbiologists of India, December 18-21,2007, Chennai,
India.
200

2. Malathi, S., Karunasagar, I. and Karunasagar, I. A bioinformatics based study of the thermostable
hemolysin (tdh) gene in Vibrio parahaemolyticus and related vibrios. Presented at the 5
th

International Conference on Bioinformatics, December 18-20, 2006, Delhi, India

3. Rekha K., Malathi, S., Karunasagar, I. and Karunasagar, I. A bioinformatics based study
of ompTS protein of Aeromonas hydrophila. Presented at the 5
th
International Conference on
Bioinformatics, December 18-20, 2006, Delhi,India.

4. Malathi, S., Karunasagar, I. and Karunasagar, I. Tandem repeats within white spot
syndrome virus genome sequences: Distribution and compositional analysis for comparative
studies. Presented at National Bioinformatics Symposium, February 1-2, 2006, Mangalore,
India

5. Rekha, K., Souche,Y. and Mourya, D.T. Bioinformatic based phylogenetic analysis of
Dengue1 and Dengue 2 virs serotypes isolated from different parts of India. Presented at
National Bioinformatics Symposium, February 1-2, 2006, Mangalore, India

6. Akash, N., Malathi, S., Karunasagar, I. and Karunasagar, I. Bioinformatics based study on
the outer membrane proteins (OMP) of Aeromonas hydrophila for DNA vaccine design.
Presented at National Bioinformatics Symposium, February 1-2, 2006, Mangalore, India
a. Comparative study of three complete nucleotide sequences of White spot
syndrome virus analysis for the distribution and composition of tandem repeats
and look for VNTR regions which could serve as markers
b. Comparative analysis of nucleotide sequence of thermostable direct hemolysin
gene in Vibrio parahaemolyticus and related Vibrio spp.
c. Comparative study of nucleotide sequence of outer membrane proteins of
aquatic aeromonads
d. Genotyping of the white spot syndrome virus
e. Characterization and evaluation of microsatellite markers in giant freshwater
prawn Macrobrachium rosenbergii .

14. Details of Training/workshop organized and total no. of user trained
The following six training programmes (consisting of lectures and demos) and one
National symposium on Bioinformatics has been conducted

Topic Month/Year Participants
Application of Bioinformatics March 21-23,2002 15
Application of Bioinformatics in
Marine culture and Marine
resource utilization
March 19-21, 2003 15
Application of Bioinformatics in
Fisheries Sciences
March 22-24, 2004 15
Bioinformatics and its applications
in marine sciences
March 21-23, 2005 15
Computer fundamentals and
Basics ( for women
March 27-28, 2006 26
201
empowerment)
Basic Bioinformatics and its
application
March 15-17,2007 35
National Symposium on
Bioinformatics
Feb.1-2, 2006 200

15. Impact shown by your center on the growth of biotechnology and
allied areas:
- The Centre has been able to deposit over 300 sequences in GenBank and
accession numbers have been assigned.
- One Ph.D thesis in the area of Bioinformatics submitted and two are registered for
PhD in Bioinformatics of Mangalore University .
- The major impact is both in terms of service and primary data generated by the
Centre using bioinformatics. This is evident from the publications in bioinformatics
and related areas (listed in item 12).
- The DBT has submitted 2 patents and two technologies based on the
patents is ready for transfer . The BCL has written to the university for the
commercialization rights.
- Based on the DBT project support and the Bioinformatics facility, PCR
based diagnostics has been developed for the White spot syndrome virus
and this kit was selected for the technology development award in 2003 by
the DBT.

The Bioinformatics Centre will be involved in the following research areas:
Studies on gene expression and development of EST Bank in the tiger shrimp P.
monodon to be continued

Identify the type III secretion system in Vibrio vulnificus using Genomics and
Proteomics approach

Comparative analysis of all the Omp genes in Aeromonas hydrophila for vaccine
studies.

Bioinformatics based analysis of virulence and omp genes for the development of a
rapid test kit for Salmonella

Bioinformatics study of sequences of shrimp viruses such as HPV and WSSV for
RNAi studies.

Genotyping of Indian shrimp viruses

Genotyping of Indian Nodavirus of prawns

In silico studies to predict immunoreactive peptides and candidate vaccines

Development of test kits for seafood pathogens

Additional details:
Name of the Coordinator : Dr. Indrani Karunasagar
Postal Address : Department of Fishery Microbiology
202
KVAFSU, College of Fisheries,
Mangalore
Phone Number : 0824-2246384; 2243755
Fax No. : 0824 - 2246384
E-mail : mircen@sancharnet.in;
fishbiotek@sancharnet.in
karuna8sagar@yahoo.com;
Website : www.mircenbiotech.com

Name of contact Person(s): 1. Dr. M.N.Venugopal (Professor)
Email: mnvenu@rediffmail.com
2. Dr. Malathi Shekar (Information Officer)
Email: malathishekar@rediffmail.com
203
Kerala Agricultural University, Thrissur
Coordinator : Dr R Keshavachandran

Bioinformatics Centre at KAU, Thrissur started functioning as a 23
rd

Distributed Information Sub Centre (DISC) since 1995 under BTISnet
programme. The Centre was upgraded to DIC during 2004. The centre has
shifted to new premises in September 2006 which also has facilities for wet
lab work.
Since its inception, the centre is carrying out research, preparing databases,
conducting training programmes in the area of bioinformatics, and supporting
plant biotechnology activities. A (2+2) credit course in Bioinformatics is
offered to the Postgraduate students of Centre for Plant Biotechnology and
Molecular Biology.
institution:
The work carried out at the Centre for Plant Biotechnology and Molecular
Biology include isolation and characterization of genes encoding disease
resistance to bacterial wilt and leaf curl virus in tomato, genomic library
construction and cloning of genes for PR proteins in black pepper, isolation of
novel strains of Bacillus thuringiensis from Western Ghats, assessing the
molecular diversity, the insecticidal activity of the crystal proteins and cloning
of novel cry and vip genes, genetic transformation for biotic stress tolerance
in bell pepper and hairy root induction in medicinal plants.
The main area of specialization is Plant Biotechnology. Apart from acting as a
supporting centre for Biotechnology research, the Centre is involved in
creating databases relevant to agriculture.
Selection of 2 Research Associates, 1 Senior Research Fellow and 1
Junior Research Fellow.
Conducting training programmes.
Insilico work mainly focusing on sequence analysis, molecular modeling,
protein structural analysis and Docking studies.
Establisment of leased line connectivity of 6Mbps speed at the
Bioinformatics centre, from AIRTEL.
Creation and maintenance of website for the College of Horticulture.
5. Infrastructure facilities in Bioinformatics Centre:
A. Computer and Communication facility
The centre has one IBM server, 6 Intel Core 2 Duo PCs, 7 PIV PCs, 7 AMD 64
Bit PCs, One Thermal Cycler, 2 HP Inkjet Printers, 2 HP LaserJet Printers (One
Monochrome and One color), One HP All in One (Printer, Scanner, Fax &
Copier), 1 Scanner, 1 LCD Projector, 1 Digital Photocopier, 1 Fax Machine.
Communication Facilities - 6 Mbps Leased Line Broadband Internet
connection from Airtel.
Omiga 2.0, Ligplot, LigandScout, Chem Axon, Maestro 8.0, Rasmol, Rastop,
Qmol, Cn3D, VMD, PyMol, MDL Chime, KING, Marvin View, Swiss PDB Viewer,
Chimera, Modeller 7v7, Genedoc, Bioedit, Treeview, Phylodraw, Mega 3.0,
Clustal X, Phylip, Python, Perl, Argus lab, Hex, AutoDock tools, Molegro Virtual
Docker, Marvin Sketch
204
ISIS Draw.
C. Databases and other information resources
Derwent Biotechnology Abstracts, Biological and Agricultural Index, Agricola,
Agrisearch.
Name of the Staff Designation Specialization Period of
working
Absorption
status
Dr.R.Keshavachandran Professor &
Coordinator
Plant
Biotechnology
1-4-02
onwards
KAU staff
Alishya Joy Research
Associate
Bioinformatics 11-10-07 till
date
Temporary
Dileep K.V Research
Associate
date
Temporary
Reena.N Senior Research
Fellow
date
Temporary
Abhilash Joseph Junior Research
Fellow
date
Temporary
Tintu George Junior Research
Fellow
date
Temporary
Training programmes for agricultural scientists, technical staff, students of
KAU and staff & students of other educational institutions.
Literature search by means of CD ROM and Internet.
Offering courses in Bioinformatics to PG students.
Support to R&D activities for PG projects in Biotechnology.
As a part of the M Sc program, the centre conducts a [2+2] credit course in
Bioinformatics for M.Sc students of the Centre for Plant Biotechnology and
Molecular Biology. As a part of the Ph.D program offered by the university, a
course on Bioinformatics has been sent for approval. An initiative for E-print
facility will be one among the future activities of the centre. Students who have
completed the course are well placed with various Biotech companies.
The research activities and regular training programmes validate the outcome of
bioinformatics resources. Scientists in the university are regularly benefitted by
the facilities of this centre. Bioinformatics resources are made use by the M.Sc.
students for their research works.
10. Collaborative works / Initiatives: Nil
11. Databases/Software packages developed:
The databases that are being developed include Database on Improved Crop
varieties at KAU, Tissue culture protocols, Database on Indian Spices, Database
on Rice Info.
12. Papers published or presented in the conference with Reference:
1. Keshavachandran,R., Nazeem P.A.,Girija, D., John P.S and Peter K.V.
2007(Eds) Recent trends in Horticultural Biotechnology.Vol.I, Vol.II New
India Publishing Agency,New Delhi.
2. Nazeem P.A., Keshavachandran,R.,Babu T.D.,Achuthan C.R., Girija, D
and Peter K.V.2007.Assessment of Genetic Variability in Black Pepper
(Piper nigrum L.) Varieties through RAPD and AFLP Analyses. Recent
trends in Horticultural Biotechnology. (eds. Keshavachandran et al.), New
India Publishing Agency, New Delhi. pp 485-490.
205
3. Keshavachandran,R., Nazeem P.A., and Karihaloo J.L. 2007. Genetic
Fingerprinting of Piper nigrum L. and Piper longum L. Cultivars Using
RAPD Markers. Recent trends in Horticultural Biotechnology. (eds.
Keshavachandran et al.), New India Publishing Agency, New Delhi. pp
635-640.
4. Rema Menon., Sunny K.M., Nisha Jose., Nazeem P.A.,
Keshavachandran,R., and Shakunthala Nair. 2007. Study of Isozyme
Polymorphism in Musa Cultivars of Kerala. Recent trends in Horticultural
Biotechnology. (eds. Keshavachandran et al.), New India Publishing
Agency, New Delhi. pp 649-651.
5. Suma, B and Keshavachandran,R. 2007. Factors affecting Agrobacterium
tumefaciens Mediated Transformation in Ginger (Zingiber officinale Rosc).
Recent trends in Horticultural Biotechnology. (eds. Keshavachandran et
al.), New India Publishing Agency, New Delhi. pp 721-726.
6. Karmarkar S.H and Keshavachandran,R. 2007. Induction of Hairy Roots in
Holostemma ada-kodien With Agrobacterium rhizogenes. Recent trends in
Horticultural Biotechnology. (eds. Keshavachandran et al.), New India
Publishing Agency, New Delhi. pp 769-772.
7. Keshavachandran,R., Ajitha, R and Lavina C.V., Deepthy P.S., Nazeem
P.A., and Girija, D. 2007. Bioinformatics: a KAU Perspective. Recent
trends in Horticultural Biotechnology. (eds. Keshavachandran et al.), New
India Publishing Agency, New Delhi. pp 967-969.
8. Fatima A.G., Girija, D., Meera C.S., Nazeem P.A. and Joseph L. 2007.
Agrobacterium mediated genetic transformation in bell pepper. Recent
trends in Horticultural Biotechnology. (eds. Keshavachandran et al.),
New India Publishing Agency, New Delhi. pp 909-916
9. Sambasivam P.K. and Girija, D. 2007. Molecular characterization of
Ralstonia solanacearum infecting ginger in Kerala. J. Ecobiol. 20:229-
237
The centre is actively engaged in plant based research on gene & protein
sequence analysis, protein structure prediction and metabolic pathways. In silico
projects carried out include:
In Silico analysis of proteins of importance and interactions in
Biocontrol agents like Trichoderma spp,.
Study of Functional Residues and Phylogenetic Analysis of Cystine
Protenases involved in programmed cell death of plants
An evolutionary analysis and structural validation of Auxin
Response Factors
Insilico analysis of insulin like proteins in plants
Bioprospecting of Chitinolytic microorganisms focusing on Serratia
marcescens Chiting binding Protein(CBP21)
In Silico study of antimicrobial properties of Ginger against Epstein
Barr virus, Aspergillus flavus and Helicobacter pylar
14. Details of Training / Workshops organized and total no: of users
trained:
Three DBT funded training programmes were conducted this Year. They
include:
1. Bioinformatics in Data Analysis of Genes and Proteins.
2. Structural Bioinformatics :Exploring Macromolecular structures
3. Bioinformatics: Current approaches & Applications.
206
Other trainings conducted include:
Training programme on Sequence Analysis
Training on Emerging Trends in Bioinformatics.
Total number of persons trained till date is 463.
areas:
The usage of Bioresources by the students have increased notably and the facilities of
the Centre are widely being made use of for research, paper presentations and other
research activities of the University as well as for interpretation of molecular marker
analysis data and sequence related work .
Papers published with the help of Bioinformatics Centre : 10
No. of papers presented in conferences : 5
No. of scientists trained till date : 418
As a supporting centre for Biotechnology division, the Centre is in charge of the Gel
Documentation system [BioRad] which is widely used by the staff and students for
molecular marker analysis.
To train faculty, students & research workers to make use of bioinformatics
techniques in scientific research.
Purchase softwares to strengthen R&D activities in Bioinformatics.
Publish practical and theory manual in Bioinformatics.
Introduce a course in bioinformatics to B.Sc and Ph.D students of
KAU.
Continuation of teaching of Bioinformatics to M.Sc Plant Biotechnology
students
Propose an E-newsletter from the Bioinformatics Centre.
To enable a E print facility to act as a repository for research articles by
integrating data generated from Biotechnology division and other affiliated
research stations
Additional details:
Name of the Coordinator : Dr R Keshavachandran
Postal address : Bioinformatics Centre, (DIC)
Kerala Agricultural
University, Vellanikkara.
Thrissur, Kerala -680 656.
Phone number : 0487-2371994
Mobile : 9388987121
Email : bic@kau.in
Website : www.kaubic.in
Name of contact person(s) : Dr R. Keshavachandran
Email : rkcs@rediffmail.com
207
Madurai Kamaraj University, Madurai
Coordinator : Prof. S.Krishnaswamy

The Centre of Excellence in Bioinformatics at School of Biotechnology,
Madurai Kamaraj University, Madurai functions as a reputed centre for
research and manpower development in bioinformatics apart from providing
service. The centre has been established as a Distributed Information Centre
(DIC) in 1986. The Centre was elevated to a Centre of Excellence in
Bioinformatics in 2003. From 1996, the centre started its extensive manpower
development activities with the initiation of the one year Advanced Diploma
Course in Bioinformatics. The centre also submitted a proposal to DBT to
upgrade the Advance Diploma course in Bioinformatics to M.Sc program in
Computational Biology from the next academic year (2008-2009) onwards.
The National High Resolution Graphics Facility started in 1993, cater to the
need of structural biologists and molecular modelers.
The Centre has been focusing its attention mainly on development of
research and manpower development as well as services in the areas of
structural bioinformatics, proteomics, database development, data mining,
molecular modeling and dynamics. The Centre has an acclaimed reputation
for service, teaching and research in the area of Bioinformatics. The staff of
the center, as an integrated activity, with the faculty of the School of
Biotechnology performs research and teaching. The Center has been a
catalyst for the growth of Bioinformatics in this region and has contributed
significantly to manpower development.

2. Major research activities in Biotechnology and its related fields at the
institution
Structural bioinformatics of membrane proteins
Structural Genomics of prophage proteins
Genome analysis for non coding RNAs
Computational biology of macromolecular interactions
Molecular Modeling and Drug design
Data mining and text mining
Proteomics and biomarkers discovery
Genetic Engineering and Strain Manipulation of industrially
important microorganisms
Genomics of antibiotic biosynthesis
Plant genetic engineering for disease resistance and stress
tolerance
Structural virology
Fungal biotechnology
Xenobiotics

Structural Bioinformatics and Genetic Engineering

1. Ten students completed Advanced Diploma in Bioinformatics (2006-07)
and Ten ongoing (2007-08).
208
2. Five PhD students completed till 2007. Seven new students registered.
3. Participation in local workshops and academic staff training.
4. In house seminars and workshops related to Bioinformatics.
5. Elective courses as part of CBCS on Programming for Computational
Biology, Structural biology and molecular modeling apart from Core
courses on Biophysics and Bioinformatics for M.Sc. Biotechnology
6. Courses on Bioinformatics, Structural genomics, proteomics for M.Phil

A. Computers and Communication Facility Systems
PCs, SGI systems, Sun workstations, Multiprocessor cluster and server
Dedicated 2Mbps RF VSNL connectivity, Structured intranet network connecting
entire School of Biotech. with Print/backup/UPS facilities.

Programs for sequence analysis and molecular modeling/dynamics including
GCG, Biosym, Accelrys Discovery Studio, GROMACS and Clementine 10.0

Databases
Beta barrel membrane porins, Prophage database, HNH database and
Noncoding RNAs
Software
Information calculation for genomes, HNH domain subclassification, PCR primer
design for whole genome, Structure analysis of Porins, Consensus based
validation of porins and a software to detect Non-coding RNAs
All databases and mirrors are available through (http://bicmku.in:8081,
http://bicmku.in:8082, http://bicmku.in:8083, http://bicmku.in:8084) .

Except for Dr. Sanjeev K. Singh in the teaching staff and all in hired under CoE
such as Database Admin, Programmer and JRFs, rest of the staff have been
taken over by the Govt. of Tamil Nadu.

Teaching Staff
N Na am me e D De es si i g gn na at t i i o on n E E- -m ma ai i l l I Id d
Dr.K.Dharmalingam Sr Professor kdharmalingam@vsnl.com
Dr.S.Krishnaswamy Sr. Professor and
Coordinator
krishna@mrna.tn.nic.in
Dr.Z.A.Rafi Reader rafi@mrna.tn.nic.in
Dr.N.Jeyakumar Lecturer n_jeyakumar@yahoo.com
Dr. Sanjeev K. Singh Lecturer sanjeevsky@rediffmail.com

Non-Teaching Staff Database admin, Programmerand JRFs
Name Designation Name Designation
Mr.M.Raghuram Sr. Technician Mr. Krishnamohan Database
Administrator
209
Mr.B.Shivakumar Sr. Technician Mrs. Mohana Priya Programmer
Mr.S.Prabakar Jr. Technician Mr. Nagoor Meeran System
Administrator
Mr.K.Rajendran Accountant Ms. Ranjana Chellam JRF (resigned)
Mr.C.Raja Stenographer Mr. Sankara Narayanan JRF
Mr.P.Muthupandi Clerk/Typist Mr.Sridharan JRF
Mr.P.Natarajasundara
m
Data Assistant
Mr.M.Nagarajan Messenger/peon

7. Types of services provided Service
Database access, Sequence analysis, Information retrieval, Molecular modeling
and Project advice
Manpower Development
Advanced Diploma Course in Bioinformatics, Elective and Core Courses under
CBCS to MSc and MPhil Biotech. students, In house workshops/seminars and
Project trainees MSc, MPhil, ADCB and PhD
Research
The Centre provides research services to college teachers, students from other
Schools in the Universities and Industries.

Eighty seven students have successfully completed the ADCB till 2007. Eighty
percent of the students are placed in different organizations from Industries to
higher education both in India and abroad. The current ADCB batch has 10
students. The students are placed in various institutions such as IARI, IBAB,
IIT, AUKBC, TN govt, local Colleges, Molecular Connections, Meta Helix, CCMB,
and also in UK, US, Canada, Germany and Switzerland. As part of the CBCS,
an elective in Programming for Computational Biology with a revised syllabus to
include perl programming has been introduced for the post-graduate and MPhil
courses.

The industry and academia utilize the services and research advice on a regular
basis. The industrial consultancy is done through the University. The research
findings are published in national and international journals.

Weizmann Institute, Israe; University of Bath, UK; University of Aalborg,
Denmark; Aravind Eye Hosptial - Medical Research Foundation, Madurai; NCBS,
Bangalore; IISc, Bangalore; AIIMS, New Delhi; Genotypic Technologies,
Bangalore; Avesthagen, Bangalore; HLL, Bangalore and CSIR NMITLI.

Databases
210
F. Beta barrel membrane porins , Prophage database, HNH database and
sRNABase.
G. Software
Information calculation for genomes, HNH domain subclassification, PCR primer
design for whole genome, SCOMPS Structure analysis of Porins, Consensus
based validation of porins and Non-coding RNA detection

1. Nishma, N. P. Sankarnarayan and K. Dharmalingam (2007). Serum
proteome of leprosy patients undergoing erythema nodosum leprosum
reaction: regulation of expression of the isoforms of haptoglobin. Journal
of Proteome Research (Available online)
2. N.S. Baalaji, M.K. Mathew and S. Krishnaswamy (2006). Functional assay
of S.typhi OmpC using reconstituted large unilamellar vesicles: A general
method for characterization of outer membrane proteins. Biochimie
(doi:10.1016/j.biochi.2006.05.010)
3. K.V. Srividhya, V.R. Geeta, L. Raghavenderan, M. Preeti, J. Prilusky, M.
Sankarnarayanan, J.L. Sussman, and S. Krishnaswamy 2006. Database
and Comparative Identification of Prophages In ICIC 2006, LNCIS D.-S.
Huang, K. Li, and G.W. Irwin (Eds.), Springer-Verlag., 344, pp. 863 868.
4. The NMITLI Bio-Suite Team (2007) BioSuite: A comprehensive
bioinformatics software package (A unique industryacademia
collaboration) Current Science 92: 29-38 (S.Krishnaswamy and group
were part of the NMITLI team)
5. K. V. Srividhya and S. Krishnaswamy (2007). Sub classification and
targeted characterization of prophage encoded two-component cell lysis
cassette. J. Biosci. 32 (in Press).
6. J. Kagavalli, P.J. Eswari, S.R. Krishnadas and S. Krishnaswamy, P.
Sundaresan 2007. In vitro and in vovo study on the secretion of the
Gly367Arg mutant myocillin protein, Muscular Vision, 13, 1161-1168.
7. Sridhar and Z.A. Rafi (2007) Small RNA identification in
Enterobacteriaceae using synteny and genomic backbone retention.
OMICS: A Journal of Integrative Biology, 11, 74-99.
8. Sridhar and Z.A. Rafi (2007) Identification of Genomic Islands using small
RNAs. In Silico Biology 7, 0053.
9. N. Jeyakumar, C. Haines, B. Berglund . DeSesa C, C.J. Hack, W.
Dubitzky and E.G. Bremer. GetItFull A Tool for Downloading and Pre-
processing Full-text Journal Articles, Proc. Intl. Workshop on Knowledge
Discovery in Life Science Literature (KDLL) in PAKDD 2006, Singapore,
139-145.
10. N. Jeyakumar, B. Daniel, W. Dubitzky, H. Catherine , Z. Yonghong, D.
Catherine, R.V.B. James and E.G Bremer. (2006) Text mining of full-text
journal articles combined with gene expression analysis reveals a
relationship between sphingosine-1-phosphate and invasiveness of a
glioblastoma cell, BMC Bioinformatics, 7:373.
11. N. Jeyakumar and R. Jawahar (2007) Functional Gene Clustering via
Gene Annotation Sentences and MeSH Keywords, INCOB, Hong Kong.
12. S.K. Singh and N.S. Ram (2007). Theoretical Studies on Cyclin
Dependent Kinase (CDK4) Inhibitors and drug receptor interaction
analysis Med. Chem. Res. 15, 367.
211
13. S.K. Singh, N. Dessalew and P.V. Bharatam (2006) 3D-QSAR CoMFA
studies on Indenopyrazole as CDK2 Inhibitors. Eur. J. of Med. Chem. 41,
1310-1319.

Comparison of Proteome Profile with Transcriptome Profile in E.coli Growing
under Oxygen Stress (K.Dharmalingam)
Infection proteomics of fungal keratitis (K.Dharmalingam)
Comparison of Homology Modeled 3D structure of M. Laprae 18KDa small heat
shock protein and its mutant (K. Dharmalingam and S.K. Singh)
Structural genomics of prophage proteins (S. Krishnaswamy)
Sub classification of HNH domain proteins (S. Krishnaswamy)
Struct. bioinformatics of membrane proteins and complexes (S. Krishnaswamy)
Detection of small RNAs in bacterial genomes ( Z. A. Rafi)
Structural bioinformatics of Protein-RNA binding proteins (Z A Rafi)
Bioinformatics Analysis of Protein Kinase Relations and Pathways from
Biomedical Data and Literature (N. Jeyakumar)
Theoretical Studies on Cyclin Dependent Kinase Inhibitors (S.K. Singh)
Modeling Studies on Non-Nucleosidic HIV-RT Inhibitors (S. K. Singh)

Workshop on Trends in Systems Biology and Bioinformatics, March 6-8, 2007 -
75 participants (and) Local workshop on Bioinformatics software September 11-
12, 2007 - 20 participants.

15.Impact shown by centre on growth of biotechnology and allied areas.
The usage of the centre has resulted in a number of research publications over
the years in referred journals, Ph.D. dissertations and project reports by the
users. The host institution and more than 80 different nearby institutions have
extensively used the infrastructure facilities of the centre. The centre is
accessible to users from different parts of the country. The National Facility on
High Resolution Graphics has acted as a catalyst to several of the south Indian
institutions. The centre has been involved in assisting several research
publications and completion of research thesis within the university and nearby
universities and colleges.

16.Future activities
New initiatives in manpower development - E-learning and content development -
Eprints archives - Bioinformatics Portal - Bioinformatics Teacher Training -
Research and Software testing for industries

Additional Details:
Name of the Coordinator: Prof. S. Krishnaswamy
Postal Address: School of Biotechnology,
Madurai Kamaraj University, Madurai 625021
Phone Number:0452 2459141
Fax No.:0452 2459105
Email: krishna@mrna.tn.nic.in,mkukrishna@gmail.com
Website: www.biotechmku.org , http://bicmku.in:8081
212
Name of Contact Person(s): Dr. Z. A. Rafi, Dr. N. Jeyakumar
Email: rafi@mrna.tn.nic.in , n_jeyakumar@yahoo.com
213
Mahatma Gandhi Institute of Medical Sciences, Sevagram (Wardha)
Coordinator: Dr. B. C. Harinath

Bioinformatics Centre at JB Tropical Disease Research Centre, Mahatma Gandhi
Institute of Medical Sciences was established in March 1999 with support from
Department of Biotechnology, as part of National Bioinformatics Network. The Centre
has thrust on Medical / Health Informatics since inception and is actively involved in
research and providing academic bibliography service. In addition to In-house
Training programme for staff involved in Hospital Information service, the Centre
organizes yearly National level Workshop / Seminar / Symposia etc. So far 10 have
been organized which were well appreciated. Further, this Centre also publishes
SEVAMED, a Quarterly Update on Infectious Disease Research and Traditional
Medicine in its 9
th
year of publication, has been well received by the medical
teachers and scientists through out India.
Centre has developed database software TbDB, FilaDB, ObSoft, GynSoft, PsySoft
for recording & retrieval of data on Tuberculosis, Filariasis, Obstetrics & Gynecology
and Psychiatry patients related information. The Centre has also developed CaDB a
database on cancer patients registry for Pathology department and JBTDRC-Res-
Pub, a database on Centres 170 research publications which are convenient for end
users. Proceedings of National Symposium on Medical Informatics & CME on
Hospital Information System as a reference book including the basics of computer to
advances & its application in Medical Informatics has also been published and
available on www.jbtdrc.org. Centre has recently launched a web portal MGIMS-
JBTDRC Health Update under its e - health info services related to emerging
infectious diseases, life style health problems and medical tourism.

2. Major research acti vities in Biotechnology and its related fields at our
institution
JBTDRC, an advanced Centre for Tropical Disease Research is the result of
sustained problem based research activity by the Biochemistry department for more
than three decades at MGIMS, with support from ICMR, CSIR, DST, WHO/TDR,
Indo US-STI, DBT, UGC & KHS. Research in tropical diseases with thrust on
diagnostics and vaccines in filariasis and tuberculosis is being carried out at this
Centre conducting Ph.D and M.D. programmes.
Filaria Repository: A National Repository facility for filarial parasites and reagents
has been set up with the support from DBT for more than 10 years. Brugia malayi
filarial infection in rodents mastomys and jirds (2
nd
Centre in India) and a filarial sera
bank with collection of about 300 sera of different clinical groups of bancroftian
filariasis from various endemic regions are being maintained. Dipstick / strip based
enzyme immunoassays (SEVA FILA CHEK) have been developed at this institute
using penicillinase / peroxidase enzymes, to detect active filarial infection in different
clinical groups. Further protein / DNA vaccine studies using cocktail antigens of ALT-
2 and VAH studies in filariasis supported by DBT are in progress.
Tuberculosis: SEVA TB ELISA system for detection of antibody, circulating free and
immune complexed (IC) antigen in tuberculosis has been developed in this Institute.
The detection of IgG antibody by Indirect ELISA against M. tb. cocktail (ES-31 + ES-
43 + EST-6 Ag) antigen in pulmonary and extra pulmonary tuberculosis and
detection of free and immune complexed (IC) antigen using affinity-purified anti
cocktail antibody by Sandwich ELISA is routinely used for hospital patients. The test
is quite helpful in childhood tuberculosis where it is difficult to obtain sputum
samples. Further antigen detection has been found helpful for detecting tuberculosis
in patients with HIV co-infection. This test is also useful in confirming tubercular
aetiology in extra pulmonary tuberculosis (lymphnode Tb, meningitis Tb, bone & joint
Tb, abdominal Tb, plural effusion Tb, occular Tb, genitourinary Tb, milliary Tb etc.).
214
Recently mycobacterial serine protease (ES-31) has been shown to have potential
as drug target for screening new anti tubercular drugs.

Patent Granted A process for isolation and purification of M. tuberculosis
excretory-secretory (M. tb ES-31) protein for use in antibody based assay or antigen
based assay by detecting the presence and monitoring of M. tuberculosis infection.
Patent No.-184510, granted on June 2, 2001.
Patents under active consideration:
1) A process for the preparation of Brugia malayi microfilarial excretory-secretory
(mf ES-22) glycoprotein.
2) Antigen detection using antibodies in tuberculosis.
3) TB diagnostics based on Mycobacterium tuberculosis Excretory-Secretory
antigens and their specific immunoglobulins.

The Bioinformatics Centre has thrust on Medical / Health Informatics and is
involved in development of databases for patients information, Quarterly updates on
advances in disease research and Health information on emerging infectious diseases
and life style health problems.

4. Major acti vi ties of the centre during the year 2007-08
SEVAMED, has entered 9
th
year of its publication and is available on
www.jbtdrc.org.
10
th
National Workshop on Medical Informatics & Biomedical Communication was
organized during November 30 - December 1, 2007. Seven Eminent Experts in
Medical Informatics, Hospital Information Systems & Biomedical Communication
and 43 delegates from all over India attended the Workshop. Mr. Senthil Kumaran
Shanmugam, Vice President, Satyam Computer Services Ltd., Chennai delivered
the keynote address.
Launching of web portal MGIMS-JBTDRC Health Update on emerging infectious
diseases, life style health problems and medical tourism.
Short term project work was carried out by Mr. Rajabrata Bhuyan & Mr.
Dibyabhaba Pradhan, in Health Information Resources and e - updates on
Medical Tourism respectively.
Computer & Communication facility:
Computer Hardware: Server-3, Workstations-3, PCs-14, LAPTOP PC-2, Printers-6,
Photoprinter1, Other equipments available include Cisco Router, Modem (2),
Wireless router. Switch, Desktop LCD projector-2, Scanner, Fax machine, Canon
B155 plain paper fax machine, Digital copier cum printer (3), Kodak Digital Camera,
etc.
Bioinformatics Centre, Lab-1 (Immunology) & Lab-2 (Molecular Biology) and Central
Library are networked through LAN.
Computer Software: Windows NT, Windows 98, 2000, XP; Microsoft Windows NT
4.0 Service Pack 4, Developer Training Service pack 3, MS office 97/ 2000, XP, Adobe
PageMaker 6.5, Wings 2000 (Accounting software), Microsoft Visual Studio 6.0
Professional Edition, with MSDN Library.
Communication Facility: Centre has got installed 512 kbps leased line from BSNL.
Centre has provided 10 nodes for benefit of students in the Library and one node for
Hospital Information System.
Scientific Software packages:
TM4 Microarry software suite 1.5.0, MEGA 4.0, Auto Dock 4.0.1, Dock 6.1, Swiss
PDB Viewer 3.7, Cn3D, TreeView, ClustalX.
215
Databases & other information resources: In-house databases developed as detailed
in 11.
The library collection of Centre includes about 68 Indian & foreign Journals, bulletins,
Newsletters etc.

Information Officer and Technical Assistant posts have been absorbed by the host
Institute. Further absorption of other staff is under consideration.

b. Publication of SEVAMED Quarterly Update on
Infectious Disease Research and Traditional Medicine.
c. Research & academic related information retrieval
by the staff & Students.
d. Yearly National level workshops on Medical
Informatics & Biomedical Communication.
e. Short term in-house training for teaching, non-
teaching staff for HIS of this Medical Institute.

Centre also extended training and research facility to the students doing post graduation
in Bioinformatics / Biotechnology for doing short term projects. So far 21 students from
various Universities such as Bharathiyar University, Coimbatore, Orissa University of
Agriculture and Technology, Bhubaneswar, Madras University, Chennai, Anna
University, Chennai, RTM Nagpur University, Bundelkhand University, Jhansi, Amravati
University etc. have successfully carried out their projects.

9. Initiati ve to validate the outcome of bioinformatics resources
We are taking initiatives to assess the effect of e-health info services portal, MGIMS-
JBTDRC Health Update to bring awareness in the people about the management of
emerging infectious diseases and lifestyle health problems and usefulness of
SEVAMED quarterly update to medical researchers.

Collaborating with SVIMS University to develop syllabus in Medical Informatics for
6 months certificate course.

The Centre has developed certain user-friendly database softwares:
i. FilaDB, TbDB, PsySoft, GynSoft, ObSoft,
CaDB for recording and retrieving patients information for better patient
management.
ii. JBTDRC-Res-Pub a Research Publications
Name Desig. Specialization Period of
working
1. Lingaraja Jena Information
Officer
System administration, Program-
ming, Database designing &
Bioinformatics tool development.
5 months

2. Mr. P. Deshmukh Technical
Assistant
Programming, Database manage-
ment, web designing and update-ion,
assistance in publications.
7 Years
3. Mrs. S. Rao DEO Data entry, retrieval, Accounting, and
Library Management
3 years
4. Mrs. T. Das DEO Data entry, assistance in Sevamed
publication
1 years
216
(1970-2007, full paper) have been developed.
iii. SEVAMED bibliography database for the
year 2001 2007 has also been developed.

i. Pramod Deshmukh, Jayant Jumde, Satish Kumar, MVR Reddy and BC Harinath.
FilaDB Database software for information storage and retrieval on detection
and management of filaria patients. Bioinformatics India. Oct-Dec 2005;3(4): 36-
46.
ii. Pramod Deshmukh, Jayant Jumde, Satish Kumar and BC Harinath. TbDB A
database software for storage and retrieval of tuberculosis patients information. -
National Bioinformatics Symposium held at KVAFSU, Mangalore, February 1-2,
2006.
iii. BC Harinath. Keynote address on Medical Informatics in Health Care and
Research - All India Medico Informatics Society (AIMIS), Nagpur, April 15 -16,
2006.
iv. Pramod Deshmukh, Satish Kumar and BC Harinath. Development of database
software for storage and retrieval of information related to tuberculosis and filarial
patients in tertiary hospital setting. - 5
th
International Conference on
Bioinformatics (InCob-2006) held at New Delhi, December 18-20, 2006.
v. Rajabrata Bhuyan, Satish Kumar and BC Harinath. Virtual Reality in Health Care:
Robots replacing Clinicians - National Conference on Healthcare Biotechnology
at IISc, Bangalore organized by Innovative Centre for Biosciences (ICBio),
Bangalore, April 20-21, 2007.
vi.Dibyabhaba PradhanSatish Kumar and BC Harinath. Medical Tourism: An emerging
area in Healthcare. - National Conference on Healthcare Biotechnology at IISc,
Bangalore organized by Innovative Centre for Biosciences (ICBio), Bangalore,
April 20-21, 2007.
e - health info services web portal MGIMS JBTDRC Health Update will help in
epidemiological research related to emerging infectious diseases and lifestyle health
problems.

Sr.
No.
Date Ti t l e of t he Tr ai ni ng / Wor kshop No. of
Participants
attended
1 8 Apr. 2000 Introduction to computer Basics & Access to Biomedical
Information
24
2 24-26 Nov. 2000 Bioinformatics & Medical Research 14
3. 26-28 Nov. 2001 Medical Informatics, Research & Communication 13
4. 23-25 Sept.2002 Medical Informatics & Biomedical Communication 30
5. 10-12 Dec. 2002 ICMR-WHO Workshop on Storage & Retrieval of Information 38
6. 29 Oct. 1 Nov, 03 Medical Informatics & Biomedical Communication 29
7. 6-7 Sept. 2004 National Symposium on Medical Informatics & CME on
Hospital Information System supported by DBT, MCI, CSIR,
DST, ICMR, MoH&FW, IAMI & KHS
40
217
8. 9 10 Dec. 2005 National Seminar on Biomedical Informatics 40
9. 1-2 Dec. 2006 National Workshop on Medical Informatics 17
10. 30 Nov. 1 Dec.,
2007
National Workshop on Medical Informatics & Biomedical
Communication
43
11. 19 March-3 April ,
2001
Inhouse computer training course
for the non-teaching staff of MGIMS
20
12. 24 Feb.14 March
2003
Inhouse computer training course for the staff of Trauma
Centre.
15
13. 3 May 9 Oct.,
2004
Inhouse computer training course for the teaching, non-
teaching and nursing staff of MGIMS as a part of
establishment of Hospital Information System.
205

15. Impact shown by the Centre on the growth of biotechnology and allied areas.
Bioinformatics Centre since its inception has been actively helping medical teachers,
post graduate students and scientists in information search for research, publication
of SEVAMED a quarterly bibliography journal for medical teachers, development of
patients information based databases & research publications. Centre has trained
about 205 of the non-teaching & nursing staff of MGIMS for operating Hospital
Information System funded by Ministry of Information Technology.
From the inception of centre 67 research papers covering disease
diagnostics and vaccines from JBTDRC and Dept. of Biochemistry have been published
in Indian and International Journals. 22 Ph.Ds and 20 MDs have been awarded.
The Centre has developed customized database software for patients information in
consultation with Psychiatry, Obst. & Gyne. and Pathology departments and for
specific public health problems namely filaria and tuberculosis. Further a database
on JBTDRC research publications (full paper) has been developed.
The Centre was very helpful in supporting active MD / Ph.D research programme with
grants from DBT, DST, UGC, ICMR, CSIR and KHS. One patent for TB antigen of
diagnostic interest has been granted. Three patent applications are under active
consideration, two in India and one in United States.

Awards:

Year Name Award
2005 Ms. K. N. Krithika GP Talwar Young Scientist
(IIS Conference, PGIMER, Chandigarh)
2005 Mr. Vijay Upadhye MGIMS Tropical Disease (ACBICON-2005, Patna)
2006 Dr. M.V.R. Reddy Fellowship of Association of Clinical Biochemists (ACBICON-
2006, Pune)
2006 Mr. V. Anandharaman MGIMS Tropical Disease and ACBI Travel Fellowship
(ACBICON-2006, Pune)
2007 Mr. V. Anandharaman Visiting Scholarship for Collaborative study at Illinois University,
USA
2007 Dr. M.V.R. Reddy Biotechnology Overseas Associationship by DBT as a visiting
Professor at Illinois University, USA
2007 Dr. M.V.R. Reddy APFCB Fellowship for Council Meeting at Beijing,
2007 Mr. Vijay Upadhye APFCB Travel Fellowship, Beijing, China
2007 Mr. Vijay Upadhye GP Talwar Young Scientist (IISConference, NARI, Pune)

218
O Evaluation of the beneficial effects of e-health info services related to Research
and Health Informatic updates and Medical Tourism to medical teachers, research
students and patients.
O Formulation of Online Certificate Course on Health Informatics for health
administrators, medical teachers & practitioners and paramedical workers.
O Continuation of SEVAMED Quarterly B An Update on Infectious Disease Research
and Traditional Medicine to bring awareness and promote research.
O Development of Clinical Decision Support System (CDSS) by analysis of the field
data of Filariasis, Tuberculosis etc.
O Organization of National Level Workshops on Medical Informatics and Biomedical
Communication.

Additional Details:
Name of Coordi nator : Dr. B. C. Hari nath, PhD (USA)
Director, JBTDRC & Coordinator, BIC
Postal Address : Bioinformatics Centre, JBTDRC,
Mahatma Gandhi Institute of Medical Sciences
Sevagram (Wardha) - 442 102
TeleFax : 07152 - 284038 Mobile: 09890776971
email : info@jbtdrc.org, bc_harinath@yahoo.com Web: www.jbtdrc.org

Name of Contact Person : Dr. Satish Kumar, MD
Professor, Biochemistry & Dy Coordinator, BIC
e-mail: sk@jbtdrc.org
219
M.S. University of Baroda, Baroda
Coordinator : Bharat B Chattoo

The Bioinformatics Centre at M.S. University of Baroda, facilitates the use of
databases and software packages required by biotechnology students and
researchers. It provides an upto-date and accurate information in the area of
Biotechnology.
Apart from answering the bibliographic queries and supplying the sequence
data, the centre also offers unique facilities for data analysis, in addition to the
use of E-Mail and internet facilities to the students and faculties.
Software package like GCG and Seqweb from the Wisconsin Genetics
Computers Group, enables us to purse several sequence analysis projects.
This also serves as a major tool in our research initiative in the area of
Genomics through the use of advance methods for database searching,
molecular modeling, sequence editing and comparison, visualization of
molecular structures, gene mapping, plasmid and primer design.
NTSYPC software has proved to be an important tool for the statistical
analysis of the quantitative biological data obtained from our studies on
microbial biodiversity and the study of population structure and dynamics of
microorganisms. The molecular modeling software of the centre, helps our
users in theoretical studies and visualizing of molecules.
The Centre provides the computing support for users in Bioprocess
simulation, prediction of trends in a process under altered parameters.
MATLAB and SIMULINK are currently being used to substantiate
experimental data of the bioprocess.
We also serve as the regional node under the ICCB-net collaboration with the
Weizmann Institute of Science, Israel. This contact has helped us to use new
approaches to data analysis in our current research and research initiatives in
Genomics and Proteomics. We jointly organized a national level workshop,
with participation of the scientists from the Weizmann Institute on the use of
contemporary methods of computer based information processing for
analyzing the structure and function of biological macromolecules.
The Centre has trained several bioinformatics students through their
dissertation project work in the area of computational biology, microarray data
analysis etc. within and from the outside institutions.

2. Major research activities in Biotechnology and its related fields :
Biotechnology training at M.S. University emphasizes the areas of
Microbial technology and the main features of the programme are Genetics,
Molecular Biology, Industrial Microbiology and Immunology. The basic
training is given in Microbiology, Biochemistry, Genetics, Developmental
biology, Genetic Engineering, Biochemical Engineering and some aspects of
Biophsysics, biostatistics, plant tissue culture and environmental biology.

- Our work in the past few years has focused on the study of molecular
basis of disease, using the interaction of the rice blast pathogen Magnaporthe
grisea with rice as a model system. We have utilized new and emerging tools
of Molecular Biology to analyse the genome and proteome of this fungus,
initiated work on functional genomics in this fungus and in a complementary
approach, we have mapped important genes for resistance to blast fungus
220
and also generated transgenic plants showing enhanced resistance to
bacterial and fungal pathogens.
- The study of genomic flux in the blast fungus, use of novel bioinformatics
tools for genome analysis, bioprocess development for important therapeutic
molecules, using non-conventional yeasts as hosts, and the use of molecular
biological tools for the documentation of microbial diversity.

3. Area of Specialization of the Centre :
Crop Biotechnology and Molecular Biology, Genome and Proteome Analysis,
Bioprocess Development

4. Major activities of the centre during the year 2007-08 :
Several bioinformatics dissertation projects were carried out in the area of
genome sequence analysis and microarray data analysis for M.Sc /
B.Tech students from various institutions.
A tool for genome-wide microRNA prediction has been developed and is
being validated.
Upgraded GCG package and implemented high speed internet line at the
centre.
A bioinformatics project has been introduced as a part of the practical
training of M.Sc biotechnology students.
We initiated activities as a regional node under the ICCB-net in
collaboration with the Weizmann Institute of Science, Israel. The focus of
this collaboration is in the specific analysis of genes and proteins involved
in plant disease. Several proteins of potential interest are being analysed
for their structural information and possible significance in host-pathogen
interactions.

5. Infrastructure facilities in the Bioinformatics Centre :
The Centre has created the necessary infrastructure for Bioinformatics
activities under Genome Research Centre.
The Centre is equipped with Computers and Communication facility. More
than 20 desktop computers and 2 servers are available for students and
faculty of the department of microbiology and biotechnology programme.
The softwares available in the centre include GCG and Seqweb from the
Wisconsin Genetics Computers Group and NTSYPC software. This facilities
are also being accessed by other departments as well as colleagues from the
local industries.

Sl.
No.
Name of the Staff Designation Working sinc Absorption
status
(Yes/No)*
1. Mr. Ramesh Menon Information
officer
September
2005
No
2. Mr. Amwillsu VargheseTechnical
Assistant
April 1991 No
221
3. Mr. Nitesh D Bhatt Data Entry
operator
November
1998
No

7. Types of Services Provided:

Apart from answering the bibliographic queries and supplying the sequence
data, the centre also offers unique facilities for data analysis, in addition to the
use of E-Mail and internet facilities to the students and faculties. The Centre
support the use of bionformatics tools in teaching and research programmes,
particularly in newly emerging areas of genomics and proteomics and in
studies on microbial diversity and bioprocess development.

The Centre has trained several bioinformatics students through their
dissertation project work in the area of computational biology and
bioinformatics. Following students from various institutions have carried out
their dissertation work in our centre during 2006-08:

Sl.
No
Name of the
student
Course University /
Institute
Project Title Duration
1 Mr. Salabh
Takkur
M.Sc
Bioinformatics
S.P
University
Computational
identification of
microRNA in
M.grisea
6 months
2 Ms. Vidhita
Sinha
B.Tech
Biotechnology
Rajasthan
Vidyapeeth
University

Analysis of MPSS
data for
upregulated genes
in aspersoria
formation
4 months
3 Mr. Purvil
Sukhadia
B.Tech
Biotechnology
Rajasthan
Vidyapeeth
University

Cluster analysis of
top 20 upregulated
appresoria genes in
M.grisea
4
months
4 Mr. Bhavesh
Dharmani
B.Tech
Biotechnology
Rajasthan
Vidyapeeth
University

Microarray data
analysis of
M.grisea genes
using Genespring
software.
4
months
5 Ms. Darshna
Ramrakhyana
M.Sc
Bioinformatics
S.P
University
Expression data
analysis of top 50
upregulated genes
of M.grisea in
Nitrogen starvation.
3 months


Our Department started a masters level course in Microbiology in 1964. We
started a post graduate course in Biotechnology in 1985 with the support from
UGC and the Dept. of Biotechnology. Over the years, we have developed a
strong base in microbial technology and molecular biology. We have started
one year Post M.Sc. Diploma Course in Genetic Engineering and Bioprocess
Development to cater to the merging needs of the industry in these areas.
This course is aimed at providing training to both in-service candidates from
industry as well as fresh students in specific application areas.
222
Most of the students are pursuing higher studies in institutes within the
country as well as abroad. Several students from the earlier batches have
been offered independent faculty or research positions in various prestigious
academic and research institutions. The department maintains a fairly close
contact with its alumni.
In 2007, 19 M.Sc students passed out of a batch of 20 and 6 Post M.Sc.
Deiploma students passed out of a batch of 6. Following are the percentage
of placement:
Higher Studies (India) 52% Higher Studies (Overseas) 28%
Working in other field 4% Working in BT related area 12%
Information not available 4%

In a span of 18 years of its existence, the centre has emphasized the
research on Genetic Engineering and Bioprocess Development. The
resources available under the centre will be utilized for this purposes. It is
planned to increase the component of bioinformatics in this programme as
well as our ongoing M.Sc. Biotechnology Course and Post M.Sc diploma
course.

We have initiated activities as a node under the ICCB-net in collaboration with
the Weizmann Institute of Science, Israel. The focus of this collaboration is in
the specific analysis of genes and proteins involved in plant disease. Several
proteins of potential interest are being analysed for their structural information
and possible significance in host-pathogen interactions.
i. Sterling Biotech: Emphasis of collaboration is on data base development,
bioprocess development and process optimization.

ii. Tel-Aviv University, Dept. of Plant Sciences, Life Science, Israel : Plant
SUMO conjugates its role in biotic stress , supported by DST under Indo-
Israeli collaboration
iii) John Innes Centre, Norwich, UK: Molecular analysis of disease resistance
signaling, supported by DBT under Indo-UK Bilateral Collaboration

Software: MIST (MicroRNA Search Tool): A tool for genome-wide
microRNA prediction using sequence and structure based strategies has
been developed.

1. Gupta, A & Chattoo, B.B. (2007) A novel gene MGA1 is required for
appressorium formation in Magnaporthe grisea. Fungal Genetics and Biology.
44:1157-1159
2. Tendulkar S.R., Saikumari Y.K., Patel V., Raghotama,S.,T.Munshi, P.Balaram and
Chattoo,B.B. (2007) Effect of surfactin from Bacillus licheniformis BC98, a soil
isolate, on the phytopathogenic fungus Magnaporthe grisea, J. of Applied
Microbiology 103(6):2331-2339.
3. Gupta, A & Chattoo,B.B. (2008) Functional analysis of a novel ABC transporter
ABC4 from Magnaporthe grisea, FEMSLE 278:1, 22-28.
223
4. Munshi, T. and Chattoo,B.B. (2008) Bacterial Community analysis of the Jute
Retting Water Environment. Applied and Environmental Microbiology (press)

13. Initiation of R&D Activities in Bioinformatics:
R & D activities related to ongoing projects in Genomics and Proteomics,
particularly the analysis of micro-array data as well as 2-D protein gels are
being initiated.

14. Details of Training/Workshop organized and total No. of user trained:
Nil

15. Impact shown by our centre on the growth of biotechnology and allied
areas.
Developments in the emerging fields of Genetic Engineering, Immunology, Plant
tissue culture, Animal cell cultures and biochemical engineering are leading to
new products and applications in the area of Health, Agriculture, Industry, Energy
etc. Progress in these areas depend on the availability, analysis and
dissemination of information.
Every year 2-5 papers with the support of bioinformatics resources were
published by the faculty in international journals.
A Centre of Excellence in Microbial Genomics has been established by
the Gujarat State Biotechnology Mission (GSBTM) and providing support for
establishing micro array facilities. The centre plans to develop the facilities as
a resource centre for gene expression studies in close cooperation with local
industry and academic institutions. One of the main projects being
undertaken at the Centre is the study of crop disease with focus on the study
of rice-blast diseases.

Development of data bases for research in the following areas :
High significant datasets on resistance genes from eukaryotes (with
reference to different domains found in resistant gene products).
Sub datasets of protein spots and their complete annotation for
proteomics research purpose.
Databases with reference to Biomedical importance.
Industries involved in R & D for therapeutic recombinant molecules,
projects undertaken, field trials, products patented and other data.
R & D institutions involved in promoting science and technology in
Gujarat and also the institutes directly working on communicable
diseases, which are prevalent in the areas of Gujarat.

Additional Details:

Name of the Coordinator: Bharat B Chattoo
Postal Address: Distributed Information Centre, Department of Microbiology and
Biotechnology Centre, Faculty of Science, M.S. University of Baroda, Baroda
390 002, Gujarat
Phone Number: 265-2794396/2750498 Fax No.265-2792508 E.Mail.
bharat.chattoo@bcmsu.ac.in ; admin@bcmsu.ac.in Web site: www.bcmsu.ac.in,
www.msubiotech.ac.in
224

Name of Contact Person(s): Prof. B.B.Chattoo
Email.bharat.chattoo@bcmsu.ac.in
225
National Brain Research Centre, Manesar, Haryana
Coordinator: Dr. Nandini C.Singh

The Distributed Information Centre has set up state of the art high speed
computing facilities at NBRC. High-end SUN and IBM servers function as
Web Servers (www.nbrc.ac.in), (www.nbrc.res.in) Mailserver
(http://mail.nbrc.res.in), DNS Server and FTP server. Centralized Network
Attached storage worth 11 TB space has been made available for high end
computing requirements. Windows 2003/ Windows 2000, Red Hat Enterprise
Linux loaded IBM servers act as File Server, Mail Server, Proxy Server with
content filters, Web Server & Application Servers respectively. In order to
access and share resources all knowledge-based systems are connected to
these servers through LAN. Pool of PCs are clustered to provide internet
access to students with their individual user Profiles. DIC has also expanded
its internal network by adding several desktops/workstations loaded with
heterogeneous operating systems, establishing interconnectivity between
buildings by using a fiber optic backbone. WiFi connection has been
implemented within the campus alongwith enhanced Internet bandwidth to 2
Mbps. The DIC staff works as a team and focuses on in-house development,
assists in technical problem solving, in addition to helping the scientists,
handling the servers and network.

institution
Computational neuroscience and neuroinformatics, which deals with the analysis,
characterization and modeling of neural data is a new emerging area. NBRC is the only
institute pursuing research and imparting training in this area in a focused and dedicated
manner. A few highlights of the research and training at NBRC in this area have been
summarized below

Image analysis Headed by Dr. P K Roy, a laboratory focused on developing
new techniques of image analysis to enable better diagnosis of MRI images has been set
up. The laboratory uses the process of stochastic resonance to amplify the response peak
in Magnetic Resonance Imaging/Spectroscopy for characterization/classification
procedures of diagnosing tumours and some neurodegenerative processes.
Speech analysis Using methods of spectral analysis, the speech and language
laboratory headed by Nandini C Singh has been analyzing speech signals from children
and those with different speech disorders. The efforts of this group have been directed at
developing novel computational tools that will enable a unified study of speech
production skills. This group has been using this approach to study the development of
various articulatory features in typically developing children and setting up quantifiers to
assess different speech disorders. This laboratory is also interested in studying the
phonological organization of different Indian languages.

19. Area of Specialization of the centre : NEUROINFORMATICS

The high speed computing facilities at NBRC have been upgraded to support
250 users. High performance SUN and IBM multiprocessor servers have
Formatted: Bullets and Numbering
226
been added to provide Active Directory Services, Mail Services, DNS
Services and Web services and high speed computing. Nokia IP390
Checkpoint High availability firewall has been configured at the gateway level
to ensure infrastructure security. A 2 Mbps dedicated Internet bandwidth line
has been provided to scientists, students and staff. Wireless access inside
the campus for roaming laptop users has also been provided. The
centralized heterogeneous network attached storage server for data
warehousing has grown to 10 Terabyte and is accessible across the network
with LDAP authentication for aiding data security and integrity.

SunFire x4100 Server-(Web server, Application Server FTP Server )
IBM xSeries 346 Xeon(Active Directory. Application Server,
Websense Content filtering)
IBM xSeries 3650 Xeon (Linux Mail server)
IBM xSeries 235 Xeon Dual processors Servers with Windows 2003
Server (File server, Mail Server)
IBM xSeries 220 server with windows 2000 server (DNS)
Network Attached Servers 11 TB, Tulsiant NAS 8420R
Desktops and ThinClients.
HP Laserjet 1300,2100,2200,2420,2300, 1020/3030/ 3050, 1320
HP Deskjet 3535, HP 800 PS Design Jet (Plotter)
Routers Cisco 2600 and1700
Switches: 3Com 10/100 Mbps 24 port, 100 Mbps 12 port 1 No.
D-Link 24 Port Xstrack DGS 3426 , D-Link 48 Port DES 3550
D-Link 24 Port DGS 1024 D
Nokia IP390 Firewall
2 Mbps Leased Line (BSNL), 512 Kpbs Leased Line (HCL)
Matlab 7.1, SPSS, E-Prime,SPM,Brain Voyager, Neurolusida
MriCro, Spot Fire (Micro Array), Silicocyte, Instrument Control Manager,
Sequence Analyzer, Phred Phrap, Consensus (Sequencer), DS
Modeling Software
Chemical Management System, Cell Lines Status in Lab's
Leave Management System
absorption status)
Sl.
No
Name of the Staff Designation
Working
Since
Absorption
status
(Yes/No)
227
1 Mrs. Reema Saxena Computer Operator 21-12-2000
2 Mr. Jothibasu Information Scientist 23-05-2001 Yes
3 Mr. Hariharan AAO 29-04-2002 Yes
4 Mr. Mahender K. Singh Jr. Information Scientist 21-03-2005 Yes
5 Mr. Kedar Singh Bajetha Computer Operator 17-07-2003 Yes
6 Mr. P.V.S. Shyam Kumar Computer Operator 29-07-2003 Yes
7 Mr. Sanjeev Bhardwaj Computer Operator 28-02-2005
8 Mr. Anoop Singh Computer Operator 28-02-2005 Yes
9 Mr. Ashish Upadhyay Computer Operator 22-03-2005
10 Mr. Punit Kumar Computer Operator 02-04-2007
11 Mr. Jeebanada Chottary Computer Operator 27-07-2007
12 Mr. Sanjay Kumar Gupta Computer Operator 12-11-2007

DIC is providing diversified services like software development, Internet,
intranet, mailing facilities maintenance of servers and network.

NBRC is a deemed University and has two training programmes in
Neuroscience namely a PhD programme and Integrated PhD programme in
Neuroscience.
25. Initiative to validate the outcome of bioinformatics resources Not
Applicable

The project on speech patterns in children with autism in the laboratory of Dr.
Nandini C Singh being carried out in collaboration with Dr. Shobha Srinath
and Dr. Shivshankar from NIMHANS, Bangalore, Dr. Amit Sen from SBISR,
New Delhi.
Joint project between Nandini C Singh of NBRC with Dr. Srinivas
Chakravarthy of IIT, Madras to explore the possibility of using speech and
handwriting patterns as markers for early diagnosis of Parkinsons disease.
Application of Stochastic Activation and Stability analysis for Brain Imaging
and Therapy In collaboration with Dr. K. L. Chakrabarty, Institute of Nuclear
Medicine & Allied Sciences, Delhi
Chemical Management System, Cell Lines Status in different laboratories in
NBRC.
228
Leave Management System

List Publications and patent applications:
Computational Neuro-science and Neuroimaging laboratory
o Subramanyam, R, Roy, P. Stochastic Resonance-Based Tomographic Transform
for Image Enhancement of Brain Lesions, J. Computer-Assisted Tomography,
2007 (in press).
o Subramanyam, R, Roy, P. Magnetic Resonance image enhancement using
Stochastic Resonance in harmonic space, Computerized Medical Imaging, 2007
(in revision).
o Roy, P. Nature of a Living State from a Thermodynamic Perspective:
Information, Fluctuation and Order in the Organism, in S Rangachari (ed). Life
and Organism, New Delhi (accepted, with revision).
o Subramanyam, R, Budhachandra, K, Upadhyay, A, Roy, P, The Self Looks at its
Brain: Symbiosis of Tensor Imaging and Functional Imaging strategies for the
Neuroinformatics Initiative, Computer Society Transactions (communicated).
Patents
o A Medical Image Enhancement Device based on Image Transform Resonance,
using a Computational Apparatus consisting of an Embedded System (submitted)
Speech and Language Laboratory
o Tanusree Das, Latika Singh, Nandini C Singh, Rhythmic structure of English and
Hindi new insights from a computational analysis, Prog. In Brain Research (in
press).
o Latika Singh, P. Shantisudha, Nandini C Singh, Developmental patterns of speech
in children, J. of Applied Acoustics, 68, 260-268, 2007.
o Latika Singh and Nandini C Singh, The development of articulatory signatures in
children, Developmental Science (in press).
o T.Padma Subhadra, Tanusree Das, and Nandini C Singh, Speech rhythms in
children learning two languages : From Heart to Brain, Springer Life Sciences
Series, (in press).
o Mohini Verma and Nandini C Singh, Cross-cultural language rhythms effects
of emotion recognition in speech, J. of cross-cultural Psychology, (in revision)
o T. Padma Subhadra and Nandini C Singh, Speech production in bilingual
children, Int. J. of Language and Commn. Disorders, (submitted)
29. Initiation of R&D activities in Neuroinformatics
As described above NBRC has initiated research in the area of the image
analysis and speech processing. With the organization of CNS workshops
every year for the past 6 years than 250 students have been trained in basic
techniques of computational neuroscience in different parts of the country.
The 3T fMRI scanner recently set up at NBRC will now enable research in the
speech and language laboratory to study undertake projects that will allow the
investigation of neural correlates of language and speech processing. It would
allow the neuroimaging laboratory headed by Dr. Roy to now undertake the
development of pulse programming sequences for efficient implementation
study of stress tensor imaging.

229
CNS course at NBRC Under intra-mural training, students undergoing MSc
(Neuroscience), Int. PhD and PhD and NBRC attended 8 week course on computational
neuroscience which also consists of tutorials and laboratory sessions. A total of 15
students were trained in this course in 2007.
CNS workshop - NBRC has been conducting a national workshop on
computational neuroscience since 2001 across different universities and IITs in an
attempt to encourage and popularize the field of computational neuroscience. A total of
35 student from India and 4 from Bangladesh and Iran kj mbb b vbvcxb vghv b bv
students were trained in various techniques of computational neuroscience at the 7
th
such
workshop which was held at Dept. of Computer Science, Delhi University in December
2007.

The computational neuroscience group at NBRC has published/submitted
around 10 publications and patent applications in 2006-07
NBRC digital library access more than 400 online scientific journals. This is
the first library of kind in that it allows inter library loan service thereby sharing
its resources 48 Network Centres across the nation. NBRC library is currently
subscripting to 521 journals of which 444 are online and others are in the hard
copy formats. A total of 245 registered users are using the digital library
facilities.
NBRC conducts Summer Training Programme every year for the Students
from different academic backgrounds and varied academic Institutions who
are in their penultimate year of their undergraduate / postgraduate course.
The summer training projects give students an exposure to neuroscience and
to encourage them to consider it as a future career option and a total of 12
students were trained in 2007.
DIC personnel actively contributed to the developments of new signal
processing tools to study speech and image analysis. The image analysis
tools have been directed towards the analysis of MRI images for better
diagnosis whilst the speech analysis techniques have been used to study
speech and language in typically developing children and those with speech
disorders children.

Creation of High end cluster computing environment for Functional
MRI analysis and Speech analysis using blade servers.
Developing specialized software for fMRI image analysis and Image
processing.
Establishment of Video conferencing facility for conducting lectures of
eminent scientist across other centres and universities.
230
Development of a portal site for neuroscience and neuroinformatics
which would provide comprehensive information to various aspects of
neurosciences research in India and abroad. This will be useful to
illustrate, catalogue and assist the latest research in neuroscience.

Additional Details:
Name of the Coordinator: Dr. Nandini C.Singh
Postal Address: National BrainResearch Centre, Manesar-122050, Gurgaon
Dist., Haryana

Phone Number : 0124-2338921 Extn: 333
Mobile :
Email : nandini@nbrc.ac.in
Website : www.nbrc.ac.in

Name of Contact Person(s): Mr. JothiBasu
Email: jothi@nbrc.res.in
231
National Dairy Research Institute, Karnal
Coordinator : Dr. D.K. Jain

The Distributed Information Sub-Centre on Animal Biotechnology started way back
in 1990 with the objective of inculcating Computer Culture in the Institute; providing
literature search facilities to the Scientists and Students; database and software
development has taken a leap forward in undertaking research and development in
the core area of Bioinformatics. In 1996, the dial up connectivity was established
using MODEM and a telephone line. Local Area Network (LAN) and KU Band
VSAT was installed in the Institute initially in 1998 which was further expanded in
2002 to cover the main buildings through optical fiber/UTP cabling and distantly
located buildings through Remote Access Server (RAS) in order to provide round the
clock E-mail/Internet services to all the scientists and other officers numbering
around 300 in their Labs/Offices.

