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VISVESVARAYA TECHNOLOGICAL UNIVERSITY, BELGAUM SCHEME OF TEACHING AND EXAMINATION FOR M.TECH.

BIOINFORMATICS (BBI)

I Semester
Subject Code Name of the Subject Teaching hours/week Practical/ Field Work/ Lecture Assignment/ Tutorials 4 4 4 4 4 -20 2# 2# 2* 2* 2 3 13 Marks for Duration of Exam in Hours I.A. Exam Total Marks

12BBI11B 12BBI11C 12BBI12 12BBI13 12BBI14 12BBI15X 12BBI16

$Data Structures in C & C++ / $$ Biomolecules, Molecular Biology and Genetic Engineering Statistical & Probabilistic methods for Bioinformatics Essential Bioinformatics Biomolecular Modeling & Simulation Elective I Seminar Total

3 3 3 3 3 -15

50 50 50 50 50 50 300

100 100 100 100 100 -500

150 150 150 150 150 50 800

Elective I 12BBI151 DNA Chips & Microarray Data Analysis 12BBI152 Computational Biology 12BBI153 Health Informatics $ Not for CSE & ISE students $$ Not for Biotechnology Students

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VISVESVARAYA TECHNOLOGICAL UNIVERSITY, BELGAUM SCHEME OF TEACHING AND EXAMINATION FOR M.TECH. BIOINFORMATICS (BBI) II Semester Subject Code Teaching hours/week Practical/ Field Work/ Lecture Assignment/ Tutorials 4 4 4 4 4 -20 2* 2# 2# 2* 2 3 13 Marks for Duration of Exam in Hours I.A. Exam Total Marks

Name of the Subject

12BBI21 12BBI22 12BBI23 12BBI24 12BBI25X 12BBI26 12BBI27

Genomics & Proteomics Systems Biology Data Warehousing & Data Mining JAVA & J2EE Elective II **Project Phase-I(6 week Duration) Seminar Total

3 3 3 3 3 -15

50 50 50 50 50 50 300

100 100 100 100 100 -500

150 150 150 150 150 50 800

Elective II 12BBI251 Chemoinformatics 12BBI252 Parallel & Distributed Computing 12BBI253 Cellular Neural Networks & Visual Computing ** Between the II Semester and III Semester. After availing a vocation of 2 weeks.

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VISVESVARAYA TECHNOLOGICAL UNIVERSITY, BELGAUM SCHEME OF TEACHING AND EXAMINATION FOR M.TECH. BIOINFORMATICS (BBI) III Semester Subject Code 12BBI31 12BBI32X 12BBI33X 12BBI34 12BBI35 Teaching hours/week Practical/ Field Work/ Lecture Assignment/ Tutorials 4 -4 4 -12 2 2 $ 3 07 Marks for Duration of Exam in Hours 3 3 3 -09 I.A. 50 50 50 50 200 Exam 100 100 100 -300 Total Marks 150 150 150 150 500

Name of the Subject

Research Methodology
Elective-III Elective-IV Project Phase II Evaluation of Project Phase I Total

Elective III 12BBI321 Artificial Intelligence 12BBI322 Neuroinformatics 12BBI323 Java for Bioinformatics & Biomedical Application $ 3 Days Course work and 3 days for Project work

Elective - IV 12BBI331 Database Management & Grid Computing 12BBI332 BioPerl, BioPython & NCBI C++ Toolkit 12BBI333Bioinformatics in Drug Design & Discovery

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VISVESVARAYA TECHNOLOGICAL UNIVERSITY, BELGAUM SCHEME OF TEACHING AND EXAMINATION FOR M.TECH. BIOINFORMATICS (BBI) IV Semester Subject Code 12BBI41 12BBI42 12BBI43 Teaching hours/week Practical/ Field Work/ Lecture Assignment/ Tutorials ----Total --3 03 Marks for Duration of Exam in Hours 3 3 3 I.A. 50 50 -Exam --100+100 Total Marks 50 50 200

Name of the Subject

Evaluation of Project Phase II Evaluation of Project work III Project work evaluation and Viva-voce

15 100 200 300 Grand Total (I to IV Sem.) : 2400 Note: Project work shall be continuously evaluated for phase I, phase II and after completion of the project.

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Note: * Lab Classes for any two core subjects are compulsory (practical will be evaluated for 20 marks and internal assessment for 30 marks. Lab journals should be maintained). # For the remaining two core subjects, it can be field work, assignment, tutorials. 1) Project Phase I: 6 weeks duration shall be carried out between II and III Semesters. Candidates in consultation with the guides shall carryout literature survey / visit to Industries to finalise the topic of dissertation. Evaluation of the same shall be taken up during beginning of III Semester. Total Marks shall be 50. Colleges have to send the synopsis after Phase I. 2) Project Phase II: 16 weeks duration. 3 days for project work in a week during III Semester. Evaluation shall be taken during the first two weeks of the IV Semester. Total Marks shall be 50. 3) Project Phase III: 24 weeks duration in IV Semester. Evaluation shall be taken up during the middle of IV Semester. Total Marks shall be 50. At the end of the Semester Project Work Evaluation and Viva-Voce Examinations shall be conducted. Total Marks shall be 50 + 50 + 100 = 200 (50 marks for guide, 50 marks for external and 100 for viva-voce). Marks of Evaluation of Project: The Marks of Project Phase I shall be sent to the University along with III Semester I.A. Marks of other subjects. The I.A. Marks of Project Phase II & III shall be sent to the University along with Project Work report at the end of the Semester. 4) During the final viva, students have to submit all the reports. 5) The Project Valuation and Viva-Voce will be conducted by a committee consisting of the following: a) Head of the Department (Chairman) b) Guide c) Two Examiners appointed by the university. (out of two external examiners at least one should be present).