Institution
The major areas of research include Embryo Biotechnology, Reproduction
Augmentation, Livestock Genomics in general and Buffalo Genomics in particular,
Probiotic attributes of milk, Development of recombinant dairy enzymes, PCR based
test kits for detection of food borne pathogens, and Structural Biology/
Bioinformatics of biological macro-molecules.

Animal Biotechnology.

A leased line of 512 kbps was commissioned by BSNL, Karnal; A
Bioinformatics Lab measuring 1200 Sq ft. has come up to house some of the
Bioinformatics facilities like Silicon Graphic Workstation. A central facility for
the Scientists and research scholars of the Institute; Video-conferencing
facility along with IP telephony connections established. Subscription to 18
on-line foreign journals and on-line availability of CD-ROM database and the
catalogue of library; the existing databases updated.

A. Computer and communication facility
Silicon Graphic Workstation, Pentium Computers, Server PII with operating
system Window NT4.0, Server DATAMINI E-8000 with operating system
Window 2000 with one workstation, Laser jet and Desk jet Printers, Fax
Machine, KU Band VSAT, Photocopier-cum-printer, UPS 3KVA and 5 KVA.
Vector NTI Advanced TM9.1 Sequence Analysis, VB. NET and
Macromolecular Simulation and Dynamics software; SYSTAT, SPSS,
LIMDEP, TORA, MATLAB, LIBSYS, Arcview GIS, In house developed
application software packages for data analysis and MIS.
Integrated Information System on Dairying.
Up-to-date CAB and FSTA literature databases.
232
Digitized inventory of Ph.D. thesis.
On-line availability of information on books and periodicals.
6. Details about staff members working in the center (Name of the staff,
Designation, Specialization and Period of working)

Name of Staff Designation Specialization
Period of
working
Dr. A.K. Sharma Scientist (CAA) &
Information Officer
(additional charge)
Computer
Applications in
Dairying
June, 1995 to
Continuing.
Ms. Aruna Pandey Computer Operator Bioinformatics Since July, 06
Mr. Sunny Bali Computer Operator Electronics &
Commun. Engg.
Selected and
yet to join

Literature search (both on-line and off-line); Training and workshops; E-mail /
Internet Access; Structure and Sequence Analysis for Proteins & DNA; Assistance in
Software development for MIS and data analysis.

The Institute runs M.Sc. and Ph.D. programmes in Animal Biotechnology, Animal
Biochemistry and Dairy Microbiology. One course on Bioinformatics for Post-
graduate students introduced from the current academic session. Use of
Bioinformatics tools in genetic engineering being offered to the students as part of
Genetic Engineering course. All the students are getting good placement.

The software developed on various aspects are being validated by the users with the
sample data and put to effective use by the researchers. Similarly, the information
system in the form of ready to use software and database on different aspects of
dairying is being used by the researchers, administrators, bureaucrats, policy makers,
industrial/ commercial organizations.

The Centre has made some initiatives towards inter-divisional research at this
Institute as well as explored possibility for collaboration with external Institutions of
excellence in research such as IITD, JNU, IASRI, Thapar University and Punjabi
University, Patiala; BISR, Jaipur and University of Qubec, Canada.
Existing Databases were updated.

Journal articles
1. Sharma, A. K., Sharma, R. K. and Kasana, H. S., 2007. Prediction of first lactation 305-
day milk yield in Karan Fries dairy cattle using ANN modeling. Applied Soft Computing
7(3): 1112-1120.
2. Yadav, Anita and Yadav, B.R. 2007. Genetic diversity among six breeds of Indian goat
using RAPD markers. Biotechnology, 6(1): 57-60.
Conference papers
3. Ruhil, A.P., Singh, R.R.B., Jain, D.K., Patel, A.A. and Patil, G.R. 2007. Development of an
artificial neural network based model for shelf-life prediction of Basundi Mix an Indian dairy
233
product. In: Proceedings of the 3
rd
Indian International Conference on Artificial Intelligence,
December 17-19, Pune, pp.1517-1524.
4. Sharma, A. K., Sharma, R. K., Kasana, H. S. and Chakarvarty, A. K., 2007. Connectionist vis--
vis conventional models for predictions of lifetime milk production in KaranFries dairy cattle. In:
Proceedings of the 2
nd
International Conference on Advanced Computing and Communication
Technologies (ICACCT2007), Nov. 03-04, Panipat, pp. 492-495.
Book chapter
5. Sharma, A. K. and Jain, D. K., 2008. Computational intelligence: state-of-the-art in research and
applications to dairying. In: Ahmad R. (editor), WTO and Agriculture Sector Opportunities,
Problems and Challenges. The editor is Professor at Department of Agricultural Economics &
Business Management, Aligarh Muslim University, Aligarh-202002

Projects were initiated in the following fields of Bioinformatics related to Animal
Sciences/Dairying.
Genomics
Structural and functional characterization of IGFBP5 gene and exploring its role
in truncation of lactation in Farm animals (Institute funded IRC Project)
Modeling & Structural analysis of proteins
Energetics and Dynamics of Protein Stability and Iron binding properties and
their modulation by domain-domain interactions in lactoferrin from various
animal species (DBT funded project).
Predictive Modeling
Prediction of economic traits in Murrah buffaloes a comparative assessment of
connectionist and conventional models (Institute funded IRC project).

14. Details of trainings/workshops organized and total number of users
trained:
A workshop is being planned in the first half of year 2008 the Institute
faculty was occupied in other assignments like organizing two International Conferences
in Animal Nutrition and Dairy Technology; and CAS Training Programme of 21 days
duration each. Also, two sponsored trainees were imparted training on Advanced
Computing techniques for Bioinformatics applications.

15. Impact shown by your center on the growth of Biotechnology and
allied areas. In this you may highlight the details like number of papers
published with the help of your center, how your center is promoting
various activities of your organization and neighboring institutions,
manpower trained, tools developed, patents & copyrights acquired and
other services offered etc.
Increased use of advanced computing techniques for effective data
management, visualization, analysis and interpretation.
Regular national level workshops and training programmes for spread
of the knowledge on emerging areas of Information Technology and
Bioinformatics to the participants drawn from various R&D institutions
including NDRI.
Attracted a large number of students for pursuing training and project
work as part of their PG degree requirements through studentship.
Availability of databases on different aspects of Dairying.
R&D activities in Bioinformatics and related areas; Publications and
presentation of research papers/invited talks.

234
Genome analysis (QTL) in bovines in relation to milk constituents from existing
on-line information search.
Comparative genomics, evolution and functional analysis of aspartic proteases:
Implication in milk clotting.
Phylogenetic lineage of indigenous animal resources.
DNA/Protein sequence analysis and genome mapping of farm animals and starter
cultures.
Structural biology of macro-molecules
Application of Soft Computing methodologies in Dairying.
Web server based Support Vector Machine to predict protein functions.
Analysis of regulatory pathways regulating mammary gland physiology during
mammary gland development, lactation and involution.

Additional Details
Name of the Coordinator : Dr. D.K. Jain
Postal Address : Principal Scientist & I/c Computer Centre
N.D.R.I., Karnal 132001
Phone Number : 0184-2259014
Fax No. : 0184-2250042
Email : dk_jain@ndri.res.in;
dkjn@rediffmail.com
: aksharma@ndri.res.in
Website : http://www.ndri.res.in
Name of Contact Person(s) Dr. D. K. Jain, Coordinator
Dr. A. K. Sharma, Information Officer.

235
National Institute of Immunology, New Delhi
Coordinator : Dr. Dinakar M. Salunke

Bioinformatics Center (BIC) at NII was set up by the Department of
Biotechnology with the mandate to serve as an information resource and
state of the art computational facility for researchers in the field of molecular
biology and immunology. The usage of the facilities provided by the center is
reflected in large number of publications from various research groups at NII.
The center has also catered to the requirements of researchers from other
institutes. The center is also engaged in advanced research in the area of
computational and structural biology. The center has contributed to the
discovery of new biosynthetic pathways and elucidation of novel mechanisms
of immune recognition.

institution
The Institute is committed to advanced research addressing the basic
mechanisms involved in body defense, host-pathogen interactions and
related areas with a view to contribute to the creation of an internationally
competitive intellectual knowledge base as a sustainable source of innovative
futuristic modalities of potential use in health care. The research interests of
the various research groups at NII coalesce in six major areas; Chemical
Biology, Genetics & Cell Signaling, Immunity & Infection, Molecular & Cell
Biology, Reproduction & Development, and Structural & Computational
Biology.

Structural Biology & Molecular Modelling

During the year 2007-2008, the center has upgraded its computational
resources by addition of a Sunfire X2200 cluster consisting of 16 dual core
2.8 GHz AMD Opteron processors and 5 TB of storage space, and several
high end LINUX and MAC OS X workstations. The center has carried out
extensive work on molecular dynamics simulations of large proteins.

The center has established major computational resources involving
Sunfire 2200 cluster with 16 dual core CPUs, Apple G5 workgroup
cluster with 16 CPUs, Mac OS X G5 and MacPro workstations, SGI
Servers and Intel linux or Windows workstations. The center is linked to
INTERNET through two independent 2 Mbps(1:1) leased lines.

The center has a large collection of commercial and public domain
softwares and they are listed at http://www.nii.res.in/bionfo-software.html
.

236
Apart from online access to various databases on the INTERNET, the
center also maintains local copies of many databases for fast access by
users. The center has online access to all the major journals in biological
sciences.

absorption status)

Name Designation Specialization Status
Dr. D. M. Salunke Staff Scientist VII Struct. Biology NII Core
Dr. D. Mohanty Staff Scientist V Comp. Biology NII Core
Ms. S. Sachdeva Technical Officer System Admin NII Core
Mr. M. S. Rao Technical Officer System Admin NII Core
Mr. Naveen Technician Comp Operations NII Core

BIC, NII manages the entire scientific and administrative computing
infrastructure at NII and ensures that most bioinformatics applications are
available on the users desktop either from INTERNET or from in house
servers. Molecular dynamics, Molecular Graphics and other CPU intensive
applications are made available from clusters or high end workstations at the
center.

Currently a number of research scholars are carrying out research work for
Ph.D. degree in bioinformatics under the supervision of scientists associated
with BIC, NII. Three students have completed Ph.D. in Bioinformatics from
BIC, NII.

Exploring the possibility of experimental validation of in silico predictions has
always been a major priority of the center. Attempts are being made to
validate the results of the structure based predictions for substrates of Ser/Thr
kinases.

The center is associated with several collaborative projects with other
experimental groups at NII as well as other institutes in India. These projects
relate to work on Mycobacterium tuberculosis and various other aspects of
immunity and infection. The center is participating in a collaborative project
involving experimental as well as computational work to understand the
molecular basis of the vitiligo disease.

A major activity of the center has been development of databases and
softwares which permit correlating the sequence and structural features of
various biosynthetic proteins to the chemical structure of the metabolites they
synthesize. Softwares have also been developed for structure based
prediction of MHC ligands and substrates for kinases.
237
During the reporting year, several new gene clusters have been
added to the NRPS-PKS database. A web based software has been
developed for predicting substrate specificity of acyl adenylate superfamily.
Most databases/softwares have been made available from NII website.

Software for
Motif Discovery http://202.54.249.131/~depak/RegAnalyst.html
Software for modeling
Protein-peptide complexes http://www.nii.res.in/modpropep.html
Substrate Specificity of ACS http://linux1.nii.res.in/~pankaj/poss.html
Software for analysis of GTr http://www.nii.res.in/searchgtr.html
Database for NRPS/PKS: http://www.nii.res.in/nrps-pks.html Genome
analysis tool: http://www.nii.res.in/genome.html


1. Kumar N and Mohanty D* (2007) MODPROPEP: A program for knowledge
based modeling of protein-peptide complexes. Nucleic Acids Res 35: W549-
55.
2. Gokhale RS*, Sankaranarayanan R and Mohanty D (2007) Versatility of
polyketide synthases in generating metabolic diversity. Curr Opin Struct Biol
17: 736-743.
3. Goyal K, Mohanty D and Mande, S. C.* (2007) PAR-3D: A server to predict
protein active site residues. Nucleic Acids Res 35: W503-5.
4. Gokhale RS*, Saxena P, Chopra T and Mohanty D (2007) Versatile polyketide
enzymatic machinery for biosynthesis of complex mycobacterial lipids. Nat
Prod Rep 24: 267-77.
5. Krishnan L, Sahni G, Kaur KJ and Salunke DM (2007) Role of Antibody
Paratope Conformational Flexibility in the Manifestation of Molecular Mimicry.
Biophysical J (in press).
6. Kaur KJ, Sarkar P, Nagpal S, Khan T and Salunke DM (2007) Structure-
function analyses involving palindromic analogs of tritrypticin suggests
autonomy of anti-endotoxin and antibacterial activities. Protein Sci (in press).
7. Krishnan L, Lomash S, Raj BPJ, Kaur KJ and Salunke DM (2007) Paratope
Plasticity in Diverse Modes Facilitates Molecular Mimicry in Antibody
Response. J Immunol 178:7923.
8. Bhowmick A, Krishnan L and Salunke DM (2007) Structural immunology:
Mechanisms of antigen recognition J Ind Inst Sci 87:35-41.
9. Kaur KJ, Pandey S, Salunke DM (2007) Design of a functionally equivalent
nonglycosylated analog of the glycopeptide antibiotic formaecin I. Protein Sci
16:309.

The center also has a number of ongoing research projects focused on
molecular modeling and analysis of protein sequences/structures.

Molecular Basis of functional mimicry (Dinakar M. Salunke)
Focus of our research has been on the elucidating the structural basis of
functional mimicry among chemically dissimilar molecular systems,
238
highlighting the possible consequences in different biological processes.
A distinguishing characteristic of our work has been the judicious
combination of structural, biochemical and immunological techniques with
bioinformatics applications.

Molecular modelling of protein-ligand complexes (Debasisa Mohanty)
The main theme of the research is to understand structural principles that
govern binding of ligands to proteins and folding of peptides/proteins to
stable conformations, and then use these principles for developing
computational approaches for specificities of protein-ligand complexes
and structures of peptides/proteins.

During the current reporting year, the center has arranged 2 hands-on
bioinformatics laboratory sessions for students and teachers of different
degree colleges. During April 2007, one day workshop with hands on training
on homology modeling and protein-ligand docking was also arranged.

areas
The major users of bioinformatics center at NII have been the large number of
scientists and researchers working at NII. The impact of the center on the
research at NII is reflected in about 50 publications every year in peer
reviewed journals. Resources of the center are also used by researchers
from JNU, ICGEB, AIIMS, Delhi University etc.

The center plans to expand the scope of the existing research projects to analyze
metabolic, regulatory and signaling pathways. Attempts are also being made to
initiate projects related to in silico design of drugs/inhibitors.
Additional Details:
Name of the Coordinator: Dr. Dinakar M. Salunke
Postal Address: NII, Aruna Asaf Ali Marg, New Delhi-67
Phone : 011-26717108 Email:dinakar@nii.res.in Website:http://www.nii.res.in
Name of Contact Person(s): Dr. Debasisa Mohanty
Email: deb@nii.res.in
239
National Institute of Oceanography, Goa
Coordinator : Dr. P.A. Loka Bharathi


Marine biodiversity is undoubtedly the most diverse, not only in terms of
number of diverse kinds of organisms but also in terms of unique habitats and
ecosystems. Compared to terrestrial biodiversity, diversity of the marine
organisms attracts more importance due to its fragile nature. Direct and
indirect effects of anthropogenic activities have proved to be of serious
concern to marine biodiversity. Therefore, conservation of marine biodiversity
is very important, particularly in the Indian context.

Bioinformatics Centre at NIO works towards improving the understanding of
the marine biota in the Indian waters. Centre has a full-fledged website
www.niobioinformatics.in to disseminate the collected data and information.
Workshops and training programmes in the emerging areas in marine
biodiversity. Recently a National workshop on Ecological Niche Modeling was
conducted to train researchers and academicians in species distribution
modeling, Remote Sensing and GIS.

institute

a. Bioactive molecules from marine environment
b. Identification and preparation of extracts of pharmacological
importance from marine organisms
c. Identification of marine organismsm for compounds with
industrial applications
d. Bioprospecting and biotechnology of marine microorganisms.
e. Habitat ecology, controlled reproduction and conservation of
marine organisms with food and medicinal values.
f. Evaluation, mechanisms and control of biofilm and biofouling

3. Area of specialization of the centre : Marine Biodiversity Informatics

4. Major activities of the centre during the year 2007 08

Website launched for dissemination of marine biodiversity data and information
www.niobioinformatics.in
Developed DigiMus-0.1, a software to digitize marine biodiversity specimen
collections.
Trained several researchers and academicians in ecological niche modeling,
through National Workshop on Ecological Niche Modeling in Biodiversity
Management, in Dec,2007.
Training imparted to students from colleges in areas such as protein sequence
analysis and various bioinformatics softwares.
Special feature on Indian Coral reefs launched on www.niobioinformatics.in for
commemorating International Year of the Reef (IYOR), 2008.
Papers in different aspects of marine biodiversity informatics have submitted in
scientific journals.
240
Initiated work on marine heat shock proteins, drug designing and databases on
protein derived from marine organisms.

The resources available at the centre
Computer Systems 6 Nos.
Notebooks 2 nos.
Printers 3Nos.
Fax 1 No.

b. Scientific Software packages : DigiMus 0.1- Marine biological specimen
digitization software.

c. Databases & Other information resources
Aquatic Science & Fishery Abstracts
Science Direct online database

6. Detailed about staff members working in the centre (Name of the staff,
Designation, specialization and period of working

Name Designation Period of working Absorption status
1 Shri Devanand Kavlekar Tech. Officer 17 Years Absorbed
2. Vishwanath Kulkarni Lab. Assistant 17 years Absorbed
3. Aditya Kakodkar Proj. Assistant 3 years Not Absorbed
4. Sarika Kerkar Proj. Assistant 1 year (Aug,06-
Aug,07)
Not absorbed
5. Neena Verghese Proj. Assistant 1 year Not absorbed
6. Ambily Nath I.V. Proj. Assistant 1 Year Not absorbed
7. Akshata Arolnekar Proj. Assistant 1 Year Not absorbed

7. Type of services provided
Main function of the centre is to provide information to the interested users on
topics pertaining to the relevant areas of marine biodiversity.

8. Educational activities with detailed of placement
Post-graduate students in bioinformatics are given facilities to complete
short term project work.

9. Initiative to validate the outcome of bioinformatics resources : NA

10. Collaborative works /initiatives
The Bioinformatics Centre of NIO and NCL, Pune have collaborated to form
the Indian Ocean Biogeographic Information System (IndOBIS) which is the
Indian Ocean regional node of the Ocean Biogeographic Information System
(OBIS).

11. Databases /Software packages developed

Web based information services through www.niobioinformatics.in
241
Biological specimen digitization software DIGIMUS Ver 0.1
NIO's digital herbarium: The NIO's Digital herbarium, is an online source
of accessing the specimen in the Herbarium collection of the National
Institute of Oceanography, it contains 741 specimen records of 142
species of marine algae.

Indian Ocean Node of Ocean Biogeographic Information Systems
(IndOBIS): Bioinformatics Centre in association with NCL, Pune has
developed a database of known organisms of the Indian Ocean. The
database contains about > 40,000 species, with their metadata.

12. Papers published or presented in conferences with reference


At present the centre has not initiated any R & D activities in Bioinformatics.

14. Details of training/ Workshop organized and total number of users
trained
The Centre has organized a National Workshop on Ecological Niche
Modeling in Biodiversity Management from 13
th
to 15
th
December 2007 at
NIO, Goa. The workshop was attended by ~25 participants from different
institutions and universities.

areas
C. T. Achuthankutty and Kakodkar A. P., (2007), Applications of
informatics in marine biodiversity conservation in the Indian Context.
Marine Biodiversity, (Eds.) S. Kannaiyan & R. Venkataraman, submitted to
National Biodiversity Authority.
Kakodkar A. P., Kerkar S. S., Kavlekar D. P.Kavlekar and C.T.
Achuthankutty, (2007), Marine Biological Museums in Real Time - from
Shelves to Screens: A Case Study, Communicated to Biodiversity
conservation.
Kakodkar A. P., C. T. Achuthankutty

and V. S. Chavan
,
(2007) Ocean
Biodiversity Information Infrastructure for India: Opportunities and
challenges, Communicated to Current Science.
Vishwas Chavan, Chandan Badapanda, Aditya Kakodkar, SwapnaPrabhu,
C.T. Achuthankutty and IndOBIS Team (2007), IndOBIS: Development of
web based informatics infrastructure todocument known Indian Ocean
biodiversity, Communicated to Marine ecology.


Database on Heat Shock Proteins from Marine organisms
Database on Marine Drugs & Designing Tools.
Databases on bio-molecules derived from marine organisms.
242
Ecological Niche Modeling in Marine Environment and its applications in
biotechnology.
Name of the Coordinator : Dr. P.A. Loka Bharathi
Postal Address : Bioinformatics Centre
National Institute of Oceanography
Dona Paula, Goa 403 004
Phone number fax number Email website
(0)832- 2450281 (0)832-2450606 loka@nio.org www.nio.org
Name of Contact Person(s) : Shri Devanand kavlekar
Email : devanand@nio.org
243
National Institute for Plant Genome Research, New Delhi
Coordinator : Dr. Gitanjali Yadav

The Sub-DIC at NIPGR is in its first year of inception, and it has already
successfully installed, operationalized and established major computational,
networking and scientific resources. Staff intake for two positions has been
completed. Installation of major computational resources, including institutes
own web & academic emailing servers is complete.

institution
Development of Genetically modified crops with increased yield and nutrition
quality. Generation of ESTs and DNA based molecular markers for Molecular
Mapping and Genome analysis. Genetic Diversity analysis, Functional
Genomics and Proteomics in Plants. Differential Gene expression and
analysis of plant stress responses

Plant computational Biology, Molecular Evolution of protein families
involved in stress response

Inception and infrastructure establishment of Sub-DIC.
Staff Intake

High end Linux and Mac Workstations & Servers, Laser
Printer, Copier and Scanner, Tape Drives for data Back up.
Accelrys Discovery Studio v 2.0

Sl.
No.
NAME DESIGNATION WORKING STATUS
1 Subhashish Mondal Data Entry Operator Since 7-1-08 Just Joined
2 Swarupa Pradhan Tech asst Since 3-1-08 Just Joined
3 Info Officer In process

244
Sequence and structural analyses, Installation of scientific software
packages, Assistance with genome sequencing efforts in Tomato.
To be started w.e.f current year
12. Papers published or presented in the conferences with reference : NA
Analysis of protein domain fusions, plant Transcription factors, and Gene
Mapping
14. Details of Training/ Workshop organized and total no. of users trained
Five Students have been trained to date.
Six students are undergoing training currently.

areas.
To conduct annual workshops and discussion meetings.
Expansion of center infrastructure.

Additional Details:
Name of the Coordinator: Dr. Gitanjali Yadav
Postal Address: National Inst of Plant Genome Research (NIPGR), Aruna
Asaf Ali Marg. New Delhi -110067
Phone Number: 26735103 Email: gy@nipgr.res.in
Website: http://www.nipgr.res.in
Name of Contact Person(s): Dr. Gitanjali Yadav
Email: gy@nipgr.res.in
245
National Institute of Technology, Raipur
Coordinator : Dr. M. K. Verma


1) Procurement of Server, Computers, softwares, Internet facilities and
other important necessary items for the development of Bioinformatics
Laboratory facilities in the center
2) Development of Bioinformatics Laboratory.
3) Development of Wet Laboratory.
4) Organized courses for students.
5) Provided center facilities to pursue research and project work in
Bioinformatics to the students of B.Tech (Bio-Medical, Bio-Technology,
Chemical Engineering, Computer Science Engineering) and M.Tech.
Computer Technology.

institution.

1) Research work in Bioinformatics was carried by students of M.Tech.
Computer Technology.
2) Research work initiated and carried in the biotechnology especially in
Environmental Biotechnology and Biotransformation.
3) Data base generation and Data mining were initiated by center.
4) Research work carried in the field of ANN and Medical Bioinformatics.

Environmental Biotechnology, Medical Bioinformatics and
Biotransformation.

Development of Center to cater the needs for the researchers, students and
teaching faculties related to biotechnology, biomedical, computer technology
and Bioinformatics including other basic science.
Development of Infrastructure facilities in center.
Initiated the research environment in related field by providing the
necessary research facilities.

5. Infrastructure facilities in the Bioinformatics Centre.
- Computer & Communication facility
- Scientific Software packages: MATLAB TOOL BOX, Genechek,
Genowitch.
- Databases & other information resources Under Generation.

absorption status)

246

1. Dr. M.K.Verma (Coordinator, Sub-DIC Bioinformatics centre)
2. Mr. R.R. Janghel (Information officer )
3. Interviewed (Technical Assistant)
4. Interviewed (Data Entry Operator)
5. Interviewed (Trainee ship)

+ Provided infrastructure facilities to pursue research and development work in
allied discipline.
+ Provided various short-term courses and workshop in Bioinformatics.

Facilities provided to in-house and other institute to pursue research activities
including carrying their project works.

Students including U.G., P.G and other research scholar were benefited by
the center.

Collaborative research works were carried out with Pt. J.L.N.M Medical
College Raipur. Like Development of expert system for the diagnosis of
cancer and diabities.

11. Databases/ Software packages developed.
1. Database under process for the cancer and diabities.

12. Papers published or presented in the conferences with reference.

List of Research Publications:
1. One paper has published in National conference on Innovation in
Science and Technology towards Industrial Development in Rungta
College of Engineering and Technology Bhilai (C.G.)

1. Research work has been initiated and ongoing in the field of
Environmental Biotechnology, Biotransformation, and Medical
Bioinformatics etc.
2. Under development an expert system for the diagnosis of cancer and
diabities.

S.no Name of the staff Designation period of
working
absorption
status
1. Dr. M.K.Verma Coordinator Oct-2006 Regular
2 Mr. R.R. Janghel Information officer Dec-2005 Non-Regular
247
1. National conference/ Training are going to be organized during the
month of January-2007, i.e. on 28-29 Jan 2007.The total no of trained
user are 30.
2. One week training programme on Tools and Technique in
Bioinformatics from 23-28 July, 2007. The total no of trained user are
30.
In this you may highlight the details like number of paper published/ number
of papers published with the help of your centre, how your centre is promoting
offered etc.

1. Center has been involve in various research activities and providing
training program to the students of B.E. biotechnology, B.E. Biomedical
Engineering and M.Tech Computer Technology by providing facilities to
carry out their research, projects etc. to the students of various nearby
and in-house institutes/ university.

16 Future activities.

1. Center will organize various short-term courses and conferences.
2. Center will continuously going to develop the basic infrastructure
facilities to make benefiting the students/ Researchers/ Faculty
members etc.

Additional Details:

We have conducted Executive meeting on 21/12/2007.
We have conducted interview for the post of Information Officer, Technical
Assistant and trainee ship.

Name of the Coordinator: Dr. M.K. Verma
Postal Address: Coordinator, SUB-DIC Bioinformatics Center
National Institute of Technology Raipur
Raipur-492010.
Phone Number: 07714062385 Fax No.:07714062385
Email: mkseem670@rediffmail.com,mkseem670@gmail.com

248
North-Eastern Hill University, Shillong
Coordinator : Prof. Pramod Tandon

The Bioinformatics Centre (BIC) at North-Eastern Hill University (NEHU) has
been setup and funded by Department of Biotechnology (DBT), Ministry of
Science & Technology under the Biotechnology Information System Network
(BTIS) program. The Centre started functioning from November 1999 with a
view to catering to the needs of the scientific community in the far-flung
northeastern region of the country and to augmenting their research activities
through information inputs. Rich in great variety of flora and fauna, the north-
eastern part of the country has been identified as one of the bio-diversity
hotspots. The forest wealth includes numerous orchids, timber-yielding trees,
medicinal and aromatic plants, animals and microbes and some unique plants
and animals from the region. For the bio-resource development, its
exploration, conservation and proper utilization, an urgent need was felt for
linkage with the Bioinformatics network. The Centre is part of the national
Bioinformatics Network and functions as an information base in various areas
of Biosciences.

The Centre has been considered for upgradation to DIC with Excellent
remarks during the XI
th
Plan period as per the Sub-DICs 2
nd
review meeting
report.

institution
The School of Life Sciences comprises four Departments: Botany,
Biochemistry, Biotechnology & Bioinformatics and Zoology, catering to the
varied research interests of faculty members at NEHU. Some of the important
areas of research are molecular characterization, genome organization and
expression in plants, animals and microbes, oncology, parasitology, crop
improvement, microbial genetics etc. The most important area of research
relevant to the northeastern region being biodiversity, the facilities of the
Centre are extensively used for preparation of databases. Besides, some
work on genomics, proteomics and metabolomics has also been initiated,
apart from providing support to all disciplines of research in biotechnology.

3. Area of Specialization of the Centre
The Centres activities focus on developing databases of scientific relevance
on biological resources of the region, training of manpower and dissemination
of information and technical knowhow (Computer Support Services) to the
end users of national community working in the arena of Biotechnology and
allied sciences.

4. Major activities of the Centre during the year 2007- 08
i) Workshop and Interaction meeting on Mapping and Quantitative
Assessment of Geographic Distribution and Population Status of Plant
Resources of Eastern Himalayan Region dated April 17-18, 2007
249
ii) A lead talk on Eco-informatics in Conservation and Database
Management by Prof. K. N. Ganeshiah, UAS, GKVK, Bangalore on April
18, 2007
iii) Organized EDUSAT Interaction for the North-East Region Vision
Document 2020 on August 10, 2007
iv) Lectures- cum- hands on training to participants of the UGC-sponsored
Refresher Course
a) in Zoology on Recent Trends in Bioinformatics during September, 2007,
b) in Botany on Ancient internet: Information flow in Cells during Nov-Dec
2007 and
c) in Political Science on E-governance and Basic Applications in IT during
December 2007.
v) Training course on Inferring Biological Relationships: A Bioinformatics
Approach during November 27- December 1, 2007
vi) Training course on Molecular Biology Databanks and Integrated Data
Analysis Tools: A Bioinformatics Approach (scheduled to be held during
March, 2008).

The Centre is functioning from a small building of its own, which has the
facilities and capacity to hold Trainings Courses and Seminars.
i. Computer & Communication facility
i. Leased Line Internet Connectivity (512 kbps)
ii. Implementation of LAN on a Structured CAT 5 UTP Cabling Network using
Switches and Hubs
iii. Servers, PCs & Workstations, Printers, Scanner, UPS, Projector, etc.
ii. Scientific Software packages
i. Accelrys Gene 2.5 (Sequence Analysis Work Bench)
ii. Matlab 7.0 (A high-level technical computing language and interactive
platform for algorithm development, data visualization, data analysis,
and numeric computation
iii. Winspirs ver 4.1 for the Biotechnological Abstracts
iv. Reference Manager for downloading and organizing data from available
online Journals.
iii. Databases & other information resources
i. Derwent Biotechnological Abstracts (July 1987 - March 2006)
ii. Reference Update Delux Edition (July 2002 - June 2004)
iii. Parasitology Database obtained through MOE&F.
iv. Other Softwares
Windows 2003 Small Business Server, Windows 2000 Professional Server,
Microsoft Small Business Server 2000, Red Hat Linux, SQL Server 2005,
Winproxy 6.0
Windows XP, Windows Millennium Edition
Macromedia Director Shockwave Studio 8.5, Dreamweaver CS3, Adobe
Photoshop 6.0, Adobe Acrobat 5.0
Microsoft Visual Studio .NET 2005, Microsoft Visual Studio 6.0, Microsoft
Office Professional 2000, Microsoft Office Frontpage 2000, iWork 2006
Prof. Pramod Tandon, Coordinator and Vice-Chancellor, NEHU
Prof. Veena Tandon, Dy. Coordinator and Dean, School of Life Sciences,
250
NEHU
S.NO. NAME OF THE STAFF DESIGNATION
WORKING
SINCE
ABSORPTION
STATUS
1. Mr. Devendra Kumar
Biswal
Information
Officer
July 2006 The process of
selection for
absorbed
position is on.
2. Mr. Manish Debnath Senior
Technical
Assistant
November
1999
Absorbed
since July
2006
3. Mr. Hamarbamutlang
Kharshiing
Computer
Operator
March 2007
4. Mr. Welfrank
Thongnibah
Computer
Operator
March 2007
5. Mr. Graciously
Kharumniud
Technical
Assistant
March 2007
6. Mr. Santosh Kumar
Vishwakarma
Technical
Assistant
March 2007
Additional
posts were
sanctioned by
UGC for the
Bioinformatics
Centre and
recruitments
have been
made.
7. Mr. Pradeep Kumar
Kar
Data Entry
Operator
November
2005
Absorbed
since July
2006

a) Training
b) Database & Software Development
c) Assisted in teaching of Bioinformatics course to the Post graduate
students of Department of Biotechnology and Bioinformatics at the
University by way of conducting lectures and providing hands on
training to them.
d) Internet Access
e) Access to Journals Subscribed (Users and on request)
f) Technical Support to University
g) Printing & Scanning
10,500 users (approx.) as per the log book maintained by the Centre.
Names of the trainee students who did their project work at BIC, NEHU
Sl.
No.
Name Affiliation Title & details of the
project work undertaken
Remarks
1 Mr. Allen Freddy
(06-07)
M.Sc. (Zoology), Madras
University
Listing of polymorphic
microsatellite markers for
chromosomes 1-7, 9 and
22 in H. sapiens
Pursuing Ph.D at
NEHU
2 Mr. Donald Jyrwa
(06-07)
M.Sc. (Zoology), NEHU Helminth Parasite of
Freshwater Fishes in India
Pursuing Ph.D at
NEHU
3 Mr. Lingaraj Jena
(07-08)
Pursuing M.Sc.(Bioinfo),
OUAT
a) Helminth Parasite of
Freshwater Fishes in India
b) Phylogenetic analysis
on ITS1 & ITS2
sequences in pathogenic
zoonotic trematodes
Working as IO, BIC,
MGIMS, JBTDRC
Wardha
4 Mr. P. Ravikumar
(07-08)
Pursuing M.Sc. (Bioinfo),
Bharatiyar University
Have joined on January 14, 2008
5 Mr. Eric Sandor
Pakma (07-08)
Pursuing M.Sc. (Bioinfo),
Bharatiyar University
Have joined on January 14, 2008
251
6 Mr. Budheswar
Dehury (07-08)
OUAT
Will be joining on February 15, 2008
7 Ms. Chinmayee
Priyadarshini
Mandhata (07-08)
OUAT
Will be joining on February 15, 2008

The quality of research has tremendously improved with the facilities of the
Centre being used by many faculty members, research scholars and M.Sc.
students of not only NEHU but neighboring institutions as well in Northeastern
region.
i) Preparation of data base on mosquito fauna of Northeastern region in collaboration
with RMRC (ICMR), Dibrugarh.
ii) Database on Seed Mycoflora of local variety of Phaseolus vulgaris Linn. in
collaboration with Department of Biotechnology and Bioinformatics, NEHU.
iii) With reference to the zoonoses of worm origin, a consortium-based programme is
supposed to be taken up by the Bioinformatics Centre at NEHU with Public-Private
Partnership (PPP) venture such as TCGA (an IGIB-IMM collaboration)
emphasizing on Whole Genome Sequencing and Analysis of the lung fluke,
Paragonimus sp. (a worm parasite), the infection of which prevails in crab-eating
populations in Near- and Far Eastern Asian countries and which mimics symptoms
of Tuberculosis.

i. The Helminth Parasite Spectrum in Northeast India
ii. Mosquito Fauna of North East India with Special Reference to the
Medically Important Vectors
iii. Traditional Fermented Foods and Beverages of the Sikkim Himalayas
iv. Medicinal Plants of Meghalaya
v. Helminth Parasite of Freshwater Fishes in India

Prasad, P. K., Tandon, V., Biswal, D. K., Goswami, L. M. and Chatterjee, A.
(2007) In silico molecular phylogenic location of the Indian liver fluke, Fasciola
gigantica (Cobbold, 1855) based on the ribosomal internal transcribed spacer
regions presented at 77th Annual Session of the NASI, Mysore during December
2007.

Tandon V., Prasad P.K., Chatterjee A. and Bhutia P.T. (2007) Surface fine
topography and PCR-based determination of metacercaria of Paragonimus sp.
from edible crabs in Arunachal Pradesh, Northeast India. Parasitology Research,
102: 21-28. DOI 10 1007/s00436-007-4.

Prasad P.K., Tandon V., Chatterjee A. and Bandyopadhyay S. (2007) PCR-
based determination of internal transcribed spacer (ITS) regions of ribosomal
DNA of giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899.
Parasitology Research 101(6):1581-7.

Tandon P., Rathore, T.S. and Kumaria S. (2007) Micro-propagation of Coptis
teeta Wall.-Threatened medicinal plant of Arunachal Pradesh, India. Indian
Journal of Biotechnology 6: 280-282

252
Tandon P., Kumaria S. and Choudhury H. (2007) Plantlet regeneration of Pinus
kesiya Royle ex. Gord. from mature embryos. Indian Journal of Biotechnology 6:
262-266.

Tandon P., Bhowmik, S. K. D., Mao, A. A. and Kumaria, S. (2007) Rapid in
vitro clonal propagation of Mantisia spathulata Schult, A rare and endemic plant
of Northeastern India for recovery. Biotechnology 6(1): 68-71.

Das, M.C., Kumaria, S. and Tandon, P. (2007) Protocorm regeneration, multiple
shoot induction and ex vitro establishment of Cymbidium devonianum Paxt.
Asian Journal of Plant Sciences 6(2): 349-353.

Tandon, P., Kumaria, S. and Abrol, Y.P. (Eds.) (2007) Biodiversity and its
Significance. I.K. International Publishers, New Delhi 370 p.

Tandon, P. and Bhattacharjee, P. (2007) Bioinformatics: An overview. In: Plant
Biotechnology and its Applications in Tissue Culture. (Eds. A. Kumar, N.S.
Shekhawat and I.D. Arya). I.K. International Publishers, New Delhi.

Tandon, P. and Bhattacharjee, P. (2007) Bioinformatics in biodiversity
mangement. In: Biodiversity and its Significance (Eds. P. Tandon, Y.P. Abrol and
S. Kumaria) I.K. International Publishers, New Delhi, pp 332-353.

Stadwelson, D., Das, M.C., Kumaria, S. and Tandon, P. (2007) Conservation of
Splendid Orchids of North-East India (Eds. P. Tandon, Y.P. Abrol and S.
Kumaria) I.K. International Publishers, New Delhi, pp 354-365.

Bhatt, B.P., Pathanaik, A. and Tandon, P. (2007) Shifting cultivation: Issues and
Strategies in N.E.H. region (Eds. P. Tandon, Y.P. Abrol and S. Kumaria) I.K.
International Publishers, New Delhi pp 262-273.

Tandon, P. and Kumaria, S. (2007). Conservation of biodiversity of North-east
India using biotechnological approaches (Eds. P. Tandon, Y.P. Abrol and S.
Kumaria) I.K. International Publishers, New Delhi, pp 157-166.

Tandon, P. and Bhattacharjee, P. (2007). Bioinformatics in bio-technological
research. In: Biodiversity and Environmental Biotechnology (Eds. P. Dwevedi,
S.K. Dwevedi and M.C. Kalita) Scientific Publishers (India), Jodhpur, pp 225-250.

The BIC at NEHU, which is being considered for upgradation to DIC,
proposes to initiate specific teaching programmes in Bioinformatics relevant
to the needs as well as undertake R & D activities pertaining to development
of dedicated and derived databases and development of innovative softwares
addressing genomics and proteomics applications.

14. Details of Training/ Workshop organized and total no. of participants
trained
I) National Training Courses
i. Basic Computer Concepts and Applications, 12-14 June 2000, 22 nos.
253
ii. Introduction to Computer Networks and Internet, 26th -29th September
2000, 16 nos.
iii. Application of Basic IT Resources, 20
th
-23
rd
June 2001, 15 nos.
iv. Basic Computer Concepts and Applications, 23rd-26th April 2002, 13
nos.
v. Application of Basic IT Resources, 21-23 January 2003, 7 nos.
vi. Introduction to Basics of Retrieval & Creation of Scientific Databases,
23-25 February 2004, 22 nos.
vii. Database Creation with Emphasis on Biodiversity, 29-31 March 2004,
17 nos.
viii. Database Creation with Emphasis on Biodiversity 22nd 24th
February 2005, 22 nos.
ix. Computer Basics & Application in Bioinformatics (Internet &
Databases) April 18 - 20, 2005, 10 nos.
x. Database Creation & Internet in Biological Applications, February 06 -
10, 2006, 16 nos.
xi. Computer & Internet Applications in Bioresource Development, March 01 -
03, 2006, 14 nos.
xii. Applications in Bioinformatics, February 13-15, 2007, 29 nos.
xiii. Bioinformatics: Recent Trends in Sequence Analysis March 28-30, 2007,
31 nos.
xiv. Inferring Biological Relationships: A Bioinformatics Approach, November
27- December 1, 2007, 22 nos.

II) Workshop & Seminars
i. Hosted the DBT National Roving Seminar on Patenting in
Biotechnology on October 26, 2002.
ii. National workshop on Conservation and Sustainable Utilization of
Medicinal Plants of North-East India during May 27-28, 2004.

III) In-house Training & Resources
i. Services of providing access to Internet and Journal Abstracts
Subscribed.
ii. Young Scientist Workshop on Identification & Diagnosis of Parasites of
Biomedical and Zoonotic Importance 6th July 2000
iii. Young Scientist National Workshop on Water Quality Assessment Bio-
monitoring and Zooplankton Diversity (Zoology Department) 5th Dec
2001
iv. Training for NEHU Ministerial Administrative Staff - 19th February - 19th
March, 2002
v. Training for NEHU Ministerial Administrative Staff - 1st - 31st May,
2002, 3rd June - 2nd July, 2002
vi. Workshop and Interaction meeting on Mapping and Quantitative
Assessment of Geographic Distribution and Population Status of Plant
Resources of Eastern Himalayan Region dated April 17-18, 2007
vii. A lead talk on Eco-informatics in Conservation and Database
Management by Prof. K. N. Ganeshiah, UAS, GKVK, Bangalore on
April 18, 2007
viii. Organized EDUSAT Interaction for the North-East Region Vision
Document 2020 on August 10, 2007
ix. Lectures and hands on training in Refresher Courses in
254
Botany: October 21-23, 2000, September 25, 2001, November-
December 2007
Zoology: December 6, 2000, December 7, 2001, November 23-24,
2004, March 5-26, 2007, August 27-September 18, 2007
Political Science: E-governance and Basic Applications in IT
during December 2007
x. Regular training on awareness and familiarization of benefits of IT
imparted to faculty members, research scholars, College teachers &
students through regular training programmes.
xi. Taking Bioinformatics theory Classes and providing hands on practical
training of the same to the Post-graduate students of the Department of
Biotechnology and Bioinformatics of the university.

15. Impact shown by your Centre on the growth of biotechnology and allied
areas.
i. The Centre started functioning from November 1999 with a view to catering
to the needs of the scientific community in the far-flung northeastern region
of the country and to augment their research activities through information
inputs.
ii. The BIC at NEHU provides the scholars with latest information in their
respective fields and brings them closer to the rest of the world as far as
scientific advancements are concerned. The Centre is part of the National
Bioinformation Network and functions as an information base in various
areas of Biosciences.
iii. Bioinformatics Training programmes, which have always been an integral
part of the Centres activity and for which connoisseurs in the field are
always invited to act as resource persons, have greatly benefited the
students and researchers of the region who otherwise because of the
location could not attend such trainings elsewhere.
iv. Successful Database preparation and information resource development in
biological sciences and Computer assisted cutting edge research in
functional annotation of bio-molecules, thereby leading to emanation of
quite a good number of publications in peer reviewed journals.
v. The Centre at NEHU, Shillong has been inducted as one of the Examination
Centers for conducting the National Level Bioinformatics Certification Exam
(BINC), 2008 onwards,catering to the much needed facility for the aspirant
students from the north-eastern region of the country.

The areas of Functional genomics, proteomics, metabolomics, and
evolutionary bioinformatics and developing e-learning bioinformatics modules
will figure prominently in our list of items for research in future. Besides, the
ongoing activity of cataloguing the biodiversity informatics will continue. The
future of bioinformatics both in teaching and research at NEHU is highly
promising. The manpower development in the discipline in a rather neglected
region will be given top priority. The following teaching/research programmes
are envisaged;
A. Teaching Programmes
Advanced P.G. Diploma in Bioinformatics (18 months)
Certificate Courses (5 months)
255
Credit Course in Bioinformatics that can be offered to the Postgraduate
and Doctoral students of the University
B. Research Programmes
Plant Sciences
Developing Grid-based Platform for Quantitative Trait Loci Analysis with
Hi-Density Molecular Markers in Orchids of North-East India
Ecological Genomics of Orchids (of medicinal importance) specific to
North-East India & Modeling of Flowering Time Control and Circadian
Oscillator in Orchids
Animal Sciences
1. Bioinformatics and Health Care
- Database development on health issues specific to North-East India, with
special reference to Malaria, Thalassaemia, Malnutrition and Zoonoses of
worm origin.
- Nutritional Genomics, which has a major role to play in Health Care
Informatics, giving special emphasis on dietary guidelines.
- With reference to zoonoses of worm origin, consortium - based programmes
can be taken up by the Bioinformatics Centre at NEHU with Public-Private
Partnership (PPP) venture such as TCGA (An IGIB IMM Collaboration).
2. Major Bioinformatics Tools to be developed at the Centre
- Developing Eukaryotic Gene Prediction tools, Gene nomenclature,
functional characterization, genome browsing and genome database
development specific to worms and Insilico study of Paragonimus under
broader areas like Proteome analysis with a focus on revelation of gene
families and duplicated genes and Evolutionary Modeling and Phylogeny
Reconstruction.
256
Additional Details:

Name of the Coordinator: Prof. Pramod Tandon
Name of the Deputy Coordinator: Prof. Veena Tandon
Postal Address: Bioinformatics Centre
North-Eastern Hill University
Shillong 793 022
Phone Number: (0364) 255 0150/ 272 1242/ 272 2214/ 272 2244
Fax No.: (0364) 255 0150/ 255 0300
Email: bioinfo1@sancharnet.in; tandon1@sancharnet.in
Website: http://www.nehu.ac.in/bic
Name of Contact Person(s): Email:
Prof. Veena Tandon bicnehu@gmail.com; bioinfo1@sancharnet.in

257
Pondicherry University, Pondicherry
Coordinator : Dr. P.P. Mathur

The Centre for Bioinformatics in Pondicherry University was started as Sub
Distributed Information Centre of the Department of Biotechnology, Govt. of
India (DBT) in 1991. The mandate of the Centre was to provide biological
information to the end users. The Centre became a focal point for providing
various communication and computational facilities to the users from the
university and also from other institutions. The Centre provides training to
teachers and students of the university, affiliated colleges and other
institutions. The Centre has so far organized 24 training National level
programs. The Centre has periodically arranged lectures by many eminent
scientists working in the areas of bioinformatics and biotechnology. Several
professionals from Industry have also delivered lectures on the opportunities
and challenges in the sector of Bioinformatics.

The Centre has been offering an Advanced PG Diploma course in
Bioinformatics with financial support from Department of Biotechnology
(DBT), Govt. of India since 2001. The also offers a Ph.D program in
Bioinformatics. The Centre has started offering M.Sc. in Bioinformatics since
2007 which is funded by the University Grants Commission (UGC) under its
scheme of Innovative Program in Emerging Areas. The Centre has been
offering a 4-credit course in Bioinformatics since 1994 to the Masters students
of Life Sciences and Biotechnology.

In the past few years, the Centre has taken up research activities in the areas
of sequence analysis, molecular modeling, database development etc., and
several papers have been published in peer-reviewed national and
international journals.

Most of the past students have got placements in various leading / research
institutions and industries.

The Centre has been identified as a Centre for Excellence in Bioinformatics
Teaching and Research by the Department of Information Technology,
Ministry of Communication & Information Technology, New Delhi.
institution
The University has several departments and affiliated institutions which are
having major research activities in Biotechnology. Some of the important
areas are DNA Protein Interactions, X-ray Crystallography Macromolecular
(Proteins), Molecular Modeling / Simulation of Biomolecules for targeted Drug
Discovery, Database & Software Development and Development of
Bioinformatics Educational Materials
258
Plant and Animal Biotechnology
Faculty and non teaching positions have been advertised and two lecturers
have joined. The Centre started offering a Ph.D program in Bioinformatics.
The Centre started offering a Masters program in Bioinformatics (M.Sc) in
2007 which is funded by the University Grants Commission (UGC) under its
scheme of Innovative Program in Emerging Areas. The Centre has
undertaken several projects in the areas of Computational Genomics,
development of Database on Zinc Finger Proteins, Homology Modeling,
Molecular Docking and Computer-based Tutorial on Bioinformatics. The
Centre has conducted various training programmes in Bioinformatics and
arranged several invited lectures.
A. Computers and Communication facilty
Xeon Cluster Servers, Itanium-Email Server, AMD Opteron Server-DS
Modeling Server, Wipro Xeon@3.0 Ghz-Web Server, Silicon Graphics Fuel
Machine, Apple IMAC, HCL Laptops, HCL Pentium Core Duo/ Dual Core/
Pentium IV Workstations (55 nos.) Works on both Windows and Linux
Operating Systems.
The Centre has a dedicated 2 Mbps internet connectivity exclusively for the Centre
for Bioinformatics from Videsh Sanchar Nigam Limited, Pondicherry
The students have the modern computing facilities and round the clock internet
facility to meet their academic and research needs.
Insight II, Amber, DS Modeling suite, Autodock, Dock, Modeller, Gromos 96,
Whatif, EMBOSS, BioEdit, Phred, Consed, GeneScan, Statistica, Endnote,
C. Resources & Services
A separate website has been maintained by the Centre for Bioinformatics.
This website was designed in-house and hosted in the web server maintained
in the Centre, can be accessed at www.bicpu.edu.in. Information about
course, admissions, syllabus, seminar notifications & various opportunities for
traineeship/ studentship / JRF are updated periodically. Bioinformatics related
tools can be downloaded from the site

D. Databases & other information resources
Books
400 books (In addition to the books available in the Central Library)
Journals
Science, Nature, Scientific American, Bioinformatics & Computational
Biology, Briefings in Bioinformatics, Bioinformatics, Nature Structural Biology,
Nature Chemical Biology, Cell, Bioinformatics Trends, Current Science
259
Magazines
Linux for U, PC Quest, PC World
Access to E-Journals
Access to Science Direct, Access to EBSCO Databases
* All the above positions including the vacant posts of Reader and Technical
Assistant are already absorbed by the University
The Centre has been providing computational and internet facilities to the
faculty and students of the University and nearby institutions.
The Centre started an Advanced PG Diploma course in Bioinformatics with
financial support from Department of Biotechnology (DBT), Govt. of India from

Sl.
No.
Posts Sanctioned
Name of the
Employee

Area of
Specilization
Date of Joining
From To
1 Lecturer Dr. D. Sundar Bioinformatics,
Proteomics &
Genomics
June
2005
Continuing
2 Lecturer Dr. R. Krishna X-ray
Crystallography
(Proteins),
Molecular
Modeling
(Protein & DNA)
Dec,
2007
Continuing
3 Lecturer Dr. M . Suresh
Kumar
Structural
Studies on Viral
Proteins,
Promiscuity of
Antibodies,
Inhibitors for
Viral Proteases
Decemb
er, 2007
Continuing
4 Information Officer M. Sundara Mohan Computer
Networks,
Database
Management
March,
1992
Continuing
5 Sr. Technical
Assistant
Ms. V. Amouda Mathematics
Modeling and
Simulation
March
1992
Continuing
6 Computer Assistant Ms. D. Venmathi - Novemb
er 2007
Continuing

260
2001. The Centre started offering a Masters program in Bioinformatics (M.Sc)
in 2007 which is funded by the University Grants Commission (UGC) under its
scheme of Innovative Program in Emerging Areas. The also offers a Ph.D
program in Bioinformatics. The Centre has been offering a 4-credit course in
Bioinformatics since 1994 to the Masters students of Life Sciences and
Biotechnology. Most of the students of the previous batches have been
placed suitably. Some of the Institutions/ Industries who have recruited our
students are as follows
Industry Placements
HCL Infosystems, Pondicherry, Molecular Connections, Bangalore, Institute
of Bioinformatics, Bangalore, Protein Lounge, Bhubaneswar, Genemines,
Chenna, BIOBASE Databases Indian Pvt. Ltd., Bangalore
Teaching/ Research Placements
Pusan National University, South Korea, Sungkyunkwan University, South
Korea, University of Madras, Chennai, Central Sericulture Research &
Training Institute, Mysore, Institute of Microbial Technology Institute,
Chandigarh, Aravind Eye Hospital, Madurai, Indian Institute of Technology,
Chennai, Jawaharlal Nehru University, New Delhi

The Bioinformatics resources created and procured in the Centre has been
subjected to peer review and suggestions have been taken from various
experts in the field. The University has nominated a Committee with external
experts to monitor the teaching/ research programmes of the Centre.
The Centre completed the following projects during the year
Sl. No. Project
1.
Comparative sequence analysis & homology modelling
studies on factors involved in the rubber biosynthesis
in rubber plant Hevea brasiliensis & Parthenium
argentatum.
2.
A comparative homology modeling study on alcohol
dehydrogenase I enzyme in Oryza sativa indica and
Oryza sativa japonica
3.
Comparative genome analysis and molecular modelling
studies of Clostridium novyi with other Clostridium spp.
for the production pf phospholipase C.
4.
Crystal structure of putative dipeptidase form Pyrococcus
horikoshii OT3
5.
Molecular docking of lead anti-retroviral non-nucleoside
reverse transcriptase inhibitors (NNRTI) compounds to
HIV-I reverse transcriptase.
6.
Homology Modelling and Molecular Docking studies of
nsp2 protease of Chikunguniya virus.
7.
Structural Analysis of Green Fluorescent Proteins
261
EnZif : A tool for targeted Genome Engineering
EnZif-dB : A database of DNA binding proteins (more information available
in Biobytes-November 2007 issue)
Molecular Visualization and Homology Modeling tools
Educational Kit on Bioinformatics
Database of Genomic Information of Sequenced Bacteria
Kandavelou, K., Sundar, D and S. Chandrasegaran (2008). Custom-
designed molecular scissors for targeted manipulation of the plant and
mammalian genomes. Methods in Molecular Biology (in press).
Kandavelou, K., Sundar, D and S. Chandrasegaran (2008). Plasmids for
gene therapy. In: Plasmids: Current Research and Future Trends,
Georg Lipps (Ed.). Horizon Press, UK (in press).
Sundar, D (2008). An improved method for interrogation of DNA-protein
interactions. Proceedings of the International Conference on Trends in
Cellar and Molecular Biology, Jawaharlal Nehru University, New Delhi,
January 2008, p. 36.
Anmol J. Hemron, J. Muthukumaran and D. Sundar (2007). Comparative
modeling of cis_IIPS domain in cis-prenyl transferase from Hevea
brasiliensis. Protein Model Data Base (PMDB identifier : PM0075092
Shankar Prasad Kanaujia, Chellamuthu Vasuki Ranjani, Jeyaraman
Jeyakanthan, Seiki Baba, Lirong Chen, Zhi-Jie Liu, Bi-Cheng Wang,
Masami Nishida, Akio Ebihara, Akeo Shinkai, Seiki Kuramitsu, Yoshitsugu
Shiro, Kanagaraj Sekar, Shigeyuki Yokoyama. Crystallization and
preliminary crystallographic analysis of Molybdenum cofactor
biosynthesis protein C from Thermus thermophilus. Acta. Cryst. 2007,
F63, 27-29.
Shankar Prasad Kanaujia, Chellamuthu Vasuki Ranjani, Jeyaraman
Jeyakanthan, Seiki Baba, Akio Ebihara, Akeo Shinkai, Seiki Kuramitsu,
Yoshitsugu Shiro, Kanagaraj Sekar, Shigeyuki Yokoyama. Cloning,
expression, purification, crystallization and preliminary X-ray
crystallographic study of DHNA synthetase from Geobacillus
kaustophilus. Acta. Cryst. 2007, F63
Gowthaman, U., Jayakanthan, M. and Sundar, D (2007). Molecular
docking studies of DTNB and its related compounds to Protein disulphide
isomerase. Proceedings of the International Conference on Bioinformatics,
University of Hyderabad, Hyderabad, December 2007.
Sundar, D (2007). Engineering DNA-binding proteins for modification of
mammalian genomes. Proceedings of the International Conference on
Cellular and Molecular Bioengineering (ICCMB 2007), Nanyang,
Singapore, December 2007, p.56.
Sundar, D. (2007). Unraveling the supply from primary to secondary
carbon metabolism. Proceedings of the International Conference on Light
and Life, Hyderabad, India, August 2007, p.21.
262
Sundar, D. and A.R. Reddy (2008). Detection of a rapidly accumulating
50 kDa polypeptide and increased rubber accumulation in guayule under
low temperatures. (Submitted)
Jayakanthan, M. and Sundar, D. (2008). Computer Aided Drug Design for
H-Ras P
21
Mutant Protein: Molecular Docking of H-Ras P
21
Mutant Protein
with Ligand Molecules. (Submitted)
Anmol J. Hemron, J. Muthukumaran and Sundar, D. (2008). Comparative
protein modeling of CIS_IPPS domain in cis-prenyl transferase from
Hevea brasiliensis. (Submitted)

A number of sponsored research projects for the period 2006-2009 are
carried out by the faculty of the Centre. Some major funding agency include
the Department of Biotechnology (DBT), Department of Science and
Technology (DST), Department of Information Technology (DIT), Govt. of
India
(2006-2007)
National Seminar on Computations in Bioinformatics, February 14-16,
2007. No. of participants : 100
National Seminar on Applications of Bioinformatics in Genome
Research, February 13-15, 2008. No. of participants : 100 (Proposed)

The Centre started offering a Masters program in Bioinformatics (M.Sc) in
2007 which is funded by the University Grants Commission (UGC) under
its scheme of Innovative Program in Emerging Areas.
The Centre has been identified as a Centre for Excellence in
Bioinformatics Teaching and Research by the Department of Information
Technology, Ministry of Communication & Information Technology, New
Delhi.
The Centre has been able to achieve many targets towards training and
manpower development in bioinformatics
The Centre has been able to advertise positions and recruit a few staff
members
Completed projects in the areas of comparative genomics, homology
modeling, molecular docking and Computer Based Tutorial on
Bioinformatics
The Centre has created a big impact in Pondicherry University and
surrounding Institutions towards teaching and research in Bioinformatics.
263
Our Centre is collaborating with many other institutions like Vector Control
Research Centre, IICT, Hyderabad and Industries.
A CD on free software on Internet has been prepared and is available for
distribution
Conducted various training programmes in Bioinformatics and arranged
several invited lectures
The Centre has helped various Universities/ Colleges for curriculum
development & training

Strengthening of R&D activities in the areas of comparative genomics,
homology modeling, molecular docking, development of Databases
Computational Analysis of Rubber biosynthetic Genes from different plant
species
Development of Database on Zinc Finger Proteins
Development of teaching aids in Bioinformatics
Strengthening and expansion of teaching and research programme

Name of the Coordinator: Dr. P.P. Mathur
Postal Address: Centre for Bioinformatics, Pondicherry University, Pondicherry
605 014
Phone Number: +91-413-2655212 Fax No.: +91-413-2655211
Email : bicpu2001@yahoo.co.in
Website : www.bicpu.edu.in

Name of Contact Person(s): Dr. P.P. Mathur
Email: ppmathur@yahoo.com ; bicpu2001@yahoo.co.in
264
Punjab Agricultural University, Ludhiana
Coordinator : Dr.(Mrs.) Parveen Chhuneja

Developed a database Pedigree Retrieval cum Morphological Diversity in
Wheat Version 1.0
Developed an online database of cultivars of wheat, rice, cotton, maize,
pulses and fodders released by PAU since 1960
Developed a database of molecular markers of wheat, Barley and Triticale
consisting of 3160 markers
Provided Leased Line Internet connectivity of 1 Mbps speed to the
researchers
Provided various information retrieval services both offline and online to the
students, research scholars and the faculty
Provided services for standardization of the mapping and the statistical
software ( IRRISTAT, J/QTL, R/QTL, Map Maker, Map Manager QTX,
ICImapping, QTLnetwok etc.) for the use of research workers
Developed an online database of Publications of the faculty of Plant Breeding,
Genetics & Biotechnology.

institution
The major emphasis of Agbiotech Center of Excellence at Punjab
Agricultural University is the germplasm enhancement in field crops using wide
hybridization, molecular marker and transgenic technology.
Introgression and mapping of new alien disease resistance genes and
productivity traits using molecular markers and molecular cytogenetic
techniques in wheat and rice
Mapping of QTLs for disease resistance, quality and domestication traits in
wheat
Pyramiding of rust resistance genes in wheat and bacterial blight resistance
genes in rice using marker assisted selection (MAS)
Improving architecture of Basmati rices using MAS
Isolation of new genes
Developing transgenic plants in rice and sugarcane

3. Area of Specialization of the centre : Bioinformatics & Agriculture
Developed an online database of cultivars of wheat, rice, cotton, maize,
pulses and fodders released by PAU since 1960.
Developed a database of molecular markers of wheat, Barley and Triticale
consisting of 3160 markers.
Standardization of the scientific softwares (IRRISTAT, J/QTL, R/QTL, Map
Maker, Map Manager QTX, ICImapping, QTLnetwok etc.) for the use of
research workers.
Maintenance of Local Area Network of (approx. 200 nodes) in the Department
of Plant Breeding, Genetics & Biotechnology.
Maintenance and updating the Sub-Distributed Information Centre and
university websites.
265
Computing and networking facilities to the students, research scholars and
the faculty.
Conducting training on the Bioinformatics: Basics and its use in gene
cloning for molecular biologists and biotechnologists of the university.
2) Computer & Communication facility
Table : List of computer and communication facilities available in the
Bioinformatics Centre

Item Total No. Item Total No.
Lease Line Internet
connectivity
1 Mbps Scanner 1
Computer System (PC) 18 Photo copier 2
Laptop (IBM) 1 Network Switch 3
Server 2 UPS Online 3 kva 2
LCD Projector 1 UPS Online 1 kva 1
Printer Laserjet 2 Computer Table 18
Printer Deskjet 1 Furniture Chairs 18
Dot Matrix Printer 1 Filing Cabinets 2
Book Case 1
3) Scientific Software packages
Bio-Chemical Interactions
J/QTL (QTL mapping)
QTX Map Manager (QTL
mapping)
Map Maker (mapping)
ICIMaping (QTL mapping)
QTLnetwork (QTL interactions)
Primer 3 (primer design)
Glimmer M
NTSYS 2.0 (diversity analysis)
IRRISTAT (statistical analysis)
SPSS Statistical Software
(statistical analysis)
Gencheck (sequence analysis)
4) Databases & other information resources
IRIS - International Rice Information System
IWIS - International Wheat Information System
ICIS- International Crop Information System
Rice Genome Sequence from TIGR Database


Sl.
No.
Name of the
Staff
Designation Working Since Absorption
status
1. Parminderdeep
Singh Mangat
Information
Officer
1
st
Dec.2006 till
date
Not absorbed
2. Jasbir Singh
Sandhu
Bioinformatic
Assistant
24
th
Nov.2006 till
date
Not absorbed
3. Gurbax Singh Data Entry
Operator
24
th
Dec.2001till
date
Not absorbed

266
Internet connectivity and computing services provided to faculty, students and
research workers of various departments of the university

Standardization of the scientific softwares (IRRISTAT, J/QTL, R/QTL, Map
Maker, Map Manager QTX, ICImapping, QTLnetwok etc.) for the use of
research workers
Searching and downloading the scientific softwares for making these
softwares available to research workers
Maintenance of Local Area Network of (approx. 200 nodes) Department of
Plant Breeding, Genetics & Biotechnology
Facilities of typing, printing, scanning and photocopying etc., are provided in
the Bioinformatics Centre, LCD, Laptop facility extended during workshops
held in different departments of the university and during the seminars.

M.Sc & Ph.D. courses in Biotechnology will commence from next
academic session

Research workers are utilizing Bioinformatics tools in their research
endeavors extensively

Providing help in the use of various mapping softwares and information
retrieval from public domains to the faculty of Genetics and Biotechnology
of PAU, Ludhiana.

Pedigree Retrieval cum Morphological Diversity in Wheat Version 1.0
Online Database of varieties of wheat, rice, cotton, maize, pulses and fodders
released by PAU since 1960
Molecular marker database of wheat, Barley and Triticale consisting of 3160
markers
Online database of Publications of the faculty of Plant Breeding, Genetics &
Biotechnology
Developed website of Sub-DIC PAU, Ludhiana (www.bicpau.org)
Online database of Bio-Tools
12. Papers published or presented in the conferences using Bioinformatics
support
Cheema K K, N S Bains, G S Mangat, A Das, D S Brar, G S Khush, and K Singh
(2007) Introgression of quantitative trait loci for improved productivity from
Oryza rufipogon into O. sativa. Euphytica (Accepted)
Chhuneja P, S Kaur, R K Goel and H S Dhaliwal (2006) Mapping of leaf rust and
stripe rust resistance QTLs in bread wheat X synthetic RIL population under
Indian field conditions. Indian J. Crop Science 1: 49-54.
Chhuneja P, S Kaur, T Garg, MGhai, S Kaur, M. Prashar,

RK Goel, NS Bains, B
Keller, HS Dhaliwal and Kuldeep Singh (2007) Mapping of adult plant stripe
rust resistance genes in diploid A genome wheat species and their transfer to
bread wheat. Theor Appl Genet (published online)
Dhillon N P S, Ranjana, K Singh, Eduardo, I Monforte, A J Pitrat, M Singh, P P
267
and N K Dhillon (2007) Diversity among landraces of Indian snapmelon
(Cucumis melo var. momordica). Genetic Resources and Crop Evolution DOI
10.1007/s10722-006-9108-2
Garg M, H S Dhaliwal, P Chhuneja, D Kumar, Quan-Wen Dou, H Elamein, H
Tanaka and H Tsujimoto (2007) Negative effect of chromosome 1A on bread
making quality shown by modification of 1D addition in durum wheat (Triticum
durum). Theor. Appl. Genet. 114:1141-1150.
Garg T, K Singh, M Ahuja, J S Sidhu, H S Dhaliwal and P Chhuneja (2007)
Validation of the molecular markers linked to a major pre-harvest sprouting
tolerance QTL mapped on wheat chromosome 3A. Indian J. Crop Science 2:
223-225.
Juneja S, A Das, S Sharma, B Patra, Y Vilkal, S Joshi, T S Bharaj, J S Sidhu
and K Singh (2006) Genetic diversity in a set of 127 accessions of wild rice,
Oryza nivara Sharma et Shastry as estimated using microsatellite markers.
Current Science 91: 1079-85
Kuraparthy V, P Chhuneja, H S Dhaliwal, S Kaur, R L Bowden and B S Gill
(2007) Characterization and mapping of cryptic alien introgression from
Aegilops geniculata with novel leaf rust and stripe rust resistance genes Lr57
and Yr40 in wheat. Theor. Appl. Genet. 114: 1379-1389.
Kuraparthy V, S Sood, P Chhuneja, H S Dhaliwal and B S Gill (2007)
Identification and mapping of tiller inhibition gene (tin3) in wheat. Theor. Appl.
Genet. 114:285-294.
Kuraparthy, V, S Sood, P Chhuneja, H S Dhaliwal, S Kaur, R L Bowden and B S
Gill (2007) A cryptic wheat-Aegilops triuncialis translocation with leaf rust
resistance gene Lr58. Crop Science (accepted).
Singh K, M Ghai, M Garg, P Chhuneja, P Kaur, T Schnurbusch, B Keller and H S
Dhaliwal (2007) An integrated molecular linkage map of diploid wheat using a
Triticum boeoticum X T. monococcum RIL population. Theor. Appl. Genet.
115: 301-312

Designing primers for mapping of genes for biotic and abiotic stresses
Comparative genomics for searching DNA sequences for heat and
drought tolerance in wheat & rice

A number of trainings have been conducted by Bioinformatics Centre for
making researchers aware of computer technology, genomic and proteomics.

Table List of trainings conducted by Bioinformatics Centre
Title of the Training Date
No. of
participants
1. Introduction to Computer Basics,
Operating Systems and their
Applications in Agriculture/Life-Sciences
October
16-18, 2001
17
2. Bioinformatics for Agricultural Sciences February
20-22, 2002
21
3. Bioinformatics Tools For Nucleic acid January 17
268
and Protein Sequence analysis 29-31, 2003
4. Internet Access For Biotechnology
Information Tools and Sources
March
25-27, 2003
17
5. Genomics & Proteomics in
Biotechnology
October
29-31, 2003
15
6. Bioinformatics tools in immunology March
16-18, 2004
15
7. Bioinformatics & Molecular Approaches
for Data Mining
December
13-15, 2004
14
8. Bioinformatics & Biotechnology December
14-16,2005
13
9. Bioinformatics: Basis & its uses in gene
cloning
December
11-14, 2007
30

areas
The Bioinformatics center has made possible the availability of 24 h
internet connectivity to the faculty and research fellows of the department which
has made possible use of Bioinformatics tools for searching and downloading
DNA sequences from NCBI and TIGR sites.

Intervention through Bioinformatics tools for utilizing the information
generated in rice and wheat genomics.
Elucidating the structure of putative novel alien genes using rice genome
sequence information
Searching for DNA sequences for heat and drought tolerance using
comparative genomics
Conducting trainings on the use of Bioinformatics in the field of genomics
Providing computing and networking facilities to the agricultural scientists
Developing a database for wild wheat & rice germplasm

Additional Details:
Name of the Coordinator : Dr. S.C. Sharma ( Feb. 2000-Oct. 2006)
Dr.(Mrs.) Parveen Chhuneja (Nov. 2006 till
date)
Postal Address : Bioinformatics Centre, Department of Plant
Breeding, Genetics and Biotechnology,
Punjab Agricultural University, Ludhiana.
PIN 141004

Phone Number
0161-2411774
Email
subdicpau@yahoo.com
Website
http://www.bicpau.org
269

Name of Contact Person:

Email:
Dr. Parveen Chhuneja

subdicpau@yahoo.com
pchhuneja@rediffmail.com

270
Rajiv Gandhi Centre for Biotechnology, Trivandrum
Coordinator : Dr. Sathish Mundayoor

The Distributed Information Sub Centre was awarded to RGCB when the
institute was in its infancy. The facility became the lifeline of RGCB and has
played a major role in its growth. The initial grant was used to procure
Computers, scanner, printers etc along with a server and a net connection.
Totally, eighteen computers have been purchased for the DISC, which
includes an SGI-Octane Machine, three SUN workstations, a Pentium Dual
Core high performance system and a Wipro Net Power Server. These were
used to provide networking and Internet facilities for all the RGCB members.
All the three personnel, viz. Information Officer, Technical Assistant and Data
Entry Operator were appointed. Eleven databases, three web servers and ten
softwares have been developed. Few databases are under development. We
are maintaining a mail server, which is accessible to all members in RGCB.
All students as well as technical staff were given basic level training in linux
platform and all routinely used bioinformatics software packages. The
bioinformatics software packages are maintained as a central facility for use
of internal as well as external students for various databases, sequence and
other analysis. Insight II procured by us was used by our students for various
molecular modeling predictions as a part of their research activities. Since its
establishment the DISC has successfully conducted three National level
seminars on Bioinformatics, in which several eminent speakers from various
research institutions/ universities have delivered their talk on frontier areas of
bioinformatics. We also organize regular training programmes. Internet
connectivity to CDAC Terascale Supercomputing Facility (CSTF) was
obtained in order to run highend bioinformatics applications.

institution
The core research teams are currently being grouped under (1) Molecular
Medicine and Cancer (2) Molecular Reproduction (3) Plant Molecular Biology
(4) Molecular Microbiology (5) Neuro and Stem Cell biology (6) Medical
Demography

Medical and Plant Bioinformatics
Softwares and databases development to support research activities in
RGCB
Molecular modeling and simulation studies to support various research
activities of groups in RGCB.
Hands-on training in Molecular Modeling for RGCB research students
Project guidance and hands-on training for B.Tech and M.Sc students
from various institutions and universities.

271
- Ingram Micro MagixTM PC 12 No
- Wipro NetPower Server 1 No
- SunBlade Workstation- 3 Nos.
- SGI-Octane Workstation 1No
- Pentium Dual Core 1 No
- 512Kbps internet connection.

- GCG Package version 11.0 (Commercial)
- EndNote v 5.0 (Commercial)
- Free/Open Softwares:- EMBOSS, Autodock.4, WHATIF,
MODELLER Clustal W, Phylip, Cn3D, Rasmol, HMMR, Staden
Package, R-statistical package, GeneDoc, Phred, Phrap &
Consed package, FTDOCK, PATCHDOCK, GROMACS-3.3,
PyMol-0.9.

- Agricola database
- Biotech Citation Index
- Current Contents Connect Life Sciences
- CD database on Indian Patents
- GENE DCFER and SEAPATH databases

absorption status)

working
K.C.
Sivakumar
(Not
Absorbed)
Information Officer Computational Biology,
Molecular Mechanics
26-08-04 to
present
date
C.
Durgaprasad
(Not Absorbed)
Technical
Assistant
Networking, PC
Maintenance
14-11-02 to
present
date
Amal. V
(Not Absorbed)
Data Entry
Operator
Web Site Design,
Documentation
02-05-05 to
present
date
- Internet facility
- Mail Server
- Network establishment and maintenance
- Biotech Citations Databases and repositories.
- Impar training to Studentship and Traineeship
- Project Guidance to MSc/B.tech Bioinformatics students
- Facilities for Sequence analysis and Molecular modeling
272

8. Educational activities with details of placement: N/A
Conformation Dynamics of Isoniazid and rifampicin bound to wild and mutant
KATG, INHA and RPOB from Multidrug resistant Mycobacterium tuberculosis
evidence by in vitro binding studies.
Molecular Simulation and Interaction Studies of HAD like Phosphatase
(Rv3813c) - A Conserved Hypothetical Protein from Mycobacterium
tuberculosis H37Rv-evidence by in vitro protein interaction studies.
Induced fit DNA recognition in a cisplatin binding groove by carbohydrazone:
structural fluctuations investigated through molecular dynamics simulations
evidence by Cytotoxicity assay and FACScan
In silico docking and dynamics of plumbagin acts through death receptor
mediated pathway in brca1 blocked ovarian cancer cells - evidence by
suppression subtractive hybridization (ssh) and microarray
New dimensions in function of fibulin, a secretory protein at embryo
implantation by molecular modeling and protein-protein interaction studies
evidence by immunoprecipitation, immunocytochemistry and western blot.
DOCK-180, a importin like molecule-plausible route for nuclear entry for
transcription factors by molecular modeling and protein-protein interaction
studies evidence by immunoprecipitation and MALDI-TOF.

10. Collaborative works/ initiatives : Nil
1. Neuro-Medicinal plants Database: A database on important neuro active
medicinal plants. The database contain information on: the genus and
species names, the common English, description of the plants, medicinal
use in literature and by the communities, preparation in literature and
communities, previous chemical and biological studies carried out etc.
2. Primer Inventory Database: A database to maintain primer inventory
information in a typical biotechnology lab. The database contains
information on: primer details, provider data, user details, storage
information, quantity details and order information etc; with advanced
search facility.
3. Psychiatric Patient Management System: This database is being
developed to assist doctors/researchers to diagnose patients with
psychiatric diseases like schizophrenia using the international diagnosis
standards such as BPRS, PANSS, AIMS etc.
4. TBCaseSheet Database: This database is developed as a case sheet
pro-forma of patients under going pulmonary tuberculosis treatment. It will
assist the research scholars in Mycobacterial research group to conduct a
survey on pulmonary tuberculosis in kerala.
5. Chemcomp Tool: A Chemical compound comparison tool to find pattern
searching between two chemical compounds in SMILES/SMARTS format.
The tool can also be used to screen a chemical dataset. Perl-Tk is used to
build the tool.
6. Chemistry 3D-Builder: A Perl-Tk GUI to generate 3D information of a
chemical compound given in SMILES/SMARTS format.

273
- Thasni K.A, Sivakumar K .C and Priya Srinivas A paper entitled
"Mechanism of action of plumbagin in brca1 blocked ovarian cancer cells:
an analysis by suppression subtractive hybridization (ssh) and micro
array" was presented on Proceedings of the 19th Kerala Science
Congress 29-31, January 27-29, 2007

- Anil Kumar A K, Sivakumar K C, Madhavi Latha G K, Ajay Kumar, Sathish
Mundayoor, Prevalence of KatG Ser315Thr Substitution and
Conformation Dynamics of Isoniazid binding among Isoniazid resistant
Mycobacterium tuberculosis isolates from Kerala, India, presented at
International Conference on New Horizons in Biotechnology, NIIST,
Trivandrum, November 26-29, 2007. (submitted to a special issue of
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY)

Please refer paragraph no: 9
In-house hands-on training in Molecular Modeling was conducted for 3 days
on 15th, 16th and 19
th
of November. 45 Research Scholars have participated
in the programe.

- Number of papers published: 1
- Number of papers published with the support of centre: 3
- Centre provides bioinformatics research and application to research
scholars in RGCB. It supports students from neighboring institutions by
providing hands-on training and allowing them to use bioinformatics
infrastructure facility. Around 30 research scholars in RGCB have utilized
this facility.
- Project Guidance and hands-on training in bioinformatics tools and its
application was given to a total of 36 MSc/B.tech students from various
institutions/ universities. Hands-on training was given to 70 internal and 16
external students.
- Databases developed: 11
- Softwares developed: 10
- Centre undertakes email server maintenance, network support for RGCB.

- Development of databases and softwares relevant to RGCB research
- Research and development in Bioinformatics.
- Human Resource Development in Bioinformatics
274

Additional Details:
Name of the Coordinator: Dr. Sathish Mundayoor
Postal Address: Rajiv Gandhi Centre for Biotechnology, Thycaud PO,
Poojappura, Thiruvananthapuram - 695 014, Kerala, India.
Phone Number: +91-0471-2342315 Mobile:
09249981969
Email: smundayoor@rgcb.res.in, sathish.mundayoor@gmail.com
Website: http://www.rgcb.res.in

Name of Contact Person(s): Sivakumar.K.C
Email: sivakumar@rgcb.res.in, sivakumar.kc@gmail.com

275
State Council of Science & Technology for Sikkim
Coordinator: B.C.Basistha

Sikkim Bioinformatics Centre in the capacity of Distributed Information Sub-
Centre (DISC) under Sikkim State Council of Science and Technology,
Department of Science and Technology was established in the year 2001. The
Centre actively involves in collection of information on various biological
resources, retrieval of biological information and creation and management of
databases. The centre serves as an Information Centre for providing in
formations on biological resources to the researchers and scholars. The centre
also aims in keeping the scientific fraternity abreast with the latest
biotechnological advancement and also aims in inculcating the scientific
temperament amongst the scholars.
The infrastructure of the centre is kept on strengthening with the latest
equipments. 512 Kbps leased line internet connectivity has also been established
in addition to previously used RF Antenna Internet connectivity provided by the
State National Informatics Centre. A new building for Science and Technology in
addition to the already existing building is also being constructed to provide
better infrastructure facility.

institution

Research activities are being carried out in the field of tissue culture,
Vermicomposting and Frankial Biotechnology. Micro-propagation of Cymbidium
orchid is carried out on regular basis. Research activities on medicinal and
aromatic plants like Geranium (Pelarrgonium graviolense), Asparagus racemose
(Kurilo), Patchouli (Pogostemom cablin), and Podophyllum are also being carried
out.
Awareness programs through trainings, workshops and seminars are
conducted at from time to time, IPR, Medicinal plants.

Tissue culture, Bioinformatics, Database Management System, Medicinal
plants and IPR:
.
The XVIIIth Annual BTISnet Coordinators meet sponsored by
Department of Biotechnology, GOI was held successfully at Sikkim at
Chintan Bhavan on 3
rd
and 4
th
of February 2007. More than hundred
participants had taken part in the Meet. It was the first Coordinators
meet held in the North East.

From 10
th
September 2006 to 16
th
September 2006 Data Entry
Operator along with the Assistant Scientific Officer toured West Sikkim
(Kyongsla Alpine Sanctuary, Changu lake and vicinity, Gnathang,
North Bengal University & Kalimgpong) for photographic
documentation of medicinal and aromatic plants.
276
Two days training program on Creation and Management of Biological
Database was held on 7/11/2006 and 8/11/2006. Scientists, lecturers
and researchers attended the training program.
Three days training program on Introduction and Scope of
Computational Biology was held from 3/12/2007 to 5/12/2007.
Science graduates, post graduates, research scholars, lecturers and
unemployed science (graduates and post graduates) youth were the
target groups. Twenty five trainees were trained in the training
program.
Animation of biological processes (cell division, protein synthesis, DNA
replication) are developed using Flash to help the scholars/students to
understand the processes in a pragmatic approach.
Timely release of the scientific news letter Bio Gyan is also done by
the centre to make the students and researchers aware of the latest
techniques in Biotechnology and Bioinformatics and to inculcate a
scientific temperament amongst the students.
The website of the Centre along with the Departments is maintained by
the Bioinformatics centre.

The Centre is equipped with a dual processor server, P-4 PCs, Two Laptops,
CD writer, Scanner, 5100C, DeskJet 810 C and a Xerox machine.
Procurement of more PCs is under process.The centre has 24 hours internet
connectivity provided by the State National Informatics Centre through RF
Antenna along with 512 Kbps leased line internet connectivity provided by
Bharat Sanchar Nigam Ltd.
Scientific Software packages:
Norton antivirus 2006, AVG 7.5, trend Micro Neat suite, PC-illin, Micro media
Flash 8 professional, Dream weaver 8.
The centre has developed database on bio resources of Sikkim Database on
450 species of orchids, 36 species of Rhododendron, and 200 species of
medicinal plants has been prepared which are available in CD ROM and shall
be launched in website.

Name of the
Staff
Design
ation
Specialization Period of
Working
Absorptio
n Status
Mrs. Rabina
Gurung
I.O Biotechnology Three
years & six
months
Co-
Terminus
Mr. Bikram Rai T.A Computer Two Years Co-
Terminus
Mr. Laydong
Lepcha
D.E.O Zoology Three
years &
four
Co-
Terminus
277
months
Mr. Prakash
Sharma
D.E.O Botany One year
six months
Co-
Terminus

The centre acts as an information centre for providing information on
various bio resources of Sikkim.
The Centre Library with a good collection of references is used by
scholars and researchers.
Free internet facility is provided to the users for searching the biological in
formations.
Prepares animations on various biological processes like protein synthesis
for better understanding the process.
Student ship is provided to the research scholars undertaking project on
Biotechnology and Bioinformatics.

The centre supports scholars pursuing courses in Bioinformatics and
Biotechnology.

Trainings are being conducted at regular intervals; number of trainee attending
the training programs is increasing every year and positive response is received
from the trainees.

Collaborative works with Sikkim Government College in terms of providing
computer, internet and library facilities. Collaborative works with North Bengal
University, G. B. Pant Institute, Botanical survey of India is being carried out.

Database on Orchids, Rhododendrons, Medicinal Plants of Sikkim Himalayas.
Animation on cell division, protein synthesis etc developed using Flash.

The centre has been categorized under Environment and Biodiversity and
hence takes the initiative to prepare database on various bio resources of Sikkim
Himalayas and conducts workshops and trainings on Bioinformatics and
Biotechnology. Encourages science graduates, post graduate students and
research scholars to take up projects in the field of bioinformatics through
studentships.

278
Three days training program on Introduction and Scope of Computational
Biology was held from 3/12/2007 to 5/12/2007. Science graduates, post
graduates, research scholars, lecturers and unemployed science (graduates and
post graduates) youth were the target groups. Twenty five trainees were trained
in the training program.

allied areas.

The Bioinformatics Centre, Sikkim plays a leading role in introducing the latest
Biotechnological advancements and Bioinformatics to the researchers through
trainings, workshops and seminars. Patent in Biotechnology is another aspect of
key interest. The centre helps the research scholars by providing informations,
library and internet facilities. validating the growing activities of the centre and
with more and more research scholars pouring in for facilities of the centre, up
gradation of the centre from Distributed Information Sub centre to Distributed
information Centre has been made by the centre to the DBT, GOI.

To bridge the communication gap between the scientific fraternity the
centre has taken up the task of preparation of database on profile of
scientific community of Sikkim.
Preparation of database on indigenous / traditional knowledge and local
health systems (Amjis, Vaids, Bumthing, Phedangba, Jhakri, etc) of
Sikkim.
Preparation of Annual working calendar of the centre to streamline the
activities of the centre.
Preparation of Software on Chemical Inventory Automation and Library
automation.
Database on Profile of Women scientists working in various fields of
Sikkim.
Further up gradation of already prepared databases, website and creation
of databases on various bio resources of Sikkim. Up gradation of library
with more reference books and journals.
To conduct more no of workshops and trainings on Bioinformatics and
Biotechnology. Training on Environment Genomic and Biodiversity shall
be conducted in the month of January 2008.

Additional Details: Shri M. L. Arrawatia, IFS
Member Secretary
Sikkim State council of Science and
Technology
Department of Science &
Technology,
Development Area
Gangtok, Sikkim-737101
279

Name of the Coordinator: Shri. B.C.Basistha

Postal Address: Sikkim State council of Science and
Technology
Department of Science &
Technology,
Development Area
Gangtok, Sikkim-737101
Phone Number: 03592-228370 Mobile: 09434109894
Email: bits_skm@yahoo.com www.dstsikkim.gov.in/disc.htm
Name of Contact Person: Shri B.C.Basistha
Email: shobar_99@hotmail.com

280
T. M. Bhagalpur University, Bhagalpur
Coordinator : Dr. R.P.Upadhayay

1. Summary of the progress made by the Centre from its inspection
The Sub-DIC University Centre of Bioinformatics, T.M.Bhagalpur University was
established in the Oct.05. Since its inception the Centre has developed good
infrastructure in the form of three Servers (Mail, Database & Firewall), 15
Computers and other communication equipments. The Sub-DIC has procured
various scientific softwares like Windows Server 2003, MS-Office 2000, SQL
Server 2000, Borland Turbo C++ Suite, Visual Studio, Emboss, EXOME Blast,
EXOME & EXOME ED etc. The Centre is providing the facilities for downloading
scientific literature and also to access various online biological databases to
research scholars and students in the Centre. So far, about 150 users comprising
of teachers, staffs and students of T.M. Bhagalpur University have availed the
services of the Centre. The centre is having 512 kbps BSNL Broadband
connectivity for Internet. The Center has published a book on "Emerging Fields in
Bioinformatics" which was released on 9th April'07 by the Hon'ble Chancellor of
Bihar. The database of "Katarni" cultivar of rice has been prepared which will be
beneficial for the socio-economic empowerment of the farmers and will also help
the researchers in improving of this and other cultivars of rice. The Centre is
engaged in preparation of one another database on "Paharia" (a primitive tribal
community of Dravidian origin) with the objective to identify the genetic reasons
for the gradual decrease in the population. The centre has started regular
classes on Computer Application and Bioinformatics for the Post and Under
Graduate students of Biotechnology. The center is acting as an integrated
information resource on all aspects of Biotechnology research, Molecular
Biological data such as Gene Bank, Nucleic Acids and Protein Sequences etc.,
are accessible over the network from worldwide resources in molecular biology.
institution :
A. Genomics
Cytogenetic studies of selected plant species.
Genetic improvement in some selected crop and ornamental plant
species.
Damage repair of DNA in animal system.
Gene sequencing of some rare plants (DBT Project).
B. Dynamics of Genomics & proteomics
General protein finger printing and isozyme polymorphism
Dynamics of genes and proteins.
The major activities of the centre are as follows:
One book on Emerging Fields in Bioinformatics was published by the
Centre.
The database of "Katarni" cultivar of rice is being prepared and it will be
beneficial for the socio-economic empowerment of the farmers and will also
help the researchers in improving of this and other cultivar of rice.
281
Biochemical and cytological study of "Katarni" cultivar of rice is almost
complete and results are encouraging enough to continue the research on
katarni.
Another database on "Paharia" (a primitive tribal community of Dravidian
origin) residing in and around the Rajmahal Hills of Santhal Pargana near to
Bhagalpur District is being prepared with the objective to identify the genetic
reasons for the gradual decrease in the population which will certainly help in
conserving the gene pool as well as the population of this aboriginal tribal
community.
Imparted regular theory and practical classes to the M.Sc. Biotechnology
students on Computer Applications & Bioinformatics.
A Bioinformatics club has been established where teachers, researchers and
students sits once in month and extent maximum utilization of the resources
available at Bioinformatics Centre. The club thus provides a platform for
collaborative scientific research work.
The Centre is assisting faculties and students from neighboring departments
and college/Institutions in updating their knowledge through different
databases / software available in the centre and also providing practical
training in Computer based applications, software analysis, computational
methods etc to Doctoral and Post graduate students.

Server: IBM Server X Series (260, 236, 226) (Tower) with 17 CRT
Monitor
12 clients workstation: IBM Think Centre with 17 TFT monitor(2), 15
TFT monitor(3), 17CRT Monitor(7)
One Laptop: IBM ThinkPad Intel P-M Processor 1.66 Hz.
Networking Equipments:
Modem: One External,
Internet Connection: 512 kbps BSNL Broadband Connectivity
Power Supply:
One SAMTEK 5 KVA Online UPS, One ELNOVA 2KVA Online UPS (2
hrs backup), Twelve ELNOVA UPS 600 VA (15 min. backup)
Printer:
One Xerox color laser Printer phaser 6100, One Xerox Mono Network
Laser Printer 3500DN, One Xerox Photocopier 5821 with star stabilizer

Exome, Exome Blast, Exome ED, Widows 2003 Server with xp clients,
Red Hat Linux 9.0, Oracle 9i, Rasmol 2.6, Embosswin 0.8,
Swisspdbviewer, Gram, Autodock, Make2DB

C. Databases and other Information resources
100 books covering various fields of bioinformatics including genomics,
proteomics, structural bioinformatics, drug designing and computational
biology etc.

282

Name Designation Area of Specialization Period of working
Dr. R.P.Upadhaya Coordinator Molecular Biology since 1-11-2005
Kumari Vandana Information Officer* Bioinformatics since 03-7-2006
Er. Rakesh Ranjan Technical Assistant* Statistics & Comp. Appl. since 22-6-2006
Mr. Saket Vinayak Data Entry Operator* Comp. Appl. & Hardware since 28-6-2006

* The university has approached State Government for permanent absorption of
manpower within the University.

7. Types of Services provided:
Use of databases and software packages required by research scholars
and Post graduate students.
Internet access and Email facilities are provided to the faculty, staff,
scholars and students of University.
Assisted faculties and students from neighboring departments and
college/Institutions in updating their knowledge through different
databases / software available in the centre.
Provided practical training in Computer based applications, software
analysis, computational methods etc to Doctoral and Post graduate
students.
Our team can assist any progressive organization / institute in developing,
integrating and maintaining valuable biological data so that it can be
accessible in a safe and comfortable manner.

8. Education activity with details of placement:
P.G. Diploma in Bioinformatics will begin from this academic session.

To be taken care of.

Collaborative works are primarily in the area of Biotechnology thus a
Bioinformatics club has been established where teachers, researchers and
students extent maximum utilization of the resources available at
Bioinformatics Centre. The club thus provides a platform for collaborative
scientific research work. Such collaborative work in Bioinformatics needs to
be further promoted at this Centre. We are preparing a database on Euryale
Ferox with the collaboration of National Research Centre for Makhana,
Darbhanga Bihar.

11. Databases / Sortware packages developed:
To cater to the regional and national needs, the centre has developed a
database on Katarni a local race of Oryza sative which is famous for its
aroma and fineness.

12. Papers published or presented in the conferences with referece:
283
Upadhyay R.P. & Singh Vandana Bioinforamtics: a pursuit of
Environmental Management International Symposium on Recent
advances in contemporary Biology, Environmental issues & sustainable
development page-70, S.K.University, Dumka September 2007.
Upadhyay R.P. & Singh Vandana Biomarkers in Cancer communicated
in Journal Bioinforamtika.
Upadhyay R.P. & Pan T.K. Database storage of Cyto-taxonomic
assessment and genetic improvement and conservation of germplasms of
Reiniwardtia Spp. (Linaceae)National Symposium on Germplasm
evaluation : present trends page-136, Punjabi University, Patiala January
2006.
Upadhyay R.P. & Pan T.K. Collection, conservation, evaluation and
preparation of Database of Germplasms of Bamboos from states of Bihar
and Jharkhand National Symposium on Germplasm evaluation : present
trends page-137, Punjabi University, Patiala January 2006.

13. Initiation of R & D activities in Bioinformatics:
Bioinformatics related problems are regularly given to M.Sc.
Biotechnology students for their work.
Near Bhagalpur, a primitive tribal community of Dravidian origin called
Paharias. residing in and around the Rajmahal Hills of Santhal Pargana.
This isolated patch of human genome has been selected for investigation
and with the objective to identify the genetic reasons for the gradual
decrease in the population. The centre is collecting relevant informations
for future genomic research to be undertaken.
14. Details of Training /workshop organized and the total number of user
trained:
Four days training course was organized by the centre on Retrieval and
Analysis of Biological Informations in Genomics & Proteomics. During the
training course, 30 participants (teachers, research scholars and students)
from the different Universities of State and outside have participated and
rigorous training has been imparted to them by highly trained professionals in
the field.

areas:
Papers published with the help of Bioinformatics Centre.
The centre has developed as an Information Hub for whole of the
University.
Bioinformatics awareness spread through the Institute web-site and by
organizing workshop.
16. Future Activities :
During ensuing year, the centre proposes to strengthen infrastructures in terms
of software tools for biological data analysis for providing better services to the
users. Besides this the following activities will also be undertaken.
Web server development and web site hosting at Institute Server.
Starting P.G. Diploma course in Bioinformatics from next academic
session.
284
To cater to the regional and national needs, the work on the specific
databases being currently developed by the centre will continue.
Students will be allotted under the studentship-scheme to accomplish the
task in bioinformatics.
To train faculty, students and research scholars who can make use of
bioinformatics techniques and tools to enhance the efficiency of scientific
research.

Additional Details:
Name of the Co-ordinator: Dr. R.P.Upadhayay

Postal Address: Coordinator Sub-DIC
University Centre of Bioinformatics
T.M.Bhagalpur University, Bhagalpur- 812007

Phone No. 0641-2501753
Mobile: +91-(94312)15481
Email: ramprakash.upadhyay@rediffmail.com
Website: www.bioinformatics-tmbu.org.in

Name of Contact Person: Vandana
Email: pn.vandana@gmail.com

285
Tamilnadu Veterinary and Animal Sciences University, Chennai
Coordinator : Dr.P.Dhanapalan

1. Summary of the progress made by the centre since its inception
The Bioinformatics centre of this institution with various inhouse facilities is
actively engaged in serving the scientific community with current technical and
scientific literature in the field of Biotechnology, Veterinary and Animal Sciences
and allied areas.

Information Dissemination
information retrieval service since 1992. 50447 research scholars
have been benefited. Provided research information to 66 universities
and 188 colleges.
Education
Offering PG Diploma in Bioinformatics course from 2004-2005 M.Sc
bioinformatics course propsoed
Software packages Developed
An applicaton tool Information Retrieval Package
Student Relational Database Management System (SRDBMS) based
on VCI syllabus
Databases created
a) Database on abstracts of Research findings on Poultry by TANUVAS
scientists (upto 2000)
b) Database on abstracts of PG theses (1996-2003) and
Database on abstracts of completed research schemes of TANUVAS
(1998-2003)
Training Programmes Conducted
25 batches on Information Retrieval System and 14 batches on
Bioinformatics and Information Technology
Studentship/Traineeship projects completed
16 studentship/traineeship projects have been completed

2. Major research activities in Biotechnology and its related fields in
our institution

2.1 Completed research schemes in Biotechnology -24
2.2 On-going research schemes in Biotechnology - 8

Veterinary and Animal Sciences including Fisheries Sciences


4.1 Education activities :
* Offering PG Diploma in Bioinformatics course
* Bioinformatics papers to M.Phil and M.V.Sc scholars

4.2 Training programmes organized:
5 batches on Information Retrieval System and 2 batches on
Bioinformatics and Information Technology.

286
4.3 Offline Information Retrieval : During 2006-2007, 708
scientists/research scholars and during 2007-2008 (Upto Dec 2007), 411
scientists/research scholars have benefited.(Total users: 15186)

4.4 Online Information Retrieval : During 2006-2007, 5636
teaching faculties and research scholars of TANUVAS and for the year 2007-
2008 (upto Dec 2007), a total of 1899 have availed the online facilities (Total
users: 35261)

4.5 Establishment of Wetlab
At Bioinformatics centre, a Wetlab was established at a cost of 2.3
lakhs with 6.5 lakhs worth of equipments

4.6 512 KBPS Leased line Internet connectivity was renewed at a
cost of Rs.1.43 lakhs for the year 2007-2008

A. Computer & Communication facility :
The center is equipped with various hardware such as
* 10 nos of IBM Desktop PCs * 10 nos of Lenovo systems
* Black and colour Printers & Scanner
* LCD Data Projector & OHP Projector etc. to facilitate online
and offline information retrieval and training
B. Communication Facilities

1. 512 Kbps leased line connectivity
2. Internet facility :
login id btismvc@giasmd01.vsnl.net.in.
broadband connection @ 128 Kbps with login id
btis90mvc@eth.net.
Seminar Hall with state of art computer aided
teaching facility
C. Scientific Software Packages and application tools
Exome Version 1.1 , Lasergene Tool
MS SQL server 2000 ,Visual studio.net .
1. Databases on CDROM :
VETCD,BEASTCD, MEDLINE , ASFA & FSTA
BIOSIS , Derwent Biotechnology Abstracts
CDROM Current Contents (CCOD) on Life Sciences &
Agricultural ,Biological and Environmental Sciences
NUCSSI
Focus on Veterinary Science and Medicine (1994 to
Jan1999) in diskette

Other Information Sources :
* Text Books : 33 Nos
* Journals : Advanced BioTech, cheiron
Indian Journal of Biotechnology , Biospectrum
* Online Access to e -journals
a) http://www.blackwell-synergy.com
287
b) http://www.bioinformatics.oupjournals.org
c) http://www.scientist.com
d) www.doaj.org
e) www.highwirestandford.edu
Name and
Qualification of Staff
working
Remarks
Dr.P.Dhanapalan,Ph.D.

Professor and
Head and Project
Coordinator
Clinical Medicine From
30.4.2007
TANUVAS
Staff
Dr.A.Wilson Aruni,Ph.D, Associate.
Professor
Microbiology From
11.12.2006
-do-
Ms.P.L.Sujatha
M.Sc., ADCNET
Assistant. Librarian Information
Science, IT
From
3.11.1999
-do-
Ms.T.Mohanasundari
M.A.,MLIS
Information Officer Library Science From
17.12.1990

DBT staff
Ms.V.Malarvizhi
D.E, D.I.T
Technical Assistant

Electronics
Engineering and IT
From
22.3.1991
-do-
Ms.M.Seethalakshmi
B.Sc, MCA, BLIS
Data Entry Operator Computer Science
and applications,
library information
Science
From
22.7.1993
-do-
= Conduct of PG Diploma in Bioinformatics One Year duration
= Conduct of Training programmes on Bioinformatics and
Information Technology and Information Retrieval System
=Online and offline Information Retrieval Services
= Database Creation
= PG course on Bioinformatics and its applications
= Studentship/traineeship projects

Conduct of PG Diploma in Bioinformatics
Courses offered for M.Phil and M.V.Sc (Animal Biotech) students.

Students were placed in teaching & research institutes and
pharmaceutical & software companies

9. Initiative to validate the outcome of the Bioinformatics resources

Development of software/application tool
9.1 Information Retrieval Package (IRP)
9.2 Student Relational Database Management System (SRDBMS

10. Collaborative works/initiatives : with the line departments and
provided research information to 66 universities, 188 colleges

11. Databases/Software packages developed :
a. Databases :
i. Abstracts of Post-Graduate Research 1996-2003
ii. Abstracts of poultry research findings of TANUVAS up to 2000
iii. Abstracts of completed research Schemes of TANUVAS (98-2003)
288
b. Software :
i. Information Retrieval Package
ii. Student Relational Database Management System

(i) Dr.A.Wilson Aruni et al, Molecular modeling of . Cancer,
(ii) P.Thenmozhi et al, Study on phylogenetic small ruminants
(iii) A.Poongodi et al, Insilico study on the proteins,
(iv) A.Wilson Aruni et al, Genome microevaluation with avian
(v) A.Wilson Aruni et al, Insilico analysis isolates of Tamilnadu,

Research projects for a period of 3 months are being carried out by
Students of other Universities on payment basis in the areas of Genomics-
Comparative and function genomics

14. Details of training/workshop organized and total no. of user
trained
a. 14 programmes on Bioinformatics & Information Technology
conducted and 246 faculties and research scholars have been benefited
b. 25 programmes on Information Retrieval System (IRS) conducted
and 402 PG scholars and 189 teaching faculties of TANUVAS have been
benefited. (Total 591)
c. One training on Computer Appreciation Programme have been
conducted and 17 technical staff of TANUVAS benefited).

15. Impact shown by centre on the growth of biotechnology and allied
areas:
Copy right obtained : Copy right has been obtained for Information Retrieval
Package, a search engine developed by Mrs.M.Seethalakshmi and Dr.G.Thulasi
through NRDC, New Delhi from Register of Copyrights

i. PG Diploma course in Bioinformatics
ii. Proposed to start of M.Sc course on Bioinformatics
iii. Conduct of training programme on Bioinformatics and
Information Technology and on Information Retrieval
System
iv. Training to participants of various in-service training
programmes , ICAR, summer institute etc
v. Literature retrieval service through offline and online
vi. Creation and Updation of database .
vii. Conduct of studentship projects on Bioinformatics


Name of the Coordinator : Dr.P.Dhanapalan

Postal Address : Professor and Head &
Project Coordinator
289
Bioinformatics Centre & ARIS Cell
Madras Veterinary College
Vepery, Chennai 600 007

Phone Number : 044-25360106/25365418/25381506
ext.264
Fax : 044-25360114
Email : btismvc@giasmd01.vsnl.net.in
Btis90mvc@eth.net

website :www.tanuvas.tn.nic.in

Name of the contact person: Dr. P. Dhanapalan
290
Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu
Coordinator : Dr. P. Balasubramanian

The Distributed Information Sub Centre (DISC) has been functioning in Tamil
Nadu Agricultural University since 1989. It is housed in the Department of Plant
Molecular Biology and Biotechnology at the Centre for Plant Molecular Biology.
In the early years of inception, the DISC was primarily involved in providing
access to literature and sequence information via online and offline databases.
Trainings were organized annually on different bioinformatics titles to the
students and scientists of life sciences. This centre is the first major science and
technology network in TNAU to establish linkage between scientific communities
at national and international levels.

1. The DISC has established an internet browsing facility @ 512 kbps for the
benefit of scientists and students
2. A bioinformatics lab has been established with facilities for sequence
analysis, molecular modeling and database development
3. The DISC had so far conducted a total of 27 bioinformatics training
programs
4. Curriculum development for MSc (Bioinformatics), B. Tech
(Bioinformatics) and for the Open and distance learning PG Diploma
program in Bioinformatics
5. Three agriculturally important databases have been created
6. External students research projects are being carried out

institution
The Department of Plant Molecular Biology and Biotechnology of TNAU conducts
research in the following areas for the genetic enhancement of crop species.

1. Development of genetically modified egg plant with cry 1Ac against shoot
and fruit borer
2. Genetic engineering of rice cv. IR64 for drought and salinity tolerance
using the gene for trehalose biosynthesis
3. Nutritional improvement in rice: Golden rice program and Iron enrichment
in rice through transgenic approach
4. Genetic engineering of rice for pest and disease resistance
5. Regeneration and genetic transformation of cotton, banana, tomato,
papaya and groundnut
6. Genetic engineering and marker assisted selection for low phytate content
maize
7. Marker aided selection for rice yellow stem borer resistance, mapping of
genes associated with brown plant hopper (BPH), white backed plant
hopper (WBPH) and bacterial leaf blight (BLB) resistance in rice
8. QTL mapping and marker aided selection for drought tolerance in rice and
cotton
9. Isolation and characterization of cry genes from native Bt isolates
10. Characterization of root proteome of rice for water stress
291
11. Cloning and characterization of abiotic stress inducible promoters from
rice
12. Database on upstream sequence of drought/ salt stress inducible genes in
rice
13. Study of the structure function relationships in GUS

3. Area of Specialization of the centre: Agricultural Biotechnology
Research and training in bioinformatics have been major activities of this centre.
Three databases have been successfully developed. They include: Rice
Germplasm Database (a database on TNAU released rice varieties), Salinity
Stress in Rice (a comprehensive database on salinity stress in rice) and Sprome:
A database on abiotic stress inducible promoters in rice. Training to the students
on bioinformatics tools have been done. Besides, our faculty members have
delivered guest lectures on bioinformatics titles to the BIF centre at the University
of Calicut, Kerala. Maintenance of the bioinformatics lab and other infrastructure
such as ensuring internet connectivity for the use of students and staff are some
of the other activities. Further, the DISC has been instrumental in updating the
curriculum of the B. Tech (Bioinformatics) during this academic year. Also, we
have taken up to host a web page exclusive for the bioinformatics centre, TNAU.

1. Ten Intel Core Duo 2.0 computers connected to an IBM server is used for
bioinformatics research purpose
2. Another ten Pentium IV machines are connected to an Intel Xeon server
and used for bioinformatics teaching and training activities
3. A 512 kbps internet connectivity has been established exclusively for the
user centre routed through an IBM proxy server
4. A Sun biocluster with 4+1 nodes have been purchased from the financial
support of TNAU for specific bioinformatics applications such as molecular
dynamics and docking
5. An Apple workstation caters to molecular modeling studies
6. UPS (5 + 5 Kva) provides uninterrupted power supply to the user centre
7. HP color, mono printers, scanner are available
B. Scientific software package
Name Purpose
Mapmaker/Mapmaker QTL Linkage map construction and QTL analysis
IRRISTAT for windows Statistical analysis of experimental data
Reference manager Literature reference data base
Adobe Photoshop, Adobe
Acrobat professional
Photo editing and documentation
EMBOSS, BioEdit, Exome
Exome BLAST, ClustalX
Analysis of protein and nucleotide sequence
RasMol, AutoDock 4.0
Discovery studio (selected
modules)
Modeling and Docking

292
MS SQL server
Visual Studio
For database backend
For database front end
BioSuite
Genocluster (server edition with
ten user license)
Windows 2003 server + twenty
client license
Sequence analysis and molecular modeling
Sequence analysis

For networking

C. Databases and information resources
On-line/Off-line information retrieval: The facilities offered in respect of
information retrieval are being used extensively by the scientists and students of
TNAU and other institutes. Internet based access to various biological databases
is being followed.

absorption status)

Mr. G. Kousikan SRF
(Systems
Administration)
Dec 26th 2006
(resigned on April
2007)
Not absorbed
Dr. N. Rajinimala SRF
(Bioinformatics)
April 2007 -
resigned
Not absorbed
Mr. M. Sujit Kumar JRF (Systems
administration)
June 2007 - till date Not absorbed
Ms. Sri Vidya SRF
(Bioinformatics)
Oct 2007 - till date Not absorbed

1. E mail access and web browsing
2. Literature search and retrieval
3. Annual training programs
4. Students project work in bioinformatics
5. Students thesis work
6. Biological database development
7. Bioinformatics research
8. Statistical analysis

The Department of Plant Molecular Biology and Biotechnology had started an
MSc program in Bioinformatics in the year 2004. Students with bachelor degree
in agriculture and allied sciences are eligible to join this program. The curriculum
encompasses the basics of computer programming, molecular biology and
genetics. The core subjects include structural and functional genomics,
computational systems biology and database management systems. From the
academic year (2006-07) a four year undergraduate program B. Tech
293
(Bioinformatics) had been started in this department. Besides, a one year PG
Diploma program in Bioinformatics had been started as an distance learning
course. So far two batches of 13 MSc (Bioinformatics) students had passed out,
most of them are pursuing further research and some have joined software
company.

9. Initiative to validate the outcome of bioinformatics resources-not yet
Industry interactions
1. ADVANTA India Ltd., Hyderabad
2. Mahyco Research Foundation, Maharastra
3. RASI seeds, Attur, Salem dt.

Interactions with other institutions
1. IRRI, Philippines
2. National Institute of Agrobiological Sciences, Japan
3. Cornell University, USA
4. IISC, Bangalore
5. Delhi University (South campus)
6. Madurai Kamaraj University, Madurai
7. Sugarcane Breeding Institute, Coimbatore
8. National Research Centre for Banana, Trichy
9. Central Tuber Crops Research Institute, Trivandrum

Rice Germ plasm database, Salinity Stress in Rice database and Sprome: A
database on abiotic stress inducible promoters in rice
Raghu et al. 2007. Morphological and simple sequence repeats (SSR) based
finger printing of south Indian cassava germplasm. International Journal of
Integrative Biology, 1: 141-149.
Senthil. 2007. Genomic tools for germplasm characterization. In: Strategies for
utilization of plant resources in Asian countries, 1 2 Nov 2007, Korea.
Elayabalan et al. 2007. Towards engineering resistance against banana bunchy
top virus through RNAi approach. In: Two day conference on
Biotechnology for human welfare, 20 -21 July 2007, Coimbatore
Bharani et al. 2007. Bacterial leaf blight resistance genes pyramiding through
molecular marker assisted selection in rice (Oryza sativa L.). In: 2
nd

International conference on Rice for the future, 5 9 Nov 2007, Thailand.
Kalaiponmani et al. 2007. Standardization of somatic embryogenesis and
regeneration in banana cultivars Rasthali (AAB) and Poovan (AAB). In
National conference on banana, 25 - 28 Oct 2007, Tiruchirapalli.
Elayabalan et al. 2007. Initiation of embryogenic cell suspension and
regeneration in hill banana virupakshi or sirumalai (AAB) through different
explants. In: In National conference on banana, 25 - 28 Oct 2007,
Tiruchirapalli.

13. Initiation of R&D activities in Bioinformatics-research has been initiated
294

14. Details of Training/ Workshop organized and total no. of user trained -
The annual training program in bioinformatics is yet to be conducted for
this year

areas
The Department of Plant Molecular Biology and Biotechnology has been into
teaching and research on Biotechnology for the last two decades. It has been
mainly involved in transgenic research and molecular breeding for ultimately
improving crop plants against biotic and abiotic stresses. The department
currently offers B. Tech programs in Biotechnology and Bioinformatics, Masters
programs in Biotechnology and Bioinformatics and a PhD program in
Biotechnology. The students of this department mostly make use of the
bioinformatics centre. Besides, the facility is also extended to outside
researchers for carrying out their research projects. A total of six outside students
were admitted this year for carrying out their project work in bioinformatics.
Further, this centre has developed three databases which are agriculturally
important. Also, a patent has been filed towards patenting an indigenously cloned
chimeric Cry2A protein of Bacillus thuringiensis with higher insecticidal activity.

16. Future activities: Development of a transcription factor database, and
strengthening research in bioinformatics
Additional details :
Dr. P. Balasubramanian
Director (CPMB)
Coordinator (DISC)
Centre for Plant Molecular Biology
Tamil Nadu Agricultural University
Coimbatore 641 003

Phone (O) : 91 - 422 - 6611262
Fax : 91 - 422- 2431672
Email : biotech@tnau.ac.in
295
Tropical Botanic Garden and Research Institute Palode, Kerala
Coordinator : Dr. P. N. Krishnan


The Department of Biotechnology, Govt. of India has sanctioned a Sub-DIC to
TBGRI in 1998. Since its inception, the Sub-DIC (Centre) has been focused on
biodiversity informatics particularly on plants and its environments. The Centre
has developed several globally competent software packages for the
organization of biodiversity data, its analysis, modeling and interpretation. The
Centre also gathered / generated mammoth quantity of valuable data and
organized into databases and made available to the users. Salient contributions
of the Centre are (1) Developed five software packages for biodiversity data
organization, analysis and interpretation and made available on the web for free
access/download. (2) Developed seven databases related to biodiversity;
primary data of about 1300 plants and detailed data of 700 plants were
incorporated into the database and made available on the web. (3) Bioinformatics
publications - three papers in peer reviewed journals, two papers communicated,
18 papers in seminars/symposia/ workshop proceedings and two training
manuals; 32 papers were published by the scientists of TBGRI using the facility.
(4) Human Resource Development - 45 students from various institutions were
carried out their M.Sc./M.C.A/B.Tech. dissertation / project works in the Centre,
12 students were trained for a period of six months with the support of DBT
studentship, 7 short-term trainings were conducted and trained 160 personnel,
organized 3 National seminars and 2 National workshops, One 21 days training
for college teachers, and the scientists of the Centre delivered 26 invited
lectures to various institutions. (5) Developed three web sites for TBGRI and a
web portal for DBT and periodically up-dating information on these sites. (6) In
order to extend the facility to more number of users and interacting with IT
industries and initiating collaborative R & D ventures, the centre has established
an extension centre near Kerala University and Technopark
Thiruvananthapuram, where the R & D programmes are going on. (7) The
Centre has also initiated programmes on Barcoding of Life Forms.

institution

The Biotechnology and Bioinformatics division of TBGRI currently focusing on
the following R & D areas: (1) Conservation Biotechnology, (2) Bioproduction of
plant specific compounds, (3) Bioprospecting and DNA-based technologies, (4)
Bioinformatics, (5) Plant tissue culture based commercial propagation, (6)
Barcoding of life forms, and (7) Training, extension and conventional
Biotechnology

Bioinformatics and Biodiversity Data Management

4. Major activities of the centre during the year 2007 - 08
Primary data such as taxonomic details, local name, habit, distribution,
phonological details, conservation status, details of useful parts, economic
296
importance, photographs, etc. of 700 plant species conserved at TBGRI
campus were collected and organized into a web enabled database.
Field exploration trips to sacred groves of Thiruvananthapuram district were
conducted and colleted detailed data and incorporated into the database.
www.tbgri.in/sacredgroveonline
Incorporated primary data of 1300 endemic plants of India into the Plant Info
database, documentation of photographs is in progress.
Developed a software package for organizing the data of endemic plants of
India. The quality testing of the software package is in progress.
Initiated the development of a software package for herbarium database
organization.
Reshaped and updated information on the websites www.bioinfotbgri.org and
www.tbgri.in
Initiated a project on Barcoding of Plant species.
Maintaining BTISNet publication and library resource web portal.
Provided facility and guidance to 5 M.Sc Bioinformatics students for
dissertations.

SI.
No
Item No. of
units
Total
No. of
Units
1. Web server (IBM) Pentium IV , III 1, 1 2
2. PCs Pentium II, III , IV 3, 2, 9 14
3. Laptop computers 1 1
4. Printers: HP Laser jet 2100, 2840, Inkjet, TVS 345
dotmatrix
1, 1, 1, 1 4
5. 2 KV UPS, 5 KV UPS 2, 1 3
6. LCD projector 1 1
7. LAN connectivity within the Bioinformatics Centre &
Leased line internet connection 512 Kbps
1

B. Scientific Software packages : Nil
C. Databases & other information resources: Nil

SI.
No.
Name Designation Specialization Periods of
Working
1 Dr. S. Sreekumar

Information
Officer /
scientist B
Ph. D. (Botany). Experience
in SQL, MS access, .net,
VB; Macromedia,
Photoshop & HTML.
Since 2001
2 Dr. C. K. Biju

JSA /
Technical
Assistant
Ph. D. (Botany), Experience
in SQL, MS access, .net,
VB; Macromedia, HTML &
Photoshop
Since 2001
3 Miss. Sawmiya Das D. E. O M.Sc. Botany & PGDCA June 2005
* Absorbed as regular employee of the institute
Web server, Internet, guidance for M.Sc. / M.C.A. dissertation, data analysis for
research papers, library, training, web portal for BTIS Centres, Web sites
maintenance and information updating.

297
Forty five students were completed their M.Sc / M.CA dissertation works, of
these, 6 of them working as teachers, 4 of them doing research work and 10 of
them got placement in private entrepreneurs. Information about others is not
available.

A committee comprising software expert, subject expert on the area of
Taxonomy, Biotechnology and Conservation biology is functioning to evaluate
the outcome of the centre.

The centre joins with apex centre and developed the web portal system for
BTISNet Publications and Library resources.


Plant Info version I: An online database package for organizing a centralized
digital database including all information related to plants and its environment.
Currently, the database comprises details of about 300 plants and taxonomic
categorization of 1300 plants . www.tbgri.in/plantinfo
Seed Pack version I: Software package for the management of Seed Bank data.
www.tbgri.in/seedpack
LitFriend version I: Software package for the personalized management of
bibliographic data and its citation. www.tbgri.in
Fungal Database Meliolales: Database comprises information about 400
species of Meliolales reported from India. www.tbgri.in/fungi
Garden Info version I: Software package for the management of germplasm
collection and monitoring data of botanic gardens & its networking. Using this
package TBGRI has digitized the details of 800 live species conserved in the
campus. www.tbgri.in/gardeninfo
BioLit: Software package for the management of publications of an institution in
digital form. Biotechnology publications of TBGRI are made available to the
public using this tool. www.tbgri.in/biolit
Sacred Groves of Kerala: An online database package for digitizing data of
sacred groves of Kerala. Currently the database provides online access to
information on more than 150 sacred groves of Kerala and 400 plant species.
www.tbgri.in/sacredgrove
Wild Ornamental plants of the Western Ghats: Database comprises information
on wild ornamental plants of the Western Ghats. This database is created in CD
version.
BTISNet Publication & Library: A Web portal site connecting all BTIS Centres and
providing centralized access to publication and library resources.
www.tbgri.in/bioinfopub
Endemic plants of Kerala: The database comprises detailed information about
284 endemic plants reported from Kerala. The database can be made available
on the web during the month of April 2008 onwards.

298
Sreekumar S., Biju C. K., Hari Sankar G. and Krishnan P. N.( 2007) LitFriend: A
Software package for personalized management of bibliographic
information and its citation. Current Science 93 (4): 456-458.
Sreekumar, S, Biju, C.K. and Krishnan, P.N. (2007) Biological database
organization in Microsoft Access. Training manual, published by TBGRI,
Thiruvananthapuram.
Sreekumar S, Biju Ck and Krishnan P N. (2007) Bio informatics an overview,
Rural Agricultural work experience programme organized by Kerala
Agricultural University, College of Agriculture, Padanakkad on 6
th

September 2007.
Biju CK, Sreekumar S, and Krishnan P N. (2007) Biodiversity with special
reference to agriculture, Rural Agricultural work experience programme
organized by Kerala Agricultural University, College of Agriculture,
Padanakkad on 6
th
September, 2007.
Sreekumar S, Biju Ck and Krishnan P N. (2007) Biodiversity with special
reference to agriculture, Rural Agricultural work experience programme
organized by Kerala Agricultural University, College of Agriculture,
Padanakkad on 7
th
September, 2007.
The Centre has developed several software tools for biodiversity data
documentation, retrieval, analysis and interpretation. Currently, the centre is
engaged in the development of protocols for barcoding of plant species and a
web portal for its data dissemination and analysis.

Organized a 5 days National workshop on Biodiversity Database Organization
and its Management from 16
th
to 20
th
July 2007. 15 participants including senior
scientists, professors and college lectures were participated in the workshop.

areas.
The major impacts made by the centre are shown below

Total
Number
i. Software packages and databases developed : 5, 7
ii. Number of plant species primary data made available
on the web
: 1300
iii. Number of plants detailed data made available on
the web
: 700
iv. Web sites developed and maintained : 3
v. Web portal developed and maintained : 1
vi. Papers published in peer reviewed journal and
communicated (Bioinformatics papers only)
: 3, 2
vii. Papers published in seminar/symposia workshop
abstract /proceedings
: 18
viii. B.Tech., B.E, M.C.A and M.Sc. bioinformatics
dissertation carried out in the Centre
: 45
ix. Students trained with DBT studentship : 12
299
x. Short term training programme organized to teachers
and research students and no. of personnel trained
: 7, 160
xi. National seminars / symposia / workshop organized
by the Centre and in collaboration with other
institutions
: 3 , 2
xii. Three week training course for college teachers : 1
xiii. Students Ph.D. thesis and Biotechnology papers
published with the support of the Centre
: 8, 32
xiv. Average number of personnel using the facility for
internet access and other services
: 300/p. m.
xv. Invited lectures delivered by the Bioinformatics staff
in various educational institutions
: 26

To establish a centre for barcoding of plant species and a National web
enabled barcoding data (sequence data) repository for the identification of
plant species.
To develop a National web portal for biodiverisity Informatics and interlink
the available information resources, thereby the users can access the
biodiversity related information from a single window.
To develop a National database repository for biodiversity informatics
comprises the preliminary data of plants such as taxonomic position,
distribution, phenological and physiological data, economic importance,
images, etc.
To develop necessary computational tools / software packages for
database organization, data mining, data analysis and interpretation, and
also develop computational models leading to novel discoveries.
To continue the ongoing database organization and complete the
organisation of comprehensive database including all information of plants
growing in Kerala State.
To establish genetic sequence database of the intraspecific variants of the
endemic plants of the Western Ghats.
To develop TBGRI as a Nodal Centre for National Plant diversity
information and computational solution provider for Biodiversity data
management, data analysis and interpretation.

Additional Details:

Name of the Coordinator: Dr. P. N. Krishnan
Postal Address: Biotechnology and Bioinformatics Division, TBGRI, Palode,
Thiruvananthapuram
Phone Number: 04722869622 Fax No.: Email:
tbgri@sancharnet.in , peringattulli@yahoo.co.uk Website: www.tbgri.in ,
www.bioinfotbgri.org , www.tbgri.in/stec.htm

300
Name of Contact Person(s): Dr. S. Sreekumar, Scientist B & Information Officer,
Saraswathy Thangavelu Extension Centre, TBGRI, Puthenthope,
Thiruvananthapuram 695 586.
Email: drsreekumar@rediffmail.com

301
University of Calcutta, Kolkata
Coordinator : Dr. Subhasis Mukherjee

1. Summary of the progress made by the center from its inception:

This center started functioning as a modest Sub-DIC since 1993 and had been
upgraded to a full DIC in 2003. This Centre also coordinates to a great extent the One
Year Advanced Diploma Course in Bioinformatics which has been running since
1999-2000 academic session. This center has been made an integral part of the host
institute, providing both extra-mural as well as intra-mural support to the appropriate
institutions and department. This center is involved in all allied activities of this
region.

institution:
i. Spinal Chord Regeneration in Zebrafish.
ii. Development of Antimicrobial drugs
iii. Study of microbial biodiversity
iv. RNMV-induced growth promotion in jute
v. Plant Somatic embryo genesis

3. Area of specialization of the center:
i. Human Resource Development The center conducts a one year
advanced diploma course in bioinformatics and plays a major role in
running a two year M.Sc. course on Bioinformatics and Biophysics.
ii. Research Structural Bioinformatics and Systems Biology


The DIC has provided facility for research for the life science groups of the
university. The Bioinformatics group of the department has been able to
publish nine papers during this period. One database on transcription
regulation by Abscisic acid in plants was developed. The center has already
organized some lectures on drug design, biochemical pathway modeling and
transcriptomic analysis of zebrafish embryo development. The center is also
planning to organize a workshop in March08 on Systems Biology.
Four students had been registered to submit their doctoral work on various aspects of
Bioinformatics during the said period from the bioinformatics group, serving as the
nucleus of the DIC and the One year Advanced Diploma activities.

5. Infrastructural facilities of the Centre

a. Computer and communication: The center has a dedicated link of 2mbps
for exclusive use of the teaching and the research activities of the center.
The center is also serving as the nodal hub of the in-campus and trans-
campus network backbone of the host institution. The center, through the
in-campus web facility, has a 200% redundancy as far as the
communication is concerned.
302
b. Scientific software packages: The center uses the GCG packages as
gifted by the DBT. A large number of bioinformatics tools like BIOPERL,
EMBOSS, PHYLIP,CLUSTALW, MODELLER, AUTODOCK and
GROMACS, etc. are available to researchers and students.
c. Database and other information resources: TRABAS,detailing the effect
of ABA induction on a plant's transcriptome, developed and maintained in-
house. It is also available at www.bioinformatics.org/trabas.

6. Details about the staff members

SL.
NO
NAME OF THE
STAFF
DESIGNATION WORKING
SINCE
ABSORPTION
STATUS
(Y/N)*
1. Ms LUNA MITRA JUNIOR
ASSISTANT
2000 NO
2. Ms BARNALI
MANNA
DO 2000 NO

7. Types of services provided: Assisting the research and educational
activities in the university.

8. Educational activities with details of placement provided:
i. The center conducts a one year advanced diploma course in
bioinformatics and plays a major role in running a two-year M.Sc. course
on Bioinformatics and Biophysics and also organizes seminars on
modern areas of biology related to bioinformatics.
ii. The students are normally placed in prestigious national and
international laboratories (TIFR, SINP, BI, Univ. of Maryland, etc.) and
related industries (Dr. Reddys laboratory, TCS).

9. Initiative to validate the outcome of the bioinformatics resources.
Presently only at the level of research publications.

10. Collaborative work/ initiatives:

i. Karolinska Institute, Sweden
ii. Institute of Bio-organic Chemistry, Poland
iii. University of California, Davis
iv. With Department of Science and Technology, Government of West
Bengal, in areas of IPR.
v. With Bengal Engineerring and Science University in the area of system
methodologies.
vi. With Machine Intelligence Unit, India Statistical Institute, Kolkata in the
area of System Biology and Bioinformatics.

11. Database/ Software packages developed

303
A fully featured database entitled "Transcriptional Regulation by ABA Signaling
(TRABAS) detailing the effect of ABA induction on a plant's transcriptome was
hosted on www.bioinformatics.org/trabas.

12. Papers published /presented :
1. Hydrophobic, hydrophilic and charged amino acids network within protein,
Md. Aftabuddin and S. Kundu (2007) Biophysical Journal, 93, 225-231
2. Dynamics of Leucine-rich Repeat Proteins (2007) A. Lahiri and S. Basu.
Biophys. Rev. Letts (In press)
3. Interactions of HIPPI, a molecular partner of Huntigntin (2007) P.
Majumdar, A. Choudhury, M. Banerjee, A. Lahiri and N.P. Bhattacharyya.
FEBS J. DOI 10.1111/j.1742-4658.2007.05922.x
4. Molecular Dynamics simulation of the preferred conformations of 2-
Thiouridine in aqueous solution (2007) A. Lahiri, J. Sarzynska, L. Nilsson
and T. Kulinski. Theor. Chem. Acc. 117, 267
5. Physics in Medical Science appreciating Physics in Everyday Life,
Subhasis Mukhopadhyay, NCSTC-NETWORK, Department of Science
and Technology, Government of India, New Delhi, 2007
6. Gene Interaction - An Evolutionary Biclustering Approach -- Sushmita
Mitra,; Ranajit Das,; Haider Banka,; Subhasis Mukhopadhyay, Information
Fusion, ( in Press)
7. Identification of Gene Regulatory Pathways: A Regularisation Method
Mouli Das, Rajat De and Subhasis Mukhopadhyay, PreMI-07, Lecture
Notes In Computer Science, pp 425-432, 2007, Springer-Verlag
8. Evolutionary Biclustering with Corelation for Gene Interaction Networks
Ranaji Das, Susmita Mitra, Haider Banka and Subhasis Mukhopadhyay, ,
PreMI-07, Lecture Notes In Computer Science, pp416-424, Springer-
Verlag
9. Jolly Basak, Sudip Kundu and Amita Pal (2007) Phylogenetic Analysis of
Divergent Structural Organization of Nucleotide Binding Domain Encoded
by Resistance Genes and Gene Homologs in the Family Fabaceae. Indian
Journal of Biotechnology 6, 9-17
Conference Presentation:
a) Analysis of regulatory element and functional class associations: Comparison in
Arabidopsis and other plants Ananyo Chaudhury and Ansuman Lahiri at
European Conference on Computational Biology (2007)
b) Domain Combinations in Leucine-rich Repeat Proteins Anindita
Banerjee, Ananyo Chaudhury, Soumalee Basu and Ansuman Lahiri at
European protein Society Meeting, Stockhlom (2007)

13. Initiation of the R&D activities in Bioinformatics
Structural Bioinformatics and Systems Biology

14. Details of the Training workshop
A lecture series on drug design by Prof. Indira Ghosh, Pune University was
organized. Total number of users trained was fourteen.

15. Impact shown
Number of papers published in the area of bioinformatics and computational
biology are nine.
Manpower trained: 30
304
Tools developed: TRABAS, a database and AminoNet, a software for network
analysis of amino acid residues in protein structures.

16. Future Plan

The TRABAS database and its subsequent modifications will be hosted in one of
the servers of the Bioinformatics Centre, University of Calcutta.
An initiative is being taken by the center to make Systems Biology a thrust area
for teaching and research in this institution.