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Data Structures in C & C++ Subject Code : 12BBI11B IA Marks No. of Lecture Hrs./Week : 04 Exam Hrs Total No. of Lecture Hrs. : 52 Exam Marks

: 50 : 03 : 100

Basic concepts: Variables, Operators, Statements, Functions and Pointers. Introduction to Classes, Objects and Object oriented design, C++ string classes. Features of Object Oriented Programming Encapsulation, Inheritance and Polymorphism. Introduction to C++ modules CORELIB, ALGORITHM, CGI, CONNECT, CTOOL, DBAPI, GUI, HTML, OBJECT MANAGER, SERIAL and UTIL module. Data structures: Stacks: Stack specifications, Lists and Arrays. Reversing a list, Information hiding, Standard template library, Implementation of Stacks, Specification of methods for Stacks. Class Specification, Pushing, Popping, and Other Methods. Encapsulation, Abstract Data Types and Their Implementations. Queues: Definitions, Queue Operations, Extended Queue Operations, Implementations of Queues - Circular Implementation of Queues, Demonstration and Testing. Application of Queues - Simulation, Functions and Methods of the Simulation. Linked Stacks and Queues: Pointers and Linked structures, Introduction and Survey, Pointers and Dynamic memory in C++. Basics of linked structures - Linked stacks, Linked stacks with safeguards, Destructor, Overloading Assignment Operator, Copy Constructor, Modified linked-stack specification. Linked queues - Basic declarations, Extended linked queues, Abstract Data Types and Their implementations. Recursion: Introduction to Recursion, Stack Frames for Subprograms, Tree of Subprogram Calls, Factorials: A Recursive Definition, Divide and Conquer (Towers of Hanoi). Principles of Recursion - Designing recursive algorithms. Tail Recursion, Refinement. Lists and Strings: List definition, Method sspecifications, Implementation of lists, Class templates, Contiguous implementation, Simply linked implementation. Variation: Keeping the Current Position, Doubly Linked Lists, Comparison of Implementations. Strings - Strings in C++, Implementation of strings, String operations. Linked lists in Arrays. Searching: Searching: Introduction Basic search types - Sequential search, Binary search, Ordered lists. Algorithm Development. Asymptotics Introduction, Orders of Magnitude, Big-O and Related Notations. Sorting: Introduction, Storable Lists. Sort types Bubble sort, Insertion sort, Merge sort, Selection sort, Shell sort, Divide-and-Conquer sorting, Merge sort for linked lists, Ordered insertion. Linked version. Analysis - Algorithm, Contiguous implementation and Comparisons. Analysis of Merge sort. Quick

sort for Contiguous lists, Partitioning the list, Analysis of Quicksort, Comparison with Merge sort. Heaps and Heapsort, Analysis of Heapsort. Two-Way trees as lists. Priority Queues. Tables and Information Retrieval: Introduction. Tables of various shapes, Triangular tables, Rectangular tables Jagged tables, Inverted tables. Tables: New Abstract Data Type, Hashing, Sparse tables. Collision resolution with Open Addressing, Collision Resolution by Chaining, Analysis of Hashing. Trees: Basic terminology. Binary trees - Binary tree representation, algebraic Expressions, Complete binary tree, Extended binary tree, Array and Linked representation of Binary trees. Traversing binary trees, threaded binary trees. Traversing Threaded binary trees, Huffman algorithm. Graphs: Terminology & Representations, Graphs & Multi-graphs, Directed Graphs, Sequential representations of graphs - Adjacency matrices, Traversal, Connected component and Spanning Trees, Minimum Cost Spanning Trees. TEXT BOOKS: 1. Nell B. Dale. C++ plus data structures, Jones Learning & Bartlett, 2007 2. Vinu V. Das. Principles Of Data Structures Using C And C++, New Age International, 2006. 3. Robert Kruse, Alexander Ryba, Data Structures and Program Design in C++, Prentice Hall, 2001. REFERENCE BOOKS: 1. S. Lipschutz. Data Structures, Mc-Graw Hill International Editions, 1986. 2. Jean-Paul Tremblay, Paul. G. Soresan. An introduction to data structures with Applications, Tata Mc-Graw Hill International Editions, 2nd edition, 1984. 3. A. Michael Berman. Data structures via C++, Oxford University Press, 2002. 4. M. Weiss. Data Structures and Algorithm Analysis in C++, Pearson Education, 2002.

Biomolecules, Molecular Biology & Genetic Engineering Subject Code No. of Lecture Hrs./ Week : 12BBI11C : 04 IA Marks Exam Hrs : 50 : 03

Total No. of Lecture Hrs. : 52 Exam Marks : 100 Overview of Biomacromolecules Introduction to Biomacromolecules, Structure, Characteristics and function of carbohydrates, proteins, lipids and nucleic acids. DNA Structure; Replication; Repair & Recombination Structure of DNA: A, B, Z and triplex DNA; Replication: Enzymes and accessory proteins, Initiation, elongation and termination in prokaryotes and eukaryotes; DNA damage and repair: Photoreactivation, Nucleotide excision repair, Mismatch repair, SOS repair; Recombination: Homologous and nonhomologous, site specific recombination. Prokaryotic & Eukaryotic Transcription Prokaryotic Transcription: Transcription unit, Promoters: Constitutive and Inducible, Operators, Regulatory elements, Initiation, Elongation, Termination (Rho-dependent and independent); Eukaryotic transcription and regulation: RNA polymerase I, II and III, Eukaryotic promoters and enhancers, General Transcription factors, TATA binding proteins (TBP) and TBP associated factors (TAF), Activators and repressors; Post Transcriptional Modifications: Processing of mRNA (splicing), 5'-Cap formation, 3'-end processing and polyadenylation, RNA editing; Nuclear export of mRNA; mRNA stability; Catalytic RNA. Transcriptional regulation-Positive and negative gene regulation; Operon concept: lac, trp operons; Transcriptional control in lambda phage; Transcriptional and post-transcriptional gene silencing; RNA interference (Role of miRNA and siRNA in gene regulation) and Antisense RNA. Translation & Transport Translation machinery; Ribosomes; Composition and assembly; Universal genetic code; Degeneracy of codons; Termination codons; Isoaccepting tRNA; Wobble hypothesis; Mechanism of initiation, elongation and termination; Co- and post-translational modifications; Genetic code in mitochondria; Transport of proteins and molecular chaperones; Protein stability; Protein turnover and degradation. Basics Concepts of Genetic engineering Introduction to genetic engineering; Restriction Enzymes; Klenow enzyme; T4 DNA polymerase; DNA ligase; Cloning Vectors: Plasmids,

Bacteriophages, M13 mp vectors, Phagemids, Lambda vectors, Cosmids, Artificial chromosome vectors (BACs, YACs), Shuttle vectors, Animal Virus derived vectors-SV-40, Expression vectors: pMal, pET, GST-tag vectors; Isolation and purification of plasmid and genomic DNA, and total RNA; Recombinant DNA technology: Cloning, screening of the recombinants, Protein purification; Isolation and purification of recombinant proteins. Native and SDS PAGE, His-tag; GST-tag; MBP-tag. Techniques in Genetic engineering Construction of genomic and cDNA libraries, Screening of the clones, PCR: Primer design, technique. Types of PCR: endpoint PCR, real time PCR, inverse PCR, cloning of PCR products, applications. Blotting techniques (Southern, Northern and Western) Radio labeled and non-radio labeled probes, Primer extension, DNA foot printing, EMSA (Electrophoretic mobility shift assay), In vitro transcription and translation. TEXT BOOKS: 1. Primrose S.B., Twyman R.M. and R.W. Principles of gene manipulation An introduction to genetic engineering, Old, Blackwell Science, 6th Edition, 2001. 2. Lewin B. Genes IX, Jones and Bartlett Publications, 2008. 3. Lodish et al. Molecular Cell Biology, ? 6th Edition, 2008. REFERENCE BOOKS: 1. Alberts B. Johnson A. Lewis J. Raff M., Robert K. and P. Walter. Molecular Biology of the cell, Garland Science, 2007. 2. Brown T.A. Gene Cloning and DNA Analysis An Introduction, Blackwell Science, 5th Edition, 2006. 3. Glick B.R. and J.J. Pasternak. Molecular Biotechnology Principles and applications of recombinant DNA, ASM Press, 4th Edition, 2008. 4. Voet D., Voet J.G. and C.W. Prott. Fundamentals of Biochemistry-Life at the molecular level, John Wiley & Sons, 2nd Edition, 2006. 5. Watson, J.D., Baker, T.A., Bell S.P., Gann A., Levine M and R. Losick. Molecular Biology of the Gene, Pearson Education, 5th Edition, 2004.

Statistical & Probabilistic Methods for Bioinformatics Subject Code No. of Lecture Hrs./Week Total No. of Lecture Hrs. : 12BBI12 : 04 : 52 IA Marks Exam Hrs Exam Marks : 50 : 03 : 100

Basics of statistics: Types of statistics Descriptive and Inferential statistics. Descriptive statistics - Frequency distributions and data presentation, Relative frequency, Histogram, Measures of central tendency. Inferential Statistics. Probability distribution functions: Binomial distribution, Poisson distribution, Uniform distribution, Normal distribution. Characteristics of a random variable. Moments of a distribution and Moment generating functions, Distribution functions of more than one random variable. Joint distributions, Conditional distributions, Marginal distributions and Independent random variables. Statistical Inference: Introduction. Classical and Bayesian methods, Classical Estimation Methods, Classical Hypothesis testing (few examples), Likelihood ratios, Hypothesis testing using Maximum as Test Statistics, Bayesian approach to Hypothesis testing and Estimation. Multiple testing. Stochastic Processes: Poison processes and Morkov chains, Homogenous poison processes and Poison distribution, poison and binomial distribution, poison and gamma distribution, pure birth test, Finite Morkov chains, Transition Probabilities and Transition Probability Matrix, Morkov chains with absorbing and no-absorbing states. Graphical representation of Morkov chains. Morkov modeling. Higher-Order Morkov Dependence. Pattern in Sequences with First-Order Morkov Dependence. Morkov Chain Monte Carlo. Continuous-Time Morkov chains. Analysis of DNA Sequences: Analysis of Single DNA sequences - Shotgun sequencing, DNA Modeling, Modeling Signals in DNA, long repeats, rScans. Analysis of patterns. Overlaps counted and not-counted. Analysis of Single Multiple DNA Sequences Frequency comparison, Sequence alignment, Simple tests for significant similarity in an alignment. Alignment algorithms for two sequences. Protein sequences and Substitution matrices. Multiple sequence alignment. Estimation and Hypothesis testing theory: Estimation theory Introduction, Criteria for Good estimators. Methods of estimation Maximum Likelihood estimation, Least squares, Multiple regression,

Multivariate and Bootstrapping. Hypothesis testing theory Introduction, Fixed sample size test, Composite fixed sample size tests, -2 log approximations. ANNOVA, Multivariate, Bootstrapping Methods. Sequence analysis. Statistical approach for sequence alignment and sequence search: Comparison of two aligned, unaligned sequences and Query sequence against a database. Minimum significance lengths. Gapped BLAST and PSI-BLAST. Hidden Morkov Models: Introduction. Algorithms Forward and Backward, Verterbi and Estimation algorithms. Applications of Hidden Morkov Models. Statistical approach for Microarray Data Analysis: Application to brain tumor data, Low level analysis of SNP Chip data, Genotyping HapMap data, Meta-analysis of genomic data. Demonstration of the methodology on the breast cancer data. Classification in genomics and metabolomics - Application to tumor data; Case study in proteomic mass-spectrometry: Coronary artery disease data; A statistical framework to infer functional gene associations from multiple biologically interrelated microarray experiments. An application to yeast and human data. Phenotypic characterization of Yersinia pestis. Detecting lineage-specific evolution of DNA. Evolutionary models: Models of Nucleotide substitution, Discrete Time Models, Continuous Time Models. Phylogenic Tree Estimation Introduction, Datasets, Tree building methods and Tree evaluation methods. TEXT BOOKS: 1. Warren J. Ewens Gregory Grant. Statistical Methods in Bioinformatics: An Introduction (Statistics for Biology and Health), Springer, 2005. 2. Warren John Ewens, Gregory R. Grant, Gregory Grant, R. Statistical Methods in Bioinformatics, Springer, 2005. 3. T. Hastie, R. Tibshirani, J. H. Friedman. The Elements of Statistical Learning, Springer, 2001. REFERENCE BOOKS: 1. Bioinformatics and Computational Biology Solutions using R and Bioconductor, edited by R. Gentleman, Springer, 2005. 2. Statistical Analysis of Gene Expression Microarray Data, edited by T.P. Chapman & Hall / CRC, Speed. 2003. 3. G. Gibson & S.V. Muse.A Primer of Genome Science , Sinauer Associates, 2001.