Coordinator: Dr. Subhasis Mukherjee
Postal Address: Department of Biophysics, Molecular Biology and Genetics
University of Calcutta, 92 APC Road, Kol-700009
E-mail: smbmbg@caluniv.ac.in

305
University of Kashmir, Hazratbal, Srinagar, J&K
Coordinator : Prof. K. I. Andrabi

The Center has developed software packages like INSUSENZ (for
computing Peripheral Insulin sensitivity using OGTT data) and an
application LIBSOFT (for library automation).
Developed a database on Medicinal & Aromatic Plants of J&K State. The
database is available on our website www.bioinfoku.org
Successfully conducted seven national level workshops.
Has its own VSAT (SCPC) with 1 Mbps bandwidth for Internet
connectivity.
Has been providing services to various Institutes of the valley and Science
departments of the University campus.
Has acquired several Software packages related to biosciences and the
research scholars from Biosciences field are getting benefited from these
packages.
Has started one-year (two semesters) PG diploma in Bioinformatics
course.

institution

Sequence variations in disease related genes and its relationship with
ethnicity
Molecular evaluation of oxidative stress as a marker for disease.
Potential of medicinal herbs to harbour signal transduction modulators.
3. Area of Specialization of the Centre:
Polymorphism studies in pure ethnic population [Kashmir].
One of the faculty member of Department of Biotechnology, has been
deputed for six months training in Bioinformatics at IBI Solutions
Chandigarh
Successfully organized a National level workshops held on Introduction
to Genomics and Proteomics in March 2007.
The Centre arranged series of online lectures related to Bioinformatics for
P.G. students of Department of Biotechnology, Kashmir University,
wherein faculty of Bioinformatics Centre, JNU, New Delhi were roped in.
The center procured Sun Fire X2100 compute server on which
BLAST,FASTA,CLUSTALW have been locally installed .This is a step
towards building a full BIOX package(Integrated bioinformatics software &
hardware solution)
Procured CLC Combined Workbench, a package enabling users to make
a large number of advanced proteins, DNA, and RNA sequence analyses,
combined with smooth data management, and excellent graphical viewing
and output options.
306
The Center has its own VSAT (SCPC) with I Mbps bandwidth from
Ernet.
Has Pentium D desktop with TFT monitors equipped computer lab.
IBM Xeon Server Core Duo and SUN Fire X2100 compute node
Properties of Organic Compounds Ver.6.0
InStat
ChemSW
EnzFitter
Sigma Plot graph library
GraFit Ver. 5.0
Softwares available online

The center recently procured Sun Fire X2100 compute server on which
BLAST,FASTA,CLUSTALW have been locally installed. This is a step
towards building a full BIOX package(Integrated bioinformatics software &
hardware solution)
CLC Combined Workbench.
Current Content Databases
a) Agriculture, Environmental Sciences and Biology.
b) Life Sciences.
working
/Absorption
Prof. K.I. Andrabi Coordinator
Molecular
Biology
18 years
Mr. Mujtaba Shafi
Information
Officer
Application &
Server side
Programming
(Java
technologies),
Linux, &
Networking
4 + years
(Yet to be
absorbed)
To be Advertised

Technical
Assistant

Ms. Arifat Ara
Data Entry
Operator

7 years.
(Yet to be
absorbed)
Literature browsing and web data mining for all research scholars of the
university.
Computational lab facility for post-graduate students, research scholars
and faculty of the science departments in general and biotechnology in
particular.
307
Project training pertaining to Bioinformatics tools, databases, data access
and data mining.
Access to BIOX grid package (integrated software/hardware solution from
SUN Microsystems) for Molecular Biology.

The center in addition to PG Diploma in Bioinformatics is offering
research-based activities to scholars/P.G Students of Science Faculty. Of
late research scholars of Department of Biotechnology, University of
Kashmir has been provided with the access to BIOX software package
(BLAST, FASTA, CLUSTALW AND VARIOUS MOLECULAR
MODELLING TOOLS).
The centre annually conducts national workshops and till date about 140-
160 personnel have been trained in various fields viz; computational
biology, Proteomics, Genomics and web based Bioinformatics tools

Centre collaborates with the department of biotechnology to provide
facility for one of the computational courses in M.Sc Biotech programme.
Centre ha entered into s collaboration with a U.S based software company
BQE Inc. to explore the possibility of developing user-friendly data mining
software.

The Center has developed a database on " Medicinal & Aromatic
Plants of J&K". The database has a GUI based Interface with Visual
Basic as its front end. Complete information on more than 133 plants has
already been collected. The information consists of folklore medicinal
uses, chemistry, medicinal uses, botany, geographical distribution etc. A
web-enabled Interface of the Database has also been developed and has
been made online on the centers website..
A software program "INSUSENZ" for computing the peripheral insulin
sensitivity from oral glucose tolerance test data has been developed.
Web enabled interface of Medicinal & Aromatic Plants in J&k has been
developed using Java server pages (JSP) technology on Macromedia
Jrun4 Server and is available on intranet.

Research Papers published in peer reviewed journals by using Bioinformatics
Support
Ishfaq Ahmed, Rohina Jan,,Riyaz A Pandit ,Tariq Qureshi & Khurshid
Andrabi, (2007), Exon10 Polymorphism in TGF Beta Gene does not
Assxcoaite with High Myopia in Pure Ethnic Pedigrees.Biochemical
Genetics (In press).
Peerzada Kaiser, Chand Raina, Rajinder Parshad
,
,Sarojini Johri
,

Vijeshwer Verma
,
Khurshid I. Andrabik and Ghulam N. Qazi

, Protein
Expression and Purification , 45(2), 2006, 262-268.
Mahrukh Hameed, Basir Ahmad, Khalid Majid Fazili, Khurshid Andrabi
and Rizwan Hasan Khan, Journal of Biochemistry, 141(4), 2007,573-
583.
308
Bioinformatics Research Papers Published, in peer Reviewed journal by your
centre.
Masood & Mujtaba Shafi, Bioinformation 1(2): 56-57 (2005).

14. Details of Training/ Workshop organized
Topic Year No. of participants
PC Familiarization & applications 2000 13
Introduction to Bioinformatics & Biostatistics-I 2001 18
Computer fundamentals & Networking 2001 06
Introduction to Bioinformatics & Biostatistics-II 2002 14
Bioinformatics & Internet 2003 17
Internet Resources & Statistics for Biologists 2004 15
Bioinformatics: Computer Methods in Biology 2005 15
Introduction to Genomics and Proteomics 2007 21

15. Imapct by the centre on the growth of biotechnology
The centre has been consistently organizing workshops to create
awareness about the potential of biotechnology in the state.
The availability of data analysis facility especially in molecular analysis
has prompted many researchers to switch their interests in biotechnology.
Our collaboration with the researchers of Deptt of Biotechnology has been
quite productive yielding data of highest quality.
The centre envisages to increase its software and data analysis resource
to cater to requirements in other areas of biotechnology viz Proteomics,
Molecular Modeling, Drug Designing etc
The center envisages starting a Postgraduate program in Bioinformatics
from next year.
Additional Details
Name of the Coordinator: Prof. K.I. Andrabi
Postal Address. Professor & Head, Department of Biotechnology &
Coordinator, Bioinformatics Center, The University of Kashmir, Hazratbal,
Srinagar(J&K) -190 006.
Phone Number: 194-2428723 Fax No.: 194-2428723
Email: andrabik@kashmiruniversity.net,
andrabik@yahoo.com
Website: www.bioinfoku.org
Name of Contact Person(s): Prof. K.I. Andrabi
Email: andrabik@kashmiruniversity.net, andrabik@yahoo.com
University of Pune, Pune
Coordinator : Prof. Indira Ghosh

Since established in 1987 Bioinformatics centre, University of Pune is
conducting the research in molecular modeling, prediction of 3D structures
and structure based drug design in bio-macromolecules. Since 2003 with the
aid of COE grants it has expanded its research area in Genome assembly
and Comparative Genomics, Metabolic pathway analysis, organization and
interaction of proteins in Virus, epitope mapping, Chemo-informatics and
309
target based drug design. During the academic year 2006-07 the Centre has
carried out several activities, viz. training, development of new databases and
programs, organization of national and international conferences and
workshops.
Prof. GNR Teaching Complex along with the main building, covering two floors in
each, houses state-of-art three lecture halls (each of 60-70 students capacity), three in-
silico laboratories for M.Sc.& CRCDM students and up-to-date library. Since 2002
we have completed 4 batches (22-30 students/year) of M.Sc students (100 Credits, 2
years course) along with 4 batches of ADB students (22 each batch) (52 credits 1 year
course). These students have completed a number of projects (30-40/year). The center
also supports Bioinformatics related all the curriculum activity of Institute of
Bioinformatics & Biotechnology, all the life sciences departments and the MBA-
Biotechnology course at University of Pune. Since 2006 the classes for integrated
course in IBB has been running at our premises for theory and practical. Experimental
research activities of the scientists of IBB are also being shared at the Bioinformatics
premises as a full scale laboratory has been established in the same premises.
The Center is able to increase the high power computing facilities (one 12
cpu, one 4 cpu & one 8 cpu server) and 60 new IBM/HP PC for research and
teaching activities in addition to updating the two Battery backup.
In addition to classroom teaching Center is conducting through its own virtual
classroom environment telecasting several web-based training programs on
MATLAB, e-Chemoinfo, Open source programs, workshops etc. in and out of
the department to our students over the whole year using the BIOGRID VPN
facility provided by DBT. Centers newly subscribed a 4Mbps(1:1) line with
STPN, Pune has been a boon to aid this activity.
A novel certificate course in Clinical research and clinical data management
has been flagged off since Nov 2005 as a part of the training activities in the
center and has created more than 300 well trained personal to help the
clinical research area in the country and abroad. This course has been
conducted as a joint venture with public private partnership and are
franchised as UoP in 5 cities including Bangalore, New Delhi, Hyderabad,
Chennai& Bhubaneswar.
Though In research fellow position presently we have two DBT-SRF, two DBT JRF,
4 COE, 2 BINC, 1 Seascape & one IBM JRF at the center and last year we were able
to fill up only the JRF, teaching associate under COE positions (3) but could not
retain the RA/faculties for 2007-08. The scientists do not appreciate temporary
positions at this level. Till now 6 JRF has been registered for Ph.D and 2 of them are
almost at the last stage of completion.
Since 2005 Bioinformatics center has been successfully coordinating the
BINC examination at the national level under the guidance of DBT. This
project will be running for three years and served the purpose of providing an
accepted standard of Bioinformatics teaching & learning to find high quality
Bioinformaticians. In February 2008 this years BINC will be held at six
centers including one at NEHU, Shillong to ease the difficulty of the students
from North East region of the country.
In addition to existing DBT-COE project, this year the center has been able to
attract one grant of COE from Ministry of Information technology and a
research project.

institution
310
More application oriented research activities have been added to the existing
portfolio of development of programs and databases research.
Comparative analysis of Metabolic Pathway in Microbial systems
Epitope mapping
Genome annotation and identification of SSR & VNTR for diagnostic tool.
Development of Interaction force field profile at the active site of protein to
map the selectivity of enzymes .
vHTS of target protein and developing a Scoring system for analysis
Searching active site using the pharmacophore: a chemo-proteome approach
to identify the receptor.
Developing physical measurement criteria to map protein interior.

Development of databases and data mining tools in the areas of Biotechnology
with stress on Virology, protein and nucleic acid sequences and structures & other
related areas.
Molecular modeling and prediction of 3D structures and interactions of bio-
macromolecules.
Genome assembly and Comparative Genomics
Metabolic pathway analysis & application to drug targets
Chemo-informatics and target based drug design

4. Major activities of the Centre during the year 2007-08
Courses were conducted with an introduction of online method (ICMS) for the
students to acquire knowledge. The course syllabus was updated during 2007
to accommodate flexibility and removing the redundancy. In addition to the
existing Databases and programming resources, new algorithms have been
developed for prediction of active sites, designing of pharmacophore, tools to
comparing metabolic pathway, scripts for conducting metabolic pathway and
flux balance analysis.
Application oriented works have been initiated using the VirGen & CEP
resources. Several High Throughput docking of relevant active sites are
completed and new scoring algorithms are in progress to identify the
probable chemical hits, this is to search for inhibitors from the known
chemical databases

a. Metabolic alphabets in bacterial system
The amount of genomic data is increasing at an overwhelming rate. As
on January 3, 2008 there are 702 published complete genomes and 3405
ongoing genome projects. One of the processes that differs living
organisms from non-living objects is metabolism. Comparative
metabolomics has become very important to understand the function;
evolution and creation of organisms by ab initio approach in laboratory.
Very few Bioinformatics tools are available to carry out comparative
metabolomics. A very efficient Bioinformatics tool has been developed
to compare genome wide metabolic pathways from KEGG database
311
using KEGG API. Using this technique and identifying a set of 34
pathways, which are essential for survival of bacteria, a set of common
metabolic alphabets have been developed for characterization of bacterial
pathway systems.

b. Epitope mapping & vaccinology
AgAbDb: Immunoinformatics provides tools for reverse vaccinology and
encompasses development of knowledge bases and algorithms for
prediction of epitopes. AgAbDb, a database archiving molecular
interactions of antigen-antibody co-crystal structures, has been developed
(http://202.41.70.51:8080/agabdb2/). The interactions are compiled at
two levels, viz. residue level and atomic level. The compilation
pertaining to the interacting residues provides insight into the geometrical
and stereochemical features of the epitope. In addition VirGen and CEP
servers have online access for accomplishing the objectives.

CEP: Conformational epitope Prediction server
(http://bioinfo.ernet.in/cep.htm) has been developed and is running on the
Bioinformatics server since September 2005. This server is used extensively
and the paper has received 22 citations. The server pages have been
updated recently and the data pertaining to the accuracy of the algorithm is
made available on the site. The work is also being carried out to improve the
accuracy of epitope prediction.

c. Genome sequencing, annotation and analysis
Genome annotation of an Indian isolate of Shigella flexneri was a project
carried out jointly by Institute of Bioinformatics & Biotechnology, at University
of Pune. The reads obtained by sequencing of the Indian isolate 1a of
Shigella flexneri were assembled using the Gap4 program. The partial
genomic sequences in terms of assembled contigs were annotated using
programs such BLAST, IS finder, GeneMark and ShiBASE.
Addition to this Bioinformatics approaches have been applied to identify the
simple sequence repeats in the genome for developing PCR based sero
typing /diagonosis tools in the virulent strains of Shigella Using the relevant
outcome of this project SSR & VNTR were designed and 40 strains of
Shigella flexneri were screened under a joint project with NICED,
Kolkata..This result experimentally validate the novel concept of using VNTR
as diagnostic tools to discriminate the strains of pathogenic bacteria.
d. Mapping of selectivity and specificity profiles
A novel method has been developed to compare the GRID potentials for
different chemical probes to build the selectivity profile for plasmepsins,
protease in Plasmodium species. Using discrimination analysis our result
shows the selectivity between Plasmepsins and human aspartic proteases.
The study illustrates the potential in analyzing the selectivity and specificity of
aspartic protease family towards receptor-ligand recognition using main
discriminating features like hydrogen bonding and electrostatics interactions.
Hence the selectivity profile will be helpful in designing novel candidate for
drug, which discriminates human aspartic protease with other pathogens.
312

e. Development of analysis tools for scoring and filtering from vHTS
Two series of high throughput in silico docking using heterologous
computing facility has been completed on 1.4 million compound set in
search of novel compound as hit in acid protease, Plasmepsin II and in
Ftase in Cancer using in-house developed script for parallel processing of
Open-eye docking SW called FRED. Development of analysis tools are
in progress for handling the appropriate clustering of the hits.

f. Pharmacophore: in search of active site to identify new target

Functional sites determine the activity and interactions of proteins and
as such constitute the targets of most drugs. However, the exponential
growth of sequence and structure data far exceeds the ability of
experimental techniques to identify their locations and key amino acids.
An attempt to device a novel in-silico protocol for active site
determination of protein has been developed using pharmacophore
approach as a search protocol. A database of orphan targets of
Mycobacterium tuberculosis H37Rv proteins, which contains the
sequence, structure and function information, has been developed in
house. A pharmacophore was built using a combinatorial library
generated from the anti-TB scaffolds identified from the previous work.
The in house program for pharmacophore docking into protein structure
is developed in C and Perl languages and successfully identified a novel
target for anti-Tb.

g. Novel measurement criteria to characterize proteins inhomogenity
Construction of an algorithmic framework to describe inhomogeneities in mass,
hydrophobicity and polarization content within protein interior assuming radial
symmetry has been developed and applied to proteins from extremophilic and
mesophilic organisms. This radial partitioning scheme of protein interior could
successfully differentiate the mass distribution pattern in extremophilic proteins from
mesophilic proteins.

A. Hardware and Network :
The center has purchased/ updated several of the servers which were
supporting the mirror database, email services, BINC server , Intranet and
IBIN project from DBT server. We have also updated our Bandwidth to
higher Mbps lines from STPN.
B. Databases & other information resources
Mirror sites at Bioinformatics Centre
EBI databases: 27 databases and EMBOSS sequence analysis
tools (Sun Solaris)
PDB database: Protein structure databank (Sun Solaris)
S-star: Bioinformatics online education (Linux)
313
C. Scientific Software packages (Acquired last year)

absorption status)
Prof. Indira Ghosh, Director, Professor, IBB
(Bioinformatics, Biotechnology& Drug Design) 01.09.03
Dr. Urmila Kulkarni-Kale, Reader (Bioinformatics) 01.09.05
Mrs. Sangeeta Sawant, (IBB) Lecturer (Bioinformatics) 01.05.03
Sanjay Londhe, Jr. Information Scientist (Information Technology)
20.04.94
Dr. Shah Vaishali, J. (IBB) Lecturer (Computational Physics) 17.12.03
Dr. A. Deshpande, Adjunct Professor ( Statistics, Environmental
science & Fuzzy Logic ) 01.02.05
Prof. A. S. Kolaskar, Advisor, NKC.
During 2007-08 total number of JRF/SRF/project assistance were 15. 6
TA/JRF from COE, one SRF & 3 JRF from DBT, 2 from BINC and 1 each
from MCIT project, from Seascape Learning & IBM have been granted to
the center.
Seven Research Fellows have already been registered for Ph.D under
Prof. A. S. Kolaskar & Indira Ghosh.

Sequence analysis user queries
Researchers / experts in life sciences who wish to analyze sequence and
structure data of genes or proteins send their queries to the center. The
experts in the center carry out the required analysis and it is sent along
with the interpretations.
Library facilities
Library has 2000 books, 5000 bound volumes and online full text
access to more than 2000 journals. This facility is made available to all
academic institutions from India. Digital Library (DL) having 400 pdf, word
and image files has been created using Greenstone Digital Library
software. DL is accessible on intranet. Center has established access to
more than 2000 full text journals and 8 bibliographic databases under the
UGC-INFONET University consortia network in November 2004.
Software Purpose
Open Eye Sw for designing
Chemicals
Small and large molecular designing and
docking, mapping etc are provided.
The Cambridge Structural Database
(CSD), Conquest etc..(Windows &
Linux )
The world repository of small molecule crystal
structures & the Interface for the CSD
Systems.
AMBER Ver. 9 Package of programs for molecular dynam
simulations of proteins and nucleic acids
CHARMM ver. Molecular dynamics and mechanics
ADF QM/MM SW
DS -Medchem Explorer A package to design pharmacophore.
314
Knowledge management
Recently, the library has established an intranet portal called InfoPath This
portal has been created using open sources content management software called
Plone. Infopath indexes electronic text image as well as audio files. InfoPath
organizes the information under different organizational processes like
administration, services, teaching, library, reports, digital library, etc. Users can
upload and download files on this portal and also submit their reviews.
Courses are ONLINE (ICMS)
A set of tools for providing online course materials and teaching utilities have
been developed . This also have been extended by developing ONLINE
Registration form for BINC , for Workshop and for admission .

M.Sc in Bioinformatics ://bioinfo.ernet.in/courses/IndexMSC.html
Under the dynamic leadership of Prof. A. S. Kolaskar, the founder
Director of the Centre the Bioinformatics Centre has highly competent
faculty, both in-house and contributory, dedicated administrative support,
state-of-the-art computer systems with full internet connectivity and
modern library facilities. The Centre have started the 2 year M.Sc.
Program in Bioinformatics from the academic year 2002-03. Given the
excellent infrastructural facilities and academic programs like active
research, interactive teaching and industry collaboration, the Centre has
gained in reputation both nationally and internationally. It is hoped that the
M.Sc. program throws open highly promising career opportunities to
aspiring students. Present input for M.Sc is 30 students/year. 50% of them
are employed in Industry and the rest opt for Ph.D or academic jobs.
Clinical Research and Clinical Data Management"(CRCDM)
http://www.clinicpune.org/ a post graduate certification 6months(weekend
course)
New Pharmaceutical Drugs, biological, herbal and natural remedies,
nutraceuticals and probiotic food products, and select cosmetics require
drug safety and efficacy testing before they are introduced in the market.
This testing for drugs on humans comprises Clinical Trials referred as
Phase I, II, III trials prior to market launch of the product & Phase IV after
market introduction. India has one of the largest patient populations for
most of the diseases with genetic diversity. Availability of highly qualified
medical practitioners is attracting conduct of global clinical trials in Indian
hospitals and clinical sites since India has implemented GCP as per ICH
global standards. It is now possible that the data from conduct of trials in
India as per GCP guidelines maybe submitted for approval of the drug in
USA, Europe, Japan, etc along with submission to authorities in India. The
clinical trial industry is doubling in revenue every 2years and as per
Mckinsey estimate India has the potential to become one billion dollar
revenue industry. This high growth has created the mandatory need for
more clinical research professionals in GCP for conduct Management of
the trials.
315
Since 2005, 300 students have passed out of this certificate course and tit
has been franchised to 5 other cities in India. 90% of the students are now
working in the Clinical research industry. A novel approach has been
taken using Public-Private partnership to support this course
The Centre is collaborating with the experimentalists to validate the
hypothesis/predictions based on bioinformatics analyses. Collaboration
with the scientists from NICAD in Kolkata, NCCS, NIV in Pune, NIPER,
Chandigarh & IRRH, Mumbai has helped in validating several predictions
done by the researchers in the wet lab.

Collaborations with national and international organizations

Functional and structural annotation and prediction of structures.

Several activities are going on to annotate unknown proteins and predict its
three-dimensional structures. One of the success story is the collaboration work
with National Institute for Research in Reproductive Health, Mumbai by
identifying a novel progesterone binding protein ER60, which has low sequence
similarity (18%) and revealed to have a Protein disulphide isomerase (PDI)
classical fold. The experimental work is in progress to validate the hypothesis.

Collaborative activities with industries and other agencies

Synergy Networks: Collaboration for Clinical research and data
management
Serum Institute, Pune : Contract R&D
IBM Life sciences : Research scholarships and IBM-CAS academy
fellowships.
Seascape Learning : OpenEye SW country wide support.
316

Databases
Name of database Mode of Access (online/offline) Size of
DB
Completion Status
Indian Bioresource
Information Network
(IBIN) portal : Web
portal for searching
any information
regarding bio
organisms.
Web based:
http://bioinfo.ernet.in/ibin/

Completed and
updated periodically
Antituberculosis
Compounds
Database : A novel
data mining
procedure to look for
new antitubercular
agents and targets
as well as to find a
minimum common
bioactive
substructure
(MCBS).
Web based:
http://203.129.231.23/indira/

Completed and
Pathophyl: Database
of phylogenetic
profiles for each
protein of
Mycobacterium
tuberculosis,
Pseudomonas
aeruginosa,
Staphylococcus
aureus.
Web based:
http://203.129.231.23/indira/

Ongoing
Virgen ver2.0
Contains genomic
data of 25 viral
families that include
2895 genomes and
23121 annotated
proteins
Web-based:

http://bioinfo.ernet.in/virgen/virgen.html

200MB Completed and
CEP server:
Conformational
epitope Prediction
server
Web based:
http://bioinfo.ernet.in/cep.htm

>GB Completed &
Updated
Metabolic pathways Web-based :
http://202.41.70.51/mpe/

1GB Ongoing in
collaboration with
Jalja tech.pvt.
PepConfDb Web-based (Proposed) 50MB Ongoing
AVIS Web-based 1GB Completed

Software/Databases with search engine developed :

Name: IBIN: Indian Bioresource Information Network (IBIN) portal :
Web portal for searching any information regarding bio organisms.
Mode of access : Online
Name: Pathophyl : Profile prediction of pathogenic bacteria.
Mode of access: Online
Name: CEP: conformational epitope prediction
317
Name: Protein Conformational state prediction
Mode of access: On request
Name: Antigen
Mode of access :Online as well as through EMBOSS and UWGCG
Name: Virus identification matrices


Papers published:

1. Rahim F*, Deshpande A, Hosseini A*. Fuzzy Expert System For Fluid Management In
General Anaesthesia. Journal of Clinical and Diagnostic Research [Serial Online] August
2007, 1:256-267.
2. Hosseini Ashraf , Ranade Suvidya H. , Ghosh Indira, Khandekar Pramod (2007). Simple
sequence repeats in different genome sequences of Shigella and comparison with high
GC and AT- rich genomes. DNA Sequence.
3. Chaitanya N. Hiremath (2007) Abbreviated Profile of Drugs (A-POD): A unique
numerical and graphical representation for compound properties and its use in ADMET
prediction, IJIB, 1(1), 44-50.
4. Greenbaum, J. A., Andersen, P. H., Blythe, M., Bui, H. H., Cachau, R. E., Crowe, J.,
Davies, M., Kolaskar, A. S., Lund, O., Morrison, S., Mumey, B., Ofran, Y., Pellequer, J.
L., Pinilla, C., Ponomarenko, J. V., Raghava, G. P., Van Regenmortel, M. H., Roggen,
E. L. , Sette, A., Schlessinger, A., Sollner, J., Zand, M., Peters, B.(2007). Towards a
consensus on datasets and evaluation metrics for developing B-cell epitope prediction
tools. J. Mol. Recognit. 20(2), 75-82.
5. Kulkarni-Kale, U., Ojha, J., Manjari, S., Deobagkar, D. D., Mallya, A.D., Dhere, R. M. &
Kapre, S. V. (2007). Mapping antigenic diversity & strain-specificity of mumps virus: a
bioinformatics approach. Virology. 359, 436-446.
6. A. Kumar and I. Ghosh (2007). Mapping Selectivity and Specificity of Active Site of
Plasmepsins from Plasmodium falciparum Using Molecular Interaction Field Approach.
Protein & Peptide Letters , 14(6), 569-574.
7. A.D. Ghate, B.U. Bhagwat, S.G. Bhosle, S.M. Gadepalli and U. Kulkarni-Kale(2007).
Characterization of Antibody-Binding Sites on Proteins: Development of a
Knowledgebase and Its Applications in Improving Epitope Prediction. Protein & Peptide
Letters, 14(6), 531-535.
Proceeding, Posters and awaiting for publications :
Poster presented by Sweta Kohli at The 18th International Conference on
Genome Informatics held in Singapore from 3rd to 5th December 2007
titled Metabolic alphabets in bacterial system


a. Our center is co-ordinating the BioInformatics National Certification
(BINC) Examination. BINC Examination, the first one was conducted on
November 12-13, 2005. This examination has been instituted by the
Department of Biotechnology (DBT), Government of India with an
objective to certify Bioinformatics professionals and to facilitate industries
318
and potential employers for recruitment. University of Pune has been
identified to continue this events for three years as a nodal agency by the
Department of Biotechnology, Govt. of India to coordinate this examination
along with four centers namely, Jawaharlal Nehru University, New Delhi;
Anna University, Chennai; West Bengal University of Technology, Kolkata
and Institute of Bioinformatics and Applied Biotechnology, Bangalore.
b. International interactions are also been strengthen by processing a
collaborative research and teaching activities with University of Utah ,
USA , under the guidance of Prof. A. S. Kolaskar. More such activities are
underway.
c. Center has received a Grant in 2007 August from Ministry of Information
technology as Center of Excellence .

The following workshop were arranged by the center (number of attendee):

1. 23.07.2007: Felicitation Day on `BioInformatics National Certification (BINC)
Examination in the hands of Prof. A.S. Kolaskar, Advisor, National Knowledge
commission and Dr. T. Madhan Mohan, Advisor, Department of Biotechnology, Govt. of
India, New Delhi (30)
2. 23.07.2007: `Bioinformatics Day, to commemorate the invaluable scientific
contributions of late Prof. G.N. Ramachandran, the department has celebrated by
arranging an oration by the eminent scientist having substantially contributed in the
areas of Bioinformatics, Genomics, Proteomics, Structural Biology and Application of
Bioinformatics. This years oration has delivered by Prof. A.S. Kolaskar on title
Bioinformatics hotter than hottest. This function was chaired by Dr. Swaminathan
Sivram, Director, National Chemical Laboratory, Pune. (100)
3. 01.08.2007: Bioinformatics Day celebration: Prof S.K. Brahmachari, Director, IGIB,
New Delhi has delivered GNR Oration lecture on Hope and reality, Prof. A.S.
Kolaskar, Chairman, National Knowledge Commission and M.D. of DSK Global
Education and Research Pvt. Ltd., was the chairman of this occasion. GNR-IGIB and
DBT Prize distribution function was also held during this time. (100).
4. December 11 -17, 2007: WORKSHOP on "Knowledge Discovery In Life Sciences:,
Modeling of Small Molecules to Macromolecules website:
http://bioinfo.ernet.in/workshop07/ (50)

allied areas. In this you may highlight the details like number of
paper published/ number of papers published with the help of your
organization and neighboring institutions, manpower trained, tools
developed, patents & copyrights acquired and other services
offered etc.
Prof. Kolaskar is deeply involved in the planning activities in human
resource generation in technology in our country being the advisor of the
Knowledge management Council led by Prime Minister. He has been
member of several national and international level committees.
Prof. Indira Ghosh in collaboration with Dr. Devapriya Choudhury, JNU has
organized a workshop to train the SAARC manpower at Thailand during
July 2007.
Prof. Indira Ghosh has been influencing the national level of teaching and
research in Bioinformatics by being active member in the group on
319
developing Bioinformatics & Medical Informatics in the Ministry of
Information technology and ICMR respectively.

Every Year our faculties attended & deliver lectures for at least 2-4 other
BIF/BIC workshops and 1-2 Colleges running Bioinformatics programs to
train the manpower .

International/Indian Conferences & Teaching

Presented papers by Indira Ghosh :

2008 Jan2-4 with Kalyani University , BIF Workshop :Macromolecule-
ligand interaction & drug design in West Bengal.
2007 Dec 16-19 Instructional workshop in Bioinformatics Jointly by the
University of Hyderabad and the C. R. Rao Advanced Institute of
mathematics, Statistics and Computer Science at the University of
Hyderabad Campus, Hyderabad, India
2007 Dec 20-22 at the"International Conference on Bioinformatics"
http://www.uohyd.ernet.in/sls/cbt/bif/Training/conf2007.htm.
2007 Nov21-23 workshop on Functional genomics and evolutionary
Biology at the Institute of Life Sciences, Bhubaneswar .
2007 Nov 29-30th. At Sophia College , Mumbai on Frontiers in
BioSciences
2007July2-6th with Biotec, Thailand and JNU, India jointly organized
and taught the workshop on Molecular Dynamics: Theory & practice in
Bangkok Thailand,
2007, May 10th. Symbiosis Institute of Health Sciences, Pune, Clinical
Data Management
2007, May 2nd., Workshop lecture at Bangalore ,Functional annotation.
At Tata Auditorium.
2007, April 6th. , Workshop lecture & Demo on in Silico Toxicity prediction at
NIRRH, Mumbai.
2007 , Feb 26-28th, CUP07 at SantaFe , USA
2007, Feb 9-12th. : Mumbai University , Bioinformatics Application in
Life Sciences, workshop inauguration lecture : Hypothesis based Biology
: a new era
2007 , Jan 22-24th : International Conference on Chemoinformatics at
NCL Pune
2007, Jan 12-14 : Kolkata Chromosomes to Neurons

Presented papers by Urmila Kulkarni-Kale:

2007, Aug23-12Sep. Teachers training program organised by Goa University.
2007 Dec 1
st
. Proteomics & genomics seminar organised by
College of Pharmacy, University of Pune .

Teaching to students of other departments at the University and
institutes

320
All life sciences departments (students~50), Institute of Bioinformatics &
Biotechnology (students~60) and MBA biotechnology dept.(students~ 70)
have Bioinformatics as a part of their syllabus. The faculty of the center
teaches these courses.
A special module based exchange program in teaching was done for the
first time with our students doing 2 credit experimental course at WBTU,
Kolkata and their students crediting the 2 credit course on structure
prediction, modeling and simulation of Proteins at out center during 3
weeks in the summer of 2007.

Specialized on site training programs

Short-term training in Bioinformatics is provided to scientists / researchers
of various institutes and industries as per their demand.

Summer training / short term projects

Students from University departments (M.Sc 30 & 5 students from IBB) and
neighboring institutions are accepted for short-term projects / summer training in
Bioinformatics. In addition to this, in 2007 we have trained 2 project student from
IIT Roorky ,1 from IIT Kharagpur and IBB, Noida.

Consultancy to industry

a. Bioinnovat(Synergy Networks) : Collaboration for Clinical research
and data management courses has been expanded to five more
centers including one at H.V. Desai Hospital, Pune , 1 at New Delhi
and one at Sankar Netralaya, Chennai, 1 at Bangalore, T. John
College and 1 at Hyderabad, LVPrasad Hospital.
b. Seascape Learning, LLC (Seascape): Advisory collaboration with the
organization has supported a JRF scholarship and provide on-line
support to international and Indian customer for the Open-eye
Software suits developed by the OE .

As a part of Center of Excellence research projects in the field of
identification of gene target and pharmacophore in the disease specific
area like infectious & parasite disease and diabetes are in progress. A few
extended works are cited as follows:
Genome annotation and comparative genomics :

Diagnostic tools using Genome annotation and comparative
genomics of Shigella flexnary 1a, an Indian isolate will be another
major activity in the future in collaboration with NICED,Kolkata.

Identification of correlated pathway using upstream comparison
of genes and operons of pathogenic bacteria :

321
A novel idea of clustering the genes belong to the same
pathway has been initiated using the upstream sequence profile
of the genes in pathogenic bacteria.

Target Identification using Metabolic pathway control analysis in
pathogenic bacteria case study with M.Tb:

MCA & Flux balance analysis are the system biology related
methods applied to understand the mechanism of persistence of
bacteria and hence to identify the appropriate way of inhibition of
the vulnerable and unique enzyme in the metabolic pathway. Flux
balance analysis of whole genome of M.Tb is the method applied to
identify the target under dormant bacteria.

Additional Details:

Name of the Coordinator : Prof. Indira Ghosh

Postal Address : Director, Bioinformatics Centre,
University of Pune,
Pune 411 007.
Phone Number : 020 2569 0195, 2569 2978
Fax No. : 020 2569 0087
Email : director@bioinfo.ernet.in
indira@bioinfo.ernet.in

Assam Agricultural University, Khanapara, Guwahati
Coordinator : Dr. Probodh Borah

Adequate infrastructure with required hardware and software has been
developed at the centre and the facilities are being used by the faculty
members and students of the institute as well as some other neighbouring
institutions of higher education. So far two training programmes have been
conducted on different aspects of bioinformatics tools and their application in
biological research and a total of 32 biology teachers/researchers of various
institutes within and outside state participated in these programmes. Another
training programme is scheduled for February 18-21, 2008. Additionally, so
far 85 faculty members/subordinate staffs of the host institute have been
trained in eight batches under a computer literacy programme conducted by
the centre.

institution:
Some noteworthy contributions made by the institute in biotechnology related
research are: molecular characterization of Salmonella enterotoxin,
standardization and application of PCR for virulence screening of Escherichia
coli and Salmonella, production of cell culture adapted duck plague vaccine,
molecular characterization of swine fever virus, development of potassium
322
thiocyanate extract vaccine of Pasteurella, cryo-preservation of ova and
application of embryo transfer technology in goat, cow and yak etc.

8. Area of Specialization of the centre: Animal Biotechnology

i. Necessary infrastructure of the centre was developed and required
hardware, software etc. were procured.
ii. Two training programmes were conducted and 32 teachers/researchers
were trained on bioinformatics tools and their application in biology
teaching and research. Another training programme is scheduled for
February 18-21, 2008.
iii. Altogether 85 faculty members and subordinate staff in eight batches of
the host institute have been offered training on computer applications.

i. Computer & Communication facility: 10 computers, 2 servers, one
Laserjet and one Inkjet printer, one Photostat machine. The computers
are connected to the faculty LAN with 24-hour 512 kpbs Internet
connectivity with adequate power backup.
ii. Scientific Software packages: Visual Studio, My SQL, Exome, Bioedit,
Phylip, ClustalW etc.
iii. Databases & other information resources: VETCD (1989-1999).

absorption status):
Name of the
staff
Designation Specialization
Period of
working
Absorption
status
Dr. P. Borah
Assoc. Professor
and Coordinator
Ph.D. Veterinary
Microbiology
Since
inception
Permanent
Dr. B.K.
Sarmah
Assoc. Professor
and Member,
Executive
Committee
Ph.D. in
Veterinary
Physiology
Since
inception
Permanent
Sri Arunav
Gupta
Research
Associate
M.Sc.
(Computer
Science)
Since
18.12.2007
Temporary
Sri Pradip
Sarmah
Typist B.A.
Since Nov.,
2007
Permanent

12. Types of services provided: Internet surfing, training and assistance on use
of online databases and bioinformatics tools, statistical analysis of biological
research data, guidance in genomic research etc.

13. Educational activities with details of placement: None so far except
conduction of training programmes. However, a proposal for opening of PG
courses in Animal Biotechnology has been submitted to DBT for approval.

323
14. Initiative to validate the outcome of bioinformatics resources: Through
publication of research articles in reputed journals.

15. Collaborative works/ initiatives: Teachers/researchers of neighbouring
institutions like Guwahati Medical College, Gauhati University, Cotton
College, B. Barooah College etc. have been trained and offered facilities for
use in their research works.

16. Databases/ Software packages developed: None so far.
17. Papers published or presented in the conferences with reference: None
so far.

18. Initiation of R&D activities in Bioinformatics: Work has been initiated.

i. Short-term hands-on training on Bioinformatics Tools and Their
Application in Teaching Biological Sciences from March 20-22, 2007, in
which 12 participants were trained.
ii. Short-term hands-on training on Bioinformatics Tools and Their
Application in Biological Research from December 03-06, 2007, in
which 20 participants were trained.
areas: The centre is encouraging faculty members and students for optimal
use of the facilities available at the centre for promoting their teaching and
research activities. An e-learning module is in the process of development
which has been available in the faculty LAN. The Internet facility is being used
extensively by the faculty members and PG students. Two papers published
with the help of the centre so far.

21. Future activities: The future activities envisaged include development of a
database of indigenous livestock and wildlife of the north-east India,
development of tools for identification of pathogenic microorganisms on the
basis of standard criteria, etc.

Additional Details:
Name of the Coordinator: Dr. Probodh Borah
Postal Address: Department of Microbiology, College of Veterinary Science,
Assam Agricultural University, Khanapara, Guwahati-22
Ph: 0361-2307329 (R), 0361-2331501 (O), Mobile: 094351-16191
Email:borahp@rediffmail.com Website: www.aau.ac.in
Name of Contact Person(s): Dr. Probodh Borah
Email: borahp@rediffmail.com
324
Alagappa University, Karaikudi, Tamil Nadu
Coordinator: Prof. S. Karutha Pandian

Bioinformatics Infrastructure Facility (BIF) was established at Alagappa
University during November 2006 and it was formally inaugurated by the
Honble Union Finance Minister on 24.11.2007. It serves to the student and
teaching community of the Alagappa University and its affiliated colleges.
M.Sc., Biotechnology students use this facility for their Bioinformatics
Practical and hence they are placed well immediately after finishing their PG
programme. One PhD was produced using this facility and 10 more research
students are using this facility. A 2 MBPS broadband internet connectivity
from BSNL is being utilized for bioinformatic purposes by the PG students,
Research Scholars and Faculty members of the host and neighbouring
Departments/Institutes. Journals with online and printed versions are being
subscribed in the area of Biotechnology, Microbial Technology and
Bioinformatics. Seven Research Papers have already been published in
International Journals with decent impact factors using the computational
facility of the Centre. Database is being generated for the 16S rRNA
sequences of marine bacteria form the Gulf of Mannar for biotechnological
prospects. This facility was also utilized to identify the bacteria associated
with goat skin which are involved in the deterioration of skin as part of the
CSIRs New Millennium Indian Technology Leadership Initiative (NMITLI)
Scheme.
institution
i) Biotechnology for Leather: Towards Cleaner Processing.
This work is being carried out with the collaboration of 11 other National
Institutes/Universities under the New Millennium Indian Technology
Leadership Initiative (NMITLI) scheme of CSIR. The culturable bacteria
associated with goat skin were identified through 16S rRNA based typing
and that in turn paved the way for coming out with suitable technologies for
bio and ambient preservation of skin without common salt. Marine bacterial
enzymes have successfully been employed for dehairing of goat skin.
ii) Study on Gene Expression technologies using C. elegans.
C. elegans is being used as a model organism for studying the host
pathogen interaction through RNAi technology through DBT funded Project
RNA-interference mediated silencing of antimicrobial genes on the
pathogenic effect of Salmonella typhi on vitamin transport of Caenorhabditis
elegans under Rapid Grant for Young Investigator. Marine natural products
are also being screened for novel antibiotics and anticancer compounds
using C. elegans as live infection model.
iii) Marine Microbial Diversity/Genomics
The microbial diversity associated with the predominant coral of Gulf of
Mannar viz Acropora digitifera is assessed/catalogued through culture
dependent and culture independent methods with an objective of coming
out with novel antiviral compounds from the coral associated bacteria
against the aquaculture pathogen blotched snakehead virus (BSNV). This
project is funded by the DBT, Government of India.
iv) Bioactive Compounds from Marine Microbes
325
Screening of antibacterial, antifungal and AHL (quorum sensing signal)
degrading molecules from marine actinomycetes are underway.
Screening of marine bacteria as a probiotics against aquaculture
pathogens is also carried out.
v) Plant Biotechnology:
Agrobacterium mediated gene transfer and ex-situ conservation of
medicinally and commercially important plants are being carried out for
increasing the tolerance to salinity and drought in commercially important
crops such as Rice. Ex-situ conservation of medicinally important plants
through synthetic seed preparation, micro and macro-propagation is also
under progress.
vi) Pharmacology of marine natural products and Antioxidant properties
of Olive Oil (DST funded Project)
Marine Microbial Biotechnology, Microbial Genomics and Proteomics and
Environmental Biotechnology
4. Major activities of the Centre during the year 2007-08
Research Projects funded by National agencies such as CSIR, DST, DBT
have been carried out. The microflora associated with the goat skin have
been identified and 16S rRNA sequences of marine bacteria associated with
coral reef ecosystem of Gulf of Mannar Marine Biosphere Reserve and
bacteria associated with the deterioration of animal (goat) skin submitted to
ribosomal data base. Marine alkaline protease from Bacillus pumilus has
been successfully applied for dehairing of goat skin. Antibacterial and
Quorum sensing signal degrading compounds have been isolated from
marine Actinomycetes. Basillus sp. has been used successfully as a probiotic
bacterial organism against Aquaculture pathogen Vibrio sp. Standardized the
protocols for ex-situ conservation of medicinally and commercially important
crops. The antioxdant properties of olive oil have been established using cell
lines. Theoretical and practical training have been given to the PG and PhD
students in bioinformatics. A National Workshop on Genome and Proteome
Analysis was conducted during January 7-9, 2008 and twenty five candidates
have got hands on training through this Workshop.
i. Computer & Communication facility:
High End Server (HP ML 350 G4/G5) with Windows Server 2003R2
Medium End Server (HP ML 110 G3) each with Windows Server 2003 R2
P4 PCs (10), High Speed Network Laser Printer (HP LaserJet P3005d)
Deskjet Printer (HP Business Inkjet 1000)
Scanner (HP Scanjet 2400)
Photocopier (Konica Minolta Bizhub 210)
2MBPS Broadband internet connectivity from BSNL with dedicated IP
address and wireless modem (WA1003A) for Wi-Fi access.
Firewall from Syntensia (White Knight).
ii. Scientific Software packages:
Windows 2003 Server with License
Red Hat Linux Enterprise Edition 4
Microsoft Visual Studio, .NET
MS SQL Server (Std.)
MS Office 2003 and Anti Virus Packages.
326
Action is being initiated for getting application software such as GCG
Wisconsin Package, Biosuite (from TCS) and Sigma Plot, DTMM,
Reference Manager and Coral Draw
iii. Databases & other information resources:
The centre currently uses the databases and resources that are freely
(open access) available over the internet like NCBI, EBI, ExPASy, etc.,
The BIF has been subscribing Nature, Nature Biotechnology, Nature
Reviews of Microbiology, Science and NISCAIR Journals.
Dr. R.A.L. Sathiyanathan RA Biochem/ Nov 19- to date
Bioinformatics
Mr. K. Syed Musthafa Tech Asst Biotech Nov 15- to date
Mr. S. R. Senthilkumar Tech Asst Biotech Nov 15- to date
(a) Training in Bioinformatics: Theoretical and practical training on
Bioinformatics is provided to the M. Sc., Biotechnology students through a
3 credit course under Choice Based Credit System. Doctoral students are
utilizing the facility for solving their research problems using bioinformatic
tools.
(b) E-Mail and Internet Facility: The BIF is regularly providing INTERNET
facility to all the interested users working in the area of biotechnology and
related areas through BSNL (2 MBPS broadband) and University server.
The scientists and researchers are regularly using this facility for literature
search and as well as for net surfing. Presently 50 M.Sc. students, 12
research scholars and 5 faculty members are regularly using this facility
apart from students and teachers/scientists from neighbouring Institutions.
(c) Access to Printed Journals and Online access to E- Journals
1. M.Sc., Biotechnology Programme- offered since 2002 in which there is a 3
credit course on Bioinformatics. All the candidates who have passes this
Programme have got placement in Research Institutes, Biotech Industries
and Academic Institutions in India and abroad.
2. Doctoral Programme in Biotechnology- offered since 2002.
3. M.E. Environmental Engineering Students of Alagappa Chettiar College of
Engineering and Technology (TN Govt. College affiliated to Anna
University) are taught on Environmental Microbilogy and recombinant
DNA Technology since 2004.
Marine bacteria which have been identified through 16S rRNA and known (by
in silico analysis) for production of antiviral compounds are being subjected to
screening for antiviral compounds against aquaculture pathogens.
1. A collaborative Project Biotechnology for Leather: Towards Cleaner
Processing is being carried out with the collaboration of 11 other National
Institutes/Universities under the New Millennium Indian Technology
Leadership Initiative (NMITLI) scheme of CSIR.
2. A DBT sponsored Project Evaluation of bacterial diversity associated with
the coral Acropora digitifera by 16S rRNA gene sequences and screening
for antiviral activity against the aquaculture pathogen blotched snakehead
327
virus (BSNV) is being carried out in collaboration with the Fisheries
College & Research Institute (Tamil Nadu Veterinary and Animal sciences
University), Tuticorin.
Ribosomal data base for the marine bacteria associated with coral reefs,
sponges, marine sediment and sea water are being established which will
pave the way for sustainable tapping of marine microbial wealth for
biotechnological prospects and protection of marine environment.
1. Ravi AV, Musthafa KS, Jegathammbal G, Kathiresan K and Pandian SK (2007)
Screening and evaluation of probiotics as a biocontrol agent against pathogenic Vibrios in
marine aquaculture. Letters in Applied Microbiology 45: 219-223.
2. Rajesekar A, Ganesh Babu T, Maruthamuthu S, Karutha Pandian S, Mohan S, and Palaniswamy N
(2007). Biodegradation and corrosion behaviour of Serratia marcescens ACE2 isolated from
diesel-transporting pipeline. World Journal of Microbiology and Biotechnology 23:1065-1074.
3. Rajasekar A, Ganesh Babu T, Karutha Pandian S, Maruthamuthu S, Palaniswamy N and
Rajendran A (2007). Role of Serratia marcescens ACE2 on diesel degradation and its influence on
corrosion. Journal of Industrial Microbiology & Biotechnology 34:589-598.
4. Rajesekar A, Ganesh Babu T, Karutha Pandian S, Maruthamuthu S, Palaniswamy N and
Rajendran A (2007). Biodegradation and corrosion behaviour of manganese oxidizer Bacillus
cereus ACE4 in diesel transporting pipeline. Corrosion Science 49: 2694-2710.
5. Kiruthiga PV, Beema Shafreen R, Karutha Pandian S and Pandima Devi K (2007). Silymarin
protection against major reactive oxygen species released in environmental toxins: Exogenous
H
2
O
2
exposure in erythrocytes. Basic & Clinical Pharmacology & Toxicology 100: 414- 419.
6. Kiruthiga PV, Beema Shafreen R, Karutha Pandian S, Arun S, Govindu and Pandima Devi K
(2007). Protective effect of silymarin on erythrocyte haemolysate against benzo(a)pyrene and
exogenous reactive oxygen species (H
2
O
2
) induced oxidative stress. Chemosphere 68:1511-1518.
7. Ramseh M, Marx R, Mathan G and Karutha Pandian S. (2007). Effect of fungicide bavistin on in
vitro plant conversion from sodium alginate encapsulated uninodal microcuttings of
micropropagated Bacopa monnieri (L.) A Pharmaceutically valuable ayurvedic herb. Journal of
Environmental Biology (In Press).

Bacterial genomic sequences associated with virulence will be analysed with
special emphasis on pathogenecity islands and M genes.
Workshop Title Duration No. of Participants
1. National Workshop on Mar 14-16, 2007 75
Genomics, Proteomics
and Bioinformatics
2. National Workshop on Jan 07-09, 2008 25
Genome and Proteome
Analysis
allied areas. In this you may highlight the details like number of paper
published/ number of papers published with the help of your centre, how
your centre is promoting various activities of your organization and
No. of M.Sc., Biotech Students trained 50
No. of Ph.D. Scholars Passed out 01
No. of Ph.D. Scholars currently availing the facility 10
No. of Papers Published 07
Workshop Manual Released 01
328
No. of candidates trained through Workshops 100
Generation of comprehensive genomic and proteomic database for the microbes from
Gulf of Mannar.
Organization of one-week training workshop for the teachers from Government and
Government aided colleges from the affiliated colleges of Alagappa University and from
other parts of the country during Nov 2008.
Undertaking research in the area of Marine Microbial Genomics for biotechnological
prospects and for protecting the environment.
Development of ribosomal database for the marine bacteria associated with coral reefs,
sponges, marine sediment and sea water for sustainable tapping of marine microbial
wealth for biotechnological prospects and protection of marine environment.
Additional Details:
Name of the Coordinator: Prof. S. Karutha Pandian
Postal Address : Coordinator
Bioinformatics Infrastructure Facility
Alagappa University
Karaikudi 630 003, Tamil Nadu
Phone Number: 04565 225215
Fax No.: 04565 225202
Email: sk_pandian@rediffmail.com
Website: www.alagappabiotech.org; www.alagappauniversity.ac.in

Name of Contact Person(s): Prof. S. Karutha Pandian
Email: sk_pandian@rediffmail.com

329
Bharathiar University, Coimbatore
Coordinator : Dr. P. Shanmughavel

The post graduate course in bioinformatics was commenced in Bharathiar
University during 2001 for the first time in India. In endorsement of the
massive research activities performed by the Bioinformatics Division, it has
become an independent department of the university during the academic
year 2006. It fosters research and developmental activities in major thrust
areas like Nano Science and Drug delivery, Molecular modeling and Drug
Design, Comparative Genomics, Computational Biology, Biodiversity
Informatics and Phytomatics. The department is engaged in various
innovative projects in the disciplines mentioned, supported by National and
International agencies like DBT, UGC & ITTO, Japan. The department also
conducts M.Phil and Ph.D courses.

institution.
Nano Science and Drug delivery, Molecular modeling and Drug Design,
Comparative Genomics, Computational Biology, Biodiversity Informatics and
Phytomatics.

3. Area of Specialization of the centre: Computational Biology and
Bioinformatics

Three Research Schemes Awarded and three conferences/Workshops
conducted.

Computer & Communication facility 11 nos of Intel Pentium, 5KVA online
UPS with 10 Nos of batteries, ISDN Router, Sun Netraj Server, Unix based
student workstation,LCD Projector and Scientific Software packages Bio-
Suite are available.
A database on The Digitized Inventory of Tropical Timber Resources of
India is completed.

absorption status)
Three Teaching staffs, two office staffs are permanent. Nearly 15 scholars
pursuing Ph.D and 8 scholars doing M.Phil in Bioinformatics.
Teaching and Research
Development of Database and Software

330
All the post graduate and diploma students were easily absorbed by the
Bioinformatics company and research institutions.

9. Initiative to validate the outcome of bioinformatics resources .
Awarded three M.Phils in the field of Bioinformatics.
10. Collaborative works/ initiatives with the following institutes.
1.Global Forest Information Service (GFIS), Vienna, Austria. 2. Global
Biodiversity Information Facility (GBIF), New Zealand. 3. Indian Institute of
Technology, New Delhi 4. Indian Agricultural Research Institute, New Delhi 5.
University of Delhi, New Delhi.

11. Databases/ Software packages developed:
Database Model for Industrial Plantations.
Digitization and Automation of Tropical Forest Biomass, 3. Nucleotide and
Protein Manipulation tool.

Ten papers and two Conference Proceedings.
13. Initiation of R&D activities in Bioinformatics .M.Phil and Ph.D.
Three seminars and workshops are conducted and more ten 800 participants
benefited.

areas.
Two Faculty development programmes (Orientation) conducted by current
academic year. (More than 40 University/college teachers trained).

Our future activities include development of Software and databases.
Additional Details:
Name of the Coordinator: D Dr r. . P P. . S Sh ha an nm mu ug gh ha av ve el l, ,
Postal Address:
D Dr r. . P P. . S Sh ha an nm mu ug gh ha av ve el l , , C Co oo or rd di in na at to or r, , B Bh ha ar ra at th hi ia ar r U Un ni iv ve er rs si it ty y, , C Co oi im mb ba at to or re e - -
6 64 41 10 04 46 6
Phone Number : +919486446101
Fax No. : +91-422-2422387
Email : shanvel_99@yahoo.co.in
Website : http://www.b-u.ac.in
Name of Contact Person(s): D Dr r. . P P. . S Sh ha an nm mu ug gh ha av ve el l, ,
Email: shanvel_99@yahoo.com
331
CCS Haryana Agricultural University, Hisar
Coordinator : Dr. Sudhir Kumar

The Bioinformatics Section, CCS HAU, Hisar was granted a fund of Rs. 20.0
lacs for the establishment of BIF. The Section has added hardware and
software and has a leased line Internet connectivity of 512 Kbps in place.

The Section started M. Sc. Programme in Bioinformatics in 2004.
A separate infrastructure with latest hardware and other infrastructural
facilities is in place in the College of Basic Sciences & Humanities.

institution:
Micro-propagation of crop plants
Development of transgenics
Molecular mapping, gene tagging and Marker assisted selection
DNA Fingerprinting
Value addition to plants and microbes
Teaching Bioinformatics
Bioinformatics in Agricultural Sciences (rice crop of interest)

Teaching
Consultancy to researchers
PCs 50
Servers 2
8-Node Cluster 1
Internet connectivity 512 KBPS
Telephone and Fax 01662-289114, 234003; 284310 (Fax)
GPL software, MOE, ChemOffice, PAUP
PDB (local mirror)
absorption status) NIL
332
Teaching, Internet access, consultancy

M.Sc. Bioinformatics started in 2004
Placement 2004-06 batch - 16/17
2005-07 batch - 9/13
NONE as the BIF is one year old only
Creation of Multimedia database of crop plant diseases (with the Department of Plant
Pathology, CCS HAU, Hisar)

Database NIL
Software One (Statistical analysis for agricultural Scientists)
1. G. Bala and Sudhir Kumar. QSAR studies on HIV-1 Reverse
Transcriptase Inhibitors. Proceedings of National Conference on
Advances in Chemical Engineering and technology. March 26-27, 2007,
101-108.
2. Jyotika and Sudhir Kumar. Virtual Screening on HIV-1 Reverse Transcriptase
Inhibitors. International Conference on Molecular Cellular Biology and
Therapeutics of HIV and Associated Viral Infection(CoMBaT HIV), 12-14
th

January,2007

Parallelization of bioinformatics algorithms
Tools for sequence analysis and gene finding
Nil, One proposed March 3-12, 2008
areas
Imparting education to PG students of Bioinformatics
Teaching basic bioinformatics course to Biotechnology students
Assisting in data analysis to researchers
To start Ph.D. in Bioinformatics
333
Plant genome annotations and analysis

Additional Details:
Name of the Coordinator: Dr. Sudhir Kumar
Postal Address: Bioinformatics Section, College of Basic Sciences &
Humanities, CCS Haryana Agricultural University, Hisar
125 004
Phone Number: 01662-289114, 234003; Mobile: 9354320276;
Email: sudhir@hau.ernet.in; Website:
http://hau.ernet.in/bioinfo
Name of Contact Person(s): Dr. Sudhir Kumar
Email: sudhir@hau.ernet.in
334
Dr. B. R. Ambedkar Center for Biomedical Research, Delhi
Coordinator : Dr. Madhu Chopra

ACBR is running courses M.Sc. and M. Sc.-Ph.D. in biomedical sciences
covering almost all subjects of biotechnology and related fields. Students at
ACBR study courses like Biochemistry, Genetics, Medicinal Chemistry. The
Bioinformatics facility thus developed over years has been strengthened by
purchasing 3 more workstations to existing 3 nos. Software licenses have
been increased from one to three on various modules of INSIGHT II. A
workshop has been organized on 28-20 January 2008 for 15 participants to
give hand on training to them on available software modules. A list of
publication in the year 2006 has been provided to show scientific progress
during this period.

institution
Following are the fields of research in biotechnology. The mandate is to
perform and promote high quality research in Biomedical Sciences, in areas
that touch human health, such as:
Medicinal Chemistry; Bio-organic Chemistry; Protein Chemistry;
Proteomics; Natural Product Chemistry; Bio-Inorganic Chemistry; Drug
Metabolism and Toxicology; Pharmacology; Medical Biotechnology;
Molecular Genetics; Developmental Biology

Medicinal Chemistry and Natural Products
Molecular Genetics and Medical Biotechnology
Clinical Biochemistry and Immunology
New drug discovery and commercialization

1. 6
th
Annual Symposium on Frontiers in Biomedical Research November
30-December 2 2006
2. Summer undergraduate Research Training Programme (Annual)

iv. Computer & Communication facility
Computer Labs with A Cs 2
Capacity of Computer Labs 12 X 2= 24
Lease Line connection provided by the University.
No. Of
Computers
Configuration Used as
1 SGI Silicon graphics, Workstation Research Facility, Insight II and
Catalyst
6 HP 4300 workstation Research Facility, Insight II and
Calalyst
17 P-4, RAM 512, HDD 80 GB Other softwares : Accelrys GCG ,
TSAR, Statistical Analysis Tool, DEEP
VIEW etc.
40 P-3, RAM 256, HDD 20 GB
11 P-2, RAM 256 + 32 MB, -Do-
335
v. Scientific Software packages
S.
No.
Software Year
(Purchase)
USEFUL TOOL
1. Insight II

2003 Protein structure prediction and
modeling Drug design. Docking
2. CATALYST 3D QSAR, pharmacophore modeling
3. Accelrys Package
-GCG
2003 Protein and nucleic acid seq analysis
tool
4. TSAR 2003 2 D QSAR
5. Statistical analysis
Tool
2006 Statistical data & Analysis tool
6. Dragon 2003 Descriptor calculator for QSAR
7. DEEP VIEW -- Basic visualiser
8. Graph Pad Statistical Analysis
9. AMBER 2005 DNA-Protein interaction and
modeling
absorption status)
Professor= 1; Reader= 2; Lecturer = 5

7. Types of services provided: Teaching and Research

Ph.D. Students : Completed : 65, Ongoing : 60
Students Qualified CSIR-UGC-NET Examination (1999-2006): 140
Career options by students: Research 97 % ; Other Jobs 3 %

9. Collaborative works/ initiatives: Various projects are under progress with
national and international Institues such as with INMAS, DEPAS (DRDO), IGIB
(Mall Road, VPCI (DU), ICPO (Noida), ST In Corporation, Italy; SIDA Sweden

Ganapathi M, Singh G.P, Sandhu K.S., Brahmachari S.K., Brahmachari
V. 2007. A whole genome analysis of 5 regulatory regions of human
genes for putative cis-acting modulators of nucleosome positioning. Gene,
391, 242-251.
Bengani H, Ganapathi M, Singh G.P. and Brahmachari V. 2007. Mining
of Putative cis-acting Elements for Chromatin Mediated Regulation of Hox
Genes in Mammals by in-silico Analysis. J. of Experimental Zoology (Mol
Devel & Evolution), 308:1-12.
Bakshi R., Mehta A.K., Sharma R., Maiti S., Pasha S., Brahmachari V.
2006. Characterization of a human SWI2/SNF2 like protein hINO80:
Demonstration of catalytic and DNA binding activity. Biochemical and
Biophysical Research Communications 339, 313320.
Madhu Chopra and Anil K. Mishra, Ligand-Based Molecular Modeling

Study on Chemically Diverse Series of Cholecystokinin-B/Gastrin
Receptor Antagonists: Generation of Predictive Model Journal of
Chemical Information and Modeling, 45, 1934-1942, 2005.

336
Invited lecture Three dimesional pahrmacophore modeling and database
searching for drug design and development of target specific
pharmaceuticals by Dr. Madhu Chopra, December 2006, Frontiers in
Biomedical Research, December University of Delhi
Workshop on Pharmacoinformatics: Tools for Drug Target Identification at
NIPER March 14
th
-16
th
,2007, Computer aided drug design of novel
NSAIDs as selective cyclooxygenase 2 inhibitors as anti cancer agents
Ruby Gupta and Madhu Chopra Poster presentation by RG

11. R &D activities in Bioinformatics
i. Design, Synthesis and Evaluation of Non Peptidic CCK-B/Gastrin
Receptor Specific Antagonists for Targeting CCK-B receptor Expressing
Tumors.
ii. Computer-Aided Design of Novel NSAIDs as Selective Cyclooxygenase-2
(COX-2) inhibitors to target tumors: Mechanistic study of anticarcinogenic
role of NSAIDs
iii. In Silico Prediction : mechanism of transacetylation activity of Calreticulin.
iv. Mining the Human Genome for Global regulatory Genes: Characterization
and Functional analysis
v. Role of Epigenetics in Genome Function and Transactions.
vi. Cloning and functional characterisation of ETO-binding protein in normal
and acute myeloid Leukemia.

12. Details of Training/ Workshop organized and total no. of user trained :
Being organized in January 2008 as detailed below:

7
th
Annual Symposium On Frontiers In Biomedical Research (Fbr-
2008):Workshop on Bioinformatics and Molecular Modeling in Drug
Design 28
th
-30
th
January, 2008
Total no. of participant to be trained: 15


Year of Course Commencement : 1998 (M.Sc.-Ph.D. Combined
Programme in Biomedical Sciences)
Visiting/Guest Faculty: 20
Research Publications (Last 6 years) : 75
Patents & Technologies Transferred : 5
Number of Projects: (i) Industrial : 3 (ii) Government Agencies : 48

Name of the Coordinator: Dr. Madhu Chopra
Postal Address: Dr. B. R. Ambedkar Center for Biomedical Research,
University of delhi, Delhi 110007
337
Phone Number 011-27666272 Mobile:09810488199
Website:www.acbrdu.edu
Name of Contact Person(s): Dr. Madhu Chopra
Email: madhu_india@hotmail.com;
mchopradu@gmail.com

338
Fakir Mohan University, Balasore,
Coordinator : Prof. Amarendra Narayan Misra


The Bioinformatics Centre of Fakir Mohan University, Vyasa Vihar, Balsore-
756017, Orissa is now established after procuring all the necessary hardware
suggested by Department of Biotechnology (Govt. of Inida, vide DBT order
No. BT/BI/04/055/2001 dt. 22 September 2006). Due to prohibitive cost and
other limitations, the softwares could not be obtained so far. Once the BIF is
shifted to the new campus of the University during February-March 2008, the
Centre will be fully functional.

institution:

Stress signaling and adaptive strategies in living systems, Marine
Biotechnology, Biosensors, Nano-biology, Blood related problems.


Teaching in Biotechnology and Biosciences.


Establishing the infrastructural facility.

A. Computer & Communication facility: Only computers are procured as per
DBT specifications. Steps are being taken by the University for the
procurement of communication facilities will be installed.
B. Scientific Software packages: Nil
C. Databases & other information resources: Nil

absorption status): Nil

7. Types of services provided: Services will start only when the Centre is
established.

8. Educational activities with details of placement: Not applicable.

9. Initiative to validate the outcome of bioinformatics resources: Not
applicable.

10. Collaborative works/ initiatives: Collaborative works are initiated with
the Department of information and Communication Technology.
339
An initiative is made to establish long term collaborative work with CIFA,
OUAT and other University Institutes having Bioinformatics and Biosciences
research and teaching programs.