Essential Bioinformatics Subject Code : 12BBI13 IA Marks : 50 No. of Lecture Hrs./Week : 04 Exam Hrs : 03 Total No. of Lecture Hrs. : 52 Exam Marks : 100 Bioinformatics & Biological Databases: Introduction to Bioinformatics, Goals, Scope, Applications in biological science and medicine and Limitations, a) Sequence Databases b) Structure Databases c) Special Databases and applications: Genome, Microarray, Metabolic pathway, motif, multiple sequence alignment and domain databases. Mapping databases genome wide maps. Chromosome specific human maps. Applications of these databases. Sequence Alignment: Evolutionary basis, Homology vs Similarity, Similarity vs Identity. Types of Sequence alignment - Pairwise and Multiple sequence alignment, Alignment algorithms, Scoring matrices, Statistical significance of sequence alignment. Database Similarity Searching: Unique Requirements of Database Searching. Heuristic Database searching, Basic Local Alignment Search Tool (BLAST), FASTA, Comparison of FASTA and BLAST, Database Searching with the SmithWaterman Method Multiple Sequence Alignment: Scoring function, Exhaustive algorithms, Heuristic algorithms, Practical issues. Profiles and Hidden Markov Models: Position-Specific scoring matrices, Profiles, Markov Model and Hidden Markov Model. Prediction Motifs and Domains: Motif and Domain databases, Identification of Motifs and Domains in Multiple Sequence Alignment using Regular expressions, Motif and Domain databases statistical models, Protein Family databases, Motif Discovery in unaligned sequences. Sequence logos. Gene and Promoter Prediction: Promoter and Regulatory elements in Prokaryotes and Eukaryotes. Promoter and Regulatory element prediction algorithms. Gene prediction. Gene prediction in Prokaryotes and Eukaryotes. Categories of Gene Prediction Programs. Prediction algorithms. Molecular Phylogenetics: Phylogenetics Basics. Molecular Evolution and Molecular Phylogenetics - Terminology, Gene Phylogeny vs Species Phylogeny, Forms of Tree Representation. Phylogenetic Tree Construction Methods and Programs - Distance-Based Methods, Character-Based

Methods. Phylogenetic Tree evaluation methods. Phylogenetic analysis programs. Predictive Methods: Predictive methods using Nucleic acid sequence DNA framework, Masking of repetitive DNA, predicting RNA secondary structure, Finding RNA genes, Detection of functional sites and Codon bias in the DNA. Predictive methods using protein sequence - Protein identity and Physical properties. Structure prediction - Prediction of secondary structure of protein, Antigenic sites, Active sites, Folding classes, Specialized structures and Tertiary structures. Microarray Bioinformatics: Sequence databases for Microarrays, Computer aided design of oligonucleotide probes, Image processing, Measuring and quantifying microarray variability and Analysis of deferentially expressed genes. TEXT BOOKS: 1. Jin Xiong. Essential Bioinformatics, Cambridge University Press, 2006. 2. V. Kothekar. Essentials of Drug Designing, DHRUV Publications, 2005. 3. Paul G. Higgs, Teresa K. Attwood. Bioinformatics and Molecular Evolution, Blackwell, 2005. 4. Bioinformatics: Sequence and Genome Analysis, CSHL Press, 2004 REFERENCE BOOKS: 1. Lukas. Bioinformatics Basics: Applications in Biological Science and Medicine, 2005. 2. Pierre Baldi and Sren Brunak. Bioinformatics - The Machine Learning Approach, 2001. 3. Andreas D. Baxevanis. Current Protocols in Bioinformatics, Published by Wiley, 2003. 4. Dov Stekel, Microarray bioinformatics, Cambridge University Press, 2003. Bioinformatics Lab 1. 2. Sequence retrieval from nucleic acid and protein databases. Retrieval of information about structure, bioassay, physical and Chemical properties of chemical compounds (such as Drugs and naturally occurring compounds). Gene sequence assembly and contig mapping and identification of Gene. Sequence searches using FASTA and BLAST. Phylogenetic analysis. Prediction of secondary structure for given protein and RNA sequences.

3. 4. 5. 6.

7. 8. 9. 10. 11. 12. 13. 14.

Retrieval of protein structure from PDB and its visualization and modification. Primer and Promoter design for a given sequences EST clustering and EST mapping Genome annotation Demonstrating Sequence structure relationship Microarray data analysis- normalization, clustering. Study of Profiles, Patterns and PSSMs Prediction of protein-protein interactions.

Biomolecular Modeling & Simulation Subject Code : 12BBI14 IA Marks No. of Lecture Hrs./Week : 04 Exam Hrs Total No. of Lecture Hrs. : 52 Exam Marks

: 50 : 03 : 100

Biomolecular Structure and Modeling: Historical Perspective, Introduction to Molecular Modeling, Roots of Molecular modeling in Molecular mechanics. Introduction to X-Ray crystallography and NMR spectroscopy. Introduction to PDB and 3D Structure data, Structure of PDB and other 3D Structure record. Protein Structure Hierarchy: Structure Hierarchy: Helices Classic Helix and Helices, Left-Handed -Helix and Collagen Helix. -Sheets Turns and Loops. Supersecondary and Tertiary structure. Complex 3D Networks. Classes in Protein Architecture Folds, -Class, Bundles, Folded leaves, Hairpin arrays. -Class folds, Anti-parallel domains, parallel and Anti-parallel Combinations. / and +-Class, / Barrels, Open twisted / folds, Leucine-rich / folds. + folds. Quaternary structure. Force Fields: Formulation of the Model and Energy, Quantifying Characteristic Motions, Complex Biomolecular Spectra, Spectra as force constant sources, In-Plane and Out-of-Plane Bending. Bond Length Potentials - Harmonic term, Morse term, Cubic and Quadratic terms. Bond Angle Potentials - Harmonic and Trigonometric terms, Cross bond stretch / Angle bend terms. Torsional potentials - Origin of rotational barriers, Fourier terms, Torsional parameter Assignment, Improper torsion, Cross dihedral/Bond angle, Dihedral terms. Van der Waals potentials. Rapidly decaying potential. Parameter fitting from experiment. Two parameter calculation protocols. Coulomb potential - Coulombs Law. Slowly decaying potential, Dielectric function and Partial charges. Molecular modeling: Modeling basics. Generation of 3D Coordinates Crystal data, Fragment libraries, and conversion of 2D Structural data into 3D form. Force fields, and Geometry optimization. Energy minimizing procedures - Use of Charges, Solvent effects and Quantum Mechanical methods. Computational tools for Molecular modeling. Methods of Conformational analysis - Systematic search procedures, Monte carlo and molecular dynamics methods. Determining features of proteins - Interaction potential, Molecular electrostatic potential, molecular interaction fields, Properties on molecular surface and Pharmacophore identification. 3D QSAR Methods. Dynamical and Stochastic-Dynamical Foundations for Macromolecular Modeling: Bimolecular sampling: Algorithms, Test molecules, and metrics. Approach to thermal equilibrium in Biomolecular simulation, Hybrid Monte