11. Databases/ Software packages developed: Nil


13.Initiation of R&D activities in Bioinformatics: Two students are enrolled for
Ph.D. degree related to Bioinformatics.

14.Details of Training/ Workshop organized and total no. of user trained:
March 24-25, 2007. Users trained 50.

services offered etc. Once the facility is fully functional at a permanent floor in
the School of Biotechnology building, which the University projects to be
ready by February 2008, various activities of the Bioinformatics Centre will be
started. This includes starting of M.Sc. Bioinformatics course initially, before
moving to other Bioinformatics activities. At present the students and faculties
of the Department are trained in various aspects of Bioinformatics.

16. Future activities: Teaching and research programs in Bioinformatics.

Additional Details:
Name of the Coordinator: Prof. Dr. Amarendra Narayan Misra
Postal Address: School of Biotechnology,
Fakir Mohan University,
Vyasa Vihar, Balasore-756019, Orissa State
Phone Number: 06782-261580
Mobile: 9437295915
Email: misraan@yahoo.co.uk

(i) Prof. Dr. Sukadev Nanda,
Vice-Chancellor,
Vyasa Vihar, Balsore-756019,
Orissa State.
iii) Mr. S. Marandi,
Controller of Finance,
Vyasa Vihar, Balsore-756019,
Or i ssa St at e.
ii) Dr. A.C. Kar,
Registrar,
Vyasa Vihar, Balsore-
756019,
Orissa State.
340
Forest Research Institute - Dehradun
Coordinator: Er. Neelesh Yadav

Forest Research Institute Dehradun is received the grant for BIF on
November, 2007. A core group has been created in the institute for the
special research initiative for Bioinformatics. FRI is the premier institute of
forestry research in the country. The Institute also administered training of
forest officers and forest rangers in the country and after Independence it was
aptly renamed as Forest Research Institute and Colleges. The separate
Bioinformatics lab is under progress, hardware/ software is available but
procurement of new tools is under process.

institution: The FRI has a well established infrastructure of laboratory,
library, herbarium, arboreta and experimental field areas for providing
scientific and training services. The genetics & tree propagation , Forest
pathology (Molecular biology lab) , tissue culture discipline , Nanotechnology
research in forest products, Statistical modeling of trees , of are the main
research domain those are working biotechnology aspect of forestry.

Forestry Biodiversity Informatics ,Bioinformatics Education & Human
Resource Development , Database of DNA fingerprinting of important tress
species like Sal, Deodar, Shisham, Eucalypts etc. ,Medicinal plants of forests,
Forest Products, Forest Soil and Land Reclamation, Genetics and Tree
Propagation, Non-wood Forest Products, Pathology, Silviculture

4. Major activities of the centre during the year 2006-07 : NA

Computer & Communication facility : The BIF centre has order to procure
the 10 Desktop computers (Core 2 duo based processor) , Web server,
database server, Internet connection is available through LAN in whole
campus, but process for separate leased line is under progress.

Scientific Software packages: SPSS, Windows server Standard 2003,
Visual studio .NET (1 User), MS-Office 2007 , SQL Server 2000, MySQL
server 5.0 , PHP 5, Apache server, (Open source soft wares),

Databases & other information resources:
vii. Web based interactive database for Botany Herbarium (Approx
3,30,000) has been develop by the centre and the data entry work is
going on.
viii. The database of Forest insects is developed.
ix. The Development of Medicinal pants of northern India in under
progress.
absorption status)
341

Sl.No. Name Designation Specialization Period of
Working
Absorption
Status
1 Er. Neelesh
Yadav
Coordinator Bioinformatics,
data mining,
Communication
,
Since Year
2003 as IT
Scientist
Permanent

7. Types of services provided : E-mailing ,Internet access, LAN management
,System management, Web designing & hosting, Software development,
Database development on forestry reserach,Hardware maintenance of FRI,
Digitization of old collections of forestry, Human Resource Development in
Bioinformatics at FRI University-Dehradun, R&D and S&T Publications,
Computational services, Information support to whole FRI.

8. Educational activities with details of placement: FRI was conferred the
status of Deemed University in 1991 with the objective of imparting education
in different branches of forestry and environment. Courses being run by the
FRI University are:

Two year Degree Courses:
M.Sc.Forestry (Economics and Management)
M.Sc. (Wood Science and Technology)
M.Sc. (Environment Management)
One Year Diploma Courses:
Post Graduate Diploma in Management of Non-Wood Forest Product
Resources
Post Graduate Diploma in Biodiversity Conservation
Six Month Certificate Course:
Certificate course in Pulp & Paper Technology
Doctoral Programme:
Under its Doctoral Programme the University also confers Ph.D. Degree in
various fields related to forestry and environment.

9. Initiative to validate the outcome of bioinformatics resources : The
activities of the center has helped in popularizing the concept, utilities and
tools of Bioinformatics among the similar organizations and individuals.
Center has successfully meet their information requirements. New databases
in the areas of forestry research have been generated. The network and
services created is playing instrumental role in communication, database
research, patent searches and market search. Centre is also very useful for
biology teaching for FRI University-Dehradun.

10. Collaborative works/ initiatives : IARI, IIT Roorkee, Forest Survey of India,
IGNAF-Dehradun, ENVIS center of FRI,

11. Databases/ Software packages developed : 1.Digital Herbarium System of
FRI. 2.Insects Information System.

342
Forestry Bioinformatics, Neelesh Yadav, a paper presented in Scientific
Data and Knowledge within the Information Society ,20
th

CODATA International conference, Beijing, China.

Role of Bioinformatics in Forestry Research, invited lecture delivered at
national Biotechnology conference -2006: CurrentTrends & Future
Perspectives at IIT-Roorkee, by Neelesh Yadav and published in
proceedings.

13. Initiation of R&D activities in Bioinformatics: Since its inception the Centre
has focused on R & D activities particularly in the area of biodiversity
database development of computational tools for its storage, retrieval,
analysis, interpretation and computer graphic modelling. The centre has also
focused on the development of appropriate tools for integrating the
information resources of BTIS Centres. The centre is tryng to become CoE for
Bioinformatics forestry Research.

NA


- NA (Because BIF FRI-dehradun recently established)
To establish a national database repository for forestry biodiversity
informatics and provides biodiversity data analytic tools and techniques.
To develop a web portal on forestry Bioinformatics and integrate the
information and all other resources of ICFRE institutes with BTISnet.
To establish a comprehensive database including all information of plants
growing in India particularly and genetical data bank of imp. Plants
species.
To establish a web portal for establishing collaborative ventures with the
institutions / researchers working on biodiversity matters and integrating
the information resources.
To establish genetic sequence database of the intraspecific variants of the
endemic plants of the Himalayan region.
The centre would link with other R & D / Educational institutions for
establishing regional sub-centres throughout Uttarakhand state for
biodiversity data documentation.
The data acquisition related with the plants of Uttarkhand, UP, Himachal
Pradesh, J&K will be carried out in these regional centres. Data
management, data analysis and interpretation, formulation of novel
strategies and R & D initiatives for sustainable utilization of the genetic
343
resources will also be carried out through cooperative functioning of the
main centre and the sub-centres.
To develop FRI-Dehradun as a Nodal Centre for National Forestry
Bioinformatics Research & Development which will be an information and
computational solution provider for forestry Biodiversity data management,
data analysis and interpretation

Additional Details:
Name of the Coordinator: Er. Neelesh Yadav
Postal Address: 1, Hill Road, FRI Campus,
P.O. New Forest-Dehradun (248006)
Phone Number:0135 2754023 ext 4234 Mobile: 9411385495
Email: neeleshy@yahoo.com Website: www.fri.res.in

Name of Contact Person(s): Er. Neelesh Yadav,
Scientist Incharge, IT Cell, FRI
Email: neeleshy@yahoo.com
344
Guru Jambheshwar University of Science & Technology, Hisar
Coordinator : Prof. J. S. Rana

i. The Executive Committee as per DBT guidelines has been approved.
ii. Three bays air-conditioned laboratory has been established from BIF.
iii. Independent Telephone line along with broad band internet by BSNL
installed from BIF.
iv. 13 HCL Computers purchase through this grant.
v. Introductory Bioinformatics course introduced in M. Sc. Biotechnology
and M.Tech. Nano Sc. & Tech

institution
Sl.
No
Name of Student Name of the Ph. D. Research title Name of the
Supervisor
Al ready Completed
1. Dr. Purkayastha
Sharmishtha
Race identification of
Macrophomina phaseolina causal
agent of root rot of cluster bean
using molecular markers.
Prof. Ashok Chaudhury
2. Dr. Anita Punia Studies on DNA fingerprinting of
Some Superior Guar Genotypes by
RAPD.
3. Dr. Pal Minakshi In Vitro Culture and induction of
Shikonin Production in Arnebia.
4. Dr. B. Kaur Identification of races of Xanth
Axonopodis pv. Cyamopsidis using
molecular markers.
Ph. Ds under Progress
5. Ms. Gaurva Priyanka Genetic Transformation of Rice for
Enhancement of Salinity Tolerance.
6. Ms. Bansal Monika Genetic Transformation of Tomato
(Lycopersicon esculentum) for
Enhancement of Salinity Tolerance.
7. Ms. Praveen Dahiya Isolation, Screening Purification &
Characterization of Microbial
Lipases.
Dr. Neeraj Dilbaghi
8. Mr. Umesh Gautam Biochemical and Molecular Marker
Studies for Bread Quality
Improvement in Wheat.
9. Ms. Pooja Arora Molecular approaches for the
development of SCAR assay as a
diagnostic tool for the detection and
distribution of dsRNA among
isolates of Macrophomina
phaseolina.

10. Mr. Rakesh Yadav Studies on Genetic Modification of
Lignin Biosynthesis Pathway in
Poplars for Low Lignin Content.
11. Mr. S. T. Bharani
Kumar
Characterization of myostatin gene
in indigenous chicken breeds.
Dr. Neeraj Dilbaghi
12. Mr. Raman Kumar Bioremediation of waste water for
heavy metals through microbes.
Dr. Namita Singh
13. Ms. Sarika Poonia Low temperature acclimatization and
its regulation in the Cyanobacterium
Spirulina.
Dr. Namita Singh
345
14. Ms. Meenu Rani Studies on genetic diversity in (Aloe
bardabensis) genotypes using
molecular markers.
Dr. Vinod Chhokar
15. Mr. Yogesh Kumar Marker assisted gene pyramiding to
enhance rust resistance in wheat.
Dr. Vinod Chhokar
16. Mr. Sandeep Jaglan DNA fingerprinting of some
important lines of Isabgol.
Dr. Priyanka Siwach
17. Ms. Priyamvada Molecular mapping of leaf rust
resistance gene LR34 in wheat.
Dr. Priyanka Siwach
18. Ms. Uma Gaur Genetic characterization of Indian
duck populations (Anas
platyrhynchos) using molecular
markers.
19. Ms. Suman Bangar In vitro culture and genetic diversity
studies of Fenugreek using
molecular markers.
20. Ms. Geetu Identification of SNP markers for
wool genes indigenous sheep
breeds.
Prof. J.S.Rana
21. Ms. Manju Rani Characterization of Helicoverpa
armigera for their insecticidal
resistance in semi and cotton eco
system.
Prof. J.S.Rana
22. Ms. Manju Yadav Molecular characterization of
mustard (Brassica juncea)
genotypes for their resistance
against mustard aphid.
Prof. J.S.Rana
23. Ms. Seema Genetic characterization of cotton
varieties for their resistance against
sucking pests.
Prof. J.S.Rana
24. Mr. Alok Pandey Study on gene expression in buffalo
in vitro matured oocytes and SCNT
produced cloned embryos.
Dr. Namita Singh
25. Ms. Sonia Kohar Production purification &
characterization of microbial
Phytase enzyme & its application in
animal feed.
Dr. Namita Singh
26. Mr. Anil Kumar Molecular characterization of major
candidate genes associated with
milk fat % in Indian buffaloes.
Dr. Vinod Chhokar
27. Mr. Vikas Beniwal Purification, characterization
molecular gene cloning, sequencing
of tannases form bacteria.
Dr. Vinod Chhokar
28. Ms. Mukta Agarwal Identification of molecular Markers
Related to Chapati Quality traits in
Wheat.
Dr. Vinod Chhokar
We specialize in the areas of food, industrial, plant and animal biotechnology
The Executive Committee as per DBT guidelines has been approved.
Three bays air-conditioned laboratory has been established from BIF.
Independent Telephone line along with broad band internet by BSNL installed
from BIF.
13 HCL Computers purchase through this grant.
Introductory Bioinformatics course introduced in M. Sc. Biotechnology and
M.Tech. Nano Sc. & Tech.
346
We have developed a full fledged alboratory with internet facilities for about
35 students. The work on further improvements in the database
management across the department is underway and would be completed
very soon.
In addition to the entire Window package we have procured the educational
tool of the basic software package for biology teaching in this laboratory
Databases & other information resources:
We plan to procure more databases of use in this laboratory on receipt of
funds for the purpose
absorption status)

Sl.
NO.
NAME OF THE
STAFF
DESIGNATION WORKING
SINCE
ABSORPTION
STATUS
(YES/NO)
*
1. Dr. J.S. Rana Professor&
Chairman
2006 YES
2. Dr. Ashok Chaudhury Professor 2001 YES
3. Dr. Neeraj Dilbaghi Reader 1998 YES
4. Dr. Namita Singh Sr Lecturer 2001 YES
5. Dr. Vinod Chhokar Sr Lecturer 2001 YES
6. Dr. Priyanka Siwach* Sr Lecturer 2001 YES
7. Anil Kumar Lecturer 2005 YES
8. Dr. Rajesh Thakur Lecturer 2006 YES
9. Santosh Kaushik Lecturer 2006 YES
10 Sandeep Kumar Lecturer 2006 YES
11. Dr. Alka Rao Lecturer 2006 YES
At the moment this laboratory is open for access by all the students
We are in the process of developing our facility for this purpose and would
update it further in the coming year for the purpose of validating the outcome
qualitatively
We collaborate with the department of Biotechnology and molecular Biology,
CCS Haryana Agricultural University Hisar, Central Institute of Research on
Buffaloes, National research centre for equines and Centre of Plant
Biotechnology Hisar on various aspects of research and teaching
10. Databases/ Software packages developed : None
We are still developing our facility for this purpose and would initiate the research
activity in the coming academic session.
We propose to organize the training in the month of February, 2008
347
14. Impact shown by your centre on the growth of biotechnology and allied areas. In this you
may highlight the details like number of paper published/ number of papers published with the
help of your centre, how your centre is promoting various activities of your organization and
neighboring institutions, manpower trained, tools developed, patents & copyrights acquired
and other services offered etc.
The Department of Biotechnology is an upcoming Department of the region and is competing
well in the research areas like food biotechnology, industrial Biotechnology, plant
biotechnology, Nano science & Technology. Within seven years of its establishment the
department has earned a reputation of a progressive department in the academic circles.
This can be judged by the fact that the department has earned several research projects from
various funding agencies like DBT, DST, Govt. of India, UGC, State level Science and
Technology department. The department is continuously working towards developing and
strengthening the existing faculties and creating the new facilities in the innovative
programme of research like Bioinformatics. Therefore it is imminent to have the facilities like
Bioinformatics for biology teaching to meet the increasing demand o the qualified technocrats
in this specialized field.
To strengthen the research facilities for Bioinformatics
To start M.Sc. Bioinformatics course specialized in the areas of Food and
industrial Biotechnology
Gene expression data analysis (using dimensionality reduction and supervised/unsupervised classification
methods, genemarker recognition and mining, and analysis of gene-expressional time series)
Protein structure alignment methods, including computational discovery of embedded sequence-structure-
functional relationships
We plan to develop our full fledged facility of Bioinformatics in the coming
year alongwith the development of

Additional Details:
Name of the Coordinator: Prof. J.S.Rana
Postal Address: Department of Biotechnology, Guru Jambheshwar University
of Sc. & Tech. Hisar-125001
Phone Number:01662-263165
Mobile: 09896300256 Email: jogenderrana@hotmail.com
Website: www.gju.ernet.in
Name of Contact Person(s): Prof. J.S. Rana
Email: jogenderrana@hotmail.com
348
HNB Garhwal University, Garhwal
Coordinator : Prof. Asha Cahndola-Saklani

We have been experimenting, at a miniscule level, with innovative methods like
computer-aided teaching (CAT), inquiry based projects, Learn-while- Serve Biology
outreach programs with a view to improve Biology & allied teaching in rural Himalaya
for several years. Since 2006 these have been brought under the frame-work of
DBT-BIF Centre catering to various levels. Thus:
Career counseling & research orientation- 10+, UG students
Training in analytical & Biological techniques including molecular,
research methodologies, internet access, search & retrieval, data base
development & mining, application of statistical and Bioinformatics tools
PG & research
Sensitization of local students through innovative student - community
interactive research projects towards Biology based programs with special
reference to biodiversity, bio-resource technology (including
entrepreneurship) and community health care, simultaneously generating
data base amenable to application of Bioinformatics tools.
Preparation of course material CD ROMs, Web based etc.
Introduction of Bioinformatics PG courses (already approved by BOS,
HNBGU)
institution.
Genome diversity of Himalayan human, bird & fish fauna (39 Acc Nos from NCBI
with CCMB); Database generation on IDD and thyroid hormone profiles,
Genetic/molecular basis of neuro-dev disorders, phyto-chemistry, natural dyes,
microbiology
Environmental Endocrinology, Immunoassay technology, Conservation Biology, Molecular
Physiology, Mol Phylogeny
BIF serves as a viable student participatory platform in a warm ambience with inquiry
based learning as an enjoyable experience motivating critical thinking thru interactive
brainstorms, audiovisual seminars, computer sessions, GDs, hands-on demos,
nature trails & bird-watching. UG PG students visit the centre daily in spare time.
Introduced m-education (mobile technology) in biology & allied subjects for e-
learning and information retrieval at SRT (rural) Campus of HNBGU
(UG/PG/Research)
Set up a network for Biology & allied teaching- support & counseling for 10+ students
via media seven schools in rural Himalaya (within 10 km radius of the BIF Centre)
Trained about 40 UG students in computer applications who in turn trained 5
students each from six neighboring schools
Organised 04 Workshops and 03 Learn-while Serve Biology outreach camps in
villages
Two Bioinformatics student projects (Elective MSc Biotech course)
Research: Molecular phylogeny of Himalayan fish Schizothorax (D Phil thesis- with
CCMB); generated data base on Iodine deficiency disorders, thyroid hormone
profiles, health & nutritional status in rural Himalaya; database on genome diversity
Him. populations; Commenced work on Mol phylogeny of Him finches & genetic
basis of neuro-dev disorders.
349
A. Computer & Communication facility : SRT Campus 02 Servers,10 computers, 02
Telephone connections. 04 Mobile modems; Chauras campus: 05 computers 02
servers
Scientific Software packages: GraphPad Prism, Costat, Instat, SPSS, MEGA,
PHYLIP


7. Types of services provided Teaching support thru CD ROMs, Internet, AV
seminars, computer sessions, WS, Sensitization to biodiversity/bioresources/health
care etc thru Bio-outreach camps. Aid student projects/research in data analysis.
8. Educational acti vities with details of placement: Bioinformatics offered as 01
compulsory credit and 09 credit Elective course in MSc Biotech/Zoo. 10 students
placed in Univs /instts (including JNU,NC ,CCMB, NII, IIT Powai etc)& MNC eg.
BIOCON, AVENTIS
9. Initiati ve to validate the outcome of bioinformatics resources
Trained 10+, UG, PG students in basic computer education, web based tools
(data mining & data compilation) & motivated them towards careers in
Bioinformatics/BT. A network for CAT was established for neighboring schools within
10 km radius of Centre. BIF services were brought through Biology outreach camps
in interior rural villages of Tehri and Chamoli (15 km from roadhead).
10. Collaborative works/ initiati ves : Following projects/PhD programs undertaken
with-
CCMB Hyderabad: Mol phylogeny of Himalayan finches, Genetic basis of strabismus
NBRI Lucknow: Mol Systematics Sapindus, NDRI Karnal: Probiotic culture,
IVRI Bareilly PCR based detection of Zoonotic Salmonella
IARI Delhi Mol studies maize.
11. Databases/ Software packages developed Database for Iodine deficiency
disorders developed from Himalayan villages & about 5,000 thyroid hormone profiles
generated.
i.A Farswan, Kiran Negi, ACS . XXIII Int Cong Ornithology, Hamburg Germany Aug 2006
ii.Application of Biotechnology and Bioinformatic tools to the science of biodiversity SC
Diyundi et al International symp Biogeography & biodiversity, HNBGU 0rganized by Int
Geography Union May 2007
iii.Adaptation to high altitude: do genes play any role? Diyundi SC et al Int Symp Human
Genetics, JNU 2006
Bioinformatics tools are used in on going researches mentioned above.
Sl.
NO.
NAME OF THE STAFF DESIGNATION WORKING
SINCE
ABSORPTION STATUS
(YES/NO)
*
1. Asha Chandola-Saklani

Coordinator Nov 2006 YES
Regular
2. Atul Kathait

Bioinformatics
Assistant
Jan 2007

No, Ad hoc
3.

Pratap S Bisht

Field Attendant Jun 2007 No, Ad hoc
4. - RA Yet to be appointed

Some Faculty members including Drs PC Lakhera, DK Sharma, N Agarwal, JS Rana
regularly visit the centre for internet and also offer help
Several past trainees are giving their services on Learn while Serve basis.

350
Student Interactive Brainstorm viz. HRD in Science & Technology: for WHAT &
HOW - a Road Map (Higher Edu in UA). Affil College Teachers, students. Lead
discussants from JNU, BHU, IIT Kanpur, RTI, Sci & Tech Councils of UA 1-2 Dec
2006 300 participants
lecture-cum-demo Workshop Diagnostic Tools (PCR/immonobased) & Med Instru
mentation for UG/PG science students. Lead speakers from NIH Bethesda USA,
AIIMS Delhi, PGIMR Chandigarh, HIMS Dehradun 14-15 January 2007. No of
users : 300
workshop on Career orientation in Biotechnology & Bioinformatics for 10+2
Students. SRT Campus, Tehri. 1-5 November 2007 No of users trained: 75
03 Learn-while-Serve student participatory Biology Outreach camps in Tehri &
Chamoli Garhwal, 7-8 days each; covered 13 villages gathering information on bio-
resources, nutrition, health & economic status for database development.
No. of users trained 10 PG, 40 UG, 30 10+2 students.
See column 04
Set up a MobEd lab (Genomic Mobile lab equipped with VSAT) for support of Biology & allied
subject teaching in rural Himalaya to cater to schools & colleges within 30 km radius
Set up a network for Biology & allied teaching- support & counseling for 10+, UG students
and faculty through Biology outreach camps in NW Himalaya (entirely rural)
Develop e-learning course material on CD ROMs, eventually to be available on web.
Commence Advance Diploma or MSc Bioinformatics from July 2008
Organisation of workshops to cater to different levels viz. 10+, UG, PG, Research
Organisation of symposia in the fields of Biological diversity & Health care with a molecules
to ecosystem approach to provide a multidisciplinary platform
Following shall be the thrusts of research (funds from other agencies shall also be generated)
Data base compilation on avifauna / ichthyofauna
Data base generation avifauna, avian song repertoire, incidence of diseases,
diagnostic facilities, mountain bio resources
Phylogeography & Genetic diversity of finches, rudraksh
Molecular basis of diseases
Vocalization analysis in birds with a view to render syllable sequence amenable
for use of algorithms e.g. UPGMA, to understand evolutionary patterns
Set up Centre of Excellence in Bioinformatics in the heart of the Himalaya and reach out to
the entire Stateand eventually to the country and the world
Additional Details:
Name of the Coordinator: Prof. Asha Cahndola-Saklani FASc
Postal Address: Post Box. 45, Srinagar Garhwal Uttarakhand-246174
Phone Number: Mobile 09412018010 Email ashachandola@yahoo.co.in
bifcentrehnbgu@yahoo.co.in Website: under preparation
Name of Contact Person(s): Atul Kathait 9997809655
Email: atulkathait@gmail.com bifcentrehnbgu@yahoo.co.in
351
Holy Cross College, Tiruchirappalli, Tamil Nadu
Coordinator : Dr. Daisy. P


The Bioinformatics Infrastructure Facility at the Dept. of Biotechnology &
Bioinformatics, Holy Cross College was set up in October 2006. BIF, HCC
procures has developed a database in the field of medicinal plants in
treatment of diabetes and a server for the prediction of CpG islands in
genomic sequences. The Facility conducts training programmes in
introductory & advanced level of Bioinformatics for college staff, researchers
and students of neighboring colleges. The Centre also aids in coursework of
the M.Sc Bioinformatics program offered by the Department, besides this two
interdisciplinary courses are offered to the postgraduate students of other
disciplines. The communication facilities at the facility is been upgraded to 1
Mbps leased line internet connectivity from BSNL from the 512 kbps
broadband connectivity.

institution:

The major research activities include isolation and characterization of active
compounds in some indigenous medicinal plants responsible for the
antidiabetic, antioxidant and antimicrobial activity. Four novel compounds
have been isolated and filed for patenting. Docking studies and Insilico
analysis of these compounds are being done


The main area of specialization is Medicinal Plant studies. Apart from
supporting Biotechnology research, the Centre is involved in creating
specialized databases of medicinal plants. Other research works include:
1. In Silico Ligand efficacy testing of a purified antidiabetic compounds
2. In Silico analysis of enzymes of functional importance in medicinal plants.
This includes the study of the whole metabolic pathway, the enzymes
interacting and its products from the annotated entries in biological
databases.

4. Major activities of the centre during the year 2007 - 08:
The DBT sponsored BIF was established in the Department of
Biotechnology, Holy Cross College in October 2006.
Established a leased line connectivity of 1 Mbps speed at the
Bioinformatics centre, from BSNL.
Maintenance and updation of the Facilitys website www.hccbif.org
A database on medicinal plants and a server for prediction of CpG islands
were created.
112 personnel benefited form the advanced & basic level training
programmes in bioinformatics.

352
Pentium IV HT Servers 2GB RAM: HP Proliant ML 110G3 - 1
Pentium IV HT Servers 2GB RAM: HP Compaq dx 7200 - 2
Pentium IV Computers IntelR PentiumR D Processor 820 with EM64T 512 MB
Scanner HP 2400c
Printer HP Laserjet 1600
Printer HP Laserjet 1005
Photo Copier: Panasonic 1520P Printer cum Copier
LCD Projector VPL ES3WT/2000 Sony
1Mbps Internet Line
GENOCLUSTERS (Developed by IGIB, CSIR & Jalaja Technologies)
GeneDcfer, Proteome Calculator, Seapath, PI Host, Proteome Calculator
GENES TO DRUGS (Accelrys Package)
GCG Wisconsin Package, Insight II, Discovery Studio, TSAR, Accord
and all other online tools

Sl. No. Name of the staff Designation Working since Absorption status
1. Dr.Daisy.P Co-ordinator 2006 yes
2. Ms.Nirmala.A Research Assistant 2007 yes

Training programmes for students, staff and researchers
Project Training for M.Sc & B.Sc students of the host institution as well as
of other institutions.
Offering courses in Bioinformatics to PG students.
Support to R&D activities of the Department


The Facility conducts two 4 credit course in Bioinformatics to the M.Sc.
Biotechnology and Bioinformatics students of the Department.
The facility is made use of for the practical coursework of the Bioinformatics
students. The passed out students are placed in Biotech companies and R&D
institutes.


The research activities and regular training programmes validate the outcome
of bioinformatics resources.

10. Collaborative works / Initiatives : nil

Database for specific Medicinal Plants : DIAB
Created a database for Medicinal plants showing positive control on the
secondary complications of Diabetes besides checking glycemic levels.
Available at: http://www.holycrossindia.ac.in/BIO-TECH-DB/home.html

353
1. Hypoglycemic and other related effects of Elephantopus scaber extracts on
alloxan induced diabetic rats. Journal of Biological Sciences 7 (2): 433-437,
2007
2. A database for medicinal plants used in treatment of diabetes and its
secondary complications. Bioinformation 2(1): 22 -23 (2007)
3. Antidiabetic effect of a novel compound from Gymnema sylvestre R.Br
leaves presented at the 28
th
Conference of Indian Association of Biomedical
Scientists, Bharathidasan University,Trichy-24.

Research efforts initiated are in the lines of:
Insilico Comparative analysis of the apoptotic proteins of Mice and
Humans

14. Details of Training / Workshops organized and total no: of users
trained:
National Level workshop on Bioinformatics: Tools & applications Jan 8th
-10th 07.
Workshop on Genome and Proteome analysis for College Staff,
Research scholars, P.G students: Aug 20th - 21st, 2007.
Workshop on Discovery Studio, by Accelrys for Researchers and
Scientist: Aug 23-24th 2007
One day training to the M.Sc., Biochemistry students of Seethalakshmi
Ramamswami College, Trichy: October 9, 2007.
An introductory class on Bioinformatics for the students of Srimad
Andavan College, Trichy.
Total number of persons trained till date is 112.

areas:
Besides the Research and academic initiatives, the facility promotes human
resource development of the students, staff and researchers.

Technical Training & Exposure in premier Commercial Drug designing softwares
for scientists.
Open source journal accessibility for M.Sc students, and procurement of
books and Journals in Bioinformatics.
To introduce a course on Bioinformatics for Ph.D (Biotechnology) students.
Hands-on Bioinformatics training for the students and staff of rural schools.

Additional details:
Name of the Coordinator: Dr. Daisy. P
Postal Address: Coordinator, Bioinformatics Infrastructure Facility
Dept of Biotechnology & Bioinformatics
Holy Cross College
Tiruchirapalli 620 002
354
Tamil Nadu
Phone Number: 0431-2700637 Fax No.:0431-2713312
Email: hcc_wc@yahoo.co.in Website: www.hccbif.org
Name of Contact Person(s): Dr.Daisy.P Email: daisylesslie@yahoo.com
355
Indira Gandhi Krishi Vishwavidyalaya, Raipur
Coordinator : Dr. D. K. Sharma

The Department has the credit to have run several national and International funded
projects. Till date more than 35 Msc. and and 6 Ph. D. have been awarded degree.
The Department of Biotechnology well developed infrastructure and laboratories to
carry out scientific research of international standards.
The Department has contributed towards HRD in the field of Biotechnology by
organizing regular training program. Bioinformatics center is in the process of
establishment.
International Conference on Plant Genomics and Biotechnolgy: Challenges and
Opportunities October 26-28th, 2005.

institution
1. Identification and characterization of biotic and abiotic responsive
transcripts in rice using cDNA microarray, gene expression changes of
selected genes and identification of the cisacting elements and their
target transcription factors
2. Tagging and mapping of gall midge resistance genes, Gene expression studies and
fine mapping of gall midge and the use of in silico data base. In silico anchoring
rice cloan contigs with putative candidate genes to QTLs associated with biotic
and abiotic stress tolerance in rice
3. Use of different DNA marker to characterize germplas of different crop
species, insect and pathogen population and beneficial microorganisms.
4. Standardization of high efficiency regeneration protocol for different crop
plants
5. Assessment of rice accessions for nutritional quality traits (protein, lysine
and micronutrient content).

3. Area of Specialization of the center :- 1) Mapping and Tagging of genes
2) Collection, isolation and characterization of microorganisms and rice
accessions 3) Standardization of high efficiency in-vitro regeneration
protocols 4) Transgenic research 5) In silico mapping 6) Screening of elite
rice line for nutritional quality traits (protein, lysine and micronutrient content
7) Mushroom breeding

4. Major activities of the center during the year 2007- 08
+ In silico construction of a new map for major abiotic stresses responsive
ESTs. and putative candidate genes, Gene expression studies for gall midge
resistance, Mushroom breeding and development of mapping population,
Collection and characteization of Trichoderma and Pseudomonas fluorescence
and Andrographis paniculata (kalmegh), Assessment of rice accessions for
nutritional quality traits (protein, lysine and micronutrient content
356
b. Computer & Communication facility:-
Purchased Computers and Servers
Software as prescribed by the Govt. of India, Ministry of Science and
Tchnology, DBT, (Bioinformatics Division) will be purchased during the
current financial year.
c. Scientific Software packages :- NIL
d. Databases & other information resources NIL

absorption status)
1) Dr. D. K. Sharma (Professor & Head, Department of Biotechnology 20
Years)
2) Dr. A. S. Kotasthane (Associate Professor, Plant Pathology,
Microbiology, Microbial genetics Molecular Host Microbe Interaction 18
years)
3) Dr. Girish Chandel (Associate Professor Plant Breeding, Nutritional
Fortification, Transgenics 15 years)
4) Dr. (Smt.) Zenu Jha Medicinal Plant Biotechnology 2 Years)



9. Initiative to validate the outcome of bioinformatics resources : High
resolution physical map for all the 12 chromosomes of rice constructed with
the use of available molecular marker databse on net is currently being used
for fine mapping and functional genomics studies for biotic stresses and
tagging of QTLs associated with biotic stresses.

10. Collaborative works / initiatives : NIL

11. Databases/ Software packages developed : NIL

12. Papers published or presented in the conferences with reference ( As In
point No 15)


Provided 5 (five trainings) on DNA marker technology since September 2000
to 2004 to 40 participants every year

15. Impact shown by your center on the growth of biotechnology and allied
published/ number of papers published with the help of your center,
how your center is promoting various activities of your organization and
357
Fifteen Thesis research related activities were carried out using
biinformatics tools
Thirty different papers were presented which are related to tagging
mapping, gene expression anlysis and in-silico mapping of genes related
to abiotic and biotic stresses

16.Future activities: Discovery of Biotic and abiotic stress tolerance gene(s),
Comparative analysis of chromosome structure among the cereals, marker
assisted breeding ,Identification and analysis of QTLs for biotic and abiotic
tolerance in rice, molecular understanding of 1) Minor gene specificity 2) Resistance
mechanism at molecular level 3)signal transduction

Name of the Coordinator: Dr. D. K. Sharma,
Professor and Head, Department of
Biotechnology,
College of Agriculture, IGKV Raipur 492006

Postal Address: Department of Biotechnology, College of
Agriculture,
IGKV Raipur 492006 India
Phone Number: 91-771-2442069 / 2444133
Mobile: 98261-39382;
Email: dkagriscientist@yahoo.com

Name of Contact Person(s): Dr. D. K. Sharma,
Professor and Head, Department of
Biotechnology,
College of Agriculture, IGKV Raipur 492006
India
Email: dkagriscientist@yahoo.com

358
Indian Institute of Technology, Madras
Coordinator : Dr. N. Manoj

The Bioinformatics Infrastructure Facility (BIF) was established in November
2006 at IIT Madras with grants from the DBT and IIT Madras. The facility is
housed at the Department of Biotechnology. The facility primarily provides
educational and training facilities by supporting the bioinformatics and
computational needs of the various academic programs conducted in the
areas of biotechnology.

2. Major research activities in Biotechnology and its related fields
Various research areas of biotechnology include: Structure function
relationship of ion channels; Biocatalysis and enzyme mechanisms;
Mechanisms of signal transduction pathways; Protein engineering; Molecular
bioremediation; Optimal bioreactor strategies; Design and synthesis of
siRNAs; Protein structure-function relationships; QSAR/QSPR and Drug
design and; Bioreactor design; Computational Neuroscience; Biomechanics
and Rehabilitation engineering; Molecular dynamics of proteins for drug
discovery; Cancer biology; Virology; Human genetics

3. Area of Specialization of the centre: None at present

The BIF has provided support for the academic programs during this period
particularly for teaching courses. The department conducts courses in
Bioinformatics, Biomechanics, Structural Biology, Computer Applications in
Biology, Biostatistics, Computational Neuroscience, Bioprocess Modeling etc
that utilize the computational facilities of the BIF.
The facility also provides research students with support for retrieval of
material for seminar presentations, online literature survey and data analysis,
bioinformatics analysis, use of specialized molecular modeling and drug
design software.

We have 12 Apple Dual core iMacs running Mac OSX; 1 High end multi
processor Mac PRO; 4 HP Pentium IV Graphics workstations; 2 HP Xeon 3D-
Graphics workstations; 7 SUN Linux workstations; 12 Pentium IV Desktop PCs; 2
SGI Octane systems; 1 HP printer/scanner/copier; Accessories like external DVD
writer, Hard disks, network switches etc. All the computers are connected to the
internet on a 33 mbps LAN.

B. Scientific Software packages: InsightII, Cerius2, Autodock, Molecular
visualization software, Bioinformatics programs

C. Databases & other information resources: The BIF is extensively used for
online literature access through the IIT Madras library e-Gateway.

1. Ms.Bhuvaneshwari Technical Assistant Information Jan 07
359
(Temporary position) Technology

7. Types of services provided: The internet facility of BIF is extensively used to
download and browse online literature. All major web resources like sequence
and structure databases are accessed for data retrieval and bioinformatics web
servers. Additionally the BIF is used by students who come for short term
projects at IIT Madras from colleges and universities around the country.

8. Educational activities: The educational activities of the biotechnology
department that the BIF supports include the B.Tech and M.Tech degree
students Additionally, the facility also provides support to research activities by
supporting the MS (by research) and the PhD students for their research projects
and course work.

9. Initiative to validate the outcome of bioinformatics resources: None

10. Databases/ Software packages developed: None at present

11. Some recent relevant papers published:
The SGNH Hydrolase Superfamily: Structural Aspects. Kiranmayee B & Manoj N. 11
th

ADNAT Convention on Structural Biology Hyderabad. Feb 2007.
The repertoire of GPCRs of the Ciona Intestinalis genome. Kamesh N, Aradhyam GK &
Manoj N. International Conference on Bioinformatics & drug Discovery, Hyderabad. Dec
2007.
Interpreting voltage-sensitivity of Gap Junctions as a mechanism of Cardiac Memory.
Krishnan J, Sachdeva G & Chakravarthy VS. Mathematical Biosciences, 2007 (in press).
Quantitative Structure Activity Relationships for Commercially available Inhibitors of
COX-2. Sivakumar PM & Mukesh Doble. Medicinal Chemistry, 2008, (in press)

12. Initiation of R&D activities in Bioinformatics: Presently bioinformatics
R&D activities here are limited to bioinformatics analysis in several BTech,
MTech and Summer projects and those of PhD projects of research scholars of
the Biotechnology dept at IIT Madras.

13. Details of workshop & total no. of user trained: None till date.

14. Impact shown by your centre on the growth of biotechnology: The
primary impact of this centre is in manpower training in Biotechnology at levels
that includes undergraduates, postgraduates and research scholars numbering
about 300, of the Biotech dept, IITM. In 2007, 11 papers that utilized the BIF
number were published in journals and conferences
15. Future activities: The BIF grant will be used for purchase of additional
software to support teaching activities and for additional 3D-graphics
workstations for Accelrys molecular modeling package. A training program in
bioinformatics involving research scholars of the dept is being planned.

Additional Details:
Name of the Coordinator: Dr. N.Manoj
Postal Address: Department of Biotechnology
IIT Madras, Chennai - 600036
Phone Number: 044-22574113 Mobile:9940149208
360
Email: nmanoj@iitm.ac.in Website: http://biotech.iitm.ac.in/
Name of Contact Person(s): Dr. N.Manoj
Email: nmanoj@iitm.ac.in

Jamia Millia Islamia, New Delhi
Coordinator : Prof. S.I.Ahson

1. Summary of the progress made by the centre from its inception in the
year 2007:The Department of Computer Science has produced two Ph.D
Thesis in the area of BioinformaticsTopics are : Microarray Gene expression
Data Analysis clustering and classification using statistical methods and
machine learning techniques , and Gene regulatory networks. The JAMIA BIF
would like to strengthen in these two areas.
The Self-finanincing M.Sc.(Bioinformatics) course (not supported by DBT),
uniquely located in the Department of Computer Science of Computer
Science of Jamia , started in 2003 is a unique blend of Computing , Maths,
Statistics and Biology.
The Department has an MoU with CDFD, Hyderabad where 3 students
every are trained for six months. The placement record is 100 % with
several students gone abroad for Ph.D and several employed in
Pharmaceutical industry, government organizations and several as
teaching in various central/state universities.
The Department of Computer Science has established a BIF Lab
consisting of SUN High-end, Medium-end servers and Workstations where
students and research scholars can excel themselves in the field of
Bioinformatics.

2. Major research activities in Biotechnology and related fields at your
institution:
The JAMIA-BIF focuses on research in AI, machine learning data mining
techniques applied to bioinformatics. The Department has publications in data
analysis of microarray data, supervised learning and data mining and analysis
of gene expression data.

Microarray Gene expression Data Analysis clustering and classification
using statistical methods and machine learning techniques , and Gene
regulatory networks. Application of Semantic Web and Ontologies.

The Department organized two 3 days national level training Programs under
BIF from 14-16 November 2007 on Databases and Data Mining in
Bioinformatics and from 9-11 January 2008 on Semantic Web and
Ontologies in Bioinformatics.
361

A. Computer and Communication facility: Sun Server Systems(Multi-
platform)- Networked Lab ,High-End X4200 SUN Server, Medium-end
X2100 SUN Server, SUN V240 Server, SUN workstations, Pentium4
Compaq PCs, Internet Connectivity through CIT, JMI.

Sun Studio 12,Sun HPC ClusterTools, Sun Grid Engine Software, Solaris 10
or Red Hat AS 4.x, Red Hat Workstation 3.0. Sun N1 Grid Engine 6.x.

6. Details of Staff members working in the Centre:
No staff member has been allocated for BIF. Some faculty members of
Department of Computer Science, JMI and some guest teachers are
associated.

*If no, the reason for the Non Absorption to be given. Likel y time of
Absorption also to be given

BIF lab set up is being used for the Project work by the internal and
external students of M.Sc.(Bioinformatics) ,M.Sc(Biotechnology) and
research scholars.
Organizing two National level Training programs in a year for
promoting Bioinformatics teaching.
The Department has an MoU with CDFD, Hyderabad where 3 students every
are trained for six months. The placement record is 100 % with several
students gone abroad for Ph.D and several employed in Pharmaceutical
industry, government organizations and several as teaching in various
central/state universities.


10. Collaborative works/initiatives: NIL

11. Databases/Software packages developed: Ontology of Avian Flu Virus H5
N1, Database of medicinal plant.

12. Papers published or presented in the conferences with references:
Following is the list of publications of research papers in the areas related to
Bioinformatics in the Department of Computer Science:
1. Jayanthi Ranjan, Goyal.D.P, Ahson.S.I. Data Mining Techniques in
Human Resource Management Systems for Better Decisions.
International Journal of Business Information systems. InderScience
Publishers. IJBIS 173. Vol 3 2007
2. Jayanthi Ranjan, Saani Khalil S.I Ahson. Developing and Implementing
successful Data Warehouses for Competitive advantage: Issues and
Challenges, International journal of information technology , Vol 2 2008
362
3. Jayanthi Ranjan. S.I Ahson. Hierarchical Cluster Analysis for Large Data
Sets. Varahamihir Journal of Mathematical Sciences Vol -1, No 1,
(2006), pp 1-16, ISSN 0973-3639.
4. Jayanthi Ranjan. S.I. Ahson. Statistical Agglomerative Clustering Methods
for Gene Expression Data A Comparison. Bioinformatics India Journal
(Peer Reviewed). Vol 6, no.3. (2006), pp. 70-80.
5. Jayanthi Ranjan. S.I. Ahson. An Overview of Data Mining Techniques.
Proceedings of the National conference on Innovations in Indian Science,
Engineering and Technology. IARI-New Delhi. (2006). Vigyan Bharathi
Proceedings. pp.62-69.
6. Jayanthi Ranjan. Abhishek Maheswari , S.I.Ahson. A study of Real Time
Scientific Data being stored by Indian Scientific Community. Journal of
Management Development and Information Technology (JMDIT- Mathura,
India). (2006) pp 34-45.
7. Jayanthi Ranjan, S.I. Ahson. A review of Statistical Clustering
Techniques Bioinformatics journal. 2006. Vol2. Abstract can be found at
http://www.bii.in/journal/BIIJOURNAL/FinalPaperAbstract.aspx?ArticleID=
238
8. Jayanthi Ranjan. S.I. Ahson. Clustering in Data Mining: Techniques and
Issues. Journal of IT-Techgenesis India, Vol 2 No 2 April 2005, pp. 17-25.
9. Jayanthi Ranjan. S.I. Ahson. Statistical Data Mining Techniques: Issues
and Challenges. Proceedings of FACM-2005, March 04-05, 2005, Allied
Publishers Pvt Ltd., pp. 429-440.
10. Jayanthi Ranjan. S.I. Ahson. Agglomerative Statistical Clustering
Techniques for Genome Databases. Proceedings of FACM-2005, March
04-05, 2005, Allied Publishers Pvt. Ltd., pp.119-131.
11. Jayanthi Ranjan. Tushar Gupta. S.I. Ahson. Information Systems: Security
Issues Threats and Challenge. Proceedings of International conference
Ludhiana (2005), pages 55-65.
12. Jayanthi Ranjan. S.I. Ahson. Tushar Gupta. Emerging Trends and
Techniques in Business Data Mining. Proceedings of International
Conference. INMANTEC (2005), Allied Publishers. pages 55-70.
13. Jayanthi Ranjan. S.I. Ahson. Nearest Neighborhood Method to Cluster
Micro Array Data. Proceedings of National Symposium in Bioinformatics.
Dept of Mathematics, IIT Roorkey, March 14, 2005, pp. 10-12.
14. S.I.Ahson, Genorobotics,AROB Conference Beppu,Japan,Jan 24-26,2003
15. T.V.Prasad and S.I.Ahson. Labeling Gene Expression Data using
LVQ,Third Annual RECOMB Sattellite Meeting on DNA Sequencing
Technologies and Computations,May 17-18,2003,Stanford University,USA
16. T.V.Prasad and S.I.Ahson, Analysis of Microarray Gene Expression
Data, Proc. Of Second International Conference on Artificial Intelligence
in Engineering and Technology, August 3-5, 2004, Kota
Kinabalu,Malayasia,Proc. Pp 588-595
17. T.V.Prasad,R.P.Babu and S.I.Ahson, GEDASGene Expression Data
Analysis Suite, Bioinformation (Online Bioinformatics Journal),vol 1,no
3,2005,pp 83-85
18. T.V.Prasad and S.I.Ahson, Visualization of Microarray Gene Expression
Data,Bioinformation,Biomedical Informatics Publishing Group,vol1,no
4,2006,pp 141-145.

13. Initiation of R & D activities in Bioinformatics:
363

The Department organized two 3 days national level training Programs under
BIF from 14-16 November 2007 on Databases and Data Mining in
Bioinformatics and from 9-11 January 2008 on Semantic Web and
Ontologies in Bioinformatics in which more than 60 participants from all over
the country participated.

allied areas:
The M.Sc.(Bioinformatics) course has attracted a number of students
throughout the country. A sizable number of students from different
universities/institutions are coming to the centre for the Project/training
programs.

Development of patents and software tools and databases related to
Bioinformatics.
Employing highly technical people for the BIF in the Department.
Extension in the existing SUN lab facility by hiring advanced Bio-cluster
Grid components.

Additional Details:
Name of the Coordinator: Professor S.I.Ahson
Postal address: DEPARTMENT OF COMPUTER SCIENCE,
JAMIA MILLIA ISLAMIA
(A CENTRAL UNIVERSITY),
JAMIA NAGAR, NEW DELHI-110025
Mobile: 9810581072
Email: drsiahson@yahoo.com

364
Jiwaji University, Gwalior
Coordinator : Dr. Ishan Patro

The one-time grant for establishing the Centre was sanctioned in September
2006. The Facility has been established. A Users Meet was held on 15.5.07
and most faculty members from all the Science Departments attended. After a
short introduction on the purpose and facilities available, a proposed list of the
areas where this facility could be used was drawn. The important areas for
database development are: Aquatic resource of MP; endangered species
and wild-life resource of MP; Microbial wealth of MP; Medicinal plants of MP;
Genomic profiles of tribes in MP; Aging population and prevalent age-related
problems in MP; Neurological disorders and disabilities in Indian population;
and Preparation of teaching aids in Biotechnology for colleges affiliated to this
University. These shall be in addition to the normal computational and
information technology facilities those could be extended to the faculty and
researchers in the University.

The ongoing research of interests are:
a) Role of microglia and inflammatory changes in neuronal apoptosis,
neurodegeneration and neurodegeneration.
b) Studies on effects of presence of resting and reactive microglia on
endogenous neurogenesis and gliogenesis from neural stem cells.
c) Aging changes in microglia per se. Does age related deterioration of
microglia and microglial cellular senescence cause increasing disability of
microglia to provide neuroprotection following injury?
d) Studies on immunophilin ligands as novel modulators of glial activity and
mediators of neuroprotection.
e) Role of glia in neurogenesis and histogenesis of neurons following
exposure to the toxicity of deltamethrin in postnatal rats.
f) Gram-negative Bacterial Endotoxin-induced Infertility.
g) Genetic Polymorphism in the Tribal Populations of North Madhya Pradesh
In Relation To Genomic Diversity and Susceptibility to Tuberculosis.
h) Genetics of susceptibility to gall stone and gall cancer
i) Genetic diagnosis and counseling for (pre-natal) abnormalities in
spontaneous abortions
j) Genetics of thalassemia and population screening
k) Conservation genetics of Gharial and turtles.

The Centre provided support to a DBT sponsored Hands-on Workshop on
Methods in Clinical Diagnosis: Cytogenetics, Biochemical, Molecular and
Bioinformatics Approaches during July 23-August 11, 2007. (Conducted by
the Centre for Genomics).
Centrs facilities were availed by the School of Studies in Neuroscience in
conducting the National Symposium on Glial Neurobiology held on October
23, 2007.
The Centre supported the teaching of Bioinformatics to the students of M.Sc.
Neuroscience (a DBT sponsored programme).
Many researchers have been using the facility for their research activity
365
leading to publications.

4. Infrastructure facilities in the Bioinformatics Centre: As sanctioned

5. Details about staff members working in the centre: The position of RA has
been advertised.

6. Types of services provided: Information, Computation and internet

7. Educational activities with details of placement: Not applicable

8. Initiative to validate the outcome of bioinformatics resources: Nil

9. Collaborative works/ initiatives: Collaborative work with several Institutes
including AIIMS, DRDO, Manipal Institute, NIMHANS, ITRC, CDRI, etc are
under progress and several others are being planned.


The researchers at this University have contributed towards publications in
the following manner:
Sequences submitted for GenBank:
By PVJ Reddy and. P.K. Tiwari
HSP genes GenBank Citations:
DQ062119 Lucilia cuprina heat shock protein 60 gene, complete CDS.
EF445946 Lucilia cuprina heat shock protein 70 (hsp70) gene, complete CDS.
EF584332 Lucilia cuprina HSP90 gene, complete CDS.

By M.S. Rohilla and P.K. Tiwari
Cytochrome-b (mitochondrial) genes GenBank Citations:
EF558361 - Aspideretes gangeticus cytochrome b-like (cytb) gene, partial sequence.
EF558362 - Kachuga kachuga cytochrome b-like (cytb) gene, partial sequence.
EF558363 - Lissemys punctata punctata cytochrome b-like (cytb) gene, partial sequence.
EF558364 - Kachuga dhongoka cytochrome b-like (cytb) gene, partial sequence.
EF558365 - Geoclemys hamiltonii cytochrome b-like (cytb) gene, partial sequence.

Papers published:
Saxena Kapil, Patro, Nisha & Patro, Ishan (2007) FK506 protects neurons
following peripheral nerve injury via immunosuppression. Cell Mol. Neurobiol.,
2007. DOI 10.1007/s10571-007-9221-6

12. Initiation of R&D activities in Bioinformatics: See 2 above.
13. Details of Training/ Workshop: A Workshop on Bioinformatics: From
genome search to phylogeny shall be held during 1-3 march 2008. We are
also planning trainings for M.Sc. Students.
areas: The Centre is helping in research and publication in various areas of
biology.

366
15. Future activities: We are planning to extend training to all biology students
in the Campus on Bioinformatics. And develop databases on aspects listed
above.

Name of the Coordinator: Dr. Ishan Patro
Postal Address: Head, School of Studies in Neuroscience & Coordinator,
Bioinformatics Centre, Jiwaji University, Gwalior 474011.
Phone Number: 0751-4016789, 2231816, 2231616 Fax No.:4016789
Email: ishanpatro@rediffmail.com,
Website: www.jiwaji.edu, www.neuroscienceju.com
367
Kannur University, Kannur
Coordinator : Dr. M. Haridas


In October 2006 we got the sanction for the establishment of Bioinformatics
Infrastructure Facility (BIF) for the promotion of Biology Teaching through
Bioinformatics (BTBI) at the Department of Biotechnology and Microbiology,
Kannur University. Rs 20 lacs was received from the DBT as initial grant and
Rs 6.82 lacs for 2007-08. The infrastructure facility has been established with
sufficient number of computers, softwares and leased line Internet
connectivity. Also steps had been taken to complete the constitution of an
executive committee has already been constituted. Now the centre is ready
for facilitating the researchers/other patrons from the outside as well. Dr. C.
Sadasivan, Reader, Department of Biotechnology and Microbiology attended
the International Conference on Bioinformatics (InCoB-2006) held at New
Delhi during December 18-20, 2006. He also attended the INSA-CAS
workshop on structural biology, IISc, Bangalore, Dec 21-23, 2007. A two
days national workshop was organized during the Jan 10-11, 2008. The
theme of the workshop was introductory structural bioinformatics.

2. Major Research activities in Biotechnology and its related fields at the
department

a. Modeling and Molecular Dynamic Study of Xeno Estrogen Targets and
Phospholipase Inhibitors
b. Anti tumor property of Butea monosperma lectin and goat milk
lactoperoxidase
c. Peptide modeling/synthesis and study of their functionally important
secondary structures/critical role of individual residues
d. Utilization of coffee treated effluent for the production of various organic
chemicals and industrially important enzymes.
e. Identification, Characterization and pharmacokinetic studies of anti
inflammatory phytochemicals/marine cyanobacterial chemical and their
derivatives biotransformed by fermentation.
f. Development of inhibitor to -lactamase from phytochemicals.
g. Sequence and structural analysis of bacterial enzymes associated with
drug resistance and designing of novel drugs to combat the problem of
antibiotic resistances using molecular modeling and other Bioinformatics
tools.
h. Modeling of inhibitors to enzymes associated with blood coagulation
such as thrombin using molecular modeling tools.
368
3. Area of specialization of the Bioinformatics Centre

Structural Bioinformatics


The infrastructure facility has been established with sufficient number of
computers, softwares and leased line Internet connectivity. Also steps had
been taken to complete the constitution of an executive committee has
already been constituted. Now the centre is ready for facilitating the
researchers/other patrons from the outside as well. A two-day national
workshop organized during the Jan 10-11, 2008. The theme of the workshop
was introductory structural bioinformatics.

5. Infrastructure facilities in the Bioinformatics centre:

a). Computer and communication facilities available in the department
1 IBM P.C. workstations with Linux and Windows OS (8 nos),IBM
Servers 2
2 PC s (14 nos.), 1 laptop computer, printers
3 Leased line internet facility (512 Kbps)
4 Photocopying machine, LCD Projector, Telephone and FAX

b). Scientific Software packages

Insight II, Discover, Affinity, SPDBV, AMBER 9, VMD, ArgusLab and
Bio-Suit (purchase order placed) for molecular modeling and
computational biology and CCP4 and many free soft wares.
a. Databases and other information resources
Fungal Database: Provided by Bioinformatics Centre, Tropical Botanical
Garden and Research Institute, Thiruvananthapuram, Kerala, India.

One RA post sanctioned was notified for appointment. But, could not get a
proper candidate in the first instance.

So far, the centre is not in a position to provide any service on demand.

Sponsorship application to start M Sc Bioinformatics is pending with
UGC/BDT.

9. Initiative to validate the outcome of bioinformatics resources: Yet to
initiate

10. Collaborative works/initiatives: nil

11. Databases/software packages developed: nil

369
12. Papers published or presented in the conferences with
references

a). Modeling of Factor XIII Activation Peptide (28-41) V34 L Mutant Bound
to Thrombin (JBSD). Divya G Nair, P N Sunilkumar and C Sadasivan.
(under revision).
b). Disruption Mechanism in the Helix of SPF Peptide by Interchanging Glu5 and
Lys10 residues: Inference from Molecular Dynamics Study (JBSD). P N
Sunilkumar, Divya G Nair, C Sadasivan and M Haridas. (under revision).
c). Role of K10 Residue in Maintaining the Helical Structure of SPF
Peptide: A Molecular Dynamics Study. ). P N Sunilkumar, C Sadasivan
and M Haridas. (accepted for the Young Scientist Award Contest, Kerala
Science Congress, Jan 2008)
d). Detoxification of Bisphenol A by Laccase: A Modeling Study. (JMM).
Divya L M, Ganesh K Prasanth and C Sadasivan (communicated)
e). Conformation of a residue substituted fragment (349-364) of human
lactoferrin protein in DMSO-d
6
by
1
H NMR and restrained molecular
dynamics.). P N Sunilkumar, C Sadasivan and M Haridas. (IJBB in
press).

13. Initiation of R&D activities in bioinformatics

a). Strengthen the ongoing research works in molecular modeling of
various drug targets and development of novel putative drug molecules
b). Sequence and structural analysis of bacterial enzymes associated with
drug resistance and design of inhibitors to these enzymes with the goal
of developing novel antibiotics against resistant strains of bacteria
using molecular modeling and other Bioinformatics tools.

Research Projects Submitted for funding

a). Synthesis, Characterization and Structure-function Correlation of a 21
Residue Peptide Misgurin, Its Analogs and Its Hibrid Sequences.(to
DBT, Rs 5,174,500)
b). Identification and Modeling of Targets of an Endocrine Disruptor:
Bisphenol A (to DBT< Rs 1,720,000)

14. Details of training/workshop organized and total no. of user
trained
A two-day national workshop organized during the Jan 10-11, 2008. The
theme of the workshop was introductory structural bioinformatics.

15. Nil

16. A series of five tutorials/workshops, from introduction to higher levels, in
structural bioinformatics has been conceived and being developed to cater
the postgraduate students.

370
Name of the Coordinator: Dr. M. Haridas,
Professor and Head

Postal Address: Department of Biotechnology and
Microbiology
Kannur University, Thalassery Campus,
Palayad P.O. Kannur-670661, Kerala
E.mail: mharidasm@rediffmail.com Phone: 04902347394,
Fax: 04902345317

Name of Contact Person: Dr. C. Sadasivan, Reader
E.mail: c_sadasivan@rediffmail.com
371
Karnatak University, Dharwad
Coordinator: Prof. B. B. Kaliwal

1. Summary of the progress made by the centre from its inception: The
grant has been received recently and arrangements are being made to set
up laboratory, purchases of computers and other facilities.
institution :Toxicology ,stress induced effects, epidemiology of
staphylococcus in northern districts of Karnataka, effect of pesticides on
microbes.

3. Area of Specialization of the centre: Reproductive Toxicology,
Fermentation Technology, Medical microbiology and Seribiotechnology
4. Major activities of the centre during the year 2006-07 : Nil
(As it is granted recently)

Computer & Communication facility : Being established
Scientific Software packages : Yet to be purchased
Databases & other information resources : Need to be done

absorption status) :Dr.R.D.Sanakal, Teaching Assistant, Ph.D in life science
with Computer Diploma and handled bioinformatics theory and Practicals.

7. Types of services provided : --
8. Educational activities with details of placement : --
9. Initiative to validate the outcome of bioinformatics resources -
10. Collaborative works/ initiatives : In touch with nearby BTIs centers and
education Institutions

11. Databases/ Software packages developed : Nil
12. Papers published or presented in the conferences with reference : See
separate page appended
13. Initiation of R&D activities in Bioinformatics : Yet to be initiated
372
14. Details of Training/ Workshop organized and total no. of
user trained : Nil

copyrights acquired and other services offered etc. : Need to be
developed.

16. Future activities: Planning to have workshop for the life science graduates
and postgraduates in Bioinformatics.

Additional Details: Nil
Name of the Coordinator: Prof.B.B.Kaliwal
Postal Address:Post graduate, Department of Biotechnology,
Karnatak University, Dharwad
Phone Number:91-0836-2779533(O) Mobile: 9449278648
Email:b_kaliwal@yahoo.com Website:www.kud.ernet.in
Name of Contact Person(s): Prof.B.B.Kaliwal
373
Kumaun University, Nainital
Coordinator : Dr. Veena Pande


Programme has been sanctioned on 22
nd
September 2006. Infrastructure and
other facilities have been established comprising of 10 desktops, two high
end servers and printing and photostat facility. The center has 24 hours
internet facility by BSNL broadband. We are exploring different available
Proteomics and Genomics softwares for purchase. A three day training was
organized from 30 Aug 1 Sep 2007 for faculty and research scholars of our
and different Universities. The facility is used exhaustively by all M.Sc. and
PhD Life Sciences students & faculty of the University for carrying out their
research smoothly. We have also subscribed print and online versions of few
journals.

institution

i. A systematic characterization of local flora and fauna at molecular level
and to develop strategy for its conservation.
ii. To develop methods for sustainable exploitation of the aromatic and
medicinal plants.
iii. To study the microbial biodiversity of the region with special emphasis
on cold tolerant microbes.
iv. Biodiversity and Biotechnological applications of mycorrhizal fungi of
Uttarakhand.
v. To study the Genetic diversity of casts and tribes of Uttarakhand.
vi. To develop protocols for in vitro micropropagation of rare, endangered
and important forest species of this central Himalayan region.


A Seminar was organized by the department entitled: and Biotechnology
Innovation systems of India: Policy Measures and Support Mechanisms
Sponsored by APCTT, DBT Govt. of India, New Delhi. Besides that a three
days training on Applications of Bioinformatics was organized from 30 Aug
1 Sep 2007 for faculty and research scholars of our and different Universities.
Department is also engaged in organizing inter school science competitions,
popular lectures by eminent scientist and educational tours to develop
scientific out look among youth.

High end server 1
Proxy Server 1
Desktop Computers 10
Laptops 3
Multi media projector 2
Scanner 2
374
Printers (high end) 2 (Laserjet), 1 (inkjet)
UPS 5 KV (1), 2 KV (1)
Xerox Machine 1
The computers are connected through LAN and 24 hrs very high speed
Broadband internet facility is available.
Scientific Software packages- Windows Office 2007, Windows XP, Red Hat
Linux, Accelrys Gene etc.
b. Databases & other information resources- Yes

absorption status)

Advertisement for the post of 1 Research Associate has been advertised and
interview is awaited.

The center provides the following services to the students, research fellows
and faculty members of the university:
(a) E-mail & internet access
(b) Training in bioinformatics
(c) Online access to public domain databases
(d) The center offers a good collection of various journals (online and
print version) to all researchers of the university

Presently department is engaged in research related with medicinal and
aromatic plants, Microbial diversity, Genetic diversity and Biotechnological
applications of Mycorrhizal fungi of Uttarakhand. After establishment of
Bioinformatics facility in the center, it will be easy to access the related
database and to proceed the research work in the oriented direction.
Department will also organize short term training programmes in
Bioinformatics for students and faculty members of nearby
institutes/organizations to enrich their knowledge in this area. It will also work
in the directions of development of new data bases.

Additional Details:
Name of the Coordinator: Dr. Veena Pande
Postal Address: Department of Biotechnology
Kumaun University, Nainital
Uttrakhand-263 001
Phone No: (05942) 235521 Fax No.:(05942) 235576
Email: veena_biotech@rediffmail.com
veena_kumaun@yahoo.co.in
Website: www.kumaununiversity.org
375
Lady Doak College, Madurai
Coordinator : Dr.R.Shenbagarathai


Established Bioinformatics Lab facility and organized one workshop.

institution

Microbial Biotechnology
Biopesticide Searching of new indigenous Bacillus thuringiensis
strain to control Spodoptera litura, Culex quinquefasciatus and
Anopheles to be used as effective ecofriendly biocontrol agent.
Biopolymer screening and characterization of indigenous mcl- phac
producer.
Identification, mapping and characterizing genes associated with
phaC1.
TB with HIV coinfection. Molecular characterization of pathogens, new
targets and novel drug delivery systems relating to viral, bacterial and
parasitic infections.

Ethnomedicine
Antimicrobial activity, biochemical properties and
immunomodulatory effects of medicinal plants used by tribes in and
around Madurai.

3. Area of Specialization of the centre Microbial Biotechnology


Organised Hands on Training in Bioinformatics tools and Applications. From
May 2
nd
to May 12
th
2007.


Computer & Communication facility: 10 from DBT-BIF and 26 from UGC
Innovative and CPE grant with internet facility at a speed of 512KB/sec
Scientific Software packages : Process of converting InsightII
software pacjage into Discovery Studio.
Databases & other information resources: Process of building database on
rural womens traditional knowledge on indigenous medicinal herbal plants
use for common ailments.