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Carlo and Newton Raphson methods. Langevin equation for generalized coordinates, Meta stability and Dominant Eigenvalues of Transfer operators. Computation of the Free Energy: Free energy calculations in Biological Systems - Drug design, Signal transduction, Peptide folding, Membrane protein association, Numerical methods for calculating the potential of mean force, Replica-Exchange-Based Free-Energy Methods. Electrostatics and Enhanced Solvation Models: Implicit solvent electrostatics in Biomolecular Simulation, New distributed multipole methods. Quantum-Chemical Models for Macromolecular Simulation: Fast and Reliable Quantum Chemical Modeling of Macromolecules, Quantum chemistry simulations of Glycopeptide antibiotics. Membrane Protein Simulations: Membrane proteins and their importance, Membrane protein environments in Vivo and in Vitro. Modeling a complex environment - Simulation methods for membranes, Membrane protein systems, Complex solvents, Detergent micelles, Lipid bilayers, SelfAssembly and Complex systems. Modeling and Simulation of Allosteric regulation in enzymes Modeling and Simulation of sGC. TEXT BOOKS: 1. Hans-Dieter Hltje, Wolfgang Sippl, Didier Rognan, Gerd Folkers Molecular Modeling, 2008. 2. Jill P. Mesirov, Klaus Schulten, De Witt L. Mathematical Approaches to Biomolecular Structure and Dynamics, Sumners, 1996. 3. Alberte Pullman, Joshua Jortner. Modeling of Bimolecular Structures and Mechanisms, 1995. REFERENCE BOOKS: 1. Tamar Schlick. Molecular Modeling and Simulation: An Interdisciplinary Guide, Published by Springer, 2nd edition, 2010. 2. Isidore Rigoutsos, G. Stephanopoulos. Systems Biology, Published by Oxford University Press US, 2006. 3. Timothy J. Barth, Michael Griebel, David E.Keyes, Risto M. Nieminen, Dirk Roose, Tamar Schlick. New Algorithms for Macromolecular Simulation, Published by Springer, 2006. 4. Peter T. Cummings, Phillip R. Westmorland, Brice Carnahan. Foundations of Molecular Modeling and Simulation, Published by American Institute of Chemical Engineers, 2001.

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1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13.

Biomolecular Modeling & Simulation Lab Prediction of 3D structure of unknown protein sequence. Homology Modeling and Docking Evaluation of Aminergic G Protein-Coupled Receptors Modeling mutations and Single Nucleotide Polymorphisms. Molecular Modeling of Antibodies with Affinity towards Hydrophobic BINOL Derivatives. Modeling Nanopores for Sequencing DNA Docking small molecules into proteins. Molecular mechanics methods for predicting protein-ligand binding Simulation of lipid bilayer. Simulation of Water Permeation through Nanotubes Simulation of Forcing Substrates through Channels Molecular dynamic study on Aggregation of Beta Amyloid 42 in Alzheimers disease. Removing organic contaminants from drinking water- understanding zeolite water adsorption Hydrogen storage for fuel cells - a density functional theory study of hydrogen adsorption on aluminum clusters. diffusion studies of small gas molecules in polymeric materials.

14. Design of polymeric membranes - modeling and simulation

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DNA Chips & Microarray Data Analysis Subject Code : 12BBI151 IA Marks No. of Lecture Hrs./Week : 04 Exam Hrs Total No. of Lecture Hrs. : 52 Exam Marks

: 50 : 03 : 100

Introduction to Biochip and Microarray Construction: Basics of Biochips and Microarray Technology, Biochip technologies. Types of Biohips - DNA Microarrays, Oligonucleotide, cDNA and genomic microarrays, Integrated biochip system. Biochip versus gel-based methods. Limitations of biochip technology. Biochip construction -Megac10ne technology for fluid microarrays, Microarray labels, Microarray scanners, Microarray robotics. Microfluidics systems, Chips and Mass Spectrometry. Electrical detection methods for microarrays. Applications of Biochips - Tissue Chip, RNA Chip, Protein Chip Technology, Glycochips, Biochip assays, Combination of microarray and biosensor technology. Bioinformatics and microarrays, Applications of Biochip Technology: Molecular diagnostics, Pharmacogenomics, application of microarray technology in drug discovery and development, Use of DNA chip technology for drug safety, drug delivery, population genetics and epidemiology. Applications of Microarray technology in Forensics. DNA chip technology for water quality management, Application of micro arrays in the agroindustry; use of microarrays in Genetic disease monitoring. Microarray Data analysis: Introduction, Image Acquisition and Analysis, Detection of differential gene expression. Pathway analysis tools. Data validation. Genomic Signal Processing: Introduction, Mathematical models, and Modeling DNA Microarray data - Singular Value Decomposition algorithm. Online Analysis of Microarray Data Using Artificial Neural Networks Introduction, Methods. Signal Processing and the Design of Microarray. Time-Series Experiments. Predictive Models of Gene Regulation: Introduction, Regression Approach to Cis-Regulatory Element Analysis, Cooperativity. Spline Models of Cooperative Gene Regulation. Statistical Framework for Gene Expression Data Analysis Materials and Methods. Analysis of Comparative Genomic Hybridization Data on cDNA Microarrays Introduction, materials and methods. Interpreting Microarray Results With Gene Ontology and MeSH Introduction, Materials and methods. Incorporation of Gene Ontology Annotations to Enhance Microarray Data Analysis Materials and Methods. DNA Computing: Introduction, Junctions, other shapes, Biochips and largescale structures. Strand algebras for DNA computing Introduction, Strand

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Algebras. Discussion of Robinson and Kallenbach's methods for designing DNA shapes, DNA cube, computing with DNA, Electrical analogies for biological circuits, Challenges, Future Trends. DNA programming - Deoxyribozyme-Based Logic Gate design processes. Renewable, Time responsive DNA Logic Gates for scalable digital circuits. Design of Bimolecular device. Commercial Aspects of Biochip Technology: Markets for biochip technologies, Commercial and Government support for biochip development, Business strategies, and Patent issues. TEXT BOOKS: 1. DNA Computing: 15th International Meeting on DNA Computing, DNA 15, Fayetteville, AR, USA, June 8-11, 2009, Springer, 2009. 2. Paul F. Predki. Functional Protein Microarrays in Drug Discovery, CRC Press Publisher, 2007. 3. Biochips and Microarrays Technology and Commercial Potential Published by: Informa Global Pharmaceuticals and Health Care, 2000. REFERENCE BOOKS: 1. DNA Arrays: Technology and Experimental Strategies, Grigorenko, E.V (ed), CRC Press, 2002. 2. Mark Schena; J. Microarry Analysis, Wiley & Sons (ed. New York), 2002.

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Computational Biology Subject Code No. of Lecture Hrs./Week Total No. of Lecture Hrs. : 12BBI152 : 04 : 52 IA Marks Exam Hrs Exam Marks : 50 : 03 : 100 and

Introduction to Computational biology: Introduction, scope applications of Computational biology. Molecular Biology databases.

Statistical approach to DNA and Protein sequence analysis: Analysis of single DNA sequence: shotgun sequencing, DNA modeling, Scanning long repeats, Analysis of patterns and Counting of overlaps. Analysis of Multiple DNA or Protein sequences: Frequency comparisons of two sequences. Simple tests for significant similarity in an alignment. Alignment algorithms for two sequences: Gapped global comparisons and Dynamic programming algorithms, linear gap model for fitting one sequence into another and local alignment. Patterns, Motifs and Signals: Pattern matching - Pattern matching with Consensus sequences Quantitative & Probabilistic pattern matching. Structural domains and Motifs - Sequence blocks & Profiles, Protein sequence motifs, Protein structural motifs, Clustering and Functional analysis of coordinately regulated genes. Discovering transcriptional regulatory Signals, Ultraconservation in the Human Genome. Restriction mapping, Map assembly and Sequencing Algorithms for restriction mapping, shotgun sequencing, DNA sequencing, Human Genome Project. DNA Arrays, Sequence Comparison sequence alignment, tuples, antichain. Finding signals in DNA - Gibbs sampling, Viterbi algorithm, Hidden Markov Models in Bioinformatics, Computational Proteomics (amino acid, C-terminal, directed acyclic graph), Problems -circular permutation, interval graph. Computational Biology and Cancer research: Mathematical modeling of tumorigenesis - Cellular automaton, tumor, angiogenesis. One hit and two hit stochastic models - Tumor suppressor gene, Kolmogorov forward equation, and retinoblastoma. Microsatellite and chromosomal instability in sporadic APC gene, colorectal cancer, point mutation. Chromosome loss. DNA damage and genetic instability - Apoptotic, Fitness landscape, unstable cells. Tissue aging and the development of cancer - Angiogenesis, Checkpoint competence, DNA damage. Basic models of tumor inhibition and promotion - Metastatic, Angiogenic tumor cells, Angiogenesis inhibition. Mechanisms of tumor neovascularization - vasculogenesis, Cancer and Immune responses

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- Dendritic cell vaccination, Viruses as antitumor weapons - Tumor load, Viral replication and Oncolytic viruses. Computational Immunology: Overview of immune system, Introduction to computational immunology Immunological databases IMGT IMGTGENE-DB, IMGT-HLA, Tools for the prediction binding affinity between peptide : TAP:MHC:TCR- MHC: Peptide Binding Prediction - SYFPEITHI, BIMAS, MHC PRED, - Future of computational modeling and prediction systems in clinical immunology -overview of models- models for HIV infection. TEXT BOOKS: 1. Darren Flower. In Silico Immunology, Springer, 2006. 2. Dominik Wodarz, Natalia L. Komarova, Computational Biology of Cancer, , Published by World Scientific, 2005. 3. Dominik Wodarz, Natalia L. Komarova,. Computational Biology of Cancer, World Scientific, 2005. 4. Neil C.Jones and Pavel .A Pevzner. An introduction to Bioinformatics Algorithms (Computational Molecular Biology), MIT Press, 2004. REFERENCE BOOKS: 1. Lukas. Bioinformatics Basics: Applications in Biological Science and Medicine, 2005. 2. Pierre Baldi and Sren Brunak. Bioinformatics - The Machine Learning Approach, 2001.

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Subject Code No. of Lecture Hrs./Week Total No. of Lecture Hrs.

Health Informatics : 12BBI153 : 04 : 52

IA Marks Exam Hrs Exam Marks

: 50 : 03 : 100

An introduction to Health care informatics: An interaction between health care and information systems. Acquisition, storage, retrieval, and use of information in health and biomedicine. Tools and techniques. Information systems in Medicine, Dentistry, Nursing, surgery and diagnosis. Future prospects. Building blocks of Health care informatics: Standards, types of standards. Modeling principles of modeling for healthcare. Architecture of Health care system models, sub systems, packages and components. Modeling framework for health care. generic health care information model. Unified modeling language. Modeling methodologies in healthcare systems. Databases, types, and applications. Database Architecture; ANSI/SPARC three tier architecture. Data warehousing; architecture. Tools and techniques in Telecare and E-Health: Introduction, conditions for telemedicine development, applications, access techniques in telecare, Internet technologies in medical systems: Requirement of Medical systems in the internet environment, internet medical architectures, and internet based telemedical services, next generation point of care information systems, internet access technologies in Telecare. Wireless communication technologies. Electronic Health records(HER): Challenges in clinical care, characteristics of good EHR, Generic EHR representation, EHR Standards and Scope of the HER. Decision support systems and Telematic networks in Medicine: Decision support systems, knowledge based and Expert based. Probabilistic and Logical decision systems. Transport layer in telematics networks, health digital data standards, E-health networks services. Applications of IT in hearing and chronic problems: Methodology of hearing screening, computer aided adjustment of hearing aids, diagnosis, tinnitus treatment. Application of IT to diagnose chronic conditions pateint centered symptom monitoring. Computer aided techniques in Medicine: Laproscopic surgery navigation, Introoperative imaging, multimodel imaging, Biosignal processing and algorithms. Biosignal databases. TEXT BOOKS:

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1. Naakesh A. Dewan, John Luo, Nancy M. Lorenz. Information Technology Essentials for Behavioral Health Clinicians, 2010. 2. Krzysztof Zielinski, Mariusz Duplaga. Technology Solutions for Healthcare (Hardcover), 2006. 3. Moya Conrick, Health Informatics, 2006. REFERENCE BOOKS: 1. Frank Sullivan, Jeremy Wyatt. ABC of Health Informatics, 2009 2. Moya Conrick. Health Informatics, 2006.