6.Details about staff members working in the centre

Name of the Staff: Ms. J.Ida Chrislyn,Designation: Research
Assistant,Specilaisation : Bioinfomatics,Period of working ::From Dec1st, 2007
onwards,Absorption status :Based on merit and interview performance.

376
7. Types of services provided Internet usage and Insilico analysis for Lab and
Project

8. Educational activities with details of placement Not applicable

Consolidated feedback from the participants of the workshop after
seven months

It was a meaningful practical experience we had during our training course on
Bioinformatics training. Really the training was very useful. We have been
applying the techniques in our research work which was taught during course
work. In fact the training was the base for our future research work in the field
of Bioinformatics. The tutorials were very good.

10. Collaborative works/ initiatives Under process.

11. Databases/ Software packages developed Under process


Publications

Sujatha. K, Mahalakshmi, A. and R. Shenbagarathai (2007),Archives of
Microbiology. 188: 451-462.
Ramakrishnan. K, Shenbagarathai. R, Uma. A, Kavitha. K, Rajendarn. R,
Thirumalaikolundusubramanian. P. (2007). Japanese journal of infectious
diseases. 60 (4): 209-10.
Mahalakshmi, A. and Shenbagarathai, R. (2007). Accepted for
publication in JBSD as color processing of US $5,000. Hence, this
manuscript was resubmitted in insilico biology.

Presentations
K.Sujatha, M.S.Dhivya Vadhana, K.Ramalakshmi, A.Mahalakshmi,
K.Anburani and R.Shenbagarathai (2007). International conference on
new horizons in biotechnology (NHBT-2007), NIST, Trivandrum, India Nov
26-29, 2007.
A.Mahalakshmi, K.Sujatha, Poornima Kkani, M.Tamilarasi, G.Geetha,
K.Anburani and R.Shenbagarathai (2007). International conference on
new horizons in biotechnology (NHBT-2007), NIST, Trivandrum, India Nov
26-29, 2007.
A.Mahalakshmi, K.Sujatha and R.Shenbagarathai (2007) 5
th

International symposium on Biocontrol and Biotechnology
(BCBT-2007). Khon Kaen University, Nongkhai Campus,
Nongkhai Province, Thailand (November 1-3, 2007).


Docking of drug for reverse transcriptase using natural products
Docking of drug for HIV 1-Protease using natural products
377
Drug designing for schizophrenia by Virtual Screening.
Drug designing for hyperthyroidism by Virtual Screening.
In silico structure based drug designing for type II diabetes.

trained 20

how your centre is promoting various activities of your organization
and neighboring institutions, manpower trained, tools developed,
Paper published-2, accepted-1.

16. Future activities Process of developing tools

Additional Details:

Name of the Coordinator : Dr.R.Shenbagarathai
Postal Address Department of Biotechnology,
Lady Doak College, Madurai.-625002
Phone Number:0452-2530527,2524575; Fax No.:091-452-2523585
Email:shenbagarathai@rediffmail.com
Website:www.ladydoak.org
Name of Contact Person(s):Dr.R.Shenbagarathai
Email: shenbagarathai@rediffmail.com.

378
Lucknow University, Lucknow
Coordinator: Prof. U.N. Dwivedi

BIF centre is only one year old. During this period the effort was to establish
the center with all the facilities. All the purchases were made and the center
was made functional. One training program is scheduled to be organized
during Feb. 12-16, 2008. The post of RA was advertised however, no
appointment has yet been made.

institution
The major research activities of the department are summarized
as follows:

Biotechnological modification of lignin biosynthesis for improved
application of biomass in paper manufacturing and fodder production.
Structure - function relationship in nitrate reductase;
Biochemical role of salicylic acid in plants;
Molecular characterization of mimosine degradation enzymes and genes in
bacteria.
Regulatory aspects of Plasma membrane linked redox mediated signal
transduction and transfer activities in eukaryotes.
Antioxidants in cardiovascular disorders.
Biochemistry of cataract development during diabetes.

The Department is collaborating in research activities with the other
departments of the University as well as with national organizations, such
as Central Drug Research Institute, Industrial Toxicology Research Centre,
National Botanical Research Institute, Central Institute of Medicinal and
Aromatic Plants, Lucknow.

The Department has earned recognition in the form of financial support
from Rockefeller Foundation, UNESCO, PL 480, UGC under special
Assistance and COSIST Programs and DST FIST, DBT etc.

3. Area of Specialization of the centre: Plant Biotechnology and Biochemistry

The thrust research areas of the department include:

1. Transgenics.
2. Enzyme Engineering.
3. Metabolism under stress and disease.

379
i. Purchase and installation of computers, servers, printer, scanner,
photocopier, softwares etc.
ii. Internal members of the department got training in the bioinformatics.
iii. One training program is scheduled to be organized during Feb. 12-16,
2008.
iv. The post of RA was advertised however, no appointment has yet been
made.

absorption status)

The post of RA was advertised however, no appointment has yet been made.

Bioinformatics tools being currently used in our research is mentioned
below:
Nucleotide and protein search at NCBI and SWISS-PROT, respectively
BLAST to check homology at nucleotide and amino acid level with the
biomolecules (DNA / RNA and protein)
EST searches at NCBI
Protein modeling :3D domain and structure of enzymes and protein at
NCBI
CLUSTAL to check homology in selected sequences at nucleotide and
amino acid level.
Entrez, Pubmed and PubMed Central to search the research articles
Molecular Beacon and Primer 3 to design gene specific primers
CUTTER, TRANSLATOR, AND ALIGNER tools at www.justbio.com
Gene runner (oligo analyzer and oligo explorer) to design and check the
suitability of oligos for conventional PCR and Real Time PCR.

8. Educational activities with details of placement Not applicable
9. Initiative to validate the outcome of bioinformatics resources N.A.
10. Collaborative works/ initiatives : N.A.
11. Databases/ Software packages developed -
12. Papers published or presented in the conferences with reference -
13. Initiation of R&D activities in Bioinformatics -

380
One training program is scheduled to be organized during Feb. 12-16, 2008.
No. 10.

offered etc.


To organize more training programs.
Developing new tools and adding to the resources that aid in the
analysis of the data.
Getting aware of the fine tools of bioinformatics and making aware of
the same to the students from neighboring academic institutions.
Exploring the various databases and anlysing the structure and
function of biomolecules
Getting access to the newly discovered bio-molecules and pathways
Getting updated in the field of genomic tools and data to analyze the
biological systems

Additional Details:
Name of the Coordinator: Prof. U. N. Dwivedi
Postal Address: Department of Biochemistry, Lucknow University,
Lucknow -226007
Email: upendradwivedi@hotmail.com lkouniv.ac.in

Name of Contact Person(s): Prof. U. N. Dwivedi
Email: upendradwivedi@hotmail.com
381
Madras Christian College, Chennai
Coordinator : Dr. D. Arul Samraj

The Centre has been established in the dept. of Zoology with the help of
Rs.20 lakhs released by DBT during the year 2006-07 and commissioned on
22, March 2007. An Extension Facility was also established in the Dept. of
Botany during April 2007. The facility is well utilized both for teaching and for
carrying out P.G. and M.Phil dissertation work.

institution
M.Phil and M.Sc. dissertation work listed under item no. 15.

Thrust area Genemic Studies, Proteomics studies & drug designing

4.1. Establishment of the facility
4.2.Teaching Bioinformatics-special paper to UG PG along with
dissertation
4.3. Workshop to the Biology Teachers of Higher Secondary Schools to
introduce Bioinformatics during June 14 16, 2007
4.4. Workshop to the Faculty of MCC on the utility of Bioinformatics
Infrastructure Facility established at MCC on August 13, 2007.

B. Computer & Communication facility
a. All Hardware and Software were purchased and installed according to the
specifications provided by DBT and in certain cases an higher
configurations were purchased..
b. All terminals are provided with DVD writer, and in addition, Web Cam and
Head Phone thereby facilitating Video Conferencing.
c. All in one Laserjet and Duplex printers have been installed.
d. An online UPS has been provided with more than two hrs backup.
e. 2Mbps Broad Band internet connectivity has been provided by BSNL
Dataone. Wireless Dial up internet connectivity has also been provided by
TATA INDICOM as a standby connectivity.
f. All these are housed in an independent air conditioned room.
g. The entire premises of the Dept. of Zoology has been provided with
wireless internet connectivity by WiFi Technology and Note Book
Computers are used in all class rooms; thereby roaming internet facility is
made available in and around the Dept. of Zoology. It is possible to
access the BIF server from the class rooms itself through this facility of
Wireless Networking while utilizing the terminals of BIF simultaneously. It
is also possible to share documents.
h. An Extension Facility has been provided to the Botany Dept. by allocating
a portion of the funds. The entire campus is to be connected with LAN
facility shortly so that the Server of the BIF could be accessed from any
part of the Campus (365 Acres campus)
382

C. Scientific Software packages
absorption status)
Ms. Jancy Joy Christy has been appointed as Research Asst. with effect from
Jan 18, 2008..

Teaching, guiding dissertations, workshop for Biology teachers of Hr. Sec.
Schools, unlimited utility by all Biology-related students

D G Thomas 2007, Splicing in DNA Computing, Proceedings of the National
Conference on Emerging Trends in Automata (ETA 07), Rajiv Gandhi
College of Engineering and Technology, Puducherry, 6
th
October 2007, pp.
14 41.

Biology Teachers of Higher Secondary Schools 12 Teachers
Faculty of MCC 20

offered etc.
15.1. Research in various aspects of Biotechnology has been encouranged
from the year1990 which is evident from the following Research
contributions
15.2. List of M Phil Dissertations in the area of Bioinformatics:
a. Hephzibah Swapna Chenchiah 2006 A basic study of inhibin alpha subunit
(INHA) using bioinformatic tools.
b. Reeba Mathew 2006 Genomic and proteomic studies on Inhibin.
c. Anulin Christhudoss 2005 Bioinformative studies on STAR protein in
steroidogenesis using bioinformative tools.
d. Rebecca Merlin 2005 Proteomic studies on 17 hydroxyl steroid
hydrogenase using bioinformative tools.
e. Satya Priya 2005 On Circular Splicing Languages
f. Hepzibah Simon 2004 Genomic and proteonomic studies on 3 hydroxyl
steriodohydrogenase using available bioinformative tools.
383
g. Kalaivani C 2000 A Study on splicing operation.
15.3. List of M Sc dissertations
Sawmsung Zuali 2007 Characterization of Gene for Haemophilia
using Bioinformatics tools
Pradeepa Jane 2006 Multiple sequence analysis of protein -
Rhodopsin from five different species of fire ants.
Mini M K 2004 Characterization and prediction of the protein pitx2 in
Homo sapiens and Gallus gallus.
Marshal Joe 1997 Seroprevalence of HIV among the rural
population of Chengalpat and South Arcot Districts.
Cynthia Anupa Isacc 1992 Transferrin polymorphism in Cattle.
Baishali Basu 1991Isolation and partial characterization of plasmid
DNA from Nocardia asteriodes, Xanthomonas oryzae.

Genomics studies, Proteomics studies, Multiple sequence analysis, Drug
Designing, DNA Computing (Studies on the splicing operation and Splicing
Languages of Circular DNA). Apart from the above mentioned areas the
following specific studies will be undertaken
Students will be trained to collect, assemble and analyze the available
data in the varied upcoming areas under Bioinformatics
Students will be motivated to develop a different software to relate and
compare different proteomics and genomics data.
Database on the fauna and flora of MCC campus.
Introduction of Optional Bioinformatics for M.Phil program from 2008-
09.
Introduction of M.Sc. in Bioinformatics during 2009-10.
Introduction of Bioinformatics as an add-on course.

Additional Details:
Name of the Coordinator: Dr. D. Arul Samraj, Madras Christian College, Chennai 600
059, (+91) 9444 284670; arulsamraj@gmail.com
Website: mccbioinformatics.htmlplanet.com
Name of Contact Person(s): Dr. (Mrs.) C. Joyce Priyakumari, Associate Coordinator,
Bioinformatics Infrastructure Facility, Madras Christian College, Chennai 600059. (+91)
9444 149280; joycebenezer@gmail.com
384
Maharanis Science College for Women, Bangalore
Coordinator : Mrs. Kavitha B

The Bioinformatics Infrastructure Facility in the college was set up the in Dec
2006. The facility now has 2 servers, 10 PCs, a network printer, scanner and
copier. A dedicated internet connection has been provided to the facility.
Software has been procured along with Pfam database. Training programs
have been conducted frequently. Last year saw various programs including
Workshops for both undergraduate and Post graduate students and faculty
from various colleges in Bangalore The facility also conducted a two month
certificate course for B.Sc. Students.

institution
M.Phil Student is being guided for her M.Phil dissertation- An assessment
of airborne fungal allergens in indoor environment: A bioinformatics approach.
3. Area of Specialization of the centre - Microbiology
Two workshops for students and one for teachers have been conducted.
A certificate course for two months duration on Basic Bioinformatics for Final
B.Sc. students of our college was conducted from 1
st
Sep to 21
st
Oct 2007 in
two batches.

Computer & Communication facility- 2 servers, 10 desktops with internet
connection
Scientific Software packages- Genious Pro Ver.3.5.6
Databases & other information resources- Pfam Database for Geneious

At present we do not have dedicated staff for the facility. The faculty of the
Microbiology Department are involved in the activities of the facility

a. Name of the staff: Mrs. Kavitha B
Designation: Senior Scale lecturer and Head of the Department
Specialization: Environmental Microbiology
Period of working: Since 1992, appointed by Karnataka Public Service
Commission

b. Name of the staff: Mr. Arun Jyothi Mathias
Designation: Senior Scale lecturer
Specialization: Environmental and Medical Microbiology
Period of working: Since 1996, appointed by Karnataka Public Service
Commission

c. One RA will be shortly appointed
385
Training programme for B.Sc. students, M.Sc Students and faculty
Access for browsing for research material is being provided for M.Phil
Students

8. Educational activities with details of placement-
9. Initiative to validate the outcome of bioinformatics resources -
10. Collaborative works/ initiatives -
11. Databases/ Software packages developed - Nil
12. Papers published or presented in the conferences with reference - Nil
13. Initiation of R&D activities in Bioinformatics- A database for airborne
fungal allergens in indoor environment is being attempted.
Date Training
programme
Participants Organized by No. of
users
trained
10
th
April 2007- One day
workshop
M.Sc.
Students
Orsby Engineering Pvt.
Ltd., Bioware division
20
18
th
and 19 April
2007
Two day
workshop
Faculty Orsby Engineering Pvt.
Ltd., Bioware division
20
23
rd
and 24
th
April
2007
Two day
workshop on
B.Sc.
Students
Department of
Microbiology
14
Sep and Oct 2007 Two months
course
B.Sc.
Students
Department of
Microbiology
21+ 21 (2
batches)

areas.
Over 75 students and 20 teachers have been trained in the field of
Bioinformatics. There have been enquires from schools and colleges to
schedule. The facility provides for literature survey to M.Sc. and M.Phil
students.
Two months course will be continued during Feb- Mar 2008.
Workshop for teachers is being planned during Feb 2008.
A state level workshop is being planned for in the month of Aug.
With over 15 new faculties being posted to our college, those interested will
also be given training in bioinformatics.
Additional Details:
Name of the Coordinator: Mrs. Kavitha B
Postal Address: Department of Microbiology, Maharanis Science College for
Women, Palace Road, Bangalore- 560001
386
Email: micromscw@rediffmail.com
Website: www.mscwb.org
Name of Contact Person(s): Same as above

387
Maulana Azad National Institute of Technology, Bhopal
Coordinator : Dr. K. R. Pardasani

The Department of Mathematics, MANIT Bhopal has already conducted a
number of activities in the area of Bioinformatics, before it received funding
from DBT for the BIF Centre. MANIT is already running M.Tech. programme
in Bioinformatics since July 2006 and started B. Tech. Program in
Bioinformatics from this session i.e. July 2007. MANIT is also conducting
Ph.D programme in bioinformatics. MANIT also intends to start B.Tech and
M.Tech programmes in the disciplines like Biotechnology, Genetic
Engineering,Biomedical engineering, Bioengineering and Pharmacy. MANIT
has already been organizing short term training programs in bioinformatics
since 2004.

institution :The institute plans to develop a versatile research team in
the following areas of computational biology-

1 Thermal modeling of cancer
2 Modeling gene expression
3 Datamining
4 Modeling and analysis of Biological sequences.
5 High performance computing for bioinformatics.
6 Computational phylogenetics
7 Neuroinformatics

3. Area of Specialization of the centre : Computational Biology.
1. Organized 12
th
Annual Conference of Gwalior Academy of Mathematical
Sciences& All India Symposium on Computational Biology during April 6-
8, 2007.
2. Organized National Workshop on Bioinformatics during May 21-25,2007
3. Organized National Workshop on Cheminformatics during May 28-June
1,2007

10 PIV computers along with one medium server, 1 laser printer and 1
Desk-jet printer and one medium server and 1 Photocopier and scanner
1 server high end (Procurement under process)
B.Scientific Software packages:
At present we use online and free softwares like BLAST, CLUSTALW,
PHYLODENDRON, RASMOL, Primers 3, EMBOSS, Webcutters etc.
Recently we have purchased GCG Accelyrs software.
388
The online databases like NCBI, EMBL, PDB etc are accessed through
internet.

absorption status) :
There are 10 Research Fellows working in the area of Bioinformatics.

7. T
ype
s of
ser
vic
es
provided:
i. Training programmes/ workshops in the areas of bioinformatics to provide
exposure to basic skills of bioinformatics to the students of
biotechnology/life science, physical sciences and IT, from other institutes
of our region and country.
ii. Guiding research for Ph.D degree and in Educational programmes in the
areas of Bioinformatics .
iii. Consultancy.

MANIT is running B.Tech,M.Tech and.Ph.D programmes in Bioinformatics
Three students of M.tech got placement in Tata Consultancy Services (TCS)
and Wipro.

(i) Feedback of participants in training/workshops.
(ii) Feedback of students and research scholars of educational programme.

We have developed collaborations with institutes like-
Bhopal Memorial Hospital and Research Centre, Bhopal.
JALMA, National Institute for Leprosy and other Mycobacterium Diseases, Agra
to create databases for their data.
International collaborations (Initialized):
Dr.Tulpupko, Department of Bioinformatics, Tel Aviv University, Isreal.
Dr.Tom Kirkwood, Director and Dr.Anil Wipat , Head department of
Bioinformatics, University of New Castle, U.K
Dr.Roman Borisyuk, Director, Centre for theoretical and computational
Neuroscience, University of Plymouth, U.K
Name of staff Designation Specialization Period of working
Dr.K.R.Pardasani Professor & Head Computational
Biology, Data Mining
23 years
Dr.Namita Srivastava Assistant Professor ComputationalGeno
mics,Intergral
Transforms
19 years
Dr.Madhvi Shakya Head Department
of Bioinformatics
Biomathematics,
Biocomputing
18 years
MrsUsha Chauhan Lecturer Computational
Phylogenetics
7 years
Mr.Chandan K.Verma Lecturer Modelling
Gene Expression
9 years
389
Dr.Daanvon Altan, University of Dundee, U.K

11. Databases/ Software packages developed :We have developed
Softwares for :
1.Haplotyping 2. Molecular cutters 3.Codon usage analysis.

12. Papers published or presented in the conferences with reference :

Papers published-5 Presented in the conferences-30

Since the faculty and students of MANIT are strong in the computational skills
therefore we will also focus on software development in the areas of
bioinformatics during 11
th
five year plan. We have Ph.D scholars with
backgrounds of mathematics, biotechnology, computer science and statistics.
We have faculty in the areas of mathematics, biotechnology, computational
science, IT and statistics .Thus we have a very good interdisciplinary group to
carry out teaching, research and software development in the area of
bioinformatics. We plan to develop computational techniques and softwares
for analysis of biological sequences to identify miRNA, siRNA, Epitopes,
egritopes, other molecular markers etc with their role in genomic and
proteomic networks, drug designing, diagnostics and therapeutics.

trained :
S.N Training/ workshops No. of
participants
1 Organized National Workshop on Bioinformatics
during May 21-25,2007
100
2 Organized National Workshop on
Cheminformatics during May 28-June 1,2007
100

offered etc. :

Among all the NITS, MANIT, Bhopal has taken lead by starting B.Tech, M.Tech and
PhD programs in the area of bioinformatics. Also MANIT has taken lead among all
NITs in organizing short term training programmes in the area of bioinformatics since
july 2004.The institute has developed collaborations with the institutes like Bhopal
Memorial Hospital and Research Centre, Bhopal, JALMA, National Institute for
Leprosy and other Mycobacterium Diseases, Agra to form interdisciplinary groups for
carrying research in the areas of mutual interest. We have developed interdisciplinary
research groups.

390
1. Proposed National Workshop on Bioinformatics during March 10 14,
2008.
2. Proposed National Workshop on Cheminformatics March 17 21, 2008.
3. International conference on Emerging Horizons of Mathematical and
Computational Sciences along with international Symposium on
Computational and Systems Biology during Dec 18 to 21, 2008.

Name of the Coordinator: Dr.K.R.Pardasani
Postal Address: Professor and Head Department of Mathematics, MANIT,
Bhopal
Phone Number: 0755-2671633 Mobile: +91- 9425358308

Email: kamalrajp@hotmail.com,
kamalrajp@rediffmail.com Website: www.manit.ac.in

Name of Contact Person(s): Dr.K.R.Pardasani
391
Narendra Deva University of Agriculture & Technology, Faizabad
Coordinator: Prof. K.N. Singh


The Project Bioinformatics infrastructure Facility (BIF) for the Biology
Teaching through Bioinformatics (BTBI) was sanctioned on 7
th
September
2007 wide letter no. BT/BI/25/001/2006 to Department of Plant molecular
Biology & genetic Engineering, Narendra Deva University of Agriculture &
Technology, Kumarganj, Faizabad (U.P.). Tenders for servers, Computers
furniture have been invited.

2. Major research activities in Biotechnology and its related research fields
at your institution

A) Novel protein corresponding cysteine protease inhibitor (CPI) has been
identified from N terminal sequencing and its homology with other protein
established.
B) Sequence characterization of one the novel Rgene fragment is in process.


Plant Molecular Biology with specific reference to Biotic and Abiotic
Stress and transformation

a) Protein Purification and raising antibody against Cysteine Protease
Inhibitor (CPI)
b) Identification of iron rich rice varieties with low phytic acid
c) Development of Mapping Population for Drought, Submergence, Salinity in
rice and also temperature tolerance in wheat (Under pipeline)

5. Infrastructure facilities in the Bioinformatics centre
B. Scientific software packages : Tenders invited for all items
C. Database and other information resources

6. Details about staff members working in the centre (Name of the Staff,
absorption status)

Faculty Member Designation Area of Specialization Working
Since
Absorb
tion Status
Dr. K.N. Singh
kapildeos@hotmail.com
Prof. & Head Gene isolation and its
manipulation
2005 Yes
Dr. Ramji Singh
rmjsingh@yahoo.co.in
Associate
professor
Molecular Biology,
Disease resistance,
Biochemistry
2005 Yes
Dr. D.K. Dwivedi
ddwivedi2000@yahoo.co.
in
Associate
professor
Genetics, Molecular
breeding, Quantitative
Genetics
2005 Yes
392
Dr. R.P. Singh
rpsbiotech@rediffmail.co
m
Assistant
professor
Proteomics of pigeon
pea to control pod borer
2005 Yes
Dr. Nawaz Ahmed Khan
nakhan_2004@india.com
Assistant
professor
Controlling YSB in rice
through transgenic
approach
2005 Yes
Dr. Shambhoo Prasad
shambhoop@hotmail.co
m
Assistant
professor
Abiotic stresses
(drought, flood, heat
etc.)
2005 Yes
Dr. Manish Kumar Singh
manishsinghmk@hotmail.
com
Prog. Asstt. Molecular Biology,
Submergence tolerance
2005 Yes
Dr. C.S. Pandey
shekharhort@india.com
Prog. Asstt. Plant tissue culture,
horticulture-Pomology,
Plant Propagation
2005 Yes
Dr. Pramila Pandey
pramila28@gmail.com
Prog. Asstt. DNA fingerprinting,
Biotic Stress
2005 Yes
Dr. Poonam Yadav
poonambiotech@gmail.c
om
Contres(III) Molecular Marker
Technology
2007 Yes
Mr. Rajiv kumar Singh
raj.singhonline@gmail.co
m
Contres (II) Transformation and
Transgenic Technology
2007 Yes

7. Types of services provided : Teaching and Research


M.Sc. Biotechnology Program and this Department is established in year
2004 and from year 2008 this M.Sc. Biotechnology Program is being run with
the help of Department of Biotechnology, GOI. Two batches of M.Sc. students
are passed out and third Batch is pursuing so far. Number of intake is
restricted to ten. Placement Details of our students are as follows:

Sr.
No.
Name of the
Student
Year of
pass
outs
Place where appointed Nature of
Job
1. Prashant Vikram 2006 International Rice Research
Institute (IRRI), Philippines,
Manila,
Ph.D.
Scholar
2. Md. Shamim 2006 Indian Institute of Pulse
Research (IIPR) Kanpur
SRF
3. Neha Singh 2006 Indian Institute of Pulse
Research (IIPR) Kanpur
SRF
4. Tarranum Nissar 2006 National Botanical Research
Institute (NBRI), Lucknow
SRF
5. Onkar Singh 2006 NRC on Plant Biotechnology,
Pusa, New Delhi
SRF
6 Aniruddh Tiwari 2006 Bajaj Hindustan Pvt. Ltd.,
Muzaffar Nagar, U.P.
Trainee
Officer
7. Shivam priya 2006 Industrial Toxicological
Research Center, lucknow
SRF
8. Amit Kumar 2007 Navodaya Vidyalaya
Barabanki, U.P.
Teaching
393
9. Brijesh Verma 2007 Eriscon, Bangalore Research
10. Vishal Singh 2007 Industrial toxicology Research
Centre (ITRC), Lucknow,
SRF



11. Databases/ Software Packages Developed ----- NA-----

12.Papers published or presented in the conference with reference

National Seminar on molecular approaches for crop improvement
Feb. 7
th
8
th
,2007
Dr. K.N. Singh
International rice Symposium , IARI , New Delhi, October 2007
Feb. 7
th
8
th
,2007
Dr. Ramji Singh
Annual Zonal meeting of Indian Phyto pathological society & National
Symposium on Advancing frontiers of Plant Disease Management
Nov. 15-17, 2007
DBT sponsored training on Gene closing Techniques and Automated
DNA Sequencing Department of Genetic Engineering School of
Biotechnology organized By SRM University, Kattankulathur Tamil
Nadu June 4 to24, 2007
National Seminar on Molecular approached for crop improvement Feb
7-8, 2007
Dr. Ramesh Pratap
Singh
National Symposium on Recent trends in Plan Science and Haerbal
Medicine. Dec., 17-18, 2007
National Seminar on Molecular Approaches for crop improvement
Feb. 7-8
th
2007 organized by Deptt. of PMB & GE, NDUAT, Faizabad
Workshop On Agricultural Biotechnology Advanced Tissue Culture
Techniques for crop improvement, 21-22 Feb., 2007, Organized the
Energy and Resource Institute (TERI) New Delhi.
Dr. C.S. Pandey
National Symposium on Research Trends in Plant Science and herbal
Medicine, Dec. 17-18, 2007. Organized by NDUAT, Faizabad in
Collaboration with APSI, India Muzaffar Nagar (U.P.)
Participated in training courage on construction of CDNA library and
its screening organized by ICAR, under advance studies in
Biochemistry from Biochemistry, IARI, New Delhi from 5-25, Jan.,
2006
Participated in 74
th
annual meeting society of biological chemistry
(India) at CDRI Lucknow from Nov. 7-10, 2005
Participated in international Symposium conference on Post Harvest
Technology and Value addition in cereals, pulses & oilseed at
CSAU&T, Kanpur , Nov., 27-30, 2006
Dr. Nawaz Khan
Participated in National symposium on Molecular approaches for crop
improvement at NDUAT, Kumarganj, Faizabad from 7-8 Feb 2007.
Dr. Shambhoo
Prasad
Activity participated in National Seminar on Molecular approaches for
crop improvement at Dept. of PMB & GE, NDUAT, Kumarganj,
Faizabad from 7-8 Feb., 2007
Participated in winter school training on Molecular Breeding
approaches for rice improvement at CRRI Cuttak, Orissa from Sep.
10
th
-30
th
, 2007.
394
Participated in International Symposium on Post Harvest technology
and value addition in cereal, pulses & oil seeds at CSAU&T, Kanpur
Nov., 27-30, 2006
Dr. Poonam Yadav
Participated in National Symposium on Molecular approaches for
crop Improvement at NDUAT, Kumarganj, Faizabad from, 7-8, Feb,
2007
National Seminar on Molecular Approaches for Crop Improvement,
NDUAT, Kumarganj, Faizabad (7-8 Feb., 2007)
International Symposium on InterDrought II: Integrated approach to
sustain and Improve Plant Production Under Drought Stress at
University of Rome La Sapienza Rome, Italy (24-28 September,
2005)
18
th
Scientific Conference of the Federation of Crop Science Societies
of the Philippines (2-6 May, 2005)
International workshop on Resilient Crops for Water-limited
Environments at CIMMYT (24-28 May, 2004)
Molecular Breeding approaches for rice improvement, CRRI (10-30
Sept, 2007)
Planning Rice Breeding Programs for Impact, IRRI (7-18 Feb, 2005)
Radiation Safety Course held at IRRI by the Department of Science
and Technology, Philippine Nuclear Research Institute (1-5 March,
2004)
Dr. D.K. Dwivedi
Microarray and Bio-informatics: Applying Genomic Technologies to
Identify Induced and Natural Variation in Stress-Response Genes,
IRRI (23-26 February, 2004)
Dr. Manish Kumar
Singh
Feb. 7
th
8
th
,2007, N.D.U.A.T., Kumarganj, Faizabad, U.P.
Km. Pramila
Pandey
Feb. 7
th
8
th
,2007 N.D.U.A.T., Kumarganj, Faizabad, U.P.
13. Initiation of R&D activities in bioinformatics : Just initiated

14. Details of training/ workshop organized and total number of user trained
Program has just started and very soon and in this calendar year training will
be organized with intake of the ten participants.

areas. In this you may highlight the details like number of papers published/
manpower trained, tools developed, patents and copyrights acquired and
other services offered etc.

Few publication in Biotechnology has just started and coming up these are as
follows:
Md. Shamim, N.A. Khan and Singh, K.N. (2007). Controlling Yellow Stem
Borer in rice using cysteine protease inhibitor from jack fruit seeds an
alternative to Bt. approach. IRRI News Letter (communicated)

Ashutosh Singh, Kapildeo N. singh, A.L. Yadav and Prashant vikram. (2007).
PCR based diagnostics of a geminivirus causing leaf curl disease in papaya.
Plant Archives. 7 (1): pp 87-89.

395
Jitendra Pratap Singh, Shambhoo Prasad, K.N.Singh and Randhir Singh
(2007). Screening of heat tolerant wheat varieties by membrane thermo
stability index in relation to yield and yield attributing trairs. International
Journal of Plant Sciences. Vol.2: 159-165.

Till date there is no any publication in Bioinformatics.


Gene prediction
Promoter analysis
Various software application like QTL cartographer, NT SYS,
secondary structure prediction etc.
Homology Search

Additional details:
Name of the Coordinator: Prof. K.N. Singh, Prof. & Head, Department of Plant
Molecular Biology & Genetic Engineering

Postal Address: Narendra Deva University of Agriculture & Technology,
Kumarganj, Faizabad, 224 229, U.P. INDIA

Phone No. 05270-262123
Mobile: 9450767369
Email: kapildeos@hotmail.com
Website:

Name of the contact person(s): Prof. K.N. Singh, Prof. & Head, Department of
Plant Molecular Biology & Genetic Engineering
Email: kapildeos@hotmail.com
396
National Institute of Pharmaceutical Education and Research, Chandigarh
Coordinator : Prof. P.V. Bharatam


Carried out research on Drug Design using Bioinformatics using Homology
Modeling, Molecular docking, virtual screening are the focus of the work.
The targets of interest are Peroxisome Proliferating Activating receptor
(PPAR,,), Glycogen Synthase Kinase (GSK3), DHFR, hERG,
acetylcholineesterase, etc. The therapeutic areas of interest are Diabetes,
Malaria, arrhythmia, Alzhemier, etc. The drugs of interest are pioglitazone,
rosiglitazone, metformin. Chemical processes like tautomerism in drugs,
reaction mechanism for the synthesis of drugs, etc. were also studied.

institution

Target identification in Insulin resistant diabetes,
Target identification in drug resistant Leishmania,
Pharmaceutical biotechnology, Microbiology & biotechnology,
Recombinant DNA technology, Protein stabilization,
Downstream processing, Nonaqueous enzymology
Genomics, Proteomics, Bioinformatics and systems biology,


Computer Aided drug design using sequence analysis, Structural
bioinformatics, Molecular Docking
Receptor based pharmacophore mapping, Virtual screening using molecular
docking


Workshop on target identification and target validation was conducted during
14-16 March 2007. A symposium on Bioinformatics for pharmacology was
conducted as a part of Annual conference of Indian Pharmaceutical Society,
SAS Nagar (2
nd
Nov. 2007). A workshop is scheduled to be held during 13-15
March, 2008.


PCs 10 Server -1
Printers 2 Storage Space NAS 1TB
Xerox machine Networking among all the systems

Drug design packages available from NIPER:
MOE, SYBYL (QSAR, Maping, docking, Unity,)
Catalyst, Gaussian, Spartan, Amber
397
Databases & other information resources available from NIPER.
CCSD (Chemoinformatics)
GCG (Bioinformatics)

absorption status)

Prof. P.V. Bharatam, Prof. in Med. Chem. (Coordinator) specialization in
computer aided drug design using molecular docking, pharmacophore
mapping, QSAR, Electronic structure methods, etc.
Dr. C.G. Mohan, Asst. Prof. in Pharmacoinformatics specialization,
pharmacoinformatics, structural biology, electronic structure analysis,
toxicoinformatics, etc.

Scientific studies based on metabolic processes (oxidation using CYPs,
FMN), pharmacophoric generation, molecular docking, QSAR analysis.
Toxicoinformatics based prediction of toxic profile of compounds.

The BIF center contributes heavily to the M.S. Pharm. (Pharmcoinformatics)
programme of NIPER. 25 MS students and 9 Ph.D. students are using this
facility. All the students of the previous batch of M.S. Pharm.
(Pharmcoinformatics) who graduated in July 2006 have found placements.
60 % are in industry, 40% joined academic research.

Computational designed drugs have been synthesized and biologically
evaluated and found to be promising.
Collaborating with scientists at Medicinal chemistry and pharmacology
department of our institute.
Collaborating with Punjab University, Chandigarh and Guru Nanak Dev
University, Amritsar.
International Collaboration with scientists at University of Turku, Finland.

Alzhemiers disease database: From Genome to Drug

Modelling and Informatics in the Design of Anti-Tuberculosis (TB) Agents, G. Ranganath, D.
Pohani, S. Sundriyal, P.V. Bharatam. J. Computer Aided Drug Design (submitted).
Metformin and Glitazones: Does Similarity in Biomolecular Mechanism Originate from
Tautomerism in these Drugs? S. Sundriyal, S. Khanna, R. Saha, P.V. Bharatam, J. Phys.
Org. Chem. 2007 (in print).
Computer Assisted Methods in Chemical Toxicity Prediction C.G. Mohan, T.Gandhi, D.Garg,
R. Shinde, Mini Review in Medicinal Chemistry, 2007, 7, 499-507.
398
XML in Motion from Genome to Drug; Available from Nature Precedings C.G. Mohan, <
http://dx.doi.org/10.1038/npre.2007.287.1 > (2007)

Target identification and validation, CADD, Cluster and High Performance
computing
Indo-Finland research collaboration is initiated in the area of structural
bioinformatics, CADD and software development. Development of
therapeutically useful databases.

Workshop on Target Identification and target validation : 14 16, March 2007
: 50 participants
Symposium on Bioinformatics during IPS annual convention : 2 Nov. 2007 :
~1000 participants

areas.
The researches at the biotechnology department at NIPER extensively use
the bioinformatics facilities. Several papers and patents were generated
during 2007 with the collaborative effort.


Research focus on drug design using pharmacoinformatics, including
structural bioinformatics, molecular docking, pharmacophore mapping,
electronic structure, metabolome informatics and toxicoinformatics, etc.

Workshop to be conducted in 13 -15 March 2008 in Pharmacoinformatics.

Name of the Coordinator: Prof. P.V. Bharatam,
(on behalf of Director NIPER)
Department of Medicinal Chemistry
A-208,Natl. Inst. Pharm. Edu. Research.
Postal Address: S.A.S. Nagar -160 062
Phone Number: 0172-2214684 Extn. 2018 Fax No.: 0172-
2214682
Email: pvbharatam@niper.ac.in
Website: www.niper.gov.in
399
Orissa University of Agriculture and Technology, Bhubaneswar
Coordinator : Dr.P.N.Jagadev

The project on Creation of Bioinformatics Infrastructure Facility (BIF) for the
promotion of Biology Teaching through Bioinformatics (BTBI) scheme of BTIS
net was implemented on 3
rd
November, 2006 in the P.G Department of
Bioinformatics, OUAT, Bhubaneswar with 100% support from the Department
of Biotechnology, Government of India, New Delhi.
During the last year (i) a well furnished computer lab with internet facility was
established for the project with two high end server and one medium end
server, ten numbers of PCs with operating system like Windows 2003
Enterprise server/Redhat Linux and needful software like Microsoft visual
studio 2005, MS Office 2007, SQL and one scanner, one HP Laser Jet 3055
printer, one HP DeskJet D2360 printer, one photo copier are available for the
project work.
institution:
The Orissa University of Agriculture and Technology is offering a two year
regular course with an intake of ten students each year, selected through the
entrance examination conducted by the JNU leading to M.sc. (Ag.) degree in
Agricultural Biotechnology with the 100% support of the Department of
Biotechnology, Ministry of Science and Technology, Government of India.
The major research activities in Biotechnology are molecular marker
technology, protein profiling, DNA fingerprinting, tissue culture, transformation
of rice and potato etc. The fields of research in Bioinformatics sequence
analysis, computational biology and development of biological databases
besides offering a two years regular course with intake capacity of 32
students each year selected through career weightage basis leading to M.Sc.
degree in Bioinformatics on self-finance scheme of the University since 2002.
3. Area of Specialization of the Centre: Biotechnology & Bioinformatics.
During the year 2006-07 four Post-Graduate students (Bioinformatics) of this
University have done their dissertation project works in the areas of database
development on medicinal plants, Fusarium species, rice crop and soil
informatics. Thirty two numbers of Post-Graduate students (Bioinformatics)
have also passed from this department by doing their theses works in leading
labs of different institutions /organizations of the country.
A. Computer & Communication facility: Thirty-seven PCs with 2048 kbps
internet connectivity in the Department of Bioinformatics and ten numbers of
PCs, two numbers of high-end servers and one medium end server with
operating system in the project are available.
B. Scientific Software packages : GCG Wisconsin package, java, LINUX,
UNIX, XL stat, Antivirus packages are available- sponsored by OUAT
C. Databases & other information resources: Oracle 10G, Microsoft SQL
Server, Ricebase, Fusabase.

BTISnet-DBT project
SL.No. Name of the staff Designation Specialization Period of
400
working
1. Mr. S.N.Rath RA Computational Biology 17.01.2008
onwards
PG Department of Bioinformatics
1. Ms.L.kanungo Asst.Proff. Proteomics 29.08.2006
Onwards
2. Mr.S.k. Pradhan Asst.Proff. Molecular modeling 01.05.2007
onwards
3. Ms.S.Mohanty Asst.Programmer Computer Science 17.04.2006
Onwards
4. Mr.M.Garanayak Data Entry Operator ------ 15.01.2003
onwards
* The absorption status of the above staffs is on contractual basis.

The centre has provided the facilities of computer lab and twenty four hours
internet facilities (fiber optics)to the post-graduate students and
teachers/scientists of the sister departments like Biotechnology, Pathology,
Horticulture, Soil Science and Biochemistry, Plant Breeding and Genetics etc. for
their dissertation and research work, besides rendering the computational
knowledge to them.
Each year, 32 Nos. of M.Sc. (Bioinformatics) students are passing out of this
department and placed in different reputed organizations and companies of
repute and also in off campus interview. During the last year our student are at
JVK Bio Science, Hyderabad, Mahatma Gandhi Institute of Medical Sciences,
Wardha, RCM, Bhubaneswar, GIET, Gunupur, Orissa, KBRC, Cuttack etc.
9. Initiative to validate the outcome of Bioinformatics resources:
Actions have been taken to validate the Bioinformatics resources. For
example booklet was developed for the initial years (2002-05) of theses research
works of students.
In the year 2006-07 students done their dissertation different reputed
institutions and laboratory like, RRL, Bhubaneswar, Wingene, Banglore, ITRC,
Lucknow, WB University, Kolkata, Biotech Park, Lucknow, ISI, Kolkata, GVK
Biosciences, Hyderabad, Satya Informatics, secunderabad, MGIMS, sevagram,
wardha for their partial fulfillment of M.Sc. Bioinformatics degree.
11. Databases / Software packages developed:
One CD-ROM database on rice genotypes available at OUAT research station is
developed.
i) Paper entitled BioRec: A biological record retrieving tool
accepted for poster presentation in InCoB (Sixth International
Conference in Bioinformatics) held at Hong Kong during August 27-
30, 2007.
ii) Paper entitled Fusabase: A database for identifying species
Fusarium accepted for poster presentation in InCoB (Sixth
International Conference in Bioinformatics) held at Hong Kong
during August 27-30, 2007
After getting this project this department has taken initiatives to develop
various CD-ROM database on Biotechnological research work, identification
401
tools for bacterial plant pathogens, database on rice genotypes of Orissa and
Fusarium are developed in the department of Bioinformatics. Initiation to develop
an online database on medicinal plants has also been taken.
14. Details of Training/ workshop organized and total no. of user trained:
A 3days National Workshop-cum Training was successfully organized from 9-11
March, 2007 with 31 numbers of participants and 15 Nos. of Resource Person
from different R &D organizations and Institutions of National repute.
15. Impact shown by your centre on growth of biotechnology and allied
areas:
Our centre is helping the students of this university and other Universities like
Amity University for their dissertation and works in the biotechnology and allied
areas.
i) To organize hands on training and seminar for familiarizing the
applications of Bioinformatics in biology teaching.
ii) To establish collaboration with other institutions and BTISnet centres
for information resources and expertise.
iii) Development of on-line databases of field and horticultural crops.

Additional Details:

Name of the Coordinator : Dr.P.N.Jagadev
Postal Address : Head, Post Graduate department of
Bioinformatics, Orissa University of
Agriculture and Technology,
Bhubaneswar-751003, Orissa
Phone Number : 0674-2530418, 09861128437
Fax : 0674-2391424/ 2394762
Email : pnjagadev@yahoo.co.in
hodbioinformatics@yahoo.co.in

Name of Contact Person : Dr. Sashikala Beura,
Associate Professor
Dept. Horticulture, OUAT,
Bhubaneswar-751003, Orissa.
Email: : skbeura2002@yahoo.co.in
402
Presidency College, Chennai
Coordinator : Prof. S. Rajarajan

The Bioinformatics Infrastructure Facility (BIF) Centre at P.G & Research
Department of Microbiology & Biotechnology, Chennai was established on
28 March 2007. The Centre had conducted two workshops. 1) State level
Workshop for 12- days on Bioinformatics for the Government College
Teachers from March 28
th
to April 10
th
2007 2) A National workshop for 11-
days on The Application of Bioinformatics in Drug discovery and Drug
development" for the benefit of Research scholars and made an indelible
impact on the target group about the activity of the centre. In addition, the
centre had created database on Antibiotics of microbial origin and will be
available in website from January 2008. The centre provides free internet
facility to all the students & all needy departments of the college.
2. Major Research activities in Biotechnology and its related fields at your
institution
Discovery of newer drugs from herbal source for microbial diseases in human
is one of the major thrust area in biotechnology conducted in P.G and
Research Department of Microbiology & Biotechnology. Screening of the
potential medicinal plants, subsequent isolation of the active principles (at
chemistry Department) and testing the efficacy of the active principle (drug) in
relation to the Pathogenomics of the microbe. Few research scholars are
working on the pharmacogenomics of efficacious drugs for very common
diseases like Diabetes, hypertension, Tuberculosis, Chickugunya etc. In
addition, in vitro cultivation of important cell lines for the estimation of toxicity
of drugs and in vitro antiviral assay are also carried out.
3. Area of Specialization of the Centre:Drug discovery & Drug development.
4. Major Acti vities Of The Centre During The Year 2007-2008:
Conducted two workshops and created a database (as mentioned in item 1)
5. Infrastructure Facilities in the Bioinformatics Centre:
a) Computer and communication Facilities:
The centre is equipped with 10 Desktop computers (IBM). 1 High end server (IBM), 1
Middle end server (IBM), with 1 HP Color Laser printer (5-in-1 model Copy, scan, fax,
print, imaging) and with software packages like Symantec Antivirus, Symantec Antivirus,
MS Windows Vista, Media Kit, MS SQL server, MS SQL server cal 2005, Redhat
enterprise linux, MS Windows, MS windows 2003, MS visual studio, MS office 2007, 1
Inkjet printer.7.5kva UPS with VSNL high speed internet connectivity to all needy
departments. The centre has been provided with split air conditioner (2 ton).
Telephone :044-64542545 Telefax:044-28589621
Email:bifcpresidencychennai@rediffmail.com Website :
www.bifcpresidency.net.in
b) Scientific software packages: CLC BIO Combined Workbench.
c) Database & other information resources: Created a database for the first time in
India on Bioinformatics of antibiotics from microbes and this will be uploaded in the
website by the end of January.
6. Details of staff members working in the centre:
Sl.
No.
Name of the
staff
Designation working since Absorption
status
(yes/no)
*
403
1. Miss. M. Niraja Asst. Coordinator
Research
Associate
December 2006
September 2006
yes
2 Miss. L. Anitha Data Entry
Operator
March 2007 yes

7. Type Of Services Provided
Four major types of services are provided 1) Free Internet facility for PG /
Research Scholars/ Teachers at the centre 2) Internet facility to all needy
departments 3) Free utilization of softwares on Bioinformatics 4) Training
programme. Also it enables the P.G. Students of Government colleges,
Government aided colleges to obtain required information on Bioinformatics.
Thus promoting the discipline of Bioinformatics among colleges in and around
Chennai. Text books and reference books on various areas of Bioinformatics
are available in the centre for the benefit of students / Teachers / Researchers.
Students of M.Sc Applied Microbiology & Biotechnology utilize this facility for
core elective paper on Bioinformatics. Besides this, students of M.Sc., M.Phil.
and Ph.D. utilize for their research data. Many of the students are well placed in
other software & knowledge process outsourcing companies.
9. Initiati ve to validate the outcome of Bioinformatics Resources:
A register is maintained on the users and membership card with finger print
entry facility is being issued to the users.
10. Collaborative Works/ Initiatives:
Collaborative work on Drug discovery & Drug development with TANUVAS
(Tamil Nadu University of Veterinary Animal Sciences) for development of drugs
for veterinary animals and with Meenakshi Medical University have been agreed
in December 2007.
11. Databases/ software packages developed:
Developed a database for the first time in India on the Bioinformatics of
antibiotics from microbes. Further, a database on vaccines is being developed.
1) Rajarajan. S. Application of Bioinformatics in drug discovery and drug
development presented at the national Conference on bioinformatics
tools for gene and protein analysis on 7-8 September, 2007 at Srimathi
Indira Gandhi College, Tiruchirapalli, Tamil Nadu.
2) Rajarajan. S., In Vitro antimicrobial assay of Medical Plants
(M.K.Nambiar oration) 28
th
Annual Conference of India Association of
Biomedical Scientists 21
st
Sept. 2007, Bharathidasan University,
Tiruchirapalli.
3). Amerjothy. S Antimycobacterial properties of Leaf extract of
Pithecellobium dulce Benth. pp. 392-395. 42 (6) Indian Drugs.
4) Amerjothy. S. In vitro assay of antifungal and antitubercular activities of
the leaf extract of Pithecellobium dulce. XXVIII All India Botanical
Conference BSI - Dehradun 2005.
5) Amerjothy. S. Pharmacognosy and Pharmaceutical Potential of Some
Plant Galls,National Seminar on Recent Advances inPlant Biology,
Abstract, p. 83, July 2006, Pondichery University, Pondicherry.
404
6) S. Amerjothy Pharmacognostic investigation on leaves of Pithecellobium
dulce (Huamuchil) A promising anti-tuberculosis drug pp. 265 275 with
S.D. Shanmuga Kumar et al. in the book Recent Trends in Plant Sciences.
7) Natarjan. C, Senthil Kumar R, Niraja M, Rajarajan. S In vitro antiviral
efficacy of lyophilized extracts of anthospira platensis (Spirulina Platensis)
on human herpes virus 2 (HH-V / HSV 2) in comparison with
acyclovir. South Zonal conference of Medical Microbiologist Sozocon
Micro 2008 20
th
January 2008 at Srimanakula Vinayagar Medical College,
Pondicherry.
8) Ganesh. B, Bakthasingh Lazarus. Y, Rajarajan. S Study on the isolation
and characterization of the etiological fungus from onychomycotic
infections at a hospital in chennai and their in vitro susceptibility to a
herbal mixture to antifungal agents. South Zonal conference of Medical
Microbiologist ,Sozocon Micro 2008 20
th
January 2008 at Srimanakula
Vinayagar Medical College, Pondicherry.
9) Praveen Irudiyaraj. R, Bakthasingh Lazarus. Y, Rajarajan. S. In vivo
experimental study on development of cutaneous hypersensitivity in albino
mice after exposure to aerosolized antigen of Aspergillus spp. South
Zonal conference of Medical Microbiologist Sozocon Micro 2008 20
th

January 2008 at Srimanakula Vinayagar Medical College, Pondicherry.
13. Initiation Of R&D Activities In Bioinformatics
The Bioinformatics centre of DBT, Presidency College and the Virology
Department of King Institute of Preventive Medicine, Chennai have agreed to
work together in its R & D activities on Bioinformatics.
14. Details of training/ workshop organized and total no. of user trained:
As mentioned in item (1) The total number of user trained in first workshop was
10 and in the second workshop was 20.
offered etc.
Through its activity and conduct of workshops it evoked interest on
bioinformatics in Tamil Nadu in relation to Drug discovery & Drug
development. In addition the facility has been used for the below mentioned
activities
M.Sc. dissertations: 61, M.Phil. dissertations: 57
Ph.D. thesis completed: 14, Papers published using this facility: 37
Database created using this facility: 2 databases
No of teachers who availed this facility: 63, PG students 215, Research
scholars 94
As this prestigious institute is to be elevated into a University from 2008 -
2009 Post Graduate & P.G Diploma programmes in Bioinformatics will be
started. Summer school programme for higher secondary students & teachers
on Bioinformatics will be conducted on Drug discovery & Drug development.
This will make an effective impression on the young minds to venture into
Bioinformatics and appreciate its role in Drug discovery & Drug development.
The centre will establish interconnectivity and exchange of information with
405
other centres working on Drug discovery & development. Databases on Drug
from plant / animal / mineral sources will be created with the coordination of
other departments.

Additional Details: Name of the Coordinator: Prof. Dr. S. Rajarajan
Postal Address: College House, No.100, Kamarajar Salai
Presidency College, Chepauk,
Chennai 600 005.
Phone Number: 044- 28547839, Mobile: 9282321575
Fax Number: 044-28589621
Email: drrajarajan@rediffmail.com
Website: www.bifcpresidency.net.in
Name of Contact Person(s): Miss. M. Niraja Email: shri_hari81@yahoo.co.in
406
Presidency College, Kolkata
Coordinator : DR. Abhijit Datta

1. Summary of the progress made at BIOINFORMATICS
INFRASTRUCTURE FACILITY (BIF-BTBI) at Presidency College, Kolkata
(NAAC A
+
Accredited and College with Potential for Excellence) Centre
since its inception:
The Centre has started working under the guidance of Dr. T. Madhan Mohan,
Advisor, DBT, during the last quarter of 2006. Following points are to be mentioned:
1. Inauguration of the site has been done (One Bioinformatics Centre, to
accommodate 20 terminals and another Server room with four terminals) in the
Central Library Building, Presidency College, Kolkata.
2. The EC meetings have been convened as per DBT guidelines;
3. LAN, 24x7 - 2 Mbps Internet connectivity and graphics facility of the
Bioinformatics Laboratory are working full time.
4. Procurement of the hardware and software has been completed as per
recommendations by the expert members.
5. List of Experts in the field of Bioinformatics is under processing, required for
the Workshop / Training Program to be conducted by BIF, Presidency College,
Kolkata from time to time;
6. Probable schedule of the Workshops / Training Program to be taken up
during the next financial year is under formulation;
7. Designing of the website bioinfopresidencycollegekolkata.edu.in is under
construction;
Presidency College, Kolkata: A full fledged Plant Biotechnology Laboratory runs
in the College, working on various medicinal plants viz. Jatropha, Chlorophytum,
Swertia and other horticultural plants including Orchids.
Plant Molecular Biology group is working on Cashew genome in collaboration with
Haldia Institute of Technology, West Bengal.
Bioinformatics work group from different constituent departments of the college is
growing to make out some inroads in near future.
Formally Inaugurated on Founders Day, National Workshop conducted on
Bioinformatics: Genomics & Proteomics Plexus 8 - 9 Dec 2007 in the Bankim
Sabhagriha which was inaugurated by Dr. T. Madhan Mohan and a National
Workshop on Clinical Research & Clinical Database Management is being held
during 31 Jan - 2 Feb 2008.
One IBM Server 226 has been installed as per DBT specifications;
Ten Desk tops are installed as terminals as per DBT specifications;
One HP Workstation is being installed for modeling works;
Software to run these systems purchased as per DBT specifications;
One independent Broadband (2 Mbps) connection with unlimited download
facility is running for the users / students;
One Fortigate Firewall has been installed for net security of the Centre.
Scientific Software packages: None purchased so far;
Databases & other information resources: Under consideration.
407
Research Assistant: Sayak Ganguly, M.Sc.; Diploma in Bioinformatics.
Laboratory Assistant: Priyanka Dhar, M.Sc.
6. Types of services to provide: Downloaded packages are being made available
to the Under Graduate and Post Graduate students of different Bio-Science
Departments as well as to the Research Scholars of the College and other Institutes
of the locality. In future all types of facilities will be offered depending on the
availability of the suitable Software.
7. Initiative to validate the outcome of bioinformatics resources: A high
profile Advisory Committee has been constituted to formulate the future
course of action at this Centre. With the help of suggestions of the honourable
members the facilities are being designed to cater not only the students of
Presidency College, Kolkata, but also the students of the nearby Government
Colleges, other affiliated Colleges and share with other National Institutions.
The excerpts of the suggestions were proposed along with the EFC inputs.
8. Collaborative works / initiatives: Collaborative work has already been
proposed with partner Dr. T.C. Ghosh of BIC, Bose Institute and collaboration
with other Institutes viz. IOCB, Bangalore and Birla Institute of Technology
etc. is under consideration. BIF, Presidency College and IOCB have held a
workshop on Clinical Research & Clinical Database Management at the
Derozio Hall, Presidency College, Kolkata.
9. Initiation of R&D activities in Bioinformatics: R & D programmes on RNAi,
Dof Domain and other interesting storage proteins are being initiated. Two
communications have been made and others are in the pipeline. Proposals
from Research work groups have been invited from different Bio-Science
Departments of the College, to be carried out utilizing the Bioinformatics
Infrastructure Facility at Presidency College, Kolkata.
10. Details of Training / Workshop organized and total no. of user trained:
One National workshop was conducted on Bioinformatics: Genomics &
Proteomics Plexus during 8-9 Dec 2007 in the Bankim Sabhagriha,
Presidency College, Kolkata with 48 participants. Inaugural address was
delivered by Dr. T. Madhan Mohan and the list of speakers includes Prof.
Pinak Chakrabarti, Dr. Subhasish Mukherjee, Dr. Debasish Mukherjee, Dr.
Kunal Mukhopadhyay and Somak Ray. Another National Workshop on
Clinical Research & Clinical Database Management is being held during 31
st

Jan 2
nd
Feb 2008 in collaboration with IOCB, Bangalore with ~ 150
participants.
11. Future activities of this Centre will include: As proposed in EFC inputs
Summer School / Winter School on Bioinformatics for Research Scholars and
Students, Training Programmes for Post graduate, Under Graduate students
and Teachers from the Undergraduate Colleges, Post Graduate Departments
of different Colleges and Universities. National level Seminars, Workshops on
emerging fields of Bioinformatics. Offer Post M.Sc. Traineeship/Studentship
to the students coming from different Bioscience disciplines. To conduct
research in the areas viz. Dedicated and derived Genomic/Clinical/
Biotechnology Database Development, Analyses using Bioinformatics tools,
In silico Modelling and Development of study modules for different levels of
teaching. To introduce (Memorial) Lecture Series in Bioinformatics. To
observe and celebrate BIOINFO-DAY each year, as annual meet, to attract
408
students in this field. This Centre aspires to become full fledged
Bioinformatics Centre in near future.

Name of the Coordinator: DR. ABHIJIT DATTA
Postal Address: PRESIDENCY COLLEGE
86/1, COLLEGE STREET
KOLKATA 700073
Phone Number: +919830116667
email: abhijit_datta21@yahoo.com
409
Sardar Vallabh Bhai Patel University of Agriculture & Technology, Meerut
Coordinator : Prof. Raghvendar Singh

The project entitled Establishment of Bioinformatics Infrastructure Facility
(BIF) for the promotion of Biology Teaching Through Bio-informatics (BTBI)
was sanctioned in the month of September 2006. The Bioinformatics lab
was established and furnished. The web site for the BIF is created and the
same is linked with our university (SVBPUA&T, Meerut) web-site. The two
week training programme on Database and Software application in biological
sciences was prepared. The six month teaching and practical courses on
Information Technology and Bioinformatics had been taught to the B.Tech
(Biotech) students of the university. The summer training on Bioinformatics
was given to the B.Tech student. The visit of the expert scientist on
Bioinformatics research in the area of structural & computational biology was
organized under VSAP. The development of the database on milk protein and
rice is in progress and will be completed shortly. Genomics and proteomic
study on wheat, rice and potato is in progress.
institution:
College of Biotechnology is established consisting of eight specialized
department as Pathology & Microbiology, Cell Biology, Biochemistry and
Physiology, Immunology & Defense Mechanisms, Recombination
Techniques, Department of Fingerprinting, Commercial biotechnology and
Department of Genetic Engineering to carry out major research and teaching
activities respectively.
3. Area of Specialization of the centre : Biotechnology
The objective of the College of Biotechnology is to train the students in
different biotechnology techniques and research areas like Finger printing,
Cell biology, Tissue culture of medicinal and other important crops of western
U.P. Molecular characterization, diagnosis and detection of pathogens,
Genetic of various traits, tagging and mapping of agriculturally important
gene(s), functional analysis of different mechanism, gene manipulation and
expression.
The major activities were establishment of Bioinformatics Lab, Creation of
Web-site, organization of BTISnet Teaching/Training / Workshop, visit of
scientist under VSAP, initiation for development of databases and
collaborative Ph. D. research projects and Participation in Meeting/ Seminar
/Conference.
The Bioinformatics lab is furnished with total ten Desktop computer system,
two Servers, two Laser Printer, internet connectivity and On-line UPS with
research and teaching material projection facility.
Designation, Specialization and period of working.
410
7. Types of services provided : Teaching, training and research
8. Educational activities with details of placement: B.Tech (Biotech) in
progress and M.Tech (Biotech) with specialization in seven different
departments is approved and under process of its implementation.
9. Collaborative works/ initiatives: Ph. D. Research project with Ch. Devi
Lal Univ. , Hisar.
10. Initiation of R&D activities in Bioinformatics : proteomic and genomic
study on lactoferrin, whey proteins, Dictyostelium discoidium.
Total 60 students of B.Tech (Biotechnology) were trained and the training on
Database and Software application in biological sciences is proposed in this
year.
To support and promote different on going teaching programme of the university
in the subjects of information technology, bioinformatics and biotechnology.
To provide a facility to different on going research programmes on mandatory
crops and other potential areas of research in the field of biotechnology and
bioinformatics of the university.
Establishment of Agri-Information center for quick transformation of advance
agricultural technology for the farmers of western U.P.
To prepare the information resources, databases on research advances on
wheat, rice, vegetable and dairy husbandry. Training on advances in
Biotechnology and Bioinformatics research including proteomics and genomics.
Development of website portal with several functionalities such as database
searching, teaching protocols, email support, user login, Query questions and
solutions and other standard information tools etc. The development of softwares
related to the bioinformatics as per the requirement of users of the universities.
To organize a refresher and Orientation courses on advances and development
in the field of bioinformatics research and to provide studentship ant traineeship
for the graduate and Post-graduate students of Biotechnology and
Bioinformatics.
Advance Diploma and post graduate degree course will be started in
Bioinformatics if approved.
Name of the Coordinator: Raghvendar Singh, Prof. & Head
Postal Address: Department of Immunology & Defense Mechanism, College of
Biotechnology, Sardar Vallabh Bhai Patel University of agriculture & Technology, Meerut
Email: raghvendar@gmail.com
Name of Contact Person(s): Dr. Jitender Singh, Co-coordinator
Email: Jeets_80@rediffmail.com
Name of the staff Designation Specialization Absorb. status
Dr. Raghvendar Singh Prof. & Head Immuno.& Biochem. Univ. employee
Dr. Jitender Singh Asst. Professor Biotechnology Univ. employee
Dr. Akash Tomar Asst. Professor Recombinant Tech. Univ. employee
Mr. Deepak Sisodia Asst. Professor Information tech. Univ. employee
Mr. Gyanendra Singh

Project fellow Information tech. No
*
411
Sant Gadge Baba Amravati University, Amravati
Coordinator : Dr. Prasad A. Wadegaonkar

Bioinformatics infrastructure Facility was established at Sant Gadge Baba
Amravati University This facility is housed in Post Graduate Department of
Biotechnology. Servers, PCs and other hardware are procured from HP
through DGS&D and 256 kbps internet leased line is obtained from BSNL.
This facility was inaugurated on 28
th
December 2007 by Honble Vice
Chancellor Dr. (Ms.) Kamal Singh, in the presence of Dr. Gulshan Wadhwa,
Principle Scientific Officer and Information Officer, Apex Centre, DBT, New
Delhi.
institution
Department of Biotechnology, SGB Amravati University is actively engaged in
research mainly in the area of microbial and plant biotechnology. DST has
sanctioned Funds DST-FIST Scheme. Prof. M.K. Rai and his groups
research is focused on the microbial growth promoters using chlorophyll
fluorescence as a biomarker (Biophysical Phenotyping). Dr. P.A.
Wadegaonkar and his research group is working on the root organ and
suspension cultures of those medicinal plants, such as Withania somnifera
(UGC sponsored), Artemisia annua (DRDO sponsored) and Rauwolfia
serpentina, Catharanthus roseus, Morinda citrifolia and Zinziber species for
production of secondary metabolites using bioreactors. Dr. (Mrs) A.S. Patil
and her group is working on bio-bleaching of paper pulp.
Establishment of infrastructure.
Server (High end) HP ML350 G4/G5 Xeon Daul processor - 01No.
Server (Medium end) HP ML110G3 Pentium IV configuration - 01No.
Desktops HP DX2060 Intel Pentium Dual Core 2.8 GHz - 10 Nos.
Laser Printer (Network) HP 2420 DN - 01 No.
Desk-Jet Printer HP BJ1200 d - 01 No.
Scanner Flat bed HP 2400 - 01 No
Lease Line 256 kbps
Bio-edit, ClustalW, GeneDoc, RasMol, TreeView, ACD/Chemsketch,
Fermisym, Polymath
o Flora of Melghat Reserve Forest (S&T Cell, Govt. Maharashtra
Funded)
o Database of Phyto chemicals (On going)
o Database of Industries India involved in phyto chemicals (On going)
absorption status) - nil
BIF has collection of books in PDF format on Bioinformatics, Genetics,
Molecular Biology, Biochemistry, Immunology etc. and other teaching
412
resources in flash animations, which are loaded on server and made available
to students through LAN. BIF is also providing Internet access and literature
search facility for academic purpose.
10. Collaborative works/ initiatives With the collaboration of Bioprocess
Laboratory, Department of Biotechnology, Sant Gadge Baba Amravati
University, attempts have been to integrate the available in silico and wet lab
facility for Metagenomic Research.
Database of Phytochemicals (On going)
Database of Industries India involved in phytochemicals (On going)
Initiation has been taken to integrate the wet lab facility of Biotechnology
Department and in silico facility of BIF.
Training Program on Bioinformatics and Information Technology was
organized from December 28-30, 2007. Total 15 participants were trained
during the period. During the training period special lectures were delivered
by Dr. Gulshan Wadhwa, Principle Scientific Officer, New Delhi, Dr. Shekhar
Mande, Scientist, CDFD, Hyderabad and Dr. (Mrs.) Sharmila Mande, Head,
Biological division, TCS, Hyderabad. Along with participants, over 150
students, research scholars and teaching faculty attended the lectures.
areas.
Ten PG students and Research scholars, who used the computational facility
of BIF, have been selected and representing the university in Inter-University
Research Festival Awishkar, at SNDT University, Mumbai.
To organize Training/Workshops for familiarizing the applications of
Bioinformatics in Biology teaching and learning activities.
To provide infrastructure facility to research students and graduate and
postgraduate students of the university.
Completion of databases.
To establish linkages with BTISnet of DBT and make available the
knowledge resources to the students, researchers and teaching faculties.