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Seminar Subject Code Field work/Assignment Hrs./Week Seminar Mechanism 1. 2. 3. 4. 5. 6. 7. A list of contemporary topics will be offered by the faculty members of the department. Student can opt for a topic of their own choice and indicate their option to the department at the beginning of the semester. Students have to do a literature survey of the selected topic from journals and web resources. A draft copy of the report should be submitted one week before the presentation, to the seminar coordinator. Students have to give a presentation in power point for about 30 minutes followed by the Q/A session. The Evaluation will be done by committee constituted by the department. The final copy of the report should be submitted after incorporating any modifications suggested by the evaluation committee. : 12BBI16 : 03 IA Marks : 50

Guidelines for Evaluation The following are the weightages given for the various stages of the seminar: 1. Selection of the topic. 05 Marks. (20%) 2. Literature survey. 05 Marks. (20%) 3. Understanding and presentation of the given topic. 05 Marks. (20%) 4. Reporting and Documentation. 10 Marks. (40%)

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Genomics & Proteomics Subject Code : 12BBI21 No. of Lecture Hrs./Week : 04 Total No. of Lecture Hrs. : 52

IA Marks Exam Hrs Exam Marks

: 50 : 03 : 100

Introduction: Introduction to Genomics & Proteomics. Structure, Organization and features of Prokaryotic & Eukaryotic genomes. Vectors. Genome mapping. Polymorphisms: Molecular markers RFLP, AFLP, RAPD, SCAR, SNP, ISSR, and Protein markers - Allozymes and Isozymes, Telomerase, FISH - DNA amplification markers and Cancer biomarkers. Genome sequences databases and Genome annotation, Gene discovery and Gene Ontology. Haplotyping and Diplotyping. Genome Sequencing: Early sequencing efforts. DNA sequencing methods Maxam-Gilbert Method, Sanger Dideoxy method, Fluorescence method, shot-gun approach and ultra-high-throughput DNA Sequencing using Microarray technology. Genome sequencing projects on E.coli. Arabidopsis and rice; Human-genome project and the genetic map. Recent developments and next generation sequencing. Raw genome sequence data, expressed sequenced tags (ESTs), Gene variation and associated diseases, diagnostic genes and drug targets. Genotyping - DNA Chips, diagnostic assays, diagnostic services. Comparative genomics and Functional Genomics - Studies with model systems such as Yeast, Drosophila, C. elegans, Arabidopsis. SAGE. Proteomics: Scope, Experimental methods for studying proteomics, methods of protein isolation, purification and quantification. Methods for large scale synthesis of proteins. Applications of peptides in biology. Analysis of proteins - high throughput screening, engineering novel proteins, MassSpectroscopy based protein expression and post-translational modification analysis. Bioinformatics analysis - clustering methods, Analysis of proteome functional information. Genome management in eukaryotes: Regulation of transcription, transcription factors and the co-ordination of gene expression, Regulation of translation and post-translational modification in eukaryotes, mitochondrial and chloroplast genome. Functional genomics: C-Values of eukaryotic genomes. Organization of microbial, plant and animal genomes, repetitive and coding sequences. Identification and tagging of markers for important traits, T-DNA & trasposon tagging. Cloning of genes by map-based cloning. Construction & Screening of cDNA libraries, differential display via RT-PCR. Micro-array in functional genomics.

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Genome analysis: Methods in mapping plant and animal genomes, Genome mapping in Plant and animal breeding, Yeast Artificial Chromosome (YAC) libraries and their uses in genome mapping. General features of mapping microbial genomes Bacterial and Fungal genomes. Genome and Proteome Annotation: Genome annotation: Extrinsic, Intrinsic (Signals and Content), Conservative information used in gene prediction. Frameworks for Information integration Exon chaining, Generative models: Hidden Morkov Models, Discriminative learning and Combiners. Evaluation of Gene prediction methods Basic tools, Systematic evaluation and Community experiments (GASP, EGASP and NGASP). Functional annotation of Proteins: Introduction, Protein sequence databases, UniProt, UniProtKB Sequence curation, Sequence annotation, Functional annotation, annotation of protein structure, post-translational modification, protein-protein interactions and pathways, annotation of human sequences and diseases in UniProt and UniProtKB. Protein family classification for functional annotation Protein signature methods and Databases, InterPro, InterProScan for sequence classification and functional annotation. Annotation from Genes and Protein to Genome and Proteome. Pharmacogenomics: Genetic Haplotyping in Natural Populations Introduction Introduction to Pharmacogenomics. Notion and definitions Notation and Definitions, Likelihoods, The EM Algorithm, Sampling variances of parameter estimates, Model selection, Hypothesis tests, Haplotyping with multiple SNP and RSNP Model, Functional Mapping Strategies for Genomic mapping of Drug Response QTL, to QTN and Functional Mapping of Drug Response. Dynamic Genetic Control, Structure of functional mapping, Estimation of functional Mapping, Hypothesis fests of functional mapping, Transform-Both-Sides model of Functional mapping, Structured ante dependence model of Functional mapping, Optimal strategy of structuring the covariance. Functional Mapping of Pharmacokinetics and Pharmacodynamics Mathematical modeling of Pharmacokinetics and Pharmacodynamics, Functional mapping of Pharmacokinetics, and Pharmacodynamics, Sequencing Pharmacodynamics. Haplotyping Drug Response by Linking Pharmacokinetics and Pharmacodynamics: Unifying model for Functional mapping Algorithms and determination of risk haplotypes, Hypothesis tests, Computer simulation, Genetic and Statistical Considerations for haplotyping of drug response.