Additional Details:
Name of the Coordinator: Dr. Prasad A. Wadegaonkar
Postal Address: Coordinator, Bioinformatics Infrastructure Facility,
Sant Gadge Baba Amravati University,
Amravati 444602
Phone Number: 0721-2662207 ext 267 Mobile: 09422157263
Email: prasadwadegaonkar@rediffmail.com,
wadegaonkar@hotmail.com
413

414
Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow
Coordinator: Dr. Sita Naik

Since the project was initiated under the BTISnet program w.e.f. 22
nd

September 2006, a computer network has been set up consisting of servers
and 14 machines. Various softwares have been procured and installed. The
center (a) provides bioinformatics support facilities to the entire institute and
neighboring institutions, (b) has designed an in-house database of research
activities of SGPGI containing searchable lists of completed and ongoing
intramural and extramural projects undertaken at SGPGI since 1988, (c)
organized two training courses on bioinformatics and (d) begun two projects
using bioinformatics tools.
institution
SGPGI is a premier medical teaching and research institution. Several departments,
including immunology, genetics, neurology, pathology, microbiology,
gastroenterology and urology have active research programs.
Research and educational activities in of Biomedical information sciences
The Centre organized the following courses during the year:
i. Three week course in Bioinformatics from 8th -26
th
October, 2007.
Objective of the course was to provide introduction and overview
bioinformatics to the medicos.
ii. Two-day training cum workshop titled First course in Bioinformatics:
Introduction, Principles & Applications on 1
st
-2
nd
December 2007. The
main objective of the course was to impart the introductory knowledge
about principles underlying bioinformatics and practical application of
bioinformatics tools and techniques for gene and protein analysis to the
students, researchers and medical personnel.
Sl. No Equipments
1
CISCO 1700 Series Router
2
CISCO 2950 Series Switch
3
XEON 3.2 GHz Processor dual processor with 2GB RAM, 72X5 GB
HDD
4
2Mbps Internet connectivity through VSNL Lease Line
5
Fourteen PCs: Intel Pentium IV with 1GB RAM, 80GB HDD
6
Hp LaserJet P3500dn Printer
7
HP Color LaserJet 3800 Printer
8
HP Scanjet 8290 digital flatbed scanner
9
Xerox Copier WC 420 CP
10
Sharp Digital DLP Multimedia Projector

Licensed Software OS and Packages
415
Sl No. Name
1 Redhat Linux Enterprise Edition 4
2 Microsoft Visual Studio Professional Edition
3 Microsoft ISA Server
4 MS Window 2003 Server Edition
5 MS SQL Server 2005 Standard Edition
6 MS Office 2007 Professional Plus
7 Semantic Antivirus Corporate Edition
8 Discovery Studio 1.6
9 GCG Package

Free Software OS and Packages
Sl No. Name
1 Fedora Core 8
2 BIOLinux 4 Live DVD
3 DNA Linux
4 BioBREW
5 The Quantian Scientific Computing Environment 7.9

Free Bioinformatics Software
Downloaded software from World Wide Web ftp sites under General
Public License:
BioEdit, spdbv, rasmol, Cn3D, Jemboss, Emboss, NCBI BLAST,
Treeview, Phylip, MEGA, DAMBE, ClustalW, Chimera


work
Absorption
status
Aditya N.
Sarangi
Senior
Research
Officer
Bioinformatics June 2007 Temporary
Bhawna Rathi Research
Officer
Bioinformatics October
2006
Temporary

The centre provides computational facilities, bibliographic searches, bioinformatics
related services like primer design, analysis of DNA and protein Sequence, database
development to researchers and medicos. More than 50 users from various department
of SGPGIMS and near by universities in Lucknow has been using this facility. Centre is
organizing short term training program in bioinformatics for students, researchers and
medicos.

The Institute considers the requests from universities and colleges for project
work towards partial fulfillment of the respective postgraduate degrees.
Currently one student from Integral University is undergoing dissertation work
on Insilico protein structure prediction and Bioinformatics strategies for
disease gene identification.
416
Efforts are on to carry out collaborative initiatives with medical universities at
Lucknow and would like to join hands with other BTIS Centers.
The Centre has designed in house database for highlighting the research
achievements of SGPGI which contains searchable lists of completed and
ongoing intramural and extramural projects undertaken by the faculty at
SGPGI from 1988. Database also includes the lists of past and current PhD
students enrolled at SGPGI under various departments.
Current work is going on Insilico studies of Hepatitis E Virus using
bioinformatics tools and techniques. Center is developing BiomedLinux Live
DVD based on knoppix, which will contain the free pre installed bioinformatics
and biomedical software packages for biomedical, molecular and evolutionary
data analysis. The centre is also developing its local WWWBLAST Server.

Sn. Training Name Duration No of
trainee
1 01 course in Bioinformatics 8 -26,October, 2007 22
2 First Course in Bioinformatics,
Introduction, Principles and
Applications
1-2,December,
2007
16
3 Second Course in Bioinformatics,
Introduction, Principles and
Applications
22-24 February,
2008.

4 Workshop titled Computers and
Informatics in Medicine
March 17-19,
2008

13 Impact shown by your centre on the growth of biotechnology and
allied areas.
The Centre has designed in house database for highlighting the research
achievements of SGPGI. The centre had organized 01 Credit Course in
Bioinformatics [8 26 October 2007] and workshop cum training on First
Course in Bioinformatics: Introduction, Principles and Applications [1-2
December 2007]. In these two training programs 38 students, researchers
and medicos were trained.
14 Future activities
The centre plans to hold short term training programs and workshop for
students, researchers and academicians on a regular basis. It also proposes
to start diploma and certificate course in the field of Biomedical Informatics for
which permission has been taken from the Institutes Academic Board. A
meeting of curriculum committee is planned in Feb 2008 and the courses are
expected to start from the coming academic year. Centre will find linkages
with different research organizations, universities to promote bioinformatics
education and research. Centre will develop various software tools and
databases related to medical sciences.

Additional Details:
417
Name of the Coordinator: Dr. Sita Naik
Postal Address: Department of Immunology
SGPGIMS, Raibareilly Road
Lucknow-226014
Phone Number: +91 522 2668700, 2668800, 2668900
Email: sitanaik@sgpgi.ac.in
Website: http://biomedinfo.sgpgi.ac.in/

Name of Contact Person(s): Dr. Sita Naik
Email: sitanaik@sgpgi.ac.in

418
Shri Mata Vaishno Devi University (SMVDU), Katra, Jammu
Coordinator : Prof. (Dr.) V. Verma

As it is a new centre after receiving the grant efforts have been made to
procure the hard and softwares. In the meantime a room has been earmarked
for housing the centre in the new Block A recently constructed in the
university and furniture for the same has been ordered. The following
equipments have also been ordered:
Servers 2 Nos.
Work Stations 4 Nos.
Computers 10 Nos.
In addition all the infra structural facilities required for the centre are already
have been put in place/ are in the process of installation.

institution
School of Biotechnology at SMVDU is carrying out research in different fields
and currently has running following research projects
Project on Bioprospecting of actinomycetes from selected niches of
North Western Himalayas in J&K state. Funded by J&K state DST. PI
Prof. V. Verma
Project on Exploitation of microbial biodi versity of North Western
Himalayas for novel enzymes, bioactive molecules and
biotransformation processes. Funded by DBT, New Delhi. PI Prof. V.
Verma & Dr. Ahmed Kamal, IICT, Hyderabad
Project on Molecular and biochemical characterization of ACC gene in
Jatropha curcas. Funded by DST, New Delhi. PI Dr. Dhiraj Vyas, lecturer.
Project on Strengthening of botanical garden at SMVDU. Funded by
Ministry of Environment & Forests, New Delhi. PI Dr. PI Dr. Dhiraj Vyas,
lecturer.
Project on Establishment of Herbal Garden-Trikuta Hills at SMVDU
campus. Funded by National Medicinal Plants Board, Department of Health
& Family Welfare, New Delhi. PI Dr. Sharda, lecturer
The centre envisages to work on the following areas:
Identification of novel ORFs from North Western Himalayas;
Development of databases for the novel actinomycestes inhabiting
North Western Himalayas;
Development of databases on Medicinal Plants of J&K state.
419
Establishment of Bioinformatics Centre in the university.
Computer & Communication facility Ordered
Scientific Software packages Ordered
Databases & other information resources In process
absorption status)
Presently no temporary staff is working in the centre
7. Types of services provided - NA
8. Educational activities with details of placement-
First batch of B.Tech IBT is expected to graduate in 2009
9. Initiative to validate the outcome of bioinformatics resources - NA
Research collaborations have been initiated/already working with the
following institutes:
IIT, Delhi;
IICT, Hyderabad;
IMTech, Chandigarh;
University of Jammu, Jammu;
University of Kashmir, Srinagar.
11. Databases/ Software packages developed - NA
Publications:
1. Sharada, M., Ahuja , A., Suri, K.A. Vij, S.P, Khajuria, R.K., Verma, V. and Kumar, A.
(2007) Withanolide production by in vitro cultures of Withania somnifera (Linn) Dunal
and its association with differentiation. Biologia Platarum 51(1): 161-164.
2. Kumar, J., Verma, V., Shahi, A.K., Qazi, G.N. and Balyan, H.S. (2007)
Development of Simple Sequence Repeat Markers in Cymbopogon Species. Planta
Medica 73(3): 262-266.
3. Soror, S. H., Verma, V., Rao, R., Rasool, S., koul, S., Qazi, G.N. and Cullum, J.
(2007) A cold-active esterase of Streptomyces coelicolor A3(2): from genome
sequence to enzyme activity. J Indus. Microbiol Biotechnol. On-line access no. DOI
10.1007/s10295-007-0224-6.
4. Verma, V., Smelcerovic, A., Zuehlke

, S., Hussain, M.A., Ahmad S.M., Ziebach

, T.,
Qazi, G. N. and Spiteller, M. (2008) Phenolic constituents and genetic profile of
Hypericum perforatum L. from India. Biochemical Systematics and Ecology 38(3):201-
206

Presentations:
420
V. Verma, Impact of Biotechnology Research on Biodiversity, Proceedings of the
National conference on Hiamlayan Biodiversity- Concerns & Issues Oct 27-29, 2007 at BGSB
University, Rajouri (J&K).
V. Verma, Biology of Cancer an over view, Proceedings of the International
Symposium on Genetic Instability and cancer, July 22-26, 2007 at University of Kashmir,
Srinagar.
V. Verma, Need for molecular characterisation of the biocontrol species for IPR and patent
purposes, Proceedings of the National Conference on Fungal Diversity: Impact & Exploration &
34
th
annual meeting of Mycological Society of India from Oct 5-6, 2007 at Thapar University,
Thapar Technology Campus, Patiala-147004.
V. Verma, Impact of Biotechnology Research on Biodiversity, Proceedings of the
National conference on Hiamlayan Biodiversity- Concerns & Issues Oct 27-29, 2007 at BGSB
University, Rajouri (J&K).
V. Verma, The concept of gene manipulation called Directed Evolution, Proceedings of the
National symposium on Biophysics: Biphysics in Medicine & Biology from Nov.15-17, 2007 at
Punjab University, Chandigarh.

The following work has already been initiated:
Development of databases for the novel actinomycestes inhabiting
North Western Himalayas;
Development of databases on Medicinal Plants of J&K state.
Course in Bioinformatics in B.Tech (IBT).

14. Details of Training/ Workshop organized and total no. of user trained -
NA
offered etc.
The BIF centre of the university will cater to the needs of Under/post
graduate and research students of various disciplines of the university.
The centre is also actively collaborating with the institutes/universities in
the region for research as well as joint collaborative studies.
The centre is also planning to organize a joint workshop in collaboration
to Department of Biotechnology, University of Jammu, Jammu.

Besides, research we propose to initiate Post Graduate Diploma in
Bioinformatics in collaboration with leading national
Biotechnology/Bioinformatics industry (s).
Establish a Chair in Bioinformatics at Professor/ Associate Professor
level.

421
Name of the Coordinator: Prof. (Dr.) V. Verma
Postal Address: Dean College of Sciences, Director School of Biotechnology,
Shri Mata Vaishno Devi University (SMVDU), Katra

Fast track postal address: PRO Office of SMVDU,15-C (2nd Ext.) Gandhi
Nagar, Opp. Bahu Plaza, Jammu 180003

Phone Number: (Direct) 01991 285691, (PABX) 01991
285524,285535, 285699 ext.2129
Mobile: 094191 31814,
E mail: nviq@yahoo.com , v.verma@smvdu.ac.in
Website: www.smvdu.ac.in

422
Sri Padmavati Mahila Visvavidyalayam, Tirupati
Coordinator : Prof. M. N. Reddy

This is only a Bioinformatics infrastructural Facility (BIF) Centre, which is still
under the process of establishment. All the arrangements have been made
for the procurement of necessary equipment, establishment of the Lab etc.,
and the facility will soon be ready in all respects.

institution :
The major areas of research activity in the Departments of Biotechnology and
Applied Microbiology and Sericulture in the University include -Agricultural
Biotechnology, Molecular Biology, Animal Biotechnology and
Seribiotechnology

Not Applicable as it is only a BIF Centre
The Facility is still in the process of establishment
The BIF Centre is in process of establishment. Arrangements have been
made to procure Computers and specific software soon.

absorption status) :
Not applicable as it is only a BIF Centre. The position of Research
Associate sanctioned in the 2007-08 budget, is to be filled up shortly.
The facility is yet to be started to open for utility by the students of different
Life Sciences Departments.

Not allocable as it is only a BIF Centre
Not applicable
423
To be initiated once the facility is established in all respects,
11.Databases/ Software packages developed : Not Applicable
12.Papers published or presented in the conferences with reference :
Not Applicable
13. Initiation of R&D activities in Bioinformatics : Not Applicable
Not Applicable

services offered etc. : Not Applicable
To conduct Workshops/Training programs atleast twice in a year for the
target groups of women students/researchers/scientists/Faculty in
Biotechnology/Bioinformatics/Microbiology and other Life Sciences, to
make them proficient and more competent for catching employment
opportunities available / being generated with increasing industrialization
of the Biotech field/Institutions as they started attracting experts from
academia
To provide effective training/awareness to the students of Life Sciences to
gain knowledge in handling different tools/techniques used in
Bioinformatics and their applications in Modern Biology, to develop
professionalism in them , as there is lot of demand for women
Bioinformatics professionals with Biotechnology/Microbiology by many
upcoming/newly established gene hunting companies, larger
pharmaceutical companies etc.
To train the students to get to know the applications of Bioinformatics and
use of computers and Data Banks in Modern Biology especially in the
fields of Molecular Biology, Industrial Biotechnology, Agricultural
Biotechnology, Animal Biotechnology, Mulberry Biotechnology etc.
To make the students confident in gaining knowledge in tools/techniques
in Bioinformatics underlying the strategies and scientific approaches
essential for understanding biological problems and successful
implementation of computer programs through guided practical training.
Inviting experts in the field to deliver Lectures and conduct demonstrations
on relevant topics, followed by hands-on sessions in computer lab

424
Name of the Coordinator : Prof M N Reddy
Postal Address: Department of Microbiology, S P Mahila
Visvavidyalayam, Tirupati-517 502, Andhra Pradesh
Phone Number: 0877 6576759 Mobile: 09849085596
Email: mopuri_nr@yahoo.com
Name of Contact Person(s): Coordinator as above
425
Sri Venkateswara College, (University of Delhi)
Coordinator : Dr. N. Latha

Bioinformatics Infrastructure Facility at Sri Venkateswara College
Inaugurated on July 27, 2007
institution.
PG Diploma in Biochemical Technology funded by DBT
Research Projects under DRDO, DBT and UGC Grants
Teaching & Training Activities
Research Activities Computer aided drug design
+ Teaching & Training Activities
Add on Course in Bioinformatics : 4 months Short Term Course for
graduates
25 final year students pursuing degree programs in Biochemistry, Botany,
Zoology, Physics at Sri Venkateswara College were selected based on an
aptitude test. This 4 month course covers lectures by experts working in
the area of Computer Fundamentals, Genomics, Proteomics and In silico
drug design. In addition, hands-on session exposes the students to
various Bioinformatics tools & softwares available in the public domain.
Short Term Training Programme in Bioinformatics: 6 months
duration for post-graduates
The following students are undergoing training program for 6 months in
the Bioinformatics Facility at Sri Venkateswara College.
Name of the Trainee Affiliated Institution Project
1. Nidhi Jatana Banasthali Vidyapith,
Rajasthan
Protein Structure
Prediction
2. Indrakshi Bhan

Amity University,
Noida
Proteomic Analyses
+ Workshops Organized :
Bioinformatics Workshop for School Teachers Jan 3-4, 2008
To promote teaching of biology through Bioinformatics, a 2-day Bioinformatics
Workshop for School Teachers was organized at Bioinformatics Facility,
Sri Venkateswara College. Around 20 participants from various
recognized schools in Delhi & around attended the workshop wherein
lectures as well as hands on training session was provided in the field of
Genomics, Proteomics & In silico drug design. The workshop was
426
inaugurated by Dr. T. Madhan Mohan, Adviser, DBT and Prof. K.
Muralidhar, Department of Zoology, University of Delhi.

The existing infrastructure includes the following hardwares/other
Equipments.

S. No Items No.
1. Sun Workstations M2 18
2. Servers (1- High End Compute &
1- Web Server)
2
3. Laser Network Printer 1
4. Gigabit Switch for LAN 1
5. UPS ( 10KV) 1
6. Internet Connectivity ( MTNL
Broadband)

Unlimited

Schrodinger package for Protein modeling & Analysis
BioBox from SUN that includes Glimmer, Artemmis, TCoffee,etc.

Bioinformatics Books 20
absorption status)

Name Designation Date of Joining Salary
Mr. Sarvesh Jangid Research Assistant 24 Sept, 2007 Rs.11000 + 30% HRA

7. Types of services provided: Training & Research Colloborations
8. Educational activities with details of placement: see section 4
Project Colloborating Scientist Commencement
Homology Modeling of proteins
derived from Mycobacterium
tuberculosis
Prof.. Anil. K. Tyagi
Department of Biochemistry
University of Delhi South
Campus
Dec 2007
Bioinformatics Analyses of
Calmodulin like protein from
Mycobacterium tuberculosis
Dr. P. Hemalatha Reddy
Reader, Dept. of Biochemistry
Sri Venkateswara College
Nov 2007
427

11. Databases/ Software packages developed : NIL
12. Papers published or presented in the conferences with reference : NIL
13. Initiation of R&D activities in Bioinformatics : Submitted a project to DBT
as a part of COE proposal
Bioinformatics Workshop for School Teachers Jan 3-4, 2008 Number of
users-20
areas.
16. Future activities: Training & Research
Name of the Coordinator: Dr. N. Latha
Postal Address: Reader, Department of Biochemistry, Sri Venkateswara
College
Mobile: 9891900122 Email: lata_svc@rediffmail.com Website:
www.svcollege.net

Name of Contact Person(s): Dr. A. Sankara Reddy, Principal, Sri
Venkateswara College
Email: sankarareddy@hotmail.com
428
Sri Venkateshwara Institute of Medical Sciences, Tirupati
Coordinator: Dr. A. Umamaheswari


Bioinformatics infrastructure facility at SVIMS was formally inaugurated on
10
th
March, 2007. On this occasion, the BIF centre organized a guest lecture
on Machine learning methods and their Applications in Biology and Prof.S.
Ramakumar, Chairman, Bioinformatics Centre, Indian Institute of Science,
Bangalore acted as a key resource person. The centre was made open to the
students, faculty and researchers of SVIMS, Tirupati to retrieve the literature
and utilize the infrastructure available at BIF, SVIMS. The infrastructure
facility is being utilized by the departments of Bioinformatics, Biotechnology,
Anatomy, Physiology and Nursing. In collaboration with BIF, SVIMS, the
department of Biotechology, SVIMS conducted a workshop on Molecular
Biology tools for 29 participants from different states and institutions of
Tirupati, in which one full day was earmarked for bioinformatics tools dealing
with genome sequence analysis. Nine students of the Department of
Bioinformatics, SVIMS were utilized the BIF infrastructure facility in pursuing
their project works dealing with identification of drug targets in pathogens,
simple sequence repeats, homology modeling and docking of proteins.

institution: Stem cell technology and drug target identification.

3. Area of Specialization of the centre: Molecular modeling, Drug designing
and sequence analysis.


The Centre is helping M.Sc. and Ph.D. students of Bioinformatics in
teaching, research projects and finalizing their dissertations/thesis.
Organized a guest lecture
Organized a workshop
Providing internet facility to the staff, research scholars and P.G students
of the institute.

a. Computer & Communication facility :
i. SERVER (High end) for Database/Application Server- 1 No.
ii. 2. SERVER (Medium) for Porxy & File Server - 1 No.
iii. 36 GB Server
iv. DESKTOP MACHINES -22
v. HP LASER JET 2420 PCL6 PRINTER - 1 No.
vi. DESKJET PRINTER - 1 No.
vii. SCANNER 2 No
viii. PHOTO COPIER 1 No.
ix. 10 KVA UPS
x. Wipro LQ DX Gold Printer
429
xi. Canon Printer
xii. Local Network Connection
xiii. 13.BSNL Dataone Broad band internet

b. Scientific Software packages:

c. Databases & other information resources: Nil

absorption status)

Sl. NO. NAME OF THE STAFF DESIGNATION
1. Dr. A. Umamaheswari Coordinator of BIF
2. Dr. S.A.A. Latheef Information Officer
3. K. Bhavana System Analyst

As partial fulfillment of graduation requirements, ten students of M.Sc.
bioinformatics carried out their dissertation work utilizing Bioinformatics
Infrastructure Facility. In addition, ten more students of M.Sc. Biotechnology
have utilized the facilities of the centre in collecting literature and utilizing
Bioinformatics tools. Furthermore, Ph.D. students of bioinformatics,
biotechnology, microbiology, biochemistry, cardiology, medicine, neurology,
plastic surgery, CT surgery and institute staff are utilizing these facilities for
research work.

8. Educational activities:
Bioinformatics Centre in the Department of Bioinformatics, SVIMS University, is
mainly involved in educational activities. The department is offering M.Sc. and Ph.D.
courses in Bioinformatics.

With the available infrastructure we identified drug targets in pathogens
causing infections ranging from tuberculosis to endocarditics. We are
modeling and analysing drug target proteins by utilizing academic softwares
like modeler 9v2 and with the available Bioinformatics Infrastructure Facility.

10. Collaborative works/ initiatives: Nil
430
Reserch activities carried out by the centre are as follows:
a. Homology modeling of cobrotoxin and human G-protein activated
inwardly rectifying potassium channel-4 and molecular docking with
blocker 3,4 pyridine diamine.
b. Substractive genomic approach for the identification of novel drug
targets in human pathogen Leptospira interrogans copenhagani str
Ficrouz L 1-130.
c. In silico identification of potential drug targets in human pathogen
Mycobacterium tuberculosis H37Rv.
d. Identification, Abundence, Distribution and Analysis of simple
sequence repeats (microsatellites) in the genomes of Leptospira.
e. A comparative study of selected scorpion toxins: binding mode of
toxins with modeled receptor and docking of scorpion toxins with L-
carnitine.
f. Analysis of Genomes of Brucella sps Brucella melitensis and Brucella
suis on simple identification abundance and distribution.
g. Studies on putative in silico drug targets and homology modeling in
organisms (Legionella pneumophila and Tropheryma whippelii )
causing endocarditis.
h. Identification of drug target proteins and homology modeling in
organisms (Coxiella burnetti and Brucella abortus ) causing infective
endocarditis.
i. study on genomes of organisms ( Neisseria gonorrhoeae and
Brucella melitensis ) causing infective endocarditis: identification of
drug targets and homology modeling.

The bioinformatics Centre has organized a guest lecture on Machine learning
methods and their applications in Biology by Prof. S. Ramakumar, Chairman
of Bioinformatics Centre, IISc, Bangalore.
The department of Bioinformatics collaborated with the department of
Biotechnology, SVIMS in conducting a workshop on Molecular Biology tools
for 29 participants from different states and adjoining regions and Ph.D.
students of our institute.

The facility is catering to the needs of staff of the centre assisting in
theoretical and practical training provided to the students of M.Sc.
Bioinformatics, M.Sc. Biotechnology and B.Sc. Nursing.
The department of Bioinformatics utilized the BIF lab in offering the following
courses to M.Sc. Bioinformatics students:
a) Biostatistics
b) Computer Fundamentals
c) C++ language and its applications
d) OOPS Programming and databases
431
e) Functional Proteomics and Genomics
f) Perl Programming
g) Molecular Modeling and Drug Designing

Apart from this the lab was used by students of M.Sc. Biotechnology by
offering two subjects.
a) Biostatistics
b) Fundamentals of Computers and Bioinformatics
The lab was also used to provide hands on training to the students of
B.Sc. Nursing who have registered the following courses:
a) Computer Fundamentals
b) Fundamentals of Computers and Information Technology

1. To organize workshops, guest lecturers, training programs in
Bioinformatics.
2. Enhance the research activities and subscribe to online Journals and
Softwares.
3. Tata Consultancy Services (TCS) has launched Tata Bio-Suite, a portable,
versatile software package for life sciences and drug discovery. This
Bioinformatics software is aimed at facilitating life science research
through information technology. As this software runs on LINUX we have
recently installed a new Pentium with LINUX on it. We are in the final
stages of procuring this software, which will provide higher capability for
computations in the areas of sequence analysis and drug designing.

Name of the Coordinator: Dr. A. Umamaheswari

Postal Address: Dr. A. Umamaheswari
Co-ordinator of BIF
Department of Bioinformatics
SVIMS University
Alipiri Road
Tirupati 517 507

Phone Number: 0877 2287727 Fax.No: 0877 2286803
Email: aminenimaheswari@yahoo.co.in
Website:http://svimstpt.ap.nic.in

Name of Contact Person: Dr. A. Umamaheswari
Email: aminenimaheswari@yahoo.co.in

432
Tezpur University, Tezpur
Coordinator: Dr. B. K. Konwar

The BIF was established in 2007 with the objective of assisting the M Sc
Molecular Biology and Biotechnology students. The allotted 10 computers
and the photocopier were purchased and installed. Students are using the
computers for the course application of computers in Biotechnology.

institution
Plant-based medicinal and aromatic compounds, petroleum biotechnology,
yeast genomics, bacterial enzymes for industrial application, malaria
immunogenetics, oncogenomics, enzymology of snake venom and
computational genomics.

Computational genomics and database on plant and microbial diversity
Establishment of the Centre with procurement and installation of computers

A. Computer & Communication facility: 10 computers purchased and
installed. Server installation will take some more time due to some
administrative and electrical problems.
B. Scientific Software packages: Procurement of DNA star etc.
C. Databases & other information resources: Medicinal plant and Petroleum
microbe database

absorption status)

Mr. K. Hazarika, Technical Officer, TU additional responsibility (part-time)
Mr. Dhiraj Sarmah, Computer Engineer, TU additional responsibility (part-
time)

7. Types of services provided: as teaching aid to M Sc students and
research use for Ph D scholars.

8. Educational activities with details of placement: The first batch of 18
Biotechnology students attending the course Use of computers in
Biotechnology in the BIF passed in the year, 3 of them secured DBT-JRF; 13
were selected for Ph D in different national institutes and Universities; 2
obtained industrial placement.
433
10. Collaborative works/ initiatives: with the Department Computer Science
and Engineering
11. Databases/ Software packages developed: Not yet, but proposed to
develop in collaboration with the Dept. of Computer Science.
Das, D., Satapathy,
S. S., Buragohain,
A. K. and Ray, S. K.
Occurrence of all nucleotide
combinations at the third and the first
positions of two adjacent codons in
open reading frames of bacteria
Curr Sci 2006, 90:
22 24.
Verma, S. K., Das,
D., Satapathy, S S ,
Buragohain, A. K. &
Ray, S.K.
Compositional Symmetry of DNA
Duplex in Bacterial Genomes.
Curr Sci. 2005.
89:374-
384
Das, D., Verma, S.
K. & Ray, S. K.
An Altered G + C% Region Within
Potential Hemagglutinin ORFs of
Ralstonia solanacearum.
Curr Sci 2005, 88:
786
792.
Ray, S. K.

Riboswitch: A New Mechanism of
Gene Regulation in Bacteria
Curr Sci. 2004, 87:
1168-
1169.

13. Initiation of R&D activities in Bioinformatics: Computational genomics
14. Details of Training/ Workshop organized and total no. of user trained: to
be taken up in 2008.

Research on computational genomics has been continued with publication of
4 papers and presentation of 1 paper in a Conference at CCMB.
16. Future activities: To start M Sc in Bioinformatics after the sanction of the
11
th
5-year plan, Manpower training
Additional Details:
Name of the Coordinator: Dr. B. K. Konwar, Professor and Head
Postal Address: Dept. of Molecular Biology & Biotechnology, Napaam,
Tezpur, Sonitur - 784028
434
Phone Number:03712-267172 Mobile:9954449468
Email: bkkon@tezu.ernet.in
Website: www.tezu.ernet.in
Name of Contact Person: Mr Kalyan Hazarika
Email: kalyan@tezu.ernet.inu

435
University of Allahabad, Allahabad
Coordinator : Prof. Dwijendra Gupta

1. Summary of the Progress made by the Center from its inception
M.Sc. Program in Bioinformatics started here with our own resources in 2002 is
presently running in its 6
th
Batch. Besides, Bioinformatics is being taught in
B.Sc.(Applied Science).Three laboratories have since been added. One Molecular
biology Lab and 2 Advanced level Bioinformatics Laboratories for
M.Sc.(Bioinformatics) and B.Sc. Applied Science students. Besides, for
experimental laboratories in Biochemistry, Molecular Biology and Biotech-nology,
the existing facilities in the Departments of Biochemistry and Biotechnology are
being used. Yet another Computer Lab for M.Sc. Bioinformatics students has 30
advanced desktop computers and with internet service.
We have procured the hardware( one High-end Database /Application
Server, one Medium end Proxy /File Server, 10 Desktop P-IV Systems as
provided in the Sanction Order of DBT. This Facility is being set up in the
space provided in Institute of Interdisciplinary Studies situated in the Faculty
of Science. The softwares suggested by the DBT have also been procured.
2. Major Research activities in Biotechnology and its related fields at University of
Allahabad
Fields of Research in Biotechnology: There are four independent research
groups working in Biotechnology and related areas, i.e. Nanobiotechnology,
Nanophosphors, GPI anchors etc (Prof. D.K.gupta, Dr.Shanthy Sundaram,Dr
Avinash Pandey and Dr. Anjana Pandey .
These projects have become operational as regards the procurement of the
equipment is concerned.

3. Area of Specialization of the center
Fields of Research in Bioinformatics & Computational Biology:
Molecular Modeling, Structural Bioinformatics, Metabolic Network
Reconstruction, Molecular Docking, Promoters of Cold-Stress Genes in
insects

4. Major activities of the Center during 2006-07:
An International Collaboration is already in force between University of
Allahabad ( Prof. D.K. Gupta and Prof. A.K.Gupta) and University of Cagliari (
Prof. Paul la Colla).

5. Infrastructure facilities in the Bioinformatics Center:
A. Computer and Communication facility We are also in the process of setting up a
16-node Red-Hat Linux Cluster (with Beowulf configuration) for the Bioinformatics
Computing lab. The whole system will be used as the very high-end computing
system for bio-molecular dynamics, genomics and computer-aided structure
prediction and computer-aided drug design.
436
B.Scientific and Software packages: GenoCluster version 1.0 procured from
Jalaja Technologies, Bangalore for functional Genomics and Proteomics .
Red Hat and MS ISA 06 are the other softwares we have procured.
C. Databases and other information resources: We are developing
our database of activities of the Center of Bioinformatics that
includes the projects carried out by the students as part of
requirement of curriculum, research papers published by the
Biotechnology and BioinformaticsCenters as well as any
softwares that we may develop in the meanwhile.

6. Details about staff members working in the Center
Presently, we have only one person temporarily employed as Office Assistant
on fixed emoluments( Rs 5000 per mensem). UGC has given 8 faculty
positions (Professor 1, Readers 2, and Lecturers 5) which remain to be filled.
Presently, the core teaching faculty comprises of faculty drawn from different
departments vide infra:
CORE TEACHING FACULTY OF BIOINFORMATICS
1. Professor Ashok K.Gupta (specialty:Macromolecular Structure, DNA-Protein interactions,
Computational Biology, Evolutionary Computing and Bioinformatics)
2. Professor Dwijendra K.Gupta, ( Recombinant DNA, Membrane Molecular Biology, Cell
Biology, Immunology, Biochemistry and Genomic DNA and cDNA cloning techniques.
Besides, hands-on experience in the area of Genomics and Proteomics and Nano-
biotechnology).
3. Dr.Shanthy Sundaram, (Immunobiology, protein structure-function and Genomics and
Proteomics
4. Professor Anoop Chaturvedi ( Econometrics, Time series, Life Testing and Reliability, and
Liner Models).
5. Professor P.N.Pandey ( Differential Geometry, Biomathematical Modeling.
8 . Dr.K.N.Uttam (specialty is Diatomic Molecular Spectroscopy).

7. Types of Service provided: None yet
8. Future activities: 1. We are developing our website 2. We will also seek link
with worldwide institutions that store primary and secondary biological
databases, like, Incyte and UniGene, SWISS-PROT, PDB, NDB, GENES and
DIPand BIND etc. Among these are National Center for Biotechnology
Information (USA), Universities of Kyoto and Tokyo, European Bioinformatics
Institute etc. The inter-action may include summer training of our students
and researchers in these international laboratories in different areas of
Genomics and Proteomics, Transcriptomics and Metabolomics.

An International Collaboration is already in force between University of
Allahabad ( Prof. D.K. Gupta and Prof. A.K.Gupta) and University of Cagliari (
Prof. Paul la Colla). A number of passed out students are working towards
their doctoral degrees on prestious Italian Govt fellowships in Universities of
Cagliari,and Turino( Italy) ,in Brno (Czech Republic) and University of South
Bohemia (Czech Republic) and a Swiss University.

10.Initiative to validate the outcome of bioinformatics resources
11.Collaborative works/ initiatives
12.Databases/ Software packages developed -- None
437
1. In silico Determination of potential drug target for curing meningococcal disease
ESFConference on Biomedicine: International Conference on Synthetic Biology-Design,
Programming, and optimization of Biological Systems Sant Feliu de Guixols (Spain) Nov
23-28, 2007.

15. Details of Training/ Workshop organized and total no. of user trained As
the facility is yet to become operational, the Workshop proposed to be
organized here in September 2007 has been postponed to sometime in
March 2008.

16 Impact shown by your centre on the growth of biotechnology and allied
areas. M.Sc. Students from different Universities outside Uttar Pradesh are
training in this Department for their Major projects. The Bioinformatics
Infrastructure Facility has not been operational as there has been inordinate
delay in processing of paperwork for purchase of computer items at various
university offices. Finally, the process for purchase and set up of the
hardware( one High-end Database /Application Server, one Medium end
Proxy / File Server, 10 Desktop P-IV Systems and softwares as provided in
the Sanction Order of DBT, has been completed. Also, the site where the
Facility is to be operational is under preparation and could not be completed
for want of funds.

17. Future activities As the facility is yet to become operational, the Workshop
proposed to be organized here in September 2007 has been postponed to
sometime in March 2008. Some of the financial requirements based on
Budget provision are appended to this Progress Report.

Additional details :M.Sc. Bioinformatics program has a novel feature amongst
all the teaching programs run at this University, i.e. it is credit-based. The
courses are divided into level 0, level 1, level 2, and level courses. Each
course has an appropriate minimum requirement. There is a minimum
number of credits(12) that each student has to complete in each semester

Name of Coordinator: Professor Dwijendra Gupta
Postal Address: Prof. Dwijendra Gupta, Coordinator, Center of Bioinformatics
Institute of Interdisciplinary Studies, Nehru Science Center & Head, Department
of Biochemistry, Faculty of Science University of Allahabad, Allahabad 211002
(U.P.)
Phone Number: 0532-2461861(o), 09335150718(Cell), Fax # 0532-2545733
Email: dwijenkumar@rediffmail.com dwijenkumar@gmail.com
Website: www.alldunivpio.org www.allduniv.edu
438
University of Bangalore, Bangalore
Coordinator : : Prof. Geetha Bali

An independent laboratory has been earmarked. The laboratory has been
equipped with computer tables and chairs. The room has been airconditioned.
The sanctioned number of desktops with TFT monitors, 2 servers, Laser Jet
and Ink jet printers, scanner and some software has been purchased. The
computers have been networked. Sanction for the purchase of UPS (5 KVA 2
nos.) has been granted by the university and the same is being installed.
Permission is being sought for installation of the UPS and necessary wiring.
Internet connection has been established. The Advisory committee has been
constituted. A meting of the advisory committee is being convened to
evaluate the progress and discuss the Bioinformatics software to be
purchased.

institution
a. Drought resistance in peanut plants
b. Anti cancer properties of Embelin and Curcumin
c. Bioactive peptides in Helicoverpa armigera and their potential as
biopesticides
d. Bioremediation of water contaminated with electroplating industrial
effluents
e. Use of Nanoparticles for diagnostics
f. Developing subunit vaccine for Blue tongue virus

3. Area of Specialization of the centre : Nanobiotechnology/Plant
Biotechnology/ Animal Biotechnology/Environmental Biotechnology/ Medicinal
Plants

In the process of being established
HP Pentium IV Server: HPML 110G3 (Sl. No.5)
HP Pentium IV Server: HPML 350 G4/G5
Processor Intel Xeon DP 3.2 GHz, 800 MHz FSB (Sl. No.38)
Hard Disk Drives
LJ 2420 DN Laser Jet Printer Monochrome Resolution 1200 x 1200 dpi, paper size A4, memory
32MB printing speed 24 PPm, 1 parallel port with inbuilt duplex with network card 10/100 (Sl.
No.143)
Desk Jet Printer 2360: Inkjet Printer Resolution 1200 x 600 dpi, paper size A4, Printing speed 17
PPM B/W and 9 PPM Colour, 1 USB
Scan Jet 5590 : Scanner Flat Bed A4 Size with USB Port with CD Technology: Scanner Flat Bed
Tupe, A2 Size, Res. 600 x 600 dpi, preview/scan speed 7 sec, colour depth 48 bit USB port with
inbluilt ADF (50 page) (Sl. No.172)
512 MB RAM for PIV Computers (Sl. No.47); TFT Monitors* (10 Desktops + 2 servers)
439
Windows 2003 Server Software (5 users) (Item No.87)
Additional CAL License (15 users)
Red Hat Linux Standrad (Sl. No.105)
Microsoft SQL Server Standard (Sl. No.110)
Additional CAL License (15 users)
Anti Virus For Server (Itemm No.91)
Microsoft ISA 2006 software
Microsoft Visual Studio 2005 Professional With Net (5 user)
Additional CAL License (15 user)
Microsoft Office 2003: Professional MOLP with Media & Documentation
Others are being purchased
6. Databases & other information resources
absorption status)
University has been requested to appoint a full time staff specialized in
Bioinformatics.

Will be provided once established completely.
Bioinformatics is being taught as one complete paper in M.Sc. courses
Training programmes will be organized as basic level for UG and PG
students and advanced training for doctoral students to undertake research in
Bioinformatics. Implementation of Bioinformatics projects and employment of
bioinformatics in biotechnology research will be a good indicator.
Biotechnology research will be initiated.

Discussions were held at Bangalore University and at the Department of Computer
Science and systems for initiating collaborative programmes Engineering,
Andhra University.

12. Databases/ Software packages developed : Not yet
1. Atmaram, T.N. Geetha Bali & K.M. Devaiah, Integration and expression of
Bluetongue VP2 gene in somatic embryos of peanut through particle
bombardment method Vaccine.(Elsevier)24, PP2994-3000, 2006

2. Atmaram, T.N.& Geetha Bali Recombinant expression of partial
bluetongue VP2 protein in E.coli, Virus Genes 35:265-271(2007)

3 S. Dwarakanath, J.G.Brunoulatha, T.N.Atmaram & Geetha Bali, Ab-QD
conjugates exhibit enhanced antibacterial action vs. unconjugated Quantum
Dots, Folia Microbiol 52(1) 01-04, 2007

440
4. K.M. Devaiah, Geetha Bali & T.N. Atmaram, Identification of two new
genes from drought tolerant peanut variety that is up regulated in response to
drought, plant growth regulation 52:249-258(2007)

Bioinformatics is being employed for current ongoing research on peanut
plants etc. More programmes are in the process of implementation

15. Details of Training/ Workshop organized and total no. of user trained : Not Yet
services offered etc. Intensive efforts will be made once the center is fully
established.

17. Future activities: Organizing training programmes, Implementing R&D in
Bioinformatics

Additional Details:
Name of the Coordinator: Prof. Geetha Bali
Postal Address: Department of Microbiology, Bangalore University,
Bangalore 56056
Phone Number:080 - 22961462 Mobile: 9845242396
Email: Geetha.bali@gmail.com
Name of Contact Person(s): Prof. S.K. Sarangi
Email: Phone No. 080-22961461 sarangisk@yahoo.co.in

441
University of Calicut, Kerala
Coordinator: Dr. M. V. Joseph

The Department of Biotechnology, University of Calicut has established the
Bioinformatics Facility with the financial support from DBT, Government of
India in the year 2006-07.

institution
A separate Department of Biotechnology has been established in 1995 with
the financial support from DBT, Government of India to start Postgraduate
programme in Biotechnology having Bioinformatics in the Course curriculum.
The department is activity engaged in research in the area of plant
Biotechnology, Immunology, Cell and Molecular Biology/recombinant DNA
technology.

3. Major activities of the centre during the year 2007 08
The BIF centre is being fully utilized by the faculty and research scholars for
their research activities. As a part of their research activities a few cloned
sequences have been deposited in the GenBank for which the accession
numbers have been obtained.

4. Infrastructure facilities in the Bioinformatics center

a. Computer and Communication facility
The department has 23 computers having 24 hours broadband internet
facility with LAN and UGC infonet facility.

Vector design (SimVector), primer premier, and free down loadable
software packages are available. A few more software packages are in
the process of procurement.

5. Details about Staff members working in the centre

a. Dr. M. V. Joseph Microbiology & Immunology 1996 onwards
Professor Secondary metabolites
Head & Co-ordinator

b. Dr. P.R. Manishkumar Cell and Molecular
Sr. Lecturer Biology & recombinant 1996 onwards
DNA technology

c. Mr. C. Gopinathan Bioprocess technology 1996 onwards
Sr. Lecturer

d. Dr. S. Pyroja Molecular Neurobiology 2002
(on Leave)

6. Details of Training/Workshop organized and total number of user trained
The BIF at Calicut University has conducted three days workshop on
Application of Bioinformatics tools in biological research for the faculty
442
members and research scholars. A total number of 25 participants have been
given training in this area.

7. Impact shown by your Centre on the growth of biotechnology and allied
areas
Four number of clone sequences have been deposited in the GenBank for
which accession numbers have been obtained.
Authors Title of the Article Journal Year
Martin K P and Joseph
Madassery
Trichopus zeylanicus subsp. travancoricus ribosomal
protein L16 (rpl16) mRNA, chloroplast
gi|155965995|gb|EU057718.1|[155965995]
GenBank
EU057718
2007
Martin K P, Gupta S,
Zhang C-L, Slater A
and Joseph Madassery
Ophiorrhiza prostrata tryptophan decarboxylase (tdc)
gene gi|155965997|gb|EU057719.1|[155965997]
GenBank
EU057719
2007
Martin K P and Joseph
Madassery
Ophiorrhiza prostrata strain albino tryptophan
decarboxylase (tdc) gene,
gi|155965999|gb|EU057720.1|[155965999]
GenBank
EU057720
2007
Kumar M P R, Manish
JPR, Rabindran R M
Physarum polycephalum sequence new GenBank
EU371923
2008

The department would like to conduct training programme in
Bioinformatics for the teachers, post graduate and research students in
Biological Sciences. We would like to databases of some important
medicinal plants and microorganisms.

Additional details:

Name of the coordinator: Dr. M. V. Joseph
Professor
University of Calicut P.O., 673 635
Kerala State
Telephone No. 0494 -2401972: Fax: 0494 -2400269, 0494 -2400361
Email: headandcoordinator@rediffmail.com
hdbiotech@sify.com

443
University of Hyderabad, Hyderabad
Coordinator : Prof. Anand K. Kondapi

The BIF has been set-up in November 2007. The first activity of the BIF was
in collaboration with CR Rao Advanced Institute of Mathematics, Statistics
and Computer science, in conducting an Instructional Workshop in
Bioinformatics and Drug discovery from Dec 16-19 2007. During the four
days, two workshops are held one on Statistical methods in Bioinformatics
and second one was on Drug Discovery. The workshop was attracted by
large number of young talents throughout India and the lectures were
delivered by Eminent scientists from India and abroad including Prof. C R
Rao himself. The workshop was inaugurated by Dr. T. Ramasami, Secretary,
DST and Dr. T. Madan Mohan, Advisor DBT has addressed in Valedictory
function. The topics discussed in the workshop were related to use of various
statistical methods and packages such as R-Package, SAS Genomics in
analysis of data collected from bioinformatics, genomics and proteomics
experiments. Drug discovery workshop covered the topics on quantum
mechanics, classical mechanics. molecular mechanics, semiemprical
methods, molecular dynamics, homology modeling, threading, Molecular
docking and Computer aided drug design. The workshop followed with an
International conference on Bioinformatics and Drug discovery, which was
inaugurated by Smt. D. Puradereswari, Honorable Union HRD Minister of
State. The conference has covered various aspects of system biology, drug
discovery including metabolomics, genomics, proteomics, drug design,
Clinical and translational research and critical issue of clinical trails etc. It was
attended by participants from academics and Industries. The scientists
actively working in academia and industry from India and abroad have
participated in the conference. In addition, the PhD students and M.Tech
students have registered and actively using the facility for research and
teaching.

institution

3. Area of Specialization of the centre Systems Biology and Drug
Discovery

Instructional workshop in Bioinformatics and Drug discovery (16-19 Dec,
2007)
International Conference on Bioinformatics and Drug Discovery(19-22 Dec,
2007)

2 HP servers, 10 HP Desktops, 2 printers & FAX with LAN network
444
SYBYL with QSAR from Tripos (3 Licenses),
Biosuite from TCS (1 License)
GOLD (1 License) from CCDC Ltd. (Under University Funds)
Public domain software Open Eye, R package, Autodock
Databases & other information resources: Public domain databases.

absorption status)
Name Designation Specialization Period of working
Anand K. Kondapi Professor Molecular therapeutics Since June 1993
K. Ramesh Naik Tech. Assistant System Administration Adhoc from April, 2007

7. Types of services provided (1) Modeling and drug design (2) Statistical
analysis

8. Educational activities with details of placement : M.Tech and PhD
programs

9. Initiative to validate the outcome of bioinformatics resources Through
Short-term projects to the students of Bioinformatics and computer sciences
from outside University.

10. Collaborative works/ initiatives: A proposal for conducting periodical
training program in collaboration with CR Rao Advanced Institute for
Mathematics, Statistics and Computer sciences, being proposed to the DBT.

11. Databases/ Software packages developed: To be taken up
12. Papers published or presented in the conferences with reference: Work
just started.

13. Initiation of R&D activities in Bioinformatics: In house database on plant
system is being created.

Instructional workshop in Bioinformatics and Drug discovery (16-19 Dec,
2007) 95 students trained

offered etc.

The facility is just started for the use of the PhD students and M.Tech.
students. We are in process of using the facility for research and Teaching in
Drug Discovery and Systems Biology. The publications, dissertations and
meeting presentations will be reported in Coming year. We are also in the
process of developing a database on plant systems to cater the community.

445
5. Training programs in Drug Discovery, Systems
Biology and Statistical methods in Proteomics and
genomics will be periodically conducted in every year.
6. Databases on plant systems being created

Additional Details:
Name of the Coordinator: Prof. Anand K. Kondapi
Postal Address: Department of Biotechnology, School of Life Sciences,
University of Hyderabad, Hyderabad 500046
Phone Number:040-23134571; Mobile:9246152654 Email:
akondapi@yahoo.com Website: www.uohyd.ernet.in
Name of Contact Person(s): Prof. Anand K. Kondapi
Email: bioinformaticsuoh@yahoo.com

446
University of Jammu, Jammu
Coordinator : Prof. M. K. Dhar


The BIF at University of Jammu, was set up in January 2007 as the
Bioinformatics Infrastructure Facility (Training Code: JUBIF-01) under the
Biotechnology Information System Network (BTISnet) programme of the
Department of Biotechnology, Government of India. During the first four
months, we set up the Bioinformatics lab and made it functional for the use of
students, research scholars, faculty and research scientists. During the last
six months, the Coordinator delivered lectures in various departments of the
University and also the affiliated colleges. The Centre organized
demonstrations, hands on training sessions and awareness programmes on
applications of Bioinformatics in solving the biological problems.
Bioinformatics is one of the courses in the M. Sc programmes in
Biotechnology, Biochemistry and Microbiology running in the University of
Jammu since last couple of years. The Bioinformatics centre extended full
support in conducting various hands on sessions and was involved in
teaching a full fledged course in these programmes. The Bioinformatics
Centre offered the dedicated internet facility and training to the students,
research scholars for using the online and offline softwares, tools to assist in
their research programmes.


The centre is focusing mainly on In silico analysis using Bioinformatics
softwares. The centre promotes Bioinformatics awareness. Research projects
and interdisciplinary research in collaboration with wet lab Biotechnology
research programmes are being carried out.


The main area of specialization is Genome and Proteome Analysis.

4. Major activities of the centre during the year 2007:

During 2007, the Coordinator delivered lectures to the College and University
teachers during the inter-disciplinary refresher courses held in the
Departments of Physics, Computer Sciences and Information Technology and
Environmental Sciences, of the University of Jammu and also the affiliated
college namely Government Degree College for Women, Udhampur. The
Centre organized short training sessions and awareness programmes on
applications of Bioinformatics in solving the biological problems. The
Bioinformatics centre extended full support in conducting various hands on
sessions and was involved in teaching full fledged course on Bioinformatics
in M. Sc Biotechnology, M. Sc Biochemistry and M. Sc Microbiology
programmes of the University. The Bioinformatics Centre offered the
447
dedicated internet facility and training to the students, research scholars for
using the online and offline softwares, tools to assist in their research
programmes.

a. Computers : Twenty (Desktop machines)
b. Printers : Two
c. Scanners : One
d. Communication facility : Telephone connection,

B. Scientific software packages : NTSys, PHYLIP, TREE VIEW, RAPDPLOT

Databases acquired: Under process

Books on Bioinformatics: (Department of Biotechnology Library)

Title Author
1. Introduction to Bioinformatics Krawetz and Womsle
2. Bioinformatics: A modern approach Srinivas
3. Algorithms in Bioinformatics Benson
4.Bioinformatics: A Practical Guide to the Analysis
of Genes and Proteins

Andreas D. Baxevanis
5. Bioinformatics (A Beginner's Guide) Clavene
6. Bioinformatics Concepts Skills and Applications Rastogi,S.C
7.Essentials of Genomics and Bioinformatics Sensen, C.W
8.Bioinformatics Sequence and Genome Mount, David
9. Bioinformatics Approaches and Applications Chakraborty
10.Bioinformatics Sequence Structure and
Databanks

Higgins and Taylor
11.Introduction to Bioinformatics Attwood and Smith
12.Bioinformatics Methods and Protocols Misener and Krawetz
13.Bioinformatics and Genomes Current
Perspectives

Andrade
14.Protein Analysis and Design Ruth Hogue Angeletti
15.Bioinformatics Sequence and Genome
Analysis (2nd Edition)

David W.Mount
16.Bioinformatics Pevsner, Jonathan
17.Bioinformatics and Molecular Evolution (Latest
edition)

Attwood and Higgs
18.Bioinformatics Lesk
19.Instant Notes Bioinformatics D.R.Westhead,J.H Parish &
448
R.M Twyman
20.Introduction to Bioinformatics (Indian edition) Arthur M.Lesk
21.Fundamental Concepts of Bioinformatics Dan E Krane, Michael
L.Raymer
22.Bioinformatics Genes Proteins and Computers C.A Orengo,D.T Jones &
J.M Thornton

23.Bioinformatics Basics Applications in Biological
Science and Medicine (Second edition)
Lukas K Buehler,Hooman H.
Rashid

24.Principles of Bioinformatics P Shanmughavel

Journal: Science
Trends in Biotechnology
Indian Journal of Biotechnology

working
Absorption
status
Prof. M. K. Dhar
Head
Biotechnology
& Coordinator
Bioinformatics
Centre
Genomics and
Proteomics
Permanent
Faculty
Mohit Kumar
Sharma
R. A Bioinformatics/
Data Analyst

Temporary

The Centre offers training on fundamental topics in Bioinformatics for
technical staff and students of Jammu University. Literature search, sharing of
resources, support to R&D activities in Biotechnology for PG student projects,
imparting teaching in Bioinformatics for PG students. Creation of awareness
among undergraduate and post-graduate students and faculty regarding the
basics of Bioinformatics and its applications is the major focus.

As a part of the M Sc program, the centre conducts Bioinformatics courses for
M.Sc students of the University of Jammu.

The large number of users at the Centre and the research activities validate
the outcome of bioinformatics resources.
449

10. Collaborative works / Initiatives:


Two papers have been submitted for presentation during 3rd J&K Science
Congress to be held w.e.f. 26 to 28th February, 2008 in the University of
Jammu, Jammu.

Title of the Papers:
1. Using Bioinformatics tools to create a database of transcription factors
binding sites.
Mohit Kumar Sharma and V. B. Bajic
2. Cloning and functional analysis of carotenoid biosynthesis genes from
carrot
Khalid Zaffar Masoodi and Manoj K. Dhar

The BIF is promoting Bioinformatics awareness and has initiated dedicated
research programmes in Bioinformatics.

14. Details of Training / Workshops organized and total no. of users
trained:
The Centre conducted various hands on sessions and was involved in
teaching full fledged course on Bioinformatics in M. Sc Biotechnology, M. Sc
Biochemistry and M. Sc Microbiology programmes of the University.

Department Users Trained
Biotechnology 12
Biochemistry 7
Microbiology 8

areas:
The Centre has initiated several programmes for introducing Bioinformatics to
the students as well as faculty of the University. The usage of e-mail and
Internet has increased notably and the facilities of the Centre are widely made
use of for presentations and other research activities. The softwares available
are being used for phylogenetic analysis by several research scholars.
The focus will be on research activities in Bioinformatics. The Centre
proposes to conduct three day workshop for University and college teachers
during first week of February 2008. The other routine services of the Centre
would be continued efficiently.

Additional details:

450
Name of the Coordinator: Prof. M. K. Dhar

Postal address : Department of Biotechnolgy
University of Jammu,
Dr. B.R.Ambedkar Road
Jammu -180006

Phone Number: 91-191- 2433655, 91-191-2456534
Fax: 0191-2456534
E-mail: hodbiotech@jammuuniversity.in,
manojkdhar@rediffmail.com

451
University of Kal yani, Kal yani, West Bengal
Coordinator : Dr. Alpana Seal

The centre was inaugurated on 28
th
March,07 .The inauguration was coupled
with one workshop on Application of Bioinformatics in Molecular Modeling,
Data Analysis and System Biology .The centre is now being used by
researchers, M.Sc. students and project workers from this University and
other Universities/Institutions. Training programs in bioinformatics and
computational biology has been arranged. Scientific Software package GCG
was bought and installed. Other scientific program packages, free for
academicians have been installed. Recently another national workshop on
Macromolecule Ligand Interaction & Drug Design has been arranged and
another national workshop on System Biology will be arranged in this
financial year.

institution :
Department of Biochemistry and Biophysics:
Molecular modeling of sulfur compounds metabolizing proteins (in
collaboration with Bose Institute, Kolkata): Sulfur compounds are
metabolized by an operon called sox operon. It codes for a number of
proteins. A considerable progress in the genetics of sulfur lithotrophy is
noted but the structural details of the proteins are not available. To predict
the biochemical aspects of the proteins involved molecular modeling
technique is employed.
Molecular modeling of protease inihibitor interaction.
Molecular Mechanism of Artificial Transformation of E.coli with Plasmid
DNA.
siRNA technology for knocking down a gene (in collaboration with SINP,
Kolkata)
Department of Molecular Biology and Biotechnology:
Molecular Phylogeny of Indian Shad Tenualosha ilisha inferred using
mitochondrial DNA partial gene sequences.
Molecular Breeding of Rice with Special Reference to Marker Assisted
Gene Pyramiding for Biotic Stress Resistant.
An Investigation on Somaclonal Variance of certain Aromatic Plants using
Biochemical and Molecular Approaches.
An Investigation on in vitro selection of Aluminium Stress Resistance of a
leguminous crop and its rhizobial counterpart for their potential exploration
in acid soil tract.
An exploration of in vitro somatic embryogenesis of two important medicinal
plants and their biomodulatory mechanism.
Identification of DNA markers associated with disease and pest resistant in
Mulberry.
A study on induction of somatic embryos and over-expression of SAM
Decarboxylase in Limonium sinensis through transgenesis.

452
I. Molecular Modeling,
II. Computational Biology

One national workshop was arranged during 2
nd
4
th
January, 08.
Another national workshop will be arranged in March,08
Some local training programs have been arranged to introduce
Bioinformatics in the neighborhood.
GCG programme package has been installed.
Other free scientific programme packages (SHELX, WINZIP, XtalView,
Rasmol, ClustalW etc.) have also been installed.
Trying to interact with local hospitals and other local institutions to generate
Medical & Pharmaceutical Databases and to start collaborative work.

1) Ten P(IV) Lenovo desktop Computers with 17 TFT monitors
2) One highend (X236) and one medium (X226) IBM server
3) One Canon black & white copier cum printer
4) One HP colour laser printer
5) One HP scanner
6) One APC Smart RT-5000 UPS with 16 batteries
7) Sony L.C.D. projector.
Internet Connection: Opted for BSNL Broadband (2 MBPS) connection
(annual).

B. Scientific software packages:
Operating System Softwares: Purchased and installed as recommended
by DBT.
Scientific Software: 1) Purchased and installed Acclerys GCG package.
2) Installed Shelex-97 package.
3) Some software free for academicians has been
installed.

C. Databases & other information resources: Developed one database on
the enzyme Dehydrogenase.
Designation, specialization and period of working. Please indicate their
absorption status):
None at present. Its a newborn centre. No staff member is attached with it till
now. Two faculties of the Department of Biochemistry and Biophysics are
working for the Centre in addition to their normal duties at the department.

7. Types of services provided: Till now we trained the students only. Project
workers are also using the facility.
8. Educational activities with details of placement: Training students,
arranging national workshops, initiated research activities. We will start
summer training programme also.

453
9. Initiative to validate the outcome of bioinformatics resources: We have
initiated.

10. Collaborative works/ initiatives: Initiatives has been taken to collaborate
with nearby Institutions and other research institutes in Kolkata.

11. Databases/ Software packages developed: Till now one database on
dehydrogenase has been developed.

12. Papers published or presented in the conferences with reference: Work
is going on.

13. Initiation of R&D activities in Bioinformatics: Nothing started yet.

We have arranged one national workshop and trained thirty two participants
in the current financial year. We will arrange another one in
March,08.Training of University students are also going on in regular basis.

areas: In this you may highlight the details like number of paper published/
services offered etc:

I. Five papers were published in last year in collaboration with other
research institutes.
II. Training programmes for University students in bioinformatics and
in computational biology are going on in regular basis.
III. We are trying to collaborate with other nearby institutions with the
view to develop various databases needed for this locality.
IV. One national workshop has been arranged in which thirty-two
participants were trained.
V. A database on dehydrogenase has been developed.

16. Future activities: We plan to
Research on:
Modeling studies of membrane system.
Structural Bio-informatics to develop novel drug molecules.
Cluster and self assembly study.
Protein ligand interactions.
Develop databases required for this locality in association with other
Institutes.
Train students and research workers in this field.
Provide service especially in this locality related to database search,
sequence analysis, use of bioinformatics tool and software packages.

454
Additional Details:

Name of the Coordinator: Dr. Alpana Seal
Postal Address: Department of Biochemistry and Biophysics, University of
Kalyani, Kalyani 741235, W.B.
Phone Number: 033 2582 3405(O), 033 2321 2106(R)
Mobile: 9830795655
Email: btis_ku@yahoo.co.in, alpana_seal@hotmail.com
Website: None
Name of Contact Person(s): Dr. Alpana Seal
Email: same as above
455
University of Madras, Chennai
Coordinatior : Prof. D. Velmurugan

An international conference on Computational drug discovery in pharma
R&D has been conducted on July 2007. About 350 candidates were
participated in the conference. A technical assistant has been appointed in
the BIF.
The following items has been purchased as per the DBT sanction rule
1. Hardware including 10 systems,2 servers, printers and scanners.
2. Software-GLIDE from Schrdinger, Bangalore.
[Quotations are invited for the purchase of other softwares like windows
2003 server with license and Red Hat Linux enterprise edition 4 or higher
version.]
3. Books on Bioinformatics
4. Furnitures and stationeries required for site preparation

institution
Medical Biotechnology and diagnostics of infectious diseases
Aquaculture Biotechnology,
Enzymology,
Environmental biotechnology.

Structural Bioinformatics.
Molecular modeling and drug designing.
Molecular dynamics

An international conference on Computational drug discovery in pharma R&D
has been conducted on July 2007. About 350 candidates were participated in
the conference.

Computer & Communication facility-10 systems and 2 servers
Scientific Software packages- Molecular docking softwares like GLIDE,
Hex, Auto dock, Modeling softwares like Swiss PDB viewer, Modeller,
visualization softwares like Pymol , Rasmol, web lab Viewer and
chemical drawing softwares like ISIS Draw, Chemsketch etc.
Databases & other information resources- Purchased about 100s of Books
in Bioinformatics
(V.C has assured for shifting to the new building with larger space. Internet
connection will be provided in the new building)
456
absorption status)
Sruthi Govind, Technical Assistant, MSc Bioinformatics from August 2007
Represented BIF in four international conferences and the research work has
been presented. (Details are given in 12)

Training will be given on the following areas
1. Three dimensional structure determination of drug molecules
2. Molecular modeling
3. Molecular Dynamics
4. Structure based drug designing
5. QSAR studies

8. Educational activities with details of placement : --
The research work done in BIF will be published as scientific papers soon. A
three days International symposium on structural bioinformatics will be
convened on first week of march wherein atleast 6 delegates will be invited
from the following institiutes.1.Genomics centre,Yokohama,Japan 2.SPring
Riken Harima, Japan 3.National University of Singapore,Singapore.

Molecular modeling studies for the compounds from marine resources,
Centre for Marine Diversity, Kerala University, Kerala, is being undertaken to
develop potential anticancer/anti malarial drugs.

11 Databases/ Software packages developed : --
12.Papers published or presented in the conferences with reference
1. Presented a paper on Crystal structure analysis and molecular modeling studies of four
novel beta lactam derivatives in the international symposium on Applied Bioengineering
conducted by sathyabhama University, Chennai.
2. Presented a Poster on Molecular docking studies of HCV NS5B polymerase inhibitors in
the international symposium on Bioinformatics and computational Biology conducted by
Kerala University, Kerala
3. Presented a Poster on Docking studies of Sulphonamide derivatives with human
Carbonic anhydrase as target in the international symposium on recent trends in
macromolecular structure and function conducted by University of Madras, Chennai.
4 Presented a Poster on Molecular Crystal structure analysis and molecular modeling
studies of four novel beta lactam derivatives inhibitors in the international symposium on
structural Bioinformatics- structure and function of Macromolecules conducted by Sri
Ramakrishna college of Arts And Science For Women, Coimbatore.
5. A paper on Antiviral Drug design: Modeling studies of HIV Integrase with dihydroxy-
pyrimidine analogues and N- Methyl Pyramidone analogues as inhibitors was accepted
by Jadavpur university, Kolkotta and will be presented in the National Seminar on
crystallography.

457
Many requests are being received from many colleges for making use of the
centre for 3 months major projects during summer .Once internet connection
has been set up this will be pursued. Since the Coordinator is applying for a
project in structural Bioinformatics wherein 2 project assistants are requested,
R &D work will begin after the recruitment of the project fellow who wll later
register for PhD in the University

An international conference on Computational drug discovery in pharma
R&D has been conducted on 26
th
july 2006. About 350 candidates were
participated in the conference .
Project is being submitted by the Coordinator, BIF on High throughput
crystallography and structural genomics. Once we move to the new building,
3 days workshop will be convened and after that research work will be carried
out in the field of Molecular modeling with novel biomolecules as potential
drug candidates.

Research students will be admitted to work on areas like QSAR, Structural
Bioinformatics etc

Additional Details:
Name of the Coordinator: Prof.D.Velmurugan
Postal Address: Dr.D.Velmurugan, Centre of Advanced Study in
Crystallography and Biophysics, University of Madaras, Chennai-25
Phone Number: 044-22202772 Mobile:09841075847
Email:d_velu@yahoo.com Website:
Name of Contact Person(s): Prof.D.Velmurugan, Sruthigovind
Email: d_velu@yahoo.com sruthigovind@yahoo.co.in
458
University of North Bengal
Coordinator: Arnab Sen

1. Summary of the progress made by the centre from its inception: Since
its inception in November 2006, we have marched forward steadily. The
centre has every modern facility of information and communication including
necessary hard ware and software. There were a number of publications in
journals and posters presented in national and international conferences on
the relevant areas.

2. Major research activities in Biotechnology and its related fields: At NBU
major research activities are clustered around the fields of molecular
genetics, microbial biotechnology, plant tissue culture, immunology, microbial
genomics, transgenics, genomics and proteomics of nitrogen fixing bacteria
and food pathogenic bacteria.

3. Area of specialization of the centre: Bioinformatics, microbial genomics,
molecular modeling.

4. Major activities of the centre during the year 2007-08: A National Level
Workshop on Bioinformatics will be held from 18
th
-20
th
January 2008. Another
National level workshop has been planned in the month of March. The
Coordinator Dr. Arnab Sen has set up International collaboration with the
University of New Hampshire, USA. He along with Prof. Louis Tisa
(Department of Microbiology, UNH, USA) has been working towards complete
genome sequencing of five Frankia strains. Considerable amount of work
relating to the characterization of bacteria on the basis of codon usage and
phylogeny has been done and are expected to be published in the coming
days. Recruitment of research fellows/ associates is in process.

5. Infrastructure facilities in the Bioinformatics Centre: Computer and
communication: 10 PCs with OS One High end server and a Medium end
server Scientific and Software packages: Two Windows 2003 Server with
license, 10 Windows XP Professional with license, Microsoft ISA Server 2005
for Proxy Server, one Microsoft Visual Studio, .NET, MS SQL Server (Std.),
MS Office 2003, 10 Quick Heal AVG Antivirus Package. GENOME
BROWSER, CODONS, CODON W, MODELLER 9v1, CLUSTAL W,
CLUSTAL X, DNAsp 4.0, MEGA 4.0, TREEVIEW, SPDBV, RASMOL,
PHYLIP, PAUP, DAMBE, Jcat, Argus Lab, C++ and PERL. Databases and
other resources: One Laser printer (network), one Desk-Jet printer, Internet
Lease line.

6. Details about staff members working in the centre: Recruitment of one
Research Associate (RA) is in process.

7. Types of service provided: The centre provides access to the faculty
members, research scholars and students from nearby universities, colleges
and research institutions interested in working in the field of bioinformatics.

8. Educational activities with details of placement: Two PhD students (S.
Sur and U.K.Mondal) are currently engaged in their research work utilizing the
459
facility. Besides students and research scholars from other departments,
institutes and nearby areas utilize this facility.
9. Collaborative work and initiatives: The Coordinator Dr. Arnab Sen has set
up International collaboration with the Department of Microbiology, University
of New Hampshire, USA.

10. Databases and softwares developed: We have developed programs for
codon usage analysis and another for phylogenetic analysis which would be
published in the coming months.

11. Papers published or presented in the conferences /workshops in the
year 2007-08:
a) Sri. Saubashya Sur participated in a National Workshop (28-30 March,
2007) on Application of Bioinformatics in Molecular Modeling, Data
Analysis and System Biology organized by Bioinformatics Infrastructure
Facility, University of Kalyani, Department of Biochemistry and Biophysics.
b)Dr. Arnab Sen presented a poster in the 107
th
Annual General Meeting
American Society of Microbiology on Codon Usage Patterns and
Predicted Highly Expressed Genes for Three Frankia Genomes and the
Implication on Life Style held in Toronto, Ontario, Canada from 21-25
th

May, 2007.
c) Dr. Arnab Sen presented a poster in the Boston Bacterial Meetings on
Codon Usage Patterns and Predicted Highly Expressed Genes for Three
Frankia Genomes and the Implication on Life Style. Boston, June 20-21,
2007 Tufts University.
d)Dr. Asim Kr. Bothra presented a paper in a National level Workshop on
Fundamental Genomics and Evolutionary Biology on Comparative
analysis of codon usage patterns and identification of predicted highly
expressed genes in five Salmonella genomes (November 21-23, 2007),
DIC, Institute of Life Science, Bhubaneswar.
e) Sri. Saubashya Sur participated in a workshop on Introduction and Scope
of Computational biology (3-5 December, 2007) organized by the
Bioinformatics Centre, State Council of Sikkim Science and Technology,
Gangtok, as a resource person. Presented a paper on Bioinformatics
Databases and provided hands on Training.

12.Initiation of R&D activities in Bioinformatics:The Coordinators group is
actively engaged in research in the field of genomics and proteomics of
nitrogen fixing bacteria and food pathogenic bacteria. Protein structure
prediction, biological sequence analysis, phylogenetic study, molecular
modeling and molecular docking are the major thrust areas. Two PhD
students (S. Sur and U.K.Mondal) are actively pursuing their research work.
13. Details of Training/ Workshop organized and total no. of user trained: A
National Level Workshop on Bioinformatics will be held from 18
th
-20
th
January
2008.

14.Impact shown by your centre on the growth of biotechnology and allied
areas: Research publications from the Centre during 2006-07:
i) Sur. S, M. Bhattacharya, A. K. Bothra, L. Tisa & A. Sen (2008).
Bioinformatic analysis of codon usage patterns in a free living diazotroph,
Azotobacter vinelandii. ANSI Biotechnology(in press).
460
ii)Sen. A, S Sur, A. K. Bothra, D. R. Benson, P. Normand & L. S. Tisa (2007)
The implication on life style of codon usage patterns and predicted highly
expressed genes for three Frankia genomes. Antonie van Leeuwenhoek
(in press).
iii) Sen. G, S. Sur, D. Bose, U. Mondol, T. Furnholm, A. Bothra, L. Tisa & A.
Sen (2007) Analysis of codon usage patterns and predicted highly
expressed genes for six phytopathogenic Xanthomonas genomes shows a
high degree of conservation. InSilico Biology 7, 0039.
iv) D. Bose, S. Sur, A.K. Bothra & A. Sen (2007). Study of the diversity of the
heavy metal resistance genes and their codon usage profiling. ICFAI
Journal of Biotechnology 1(3) 49-58.
v) Sur. S, A .Sen & A. Bothra (2007) Mutational drift prevails over
translational efficiency in nif operons of Frankia. Indian Journal of
Biotechnology. (6) 321-328.
vi) Mondol. U.K, S. Sur, A. Sen & A.K. Bothra (2007). Codon Volatility: An
Efficient Tool to Detect the Purity of Genes. ICFAI Journal of Biotechnology
1(2) 45-49.

15. Future activities: Development of software for the analysis of DNA
sequencing data and protein. Annotation of five Frankia genomes whose
sequencing has been undertaken Bioinformatics analysis of nitrogen fixing
and food pathogenic bacterial genomes. Molecular modeling of some nitrogen
fixing proteins. Publication of Newsletter and conducting various training
programs/workshops in bioinformatics.

Additional details:
Coordinator: Dr. Arnab Sen
Department of Botany,
University of North Bengal,
Siliguri-734013 Tel: 0353-2699106;
Fax: 0353-2699001 E-mail: senarnab_nbu@hotmail.com
Deputy Coordinator: Dr. Asim Kr. Bothra
Chemiinformatics
Bioinformatics Laboratory, Department of Chemistry,
Raiganj College (University College)
Raiganj- 733134 Phone: 9474441570;e-mail: asimbothra@gmail.com.
461
University of Rajasthan, Jaipur
Coordinator : Prof. S. L. Kothari

The sanction for the establishment of BIF was issued by DBT through its
order number BT/BI/04/055/2001 dated 22-9-06.
University in its centre for converging technologies has provided independent
accomodation suited for BIF.The area of the facility is about 600 sq. ft.It is
provided with four units of split air conditioners.
Furniture and site Preparations have been completed. The university has
provided one direct telephone line.
The executive committee has been constituted.
One R.A has been appointed from 01-12-2007.

institution
The institution has biotechnology and its related fields of study in the
departments of Botany, Zoology, Biotechnology, Microbiology, Chemistry and
Centre for Converging technologies (CCT). The broad research activities in
these departments include transgenesis, plant tissue culture, secondary
metabolites, molecular taxonomy, biodiversity, reproductive biology, microbial
genetics, environmental biotechnology, radiation and cancer biology,
immunology, biochemistry, and bioinformatics.

The CCT has four components of Converging technologies that are:
N : Nanomaterials & Nanotechnology
B : Bioinformatics & Biotechnology
I : Information & Communication Technology
C : Cognitive Neuroscience

Converging Technologies namely :
N : Nanomaterials & Nanotechnology
B : Bioinformatics & Biotechnology
I : Information & Communication Technology
C : Cognitive Neuroscience

The centre came into existence in December 2006.The R.A joined on 01-12-
2007.
The centre will hold a 3 day workshop on Bioinformatics : Introduction and
Application from 7
th
-9
th
feb,2008.

462
Computer & Communication facility : 10 Desktop Computers with all the
accessories,1 Hp Laser jet printer & 1 HP Inkjet Printer.
1) Microsoft visual studio net Proffesional
2) Microsoft ISA server 2005 for proxy serve with media kit.
3) Freeware (Linux, Apache F Server, My SQL, PHP)

absorption status)
Ranjeeta Bonal : R.A : M.Sc (Bioinformatics) : 01-12-2007

The 5 Yr integrated course in Converging Technologies take the help of
BIF.Other students, research scholars and faculty also take the advantage of
the facilities at BIF.


It is proposed to take Ph.D level students in the subject area of
Bioinformatics.

A workshop is going to be held in BIF on Bioinformatics : Introduction and
Application between 7
th
-9
th
Feb, 2008. Total no. of participants expected is
25..

463
CCT is providing help to the 5yr integrated course in M.Sc(Converging
Technologies) and is on the way to start PhD programmes and M.Sc-Honours
in Converging Technologies.

BIF is actively working to start PhD programme & CCT- M.Sc (Honours)
Programme is already running.

Additional Details:
Name of the Coordinator: Prof. S.L Kothari
Name of the Dy. Coordinator : Dr.Ashok .K. Nagawat
Postal Address: Bioinformatics Infrastructure Facility
Centre for Converging Technologies
University of Rajasthan
Jaipur-302004

Phone Number: 0141-2712489; 0141-2703439; 0141-2700370

Email: slkothari@lycos.com; kothari-sl@uniraj.ernet.in
Website: www.uniraj.ernet.in

Name of Contact Person(s): Dr.A.K. Nagawat, Dy. Coordinator CCT,
Email: nagawat@uniraj.ernet.in
464
Vidyasagar University, Midnapur, West Bengal
Coordinator : Prof. Bikas Ranjan Pati

Bioinformatics laboratory of our center is start to functioning since August
2007. Inauguration of center was made by our Honble Vice Chancellor Prof.
Swapan Kumar Pramanick and in presence of the chief guest, Prof. Pinak
Chakraborty, Co-ordinator of BIF, Bose Institute on 8
th
October 2007.
From the inception of this laboratory our aim was to popularize the
Bioinformatics in our surrounding as our center is situated in the remote
corner and rural part of West Bengal. We have been able to complete the four
training programme in different aspects of Bioinformatics like Structural
Bioinformatics, Computational Biology, Database & data mining, and
Evolution & Phylogeny.

institution.
Biotechnology related research activities of our University are
1. Microbial enzyme (amylase, tannase, xylanase, chitinase) production and
scale up process.
2. Production of microbial polysaccharides and antibiotics.
3. Biofertilizer production and transfer of technology.
4. Anticancer substances from mashroom.
5. Antioxidant and antidiabetic constitute from medicinal plants.
6. Joint forest management (JFM).
7. Development of new fish feed.
In the last year we have received two research projects from different
funding agencies like UGC, DRDO, New Delhi.
a. Microbial fermentation; b. Biofertilizer ; c. Medicinal plants;
d. Mashroom polysaccharides; e. Fish feed
4. Major activities of the center during the year 2007 - 08
After establishment of the center we have organized four short-term
workshops for different group of students and teachers. Post graduate students,
Ph. D. scholars and faculties of different department of our Institute and
surroundings are enjoying different softwares, internet and e-journal facilities
regularly. Now we are starting some shorts of proteomics research work in our
center.
In the department there is already five existing computer, two printers (one laser
and other dot matrix) and one scanner. Apart from these, 10 computers, one
printer, one scanner and one copier machine procured from the BIF scheme and
all are functioning.
Twenty four hours internet facility and one dedicated telephone (no. 03222
274173) is available in this center.
a. Scientific software packages
Target to install the following softwares -
Sequence analysis software:
EMBOSS, Phylip 3.6, MEGA 2.0, TreeconW, Boxshade, OMIGA 2.0
Molecular modeling software :
465
MSI Insight II, Modetter, Procheck, Chemsketch, Rasmol, Swiss PDB viewer.
b. Databases & other information resources
Some free software collected from the internet and used regularly

GenBank
http://www.ncbi.nlm.nih.gov/Web/Gen
Bank/index.html
EMBL http://www.ebi.ac.uk/embl.html
DNA sequence motifs
TRRD http://www.bionet.nsc.ru/trrd/
ooTFD http://www.isbi.net
Gene expression
ASDB http://cbcg.nersc.gov/asdb
Some specific software could not purchase due to shortage of fund.
We can procure it whenever next allotment is available.
absorption status).
There is no permanent staff in our center. Following departmental
faculty and staff are actively engaged in this center
Prof. B. R. Pati (Head of Microbiology Department & Coordinator of
BIF center)
Dr. K. C. Mondal (Faculty, Microbiology Department)
Dr. D. Banerjee (Faculty, Microbiology Department)
Dr. P. Das Mohapatra (Staff, Microbiology Department)
Mr. J. Chalak (Staff, Microbiology Department)
Mr. Biplab Chakraborty, [Information scientist] BE (Computer
Science)
Mr. Krishnakanta Ojha, [Technical assistant] Graduate
Second installment of BIF grant is very much necessary to appoint a
contractual research associate.

a. Laboratory supports to our students for learning their course curriculum.
b. Internet & e-journal facilities to the PG students, Ph D scholars and
faculties.
c. Computational facility to all users of the University.
d. Short term training & workshops are given to different scientific
communities.
At present we are not able to provide any type of conventional course on
Bioinformatics. However our students completed their M. Sc. dissertation works
and most of them are now engaged in industry or in research.
9. Initiative to validate the outcome of Bioinformatics resources.
As such there is no committee in our center to evaluate the outcome of the
Bioinformatics resources. We are planning to request the BIF executive
committee of our center to take initiative to evaluate the outcome of
biotechnology related works in our University.
The center made primary discussion to tie-up with Bioinformatics center,
Bose Institute, Kolkata for exchange of resource person, software and others.
466

11. Databases/software packages developed.
We are not able to develop any software / databases from our center. We
have only collected free and available softwares from the internet.
Paper
Das Mohapatra
P.K., Mondal K.C.
and Pati B.R.
Production of tannase by the
immobilization of Bacillus
licheniformis KBR6 in Ca-alginate
beads.
Journal of Applied Microbiology
102, 1462- 1467, 2007
Das Mohapatra
P.K., Mondal K.C.
and Pati B.R.
Effect of amino acids on tannase
biosynthesis by Bacillus licheniformis
KBR6.
Journal of Microbiology,
Immunology and Infection.
(Accepted)
K. Krishna Prasad,
S. Venkata Mohan,
B. R. Pati and P. N.
Sarma.
Immobilization of Pleurotus ostreatus
1804 on PUF cubes: Influence of
mycelial growth pattern on laccase
yield.
Indian J. of Biotechnology
(Accepted).
S. M. Mandal, K. C.
Mandal, B. R. Pati

Optimization of IAA production by a
Rhizobium isolate from V. mungo.

Res. J. Microbiol (In
press), 2007

S. M. Mandal, K. C.
Mandal, B. R. Pati

A rapid colony screening method for the
detection of arsenate reducing bacteria

Ind. J. Microbiol, 47,
2007

S. M. Mandal, K. C.
Mandal, B. R. Pati
Production and composition of
extracellular polysaccharide synthesized
by a Rhizobium isolate of Vigna mungo.

Biotecnol. Lett 29, 1271-1275,
2007.
S. M. Mandal, K. C.
Mandal, S. Dey, B.
R. Pati

Optimization of cultural and nutritional
conditions for Indole 3-acitic acid (IAA)
Production by Rhizobium sp. isolated
from root nodules of Vigna mungo (L.)
Hepper.
Res. J. Microbiol 2 (3) 239-246
(2007).
S. M. Mandal, ,B. R.
Pati, A.K. Ghosh,
A.K.Das.

Letter: Influence of experimental
parameters on identification of whole cell
Rhizobium by matrix assisted laser
desorption/ionization time of flight mass
spectrometry.
Eur. J. Mass. Spectrom 13. 165-
171 (2007).
Debdulal Banerjee,
Keshab.C. Mondal,
Bikas R. Pati.
Tannase Production by Aspergillus
aculeatus DBF9 Through Solid State
Fermentation.
Acta Microbiologica et
Immunologica Hungarica 54 (2):
159-166 (2007)
Debdulal Banerjee
and Bikas R. Pati.
Optimization of Tannase Production by
Aureobasidium pullulans DBS66.
Journal of Microbiology and
Biotechnology 17 (6) 1049-
1053 (2007)
Publication in proceedings
1. Pradeep K. Das Mohapatra, Keshab C. Mondal and Bikas R. Pati. 2007. Solid state fermentation
for tannase production by Bacillus licheniformis KBR6. Proceeding of the International
Conference on New Horizons in Biotechnology [NHBT-2007], pp 131-132.
2. Parag Dandapat, Pradeep K. Das Mohapatra, Chiranjit Maity, Bikas R. Pati and Keshab C.
Mondal. 2007. In vitro antimicrobial activity of leaf extracts of Anacardium occidentale (L)
against human pathogens. Proceeding of the National Seminar on Medicinal Plants, pp 27.
3. Chiranjit Maity, Sapdip Samanta, Chandrani Mishra, Sasmita Jana, Pradeep K. Das Mohapatra,
Bikas R. Pati and Keshab C. Mondal. 2007. Production and partial characterization of amylases
by a local bacterial isolate, Bacillus sp. CKB19 under immobilization in Ca-alginate beads.
Proceeding of the International Conference on New Horizons in Biotechnology [NHBT-2007], pp
244.
4. Mahapatra S, Manna S, Dey BK, Pandey A, Roy S, Basu M, Banerjee D. 2007. Endophytic fungal
assemblage in tulsi (Oscimum sanctum) plant. Proceeding of 2
nd
Asian Congress on Mycology &
Plant pathology, pp 436.
5. Banerjee D, Roy S, Mahapatra S. 2007. Antimicrobial activities of some endophytic bacteria
isolated from Vinca rosea and Centella asiatica. Proceeding of joint bilateral seminar on
Antimicrobial Drug Resistance and the development of new Antibiotics.

467
13. Initiation of R & D activities in Bioinformatics.
Till we are not able to start R & D activities on Bioinformatics. Two M. Sc.
students started project work in Bioinformatics in our center with active support of IIT,
Kharagpur and Bose Institute, Kolkata.
14. Details of Training / workshop organized and total no. of user trained

Name of the training
programme
Nature of
Participants
Number of
Participants attended
Structural Bioinformatics M.Sc. students: 26
Computational Biology B.Sc. students 28
Database & data mining Biology teachers 20
Evolution & Phylogeny H.S. students 20

15. Impact shown by your center on the growth of biotechnology and allied
published /number of papers published with the help of your center,
how your center is promoting various activities of your organization
and neighboring institutions, manpower trained, tools developed,
Paper published: 06
Manpower trained: 94
a. Initiation of refresher course for college teachers on Bioinformatics &
Advance Biology.
b. Regular workshop and training on different fields of bioinformatics for UG
& PG students.
c. Purchase of software and appointment of a research associate.
d. Introduction of certificate / diploma course on Bioinformatics.

Additional details:
Name of the Coordinator (& contact person): Prof. Bikas Ranjan Pati
Postal Address: Dept. of Microbiology, Vidyasagar University, Midnapur,
WB
Phone : 03222-276554/555 (Ext. 477)
Fax : 03222 275329 / 264338
Mobile: 09232743348
Email : brpati@yahoo.com
Website: www.vidyasagar.ac.in

468
West Bengal University of Technology, Kolkata
Coordinator : Prof. Ashoke R. Thakur

H. Summary of the progress: The Dept. of Bioinformatics was founded for PG
teaching and research in the year 2005. The courses offered in Bioinformatics I. M.
Tech. In Bioinformatics and II. Post B.SC. Int. Ph.D in Bioinformatics. For details :
www.wbut.ac.in , www.utechbiotech.org. A Credit Exchange Programme has
been initiated with the Bioinformatics Centre, University of Pune, a COE under DBT,
New Delhi. Admission: Students are selected through a written test followed by PI.
Intake: 18 (app. By AICTE). Fellowship: Students scoring above GPA 8.0 are
awarded a monthly fellowship of 4000 INR. Other Activities: The Department
regularly organizes workshops on different topics. Eminent Scientists from different
research institutes, Universities, R&D organizations from all over the country
delivered seminars on current research topics. The Department has recieved Rs.
26.50 lacs in grants from the DBT, New Delhi for Eshtablishment of Bioinformatics
Infrastructure Facility (BIF) for the promotion Biology Teaching through
Bioinformatics (BTBI). It is also the DBT nodal centre for Eastern Region and have
held the National Eligibility Test for Bioinfo-NET (rechristened BINC). An MoU has
been signed for DOEACC-B level programme for M.Sc.(Tech) in Bioinformatics.

I. Major Research Activities in Biotechnology and its Related Fields: Ongoing
research stresses on Microbial Biodiversity, Plant Biotechnology(heavy metal
homeostasis in plants), Protein trafficking in Giardia lamblia. Human Molecular
Genetics and Human Cordblood Stem Cell. Experimental techniques on Molecular
Biology and Microbiology to students of M.Sc. In Bioinformatics, Sikkim Manipal
University.

J. Areas of Specialization of the Centre: ZTUS Zero Tolerance in Unlicensed
Software

K. Major acti vities of the centre during the year 2007-2008: 1. Mirror Sites: The
University website(www.wbut.ac.in) now hosts mirror sites for: 1. Fedora 2.
Ubuntu 3. Mozilla 4. CRAN and 5. OpenOffice. 2.Workshops Organized:
Bioiformatics 5, Biotechnology 3 on R, QSAR etc. 3. 1
st
Annual JC Bose
Memorial lecture by Sir Gregory Winter (Feb 24
th
2007). 4.2
nd
Annual JC Bose
Memorial lecture by Prof. B. Sanyal, honored by the French Govt. with Legion de
honor (Scheduled Feb 22
nd
2008).
L. Research Activities: Ongoing research stresses on Microbial Biodiversity,
Plant Biotechnology(heavy metal homeostasis in plants), Protein trafficking in
Giardia lamblia. Human Molecular Genetics and Human Cordblood Stem
Cell. MD.
M. Projects Approved: 1. Design of 'anion recognition' short peptide motifs
2. Molecular Investigation of Heavy Metal Tolerance/
Hyperaccumulation in Plants Growing on the Uranium Tailings Ponds
in Jaduguda 3. Role of phosphoinositide in intracellular protein
transport of Giardia lamblia 4. Co-ordinated Research & Development
Project on the use of Kalanchoe pinnata(Patherkuchi) as a green
manure crop to increase the yield of medicinal plants cultivated on
degraded wasteland 5. Imparting Training to progressive farmers,
growers, women members of self-help groups, traders and educated
unemployed youths on cultivation, processing, extraction of medicinal
& aromatic plants including entrepreneurship development
N. Publications in peer-reviewed National and International Journals:
469
Bioinformatics 4 2. Biotechnology 8 3. Presentations in Conferences
& Seminars 4.
O. Infrastructure facilities in the Bioinformatics Centre: Computer & Communication
facility
Hardware Servers 6, Thin Clients 25, 12 desktops, workstation 1, 30 TFT
monitors, 4 switches Scientific Software EMBOSS, EMBASSY,
CLUSTALV, ARB (Phylo. Anal.), Helix packing, netblast, dssp, OpenBabbel,
Genoculster(Jalaja Technologies),GROMACS, YASARA, CHARMM, Mopac,
VMD, RASMOL,SPDB Viewer, YASARA, RASTER3D, Pymol, AUTODOC,
MOLWORKS, Bkchem, Cerius2 from Accelrys Databases and other
Information Resources Our Digital library based on KOHA and D-space
platforms permit network bassed access to 13500, e-books & 1800 e-journals
from Springer link along with CSIR, Academy of science, Science Direct and
IOE journals.

P. Details about staff members working in the centre:
ix. Prof. Ashoke Ranjan Thakur, Vice-Chancellor, Microbial Biodiversity &
Bioinformatics 4yrs 2.Professor Rabi Majumdar, Advisor, Molecular Biophysics,
2yr 3.Dr. Raja Banerjee, Reader, Spectroscopy & Structural Biology, 2.5 yr 4.Dr.
Soumalee Basu, Lecturer, Computational Biology & Bioinformatics, 2.5yrs 5.Mr.
Subhrangshu Supakar, Project Officer, Pharm. & Bioinformatics, 2yr. 6.Ms. Aulie
Banerjee, Project Officer, Botany & Bioinformatics, ~2yr 7.Ms. Sujata Roy,
Project Officer, Molecular Modelling, 1.5 yr 8.Md. Aftabuddin, Project Officer,
Protein Networks & Comp. Appl. ~1.5yrs
Advisor and project officers are on contractual appointment.

Q. Types of service provided: The centre provides training programmes.

R. Educational activities with details of placement: Cognizant, wipro, IICB, CU,
Labvantage, Bose Institute, NIT, DOEACC, Cennexios life sc.

S. Initiati ve to validate the outcome of bioinformatics resources:
T. Placement of students Cognizant, wipro, IICB, CU, Labvantage, Bose
Institute etc
U. Research papers 12
V. Projects 5

W. Collaborative works/initiatives: We have Ekta Incubation Centre, a Technology
Business Incubator which proposes to build on competencies of its own resources
and those of the networked incubator Entrepreneurship Development Cell (EDC).
Dabur has signed an MOU.M/S Solutron based in USA is a company that specialises
in development of software related to Patent database and has signed an
Agreement.Hinovation Research Centre Pvt.Ltd. is another incubatee.

X. Databases/software packages developed : None.
Y. Papers published/ presented in Conferences with reference: 12
Z. Initiation of R&D acti vities: Dabur has signed an MOU.M/S

AA. Details or training/ workshop organized and total no of users trained: 5 Nos. on
R, QSAR and drug Design, Phyllogenetics.

BB. Impact shown by your centre on the growth of biotechnology and allied areas:
Many research papers published, good placement for students, 5 projects awarded.

CC. Future workshops: python, QT, Molecular Dynamics
470

Additional details: Name of the Coordinator: Prof. Ashoke R. Thakur

Postal Address: West Bengal University of Technology,
BF-142, Sector-1, Salt Lake, Kolkata -700064
Phone Number: 033-23217578,
Fax No.: 2334-1030
Email:vc@wbut.ac.in www.wbut.net, www.utecbiotech.org

Name of Contact Person(s): Prof. Ashoke R. Thakur vc@wbut.ac.in
471
Jawaharlal Nehru University , New Delhi
Coordinator : Prof. Alok Bhattacharya,


Bioinformatics Center (BIC) was established in Jawaharlal Nehru University, New
Delhi in 1989 under Biotechnology Information System Programme funded by the
Department of Biotechnology, Government of India. The original objective of the
center was to provide information to the researchers in Northern Region. In the first
decade the Centre assisted biologists by providing bibliographic references with
abstracts, retrieving sequences and structural data, analyzing the sequences and
structural data, imparting skills in bioinformatics and providing computational
facilities for research purposes in any area of bioinformatics. Last few years the BIC-
JNU has embarked on research and development in the broader area of
Computational and systems biology.
The advancements in the field of Bioinformatics is leading to more focused area of
study at Systems level. Taking note of this trend BIC-JNU has renamed its centre as
Centre for Computational Biology and Bioinformatics (CCBB). Our main objective
of human resource development activities and research in frontier areas of
computational biology is has taken a shape and recognition within the country. We
are also making concrete effort in interinstitutional collaboration in research
projects. To keep pace with the development in the field, impetus is given to set up
the necessary infrastructure and resources for the academic community

institution
Application and development of computational tools and Techniques to
analyze, visualize and interpret sequence, structure and gene expression
data on a large scale.

Computational Comparative genomics
Large scale Microarray data analysis
Homology modeling and molecular simulation
Systems biology
Evolutionary mechanisms
Computer based drug discovery

4. Major activities of the centre during the year
472
Faculty recruitment
Setting up of a high performance computing facility
Started M.Tech program in Computational and Systems Biology
Academic activities, such as conference and lectures
Research in Computation Biology


A. Computer Facilities
High Performance Computing Facilities (HPCF) as part of the UPOE, JNU.
HPCF will be not only be used by the Bioinformatics community but also by other
faculty doing large scale system level simulation. School of Information
Technology has signed an MOU with C-DAC Pune to set up a 256 processor
Cluster system for high performance computing initiative.
Internet Connectivity : Our host organization has high speed connectivity through
Software Technology Park of India (STPI), Noida and a fibre optic based campus
wide LAN is fully functional. Beside this SIT JNU has a connection of 2 Mbps
from DBT.72 PCs and 10 serversImplemented Video Conferencing as a method
to share teaching and other resources
A specialized library

Discovery Studio Windows & Linux Server, Discovery Studio DS Modeling 1.2,
Discovery Studio DS MedChem Explorer 2.2,DS Project KM Plus 1.0, MS SQL
Server 2000, What IF,Gold 2.1.2,CORINA Structure Generator 2.6,Catalyst NS
(SGI Workstations) 3.1, SYBYL 6.5,Chem Office, SigmaStat 2.0.3, SigmaPlot,
MATLAB Unix & Windows, AMBER 7, Chamm32

absorption status)
University has merged the centre along with the staff w.e.f. 2000

Sl.
#
Name of the staff Designation Specialization Period of
working
01. Dr. N. Subbarao System Analyst Molecular Modeling 1996
02. Dr. A. Krishnamachari Assistant
Professor
Bioinformatics 1995
03. Debasish Mondal Accountant Accounts 1997
04. K.Ganesan Technical
Assistant
Computer Hardware
& Software
1998
05. Arun Kumar Thakur Xerox Operator Xerox / Fax operation 1995
06. Mahesh Ram Office Assistant Office Assistance 1999

7. Type of services provided
Provide access to biological databases and tools to research scientists on-site as
well as through the network. This is supplemented with trained manpower to guide the
new user. The Center has several high-end workstations with considerable storage
capacity processing capabilities, and are available for the user community. External
473
users from surrounding institutes and users from within campus routinely use the centers
facilities for sequence data analysis as well as use the expertise in different area, such
as molecular modeling etc.

We are offering M.Tech and Direct Ph.D programme in the area of computational
and systems biology.

a) M.Tech in Computational and Systems Biology : Present batch is about 15
students drawn from diverse background. This two year programme grooms
them to become professional in the area of Computational Biology.
Year Applied Interviewed Admitted
2006-07 576 26 06
2007-08 43 36 12

b) Ph.D in the broad area of computational biology and bioinformatics : During the
current year , Ms. Sonika Tyagi became our first Ph.D scholar form the centre and Ms.
Anchal Vishnoi submitted her thesis. We expect four students may submit their Ph.D
thesis by July 2008. Besides these seven students are currently working on their
research problem.

c) Long-Term and Short-term trainees : Through this programme we provide an
opportunity to young minds from any area to work on a specific problem and the duration
is generally 3 months for short-term and 6-12 months for long term. We get tremendous
response and we plan to strengthen this in the coming year.
Year No. of students
2006 29
2007 34

d) Post-Doctoral Fellowship : Our centre also provides fellowship to attract Ph.D
scholars from diverse background and motivate them to undertake research
investigations in the broad area of computational biology.

e) Placements : Majority of the students have gone into Ph.D. program in India and
abroad. Some of the places where these students have enrolled for Ph.D. are JNU, IISc,
number of Institutes in Europe and USA. Some of the students have joined as faculty
including in one Central University. A substantial fraction about 30-40% are in private
sector. Many of these students did not stay long in Industry and decided to go for Ph.D.
programme. Since we started M. Tech program in 2006 the first of batch of srydents will
be graduating in 2008.

f) Workshops / seminars/ conferences
(a) Participated in eight national workshops:
(b) Thirteen Invited Lectures were organized by CCBB
(c) Thirteen Lectures were delivered outside JNU

The number of collaborative projects involving computation biology is increasing as
evident from number of publications and we plan to increase this aspect so that
larger community can benefit from the expertise.

Year Applied Interviewed Admitted
2006-07 17 12 03
2007-08 06 03 01
474

A major project involving researchers from AIIMS, JNU, IIT and ICGEB has
been initiated i.e Deciphering RNA regulons : Construction, analysis and
validation of a miRNA based regulatory network.
We have started a Complexity Group with an aim to attract researchers
working in diverse areas to take up research problems in complexity studies
at systems level. Several meetings and seminars have been organized in this
regard.

11. Databases / Software packages developed
(a) No. of Software Created
http://gopam.jnu.ac.in GOPAm Database contain the relation between
Gene, Genbank accession number, Gene Aliases, Chromosomal
Location, SwissPort, Accession No. Annotation in Gene Ontologies,
UniGene Cluster, UniGene and Locus Link Ref. Seq
MGDD : The database contains divergent regions present in members of
tuberculosis complex. SNPs, repeats causing indels are also included in
the database.
ABWGC, a comparative genomics method

1. Thakur, V., Azad, R. K., Ramaswamy, R. (2007) Markov models of Genome
segmentation Physical Review E. 75, 011915.
2. Srivastava, P. K., Desai, D. K., Nandi, S., Lynn, A. M. (2007) HMM-ModE - Improved
classification using profile hidden Markov models by optimising the discrimination
threshold and modifying emission probabilities with negative training sequences. BMC
Bioinformatics. 8,104.
3. Vishnoi, A., Roy, R., Bhattacharya, A. (2007) Comparative analysis of Bacterial
genomes: Identification of divergent regions in Mycobacterial strains using an anchor-
based approach. Nucleic Acid Res. 2007;35(11):3654-67. Epub 2007
4. Ramachandran, V., Subbarao, N., Mallick, B. N. (2007) In silico modeling of 1A-
adrenoceptor: Interaction of its normal and mutated active sites with noradrenaline as
well as its agonist and antagonist. American Journal of Biochemistry & Biotechnology
American Journal of Biochemistry and Biotechnology 3 (4):216-224, 2007.
5. Stephen, P., Ramachandran, V., Subbarao, N., Bamezai, R. N. K. (2007) Molecular
Modeling Pyruvate Phosphate Dikinase of Entamoeba Histolytica and Insilico Virtual
Screening for novel inhibitors. Special Issue in Drug Discovery of Journal of Computer
aided Molecular Design (E publicated in Aug. 2007)
6. Anupama Singh, Hemant R. Kushwaha, Pawan Sharma Molecular Modeling and
Comparative Structural Account ofAspartyl beta -semialdehyde dehydrogenase of
Mycobacterium tuberculosis (H37Rv) Journal of Molecular Modeling (In Press)
Genome analysis using statistical and other methods
Comparative genomics
Systems biology
Microarray and other large scale data analysis
Motif finding and analysis
Pathway analysis and identification of drug targets
In silico drug discovery
475

We have already mentioned before under educational programs.

allied areas. In this you may highlight the details like number of
paper published/ number of papers published with the help of your
organization and neighboring institutions, manpower trained, tools
developed, patents & copyrights acquired and other services
offered etc.
a. Some of the papers published by us are getting citation as well as are
highly accessed.
b. The students produced by us are being considered to be one of the best
in the field are working in the top industries and also in top Institutions.
c. Some of the potential drugs identified by us by computational methods
are currently being experimentally verified.
d. The teaching programs are in the forefront of the subject.


Setting of a software development centre :
Setting up of a large scale data analysis centre
Setting up of Interdisciplinary group on complex system
Starting a Ph.D. program with M.Sc./B.Tech as input students
Continuation of Post Doctoral Fellow / Long Term Training Programme in
Bioinformatics

Additional Details:
Name of the Coordinator: Prof. Alok Bhattacharya,
Postal Address: Centre for Computational Biology & Bioinformatics,
School of Information Technology
Jawaharlal Nehru University
Hall # 4, Lecture Hall Complex,
New Delhi-110 067
Phone Number:26741699 Mobile: Email: alok0200@mail.jnu.ac.in
Website: http://ccbb.jnu.ac.in/

Name of Contact Person(s): Prof. Alok Bhattacharya,
Email: alok0200@mail.jnu.ac.in

476

National JALMA Institute for Leprosy & Other Mycobacterial Diseases
Agra
Coordinator: Dr. VM Katoch

Title: Creation of Bioinformatics Infrastructure Facility (BIF) for the promotion of
Biology Teaching through Bioinformatics (BTBI) scheme of BTISnet

Installation of Bioinformatic softwares: Following Bioinformatic softwares
have been / are being purchased for the facility.

Biointerpreter
GeneSpring
Geno-cluster
Discovery Studio 2.0
GCG

Research work done:

Homology modeling: We have prepared homology models for proteins recently
identified in the Institute to have role in efflux mediated drug resistance in
Mycobacterium tuberculosis as well as for metabolic proteins of M.leprae.

Phylogenetic analysis: We have done phylogenetic analysis of M.tuberculosis
efflux pump proteins. The study was done to investigate close relationship of
efflux pump proteins within other genera having similar functions. Phylogenetic
analysis of M.tuberculosis was also done based on VNTR typing.

Evolutionary relationship of M.leprae strains: Evolutionary relationship of
M.leprae strains has been studied to investigate their origin in India. The copy
numbers of micro and minisatellites regions in M.leprae determined by Molecular
Biological methods have been correlated with Bioinformatic analysis to
investigate their ancestral origin.

Other studies: A number of online Bioinformatic tools have been used for
ongoing studies in the Institute like primer designing, BLAST analysis,
Transmembrane region prediction of efflux proteins, multiple sequence
alignments etc.

Workshop cum Orientation Training Programmes: The Institute has
organized three workshops during the period of August to December 2007. The
selection of students as well as teaching faculty for Orientation Training cum
Workshop was based on a write-up submitted by them covering their present
work and motivation for future research / teaching involving Bioinformatic
aspects.

1. Bioinformatics Orientation Training cum Workshop held from 27
th
31
st

August 2007

477
In this training 25 candidates were selected including 8 teachers and 16
students from Agra as well as other cities such as Indore, Bharatpur, Jabalpur
and Bhopal. Lectures on advanced tools and techniques related to sequence
analysis, genomic data mining, protein modeling, docking and structure based
drug designing etc. were given by the Institutional faculty as well as invited
speakers from various places like MANIT, Bhopal (Prof. KR Pardasani),
Jaypee Institute of Engineering & Technology, Guna (Dr. Neeru Adlakha),
AIIMS, New Delhi (Prof. Punit Kaur), JNU, New Delhi (Prof. Alok
Bhattacharya) and Madurai Kamraj University, Madurai (Dr. Sanjeev Singh).
Hands-on training was also provided in various aspects of Bioinformatics.

2. Short-term Training cum Workshop held from 25
th
September 6
th
October,
2007

This training programme was organized for students studying at the Institute /
who had come for short-term training from Agra and nearby regions to
provide them exposure about various bioinformatic tools. Twenty students
were selected for this training and hands-on training was provided to them
alongwith lectures by the Institutional faculty.

3. Bioinformatics Orientation Training cum Workshop held from 24
th
30
th

December 2007

The selection procedure for the second Bioinformatics Orientation Training
cum Workshop was based on same procedure followed earlier. 40 candidates
were selected for the training including 9 teachers and 31 students from Agra
as well as other cities such as Datia, Lucknow, Meerut, Moradabad and
Ghaziabad. The training programme was inaugurated by Prof. VP Saxena,
Former Vice Chancellor, Jiwaji University, Gwalior and Lectures as well as
hand-on training on various aspects of Bioinformatics were provided by the
Institutional faculty as well as invited speakers from various places like
MANIT, Bhopal (Prof. KR Pardasani), Jaypee Institute of Engineering &
Technology, Guna (Dr. Neeru Adlakha) and CDFD, Hyderabad (Dr. Akash
Ranjan).

Dr. VM Katoch
Director &
Coordinator
Bioinformatics Infrastructure Facility (BIF)

478
Ch. Charan Singh University, Meerut
Coordinator: H. S. Bal yan

1. Summary of the progress made by the centre from its inception: The BIF
facility was established in the Department of Genetics and Plant Breeding and
is open for use by all biology students. The first workshop will be organized
during March 2008 to train students.
institution: Genetic and physical mapping, QTL analysis, Molecular marker
assisted selection, gene pyramiding, association analysis, comparative
genomics involving wheat, rice, rye, barley, Mycobacterium tuberculosis and
M. bovis, database searches, sequence retrieval, in silico correlated gene
expression in bread wheat, genome-wide analysis of promoter and coding
sequences in Mycobacterium tuberculosis, homology modeling and docking
studies for various enzymes, Development of web-based interface for food
safety, computer aided drug designing (Cadd); designing of self-assembling
peptides
3. Area of Specialization of the centre: The major area of specialization is
Genetics, Plant Breeding & Crop Biotechnology. Although master courses in
Biotechnology and Bioinformatics are also offered by the university under
self-finance scheme.
4. Major activities of the centre during the year 2007-08: The facility is open
to all biology students. We also propose to organize a workshop Databases,
data mining and retrieval of information during March 2008.
(i) IBM THINK CENTRE: 10 Numbers; RAM 256 DDR-2 (Make IBM
additional 256 MB DDR 2 Ram): 10 Numbers; IBM TFT 17 (in lieu of
17 monitor): 10 Numbers
(ii) IBM SERVER with 2 Dual Core Processor: One Number; IBM TFT 17
In lieu of 17 monitor): One Number
(iii) IBM SERVER Intel Xeon 3.00 Ghz Dual Core Processor EM 64 T: One
Number; RAM 1 GB (Make IBM additional 1GB DDR2 RAM, 2512 MB):
One Number; IBM TFT 17 (in lieu of 17 monitor): One Number
(iv) 420 CP Multifunction Xerox Machine: One Number
(v) HP Laser Jet Printer (Model 5200 series): One Number
(vi) Scanner HP 2400C: One Number
(vii) Desk Jet HP 1360 Laser Jet Printer: One Number
(viii) Softwares: Windows 2003 Server 10 clients: One Number; Microsoft ISA
Server 2005: One Number; Microsoft Visual Studio Standard 2005: One
Number; MS SQUL Server 2005 Standard: One Number; MS Office
2003: One Number

absorption status): The facility is being looked after by the staff of the
Department of Genetics & Plant Breeding. Separate staff has not been
recruited as yet.
479
7. Types of services provided: The facility is available for all those who are
interested
8. Educational activities with details of placement: Not Applicable
9. Initiative to validate the outcome of bioinformatics resources: Not
applicable
10. Collaborative works/ initiatives: Not applicable
11. Databases/ Software packages developed: Not Applicable
Mohan A., Goyal A., Singh R., Balyan H.S., Gupta P. K. (2007). Physical mapping of wheat
and rye expressed sequence tag-simple sequence repeats on wheat chromosomes. The
Plant Genome (A supplement to Crop Sci.) 47: 3-13

13. Initiation of R&D activities in Bioinformatics: Not Applicable
14. Details of Training/ Workshop organized and total no. of user trained: A
workshop on Databases, data mining and retrieval of information will be
organized during March 2008 for training of students.
areas: The facility is being put to use by students and scholars as evident by
the above publication. The organization of the workshop will also help in
training manpower in the use and application of bioinformatics.
16. Future activities: Conduct of workshop
Name of the Coordinator: H. S. Balyan
Postal Address: Dr. H. S. Balyan, Professor & Head, Department of Genetics
& Plant Breeding, Ch. Charan Singh University, Meerut-250 004
Phone Number:0121-2763564 Mobile: 9412515497
Email:hsbalyan@rediffmail.com Website: www.ccsuniversity.org

Name of Contact Person(s): H. S. Balyan
Email: hsbalyan@rediffmail.com, hsbalyan@gmail.com

480
Maharani Lakshmi Ammanni College for Women, Bangalore.
Coordinator : Prof. M.B. Nagaveni

From the time of receipt of grants, our college BIF centre has successfully
conducted one national conference and 3 workshops on bioinformatics.

National conference: College conducted two day national conference on
computational biology, bioinformatics and life sciences (NCCBL
07) on May 2 and 3, 2007.

Workshops:

A. 15 days hands-on workshop on In silico drug designing and molecular
modeling, was held with the collaboration with Institute of Computational
Biology from July 25, 2007 to August 10, 2007. After the completion of the
workshop, students /faculties are well-versed in drug designing softwares as
ligand scouts, marvin sketch, smiles, quantum, vmole, autodock, argust lab
etc. Sessions were handled by experienced faculties from industries (Biocon,
IOCB, Accenture, PDP), academia (IIIT, Hyderabad, Maharani Lakshmi
Ammanni College for Women).
B. Two days hands-on workshop for faculty members alone, was conducted with
the collaboration of Accelrys, Sai foundation, Apsara Innovation specificifally
only on GCG wiscon package.
C. The other workshop was conducted in collaboration with the company named
Orsby Engineering Pvt. Ltd., BIOWARE Division, Bangalore. The workshop
was conducted on April 11, 2007 on Genious Pro software for Post graduate
students for enhancing their bioinformatics skills. This software is used for
mainly for teaching basic bioinformatics tools.

Apart from the above mentioned scientific activities, BIF centre made few
progresses as listed below:

A. Upgradation of the systems
B. Speed enhancement of the systems which has enabled us to use the
softwares effectively
C. BIF has given free access to undergraduate students, to enable them to have
bioinformatics software knowledge and to make them focused towards
research
D. Using BIF, our colleague, Mr. Sushil Kumar Middha has won first prize in
paper poster presentation at international bioinformatics symposium held at
Bhubaneshwar.
E. Our M.Sc. students Ms. Keya, Ms. Ashwini have presented a paper at national
conference Motif 06 at Bharatiyar university at Coimbatore on cystic fibrosis
Title of the paper: CFTR genome analysis with the help of bioinformatics
tools. Authors: Keya M, Ashwini, Sushil Kumar Middha

2. Major research activities in Biotechnology and its related fields at our
institution
481
Many faculty members have taken up the research projects for their M.Phil
and Ph.D. degrees.

3. Area of specialization of the center : Biotechnology
BIF centre has successfully conducted 2 days national conference on
computational biology, bioinformatics and life sciences on May 2 and 3, 2007,
short term training programs for students of our and other colleges.
a. Computer and communication facility: 25 computers, A dedicated BSNL
line for internet access, High end Server for internet.
b. Scientific software packages: Accelrys GCG package, Discovery studio,
Quantum software (all are commercial packages and free ware
Hex,RasMol,Qmol etc. )
c. Databases and other information resources: PFam (Protein database)
Mr. Suhil Kumar Middha : Bioinformatician
Mrs. Aruna H.K. : Bioinformatician
Mrs. Saraswati B. : Bioinformatician
Mrs. Harini : Lab Assistant
Mr. Venkatesh : Bioinformatician .
(All are appointed on permanent basis since 2006)

We have trained our students and faculty members to use bioinformatics tools
for teaching and enhance their bioinformatics skill

Students are placed in companies like Accenture, Apsara Innovation center
as bioinformatician, data management professionals etc.

Want to collaborate, have discussions and interact with BTISnet Centres and
other BIF centers.

With IOCB we want to do database designing
With Apsara Innovation for conducting work shop in future.

11. Databases/software packages developed : Still working


13. Initiation of R&D activities in Bioinformatics: Initiated database
creation

14. Details of Training/workshop organized and total no. of user trained
5 days hands-on workshop on In silico drug designing and molecular
modeling, was held with the collaboration with Institute of Computl.
Biology from July 25-Aug 10, 2007.

482
Two days hands-on workshop for faculty members alone, was conducted
with the collaboration of Accelrys, Apsara Innovation specifically only on
GCG wiscon package.

One day workshop in collaboration with the company named Orsby
Engineering Pvt. Ltd., BIOWARE Division, Bangalore
Total number of users trained: 130

15. Under progress

Working on database designing and drug designing, Organizing national
level workshop on clinical research during March, 2008

Additional details:
Name of the Coordinator: Prof. M.B. Nagaveni
Postal Address: Maharani Lakshmi Ammanni College for
Women, Malleswaram, Bangalore- 560 012
Phone Number: 26692137
Mobile: : 9886205533
Email : nagavenimb_yahoo.co.in

Name of Contact Person: Mr. Sushil Kumar Middha
Email: sushilmiddha@yahoo.com
483
University of Kerala
Coordinator : Dr.Achuthsankar S. Nair

The Centre for Bioinformatics was established by the University of Kerala in
January 2005 to take up teaching, research and extension activities in
bioinformatics and computational biology. This inter-disciplinary centre
focuses on the computational applications in biology, drawing knowledge
from mathematics, statistics, computer science, information technology,
biology and bio-technology. The centre has currently a post-graduate
programme (MSc in Computational Biology) and a post-masters
programme (MPhil in Bioinformatics) in addition to a research programme
leading to PhD in Bioinformatics/Computational Biology. The research
areas identified are genomic and proteomic signal processing (applications
of digital signal processing), protein sub-cellular localization, chaos game
representation of bio-sequences, bio-sequence compression, systems
biology and molecular modeling.
The Centre has attracted funding from various state and national agencies
such as Kerala State IT Mission, Dept of Information Technology, Govt of
India, Dept of Bio-Technology, Govt of India, University Grants Commission,
Dept of Science, Technology and Environment, Govt of Kerala.
In 2006-2007, DBT-BIF was granted to the centre and the first phase of
implementation is now complete. A number of programmes were conducted
under the auspices of DBT-BIF and the major one was Bioinformatica Indica
08 International Symposium on Computational Biology, Bioinformatics
and Synthetic Biology.
your institution.
Major research activities in Biotechnology and its related fields at your
institution The research areas identified are genomic and proteomic signal
processing (applications of digital signal processing), protein sub-cellular
localization, chaos game representation of bio-sequences, bio-sequence
compression, systems biology, Drug Discovery against Hepatitis C virus and
isolation and analysis of active compounds present in Trichopus
zeylanicus (Arogyapacha).

Computational Biology & Rational Drug Discovery
x. Bioinformatica Indica 08: International Symposium on Computational
Biology, Bioinformatics and Synthetic Biology. This was a major event
with 41 institutions from India and abroad represented. It had 120
participants. Key note address was delivered by Dr Todd Taylor of the
Riken Genomic Sciences Centre in Japan. Dr Limsoon Wong from
National University of Singapore, Dr Pawan Dhar from Riken Genomic
Sciences Centre in Japan (Editor in chief International Journal Systems
& Synthetic Biology), Dr Kumar Selvarajoo from University of Kew,
Japan, Dr. G. Narahari Sastry, IICT, Hyderabad, India, Dr. D.
Karunagaran, IIT, Chennai, India, Dr. D. Swati, Banaras Hindu
484
University, India, Dr. Ramakrishna Ramaswamy, JNU, New Delhi were
the key speakers. Proceedings has been published.
xi. A number of training programmes/workshops were conducted which are
listed in section 13.

The centre has a full-fledged Informatics Lab, whereas wet labs are shared
with the Life science Depts. Facilities ranging from Gel electrophoresis and
RTPCR to electron microscope are at the disposal of the students. In
addition, the Rajiv Gandhi Centre of Biotechnology (RGCB) in
Thiruvananthapuram also supports our programme with expert human
resources and short workshops at their Labs which include DNA & Protein
sequencing systems, DNA finger printing facility and Molecular Imager. An
excellent collection of over 600 books on Bioinformatics and allied areas are
available at the Centre, in addition to facilities of the Campus Library and the
University Library.
With DBT-BIF funds, 2 servers and 10-node network has been installed.
Both broad-band fiber-optic connection and Wi-Fi connection has been
established.

Scientific Software packages : Scilab, MATLAB, GenoCluster, GOLD.
Databases & other information resources. Through Campus WAN has access
to bundled on-line subscription of 1800 Journals.

absorption status)
Dr Achuthsankar S Nair,
(Hon. Director, Computational Biology, Since 2005, Permanent)
Being appointed
Lecturers (2 Nos): Contract
Lecturer (1 No): Permanent (UGC)
Training, Consultancy
MSc (Computational Biology) 8 seats: Started in 2008
MPhil (Bioinformatics) 15 Seats: Placement in SooryaKiran Bioinformatics
Pvt Ltd, Kerala Agricultural University, Rajiv Gandhi Centre for Biotechnology,
Saurashtra University, Rajkot, 5 students have registered for PhD at the
centre.
The MPhil (Bioinformatics) programme has an intake of 15 seats, admits
students with masters degree in life science/computer science and all allied
areas. The courses include: Bio-Mathematics & Statistics, Web Programming,
Computational Genomics, Computational Proteomics and Computer-Aided
Drug Discovery, Micro Array Bioinformatics, Introduction to IT (E),
Introduction to Life Sciences (E), Algorithms in Computational Biology (E),
Applied Bioinformatics (E), Seminar, Project & Viva Voce.
485
The Msc(Computational Biology) programme with an intake of 8 seats, admits
students from computing and allied areas (BSc (Computer Science), BSc
(Electronics), BCA, BSc Physics and Computer Applications, BSc in any
branch with PGDCA, BTech (Biotechnology)). It covers the following courses:
Introduction to Life Sciences, Bio Mathematics & Statistics, Bio-Physics,
Computational Genomics, Introduction to Biotechnology, Computational
Proteomics & Metabolemics, Computational Transcriptomics, Molecular
Phylogenetics, Advanced Programming Tools, Computer Aided Drug Design,
Micro Array Image Processing, Project & Viva Voce, and Elective courses
(Systems Biology, Data Mining, Professional Studies, Synthetic Biology,
Advanced Topics, Programming in Perl, Soft Computing methods in
Bioinformatics)

- Informal Collaboration with Scientists of Riken Genomic Sciences
Centre, Japan
- Sooryakiran Bioinformatics Pvt Ltd (A company launched by alumni of
the centre and incubated in the centre).

CGRex: A Software for generating CGR Signatures of Biosequences
Developed with DIT, Govt of India support)

Contributions to International Data Banks
[1] Achuthsankar S Nair , Sugunan V S, Amjesh R, Prasanth V, Theoretical model for the
structure of HCV NS3 Protease (Indian Strain), Brookhaven Protein Data Bank, Pdb id
:2ijs, Released on 17 Oct 2006.
[2] Achuthsankar S Nair , Amjesh R, Theoretical model for the structure of Cholestryl Ester
Transfer Protein, Protein Model Data Base, Pmdb id: pm0074708, Released on 30 Oct
2006.
[3] Amjesh R., Achuthsankar S. Nair & Sugunan V.S. Homo sapiens isolates of 1 to 19
microRNA, complete sequence. Submitted to NCBI Database. Accession Code: EF629327,
EF629328, EF629329, EF629330, EF629331, EF62932, EF629333, EF629334, EF629335,
EF629336, EF629337, EF629338, EF629339, EF629340, EF629341, EF629342, EF629343,
EF629344, EF629345.
[4] Amjesh R, Achuthsankar S Nair, Sugunan V.S, Sequence Alignment of Hepatitis C Virus
Indian Strain, European Molecular Biology Laboratory. Align Id-001119.

[1] Achuthsankar S. Nair and T. Mahalakshmi
"
Are categorical periodograms and indicator
sequences of genomes spectrally equivalent?, In Silico Biology, International Journal of
Computational Molecular Biology , IOS Press, 6(2006), pp 215-222.
[2] Achuthsankar S. Nair and Sivarama Pillai Sreenadhan, A coding measure scheme employing
electron-ion interaction pseudopotential (EIIP), Bioinformation 1(6), 2006, pp. 197-202.
[3] Achuthsankar. S. Nair

and Sreenadhan.S, An improved digital filtering technique using
nucleotide frequency indicators for locating exons. Journal of the Computer Society of
India, Vol. 36, No.1 , 2006, pp 60-66.
[4] Achuthsankar S Nair, Combatting Diseases with Computer-Aided Drug Design, IEEE
Potentials, Vol 25, No. 6 Nov/Dec 2006, pp 39-41,
[5] Gopikrishnan, Achuthsankar S. Nair and S. Sivakumar, "Optimization in DNA Microarray
Manufacture", Conference proceedings, NCTT 2006, Thiruvananthapuram, Volume II, pp.
M23-M28, November 2006.
[6] Achuthsankar S Nair , Amjesh R, Sugunan V.S , Homology Modeling as a tool for Drug
Action Analysis A study on HCV NS3 Protease, Proceedings of the Kerala Science
Congress, 2007.
486
[7] Achuthsankar S. Nair, Koshy P. Vaidyan, "Homology Modeling of Myoglobin using Adaptive
Neurofuzzy Systems", Proceedings of International Conference on Bioinformatics and
Computational Biology ( BIOCOMP 2006), Las Vegas, USA, June 26 29, 2006, pp. 24-30.
[8] Koshy P. Vaidyan, Achuthsankar S. Nair, "Applying Nonlinear Control system Principles to
Structural Bioinformatics", National Seminar on Bioinformatics and Computational Biology at
Banaras Hindu University, Varanasi, March, 2006.
[9] Koshy P. Vaidyan, Achuthsankar S. Nair, "Protein Sequence to Structure Mapping as a
Causal, Non-linear System: A Study Using Adaptive Neuro Fuzzy Techniques", Proceedings
of Kerala Science Congress, January 29 31, 2006, Thiruvananthapuram, pp. 288 290.
[10] Achuthsankar S. Nair and Sreenadhan S., "Design of an anti-notch digital filter for exon
identification from genomic signals", Paper presented at the National Seminar and
Workshop on Bioinformatics and Computational Biology Benarus Hindu University,
Varanasi, March 2006 22-24,
[11] Achuthsankar S Nair & T Mahalakshmi, Visualisation of Genomic Data Using Inter-
neucleotide Distance Signals, Paper presented in the IEEE International Workshop on
Genomic Signal Processing, Bucharest, July 2005.
[12] Achuthsankar S Nair & T Mahalakshmi, GSP Using Bi-neucleotide Distance Signals, Paper
presented in the 13
th
International Conference on Advanced Computing and
Communications, Coimbatore, December 2005.
[13] T Mahalakshmi & Achuthsankar S Nair, Digital Signal Processing of Categorical Series Data
in Bioinformatics, Proceedings of the Kerala Science Congress, January 2006.
[14] Aneesha M. S, Vidhya R. V, Sugunan V. S, Achuthsankar S. Nair. Comparative study of
genomes of Hepatitis C virus and Chikungunya virus. Proceedings of Bioinformatica
Indica08, Jan17-19. p: 76.
[15] Anu James, Sukanta Mondal, Suryanarayanarao Ramakumar. A comparative sequence-
structure-function analysis of molluscivorous and piscivorous -conotoxins. Proceedings of
Bioinformatica Indica08, Jan17-19. p: 69.
[16] Sreenadhan S, Mahalekshmi T, Koshy Vaidyan, Betsy Sheena Cherian, Achuthsankar S.
Nair. Genomic signal processing-contributions of Kerala University computational biology
research group-a brief overview. Proceedings of Bioinformatica Indica08, Jan17-19. pp:
35-42.
[17] Vinod Chandra S. S, Betsy Sheena Cherian. Exploring features of RNA sequences.
Proceedings of Bioinformatica Indica08, Jan17-19. p: 72.
[18] Subesh M. P, Umesh P, Gopakumar G, Achuthsankar S. Nair. Computational Approach to
the study of the significance of mitochondrial DNA mutations causing diseases and
identification of haplogroups. Proceedings of Bioinformatica Indica08, Jan17-19. p: 66.
[19] Sithara S, Gopakumar G, Achuthsankar S. Nair. Fractal analysis of genomic sequences.
Proceedings of Bioinformatica Indica08, Jan17-19. p: 75.
[20] Keerthy A. S, J. S. (Pat) Heslop-Harrison, Achuthsankar S. Nair. Heterozygosity and allelic
variation within and between Musa accessions. Proceedings of Bioinformatica Indica08,
Jan17-19. p: 71.
[21] Renu S, Manoj Kumar, TejP. Singh, Achuthsankar S. Nair, Punit Kaur. In silico design of
peptide inhibitors for Mycobacterium tuberculosis based on the structure of
dihydrodipicolinaste reductase. . Proceedings of Bioinformatica Indica08, Jan17-19. p:
54.
[22] Suma L. S, Smitha Dharan, Abdul Nazeer K. A, Microarrary data analysis using non negative
matrix factorization with sparseness constraint. Proceedings of Bioinformatica Indica08,
Jan17-19. p: 44.
[23] Smitha Dharan and Achuth Sankar S. Nair, Non- Negative Matrix Factorization for Clustering
Gene Expression Data from Microarray Digital Images, In National Conference on Recent
Trends in Optoelectronics and Laser Technology, p.44-45, Apr 9-11, 2007.

The Centre has 6 Full Time research students working in the areas
mentioned in Section 2. Also one DIT funded project on Development of one
open Source software CGREx (Chaos Game Representation Explorer)

13. Details of Training / Workshop organized and total no. of user trained.
487
The Centre organized a series of training programmes / Workshops in the
field of Bioinformatics.

Workshop on Biosequence Analysis on 15
th
of June 2007. (40 participants).
One day Seminar on Scilab on 20
th
July, 2007 (65 participants).
A Seminar cum workshop on Molecular Visualization Softwares on 17
th
August, 2007(45
participants).
The Centre in association with Sree Chithira Thirunal Engineering College, Trivandrum,
organized a seminar cum workshop in Bioinformatics on 6
7 November, 2007 and was

attended by over 300 delegates.
A seminar cum workshop on Perl on 30 Nov (50 participants)
A seminar cum workshop on Hidden Markov Models on 1
st
Dec (20 participants)
Bioinformatica Indica 08: International Symposium on Computational Biology,
Bioinformatics and Synthetic Biology. This was a major event with about 40 institutions
from India and abroad represented:

promoting various activities of your organization and neighboring
institutions, manpower trained, tools developed, patents & copyrights
acquired and other services offered etc.

Already noted in Sections 4, 5C, 11 and 13.

To continue routine training activities.
To organize Bioinformatica Indica on a yearly basis*
To launch an open-source e-content on Bioinformatics*
Organize a International workshop on E-cell.
To launch a 3-6 month training programme for students*, whereby students will be given
stipend and trained to work on chosen research/industry problem.
(*subject to DBT support)

Additional Details:
Name of the Coordinator: Dr.Achuthsankar S. Nair
Postal Address: Centre for Bioinformatics, University of Kerala, Karyavattom Campus,
Thiruvananthapuram 695581, Kerala
Phone Number: +914712412759
Email: sankar.achuth@gmail.com
Website: www.achu.keraluniversity.edu

Mysore Proceeding

Hochgeladen von

Dokumentinformationen

Originaltitel

Copyright

Verfügbare Formate

Dieses Dokument teilen

Dokument teilen oder einbetten

Freigabeoptionen

Stufen Sie dieses Dokument als nützlich ein?

Sind diese Inhalte unangemessen?

Copyright:

Verfügbare Formate

Mysore Proceeding

Hochgeladen von

Copyright:

Verfügbare Formate

1

Madhu Chopra and Anil K. Mishra, Ligand-Based Molecular Modeling

7 November, 2007 and was

Das könnte Ihnen auch gefallen