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TEXT BOOKS: 1. Dmitrij Frishman, Alfonso Valencia, Modern genome annotation: the BioSapiens Network, Springer, 2008. 2. Rongling Wu, Min Linen. Statistical and Computational Pharmacogenomics (Interdisciplinary Statistics), Chapman & Hall/CRC, 2008. 3. Benjamin Lewis. GeneVIII, Jones and Bartlett Publisher, 2006. 4. Werner Kalow, Urs A. Meyer, Rachel F. Tyndale. Pharmacogenomics, Informa Healthcare, 2005. 5. Sndor Suhai, Genomics and Proteomics, Springer Publisher, 2000. REFERENCE BOOKS: 1. A. Malcolm Campbell, Laurie J. Heyer. Discovering genomics, proteomics and bioinformatics, Published by Pearson/Benjamin Cummings, 2006. 2. Ann Batiza, Ann Finney Batiza. Bioinformatics, Genomics, and Proteomics, Chelsea House Publishers, 2005. 3. Christopher A. Cullis. Plant Genomics and Proteomics, Wiley-Liss, 2004. Genomics & Proteomics Lab 1. 2. 3. 4. 5. 6. 7. 8. 9. Virtual sequencing (base calling, Sequence assembly, Mapping assembly, Contig mapping) Analysis of next generation sequencing data Genome annotation. Structure and sequence detection. Study of vector and virtual subcloning Chromatographic data analysis. Chromatogram sequence alignment and editing. CGH and Genotype Array Analysis. Analysis of X-Ray data and spectroscopic data.

10. 2D PAGE image analysis. 11. Prediction of secondary and tertiary structure of unknown proteins. 12. Protein annotation. 13. Prediction of protein functional sites in Protein 14. Microarray data analysis.

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Systems Biology Subject Code No. of Lecture Hrs./Week Total No. of Lecture Hrs. : 12BBI22 : 04 : 52 IA Marks Exam Hrs Exam Marks : 50 : 03 : 100

Introduction to Systems Biology: Scope, Concepts, Implementation and Applications. Information and Integration Technologies for Systems Biology: Databases for Systems Biology, Natural Language Processing and Ontology Enhanced Biomedical Data Mining, Text Mining. Integrated Imaging Informatics. Modeling tools - SBML, MathML, CellML, Petri Nets, Standard Platforms and applications in Systems Biology. Models and Applications: Metabolic Control Analysis, Glycolysis, Michaelis-Menten Kinetics, and Flux Balance Analysis. Signal Transduction - Phosphorylation, JAK-STAT Pathway, MAP Kinase. Biological Processes Mitochondria, Cyclin, CDC2. Evolution and Self organization - Hypercycle, Quasispecies model, Self Replication. Integrated Regulatory and Metabolic Models: Metabolic Network, Reconstruction of Metabolic Network from Genome Information. Mapping Genotype Phenotype relationship in Cellular Networks. Estimation Modeling and Simulation Computational Models of Circadian Rhythm. ,Gene Regulatory Networks, Attractor, and Boolean functions. Modeling of Gene Expression: Modeling of Gene Expression - Lactose, Lac Operon, tRNA. Analysis of Gene Expression Data - Support Vector Machines, Identifying Gene Regulatory Networks from Gene Expression Data. Modeling and Analysis of Gene Networks using Feedback Control. Global Gene Expression Assays. Multiscale representations of cells and Emerging phenotypes: Multistability and Multicellurarity, Spatio-Temporal Systems Biology, Mass Spectrometry and Systems Biology, Cytomics from cell state to predictive medicine, The Human Interactome - Protein-DNA and Protein-Protein Interactions. TEXT BOOKS: 1. Andres Kriete, Roland Eils. Computational Systems Biology, Academic Press, 2006. 2. Andrzej K. Konopka. Systems Biology, CRC, 2006. 3. Edda Klipp. Systems biology in practice: concepts, implementation and application, Wiley-VCH, 2005.

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REFERENCE BOOKS: 1. Corrado Priami. Transactions on Computational Systems Biology I. Springer Publisher, 2009. 2. Fred C. Boogerd, H.V. Westerhoff. Systems Biology, Elsevier Publisher, 2007. 3. Glenn Rowe. Theoretical Models in Biology , Oxford University Press Publisher, 2004.

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Data Warehousing & Data Mining Subject Code No. of Lecture Hrs./Week Total No. of Lecture Hrs. : 12BBI23 : 04 : 52 IA Marks Exam Hrs Exam Marks : 50 : 03 : 100

Introduction to Data Warehousing: Heterogeneous information, Integration problem. Warehouse architecture. Data warehousing, Warehouse vs DBMS. Aggregations: SQL and Aggregations, Aggregation functions and Grouping. Data Warehouse Models and OLAP Operations: Decision support; Data Marts, OLAP vs OLTP. Multi-Dimensional data model. Dimensional Modelling. ROLAP vs MOLAP; Star and snowflake schemas; the MOLAP cube; roll-up, slicing, and pivoting. Issues in Data Warehouse Design: Design issues - Monitoring, Wrappers, Integration, Data cleaning, Data loading, Materialised views, Warehouse maintenance, OLAP servers and Metadata. Building Data Warehouses: Conceptual data modeling, Entity-Relationship (ER) modeling and Dimension modeling. Data warehouse design using ER approach. Aspects of building data warehouses. Introducing Data Mining: KDD Process, Problems and Techniques, Data Mining Applications, Prospects for the Technology. CRISP-DM Methodology: Approach, Objectives, Documents, Structure, Binding to Contexts, Phases, Task, and Outputs. Data Mining Inputs and Outputs: Concepts, Instances, Attributes. Kinds of Learning, Kinds of Attributes and Preparing Inputs. Knowledge representations - Decision tables and Decision trees, Classification rules, Association rules, Regression trees & Model trees and Instance-Level representations. Data Mining Algorithms: One-R, Nave Bayes Classifier, Decision trees, Decision rules, Association Rules, Regression, K-Nearest Neighbour Classifiers. Evaluating Data Mining Results: Issues in Evaluation; Training and Testing Principles; Error Measures, Holdout, Cross Validation. Comparing Algorithms; Taking costs into account and Trade-Offs in the Confusion Matrix.

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TEXT BOOKS: 1. J. Han and M. Kamber. Data Mining: Concepts and Techniques, Morgan Kaufman, 2000. 2. Fundamentals of Data Warehouses, M. Jarke, M. Lenzerini, Y. Vassiliou, P. Vassiliadis (ed.), Springer-Verlag, 1999. 3. I. Witten and E. Frank. Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations, Morgan Kaufman, 1999. 4. Ralph Kimbal. The Data Warehouse Toolkit, Wiley, 1996. REFERENCE BOOKS: 1. M. H. Dunham. Data Mining: Introductory and Advanced Topic, Prentice Hall, 2003. 2. Zhengxin Chen. Intelligent Data Warehousing, CRC Press, 2002. 3. D. Hand, H. Mannila and P. Smyth. Principles of Data Mining, MIT Press, 2001.

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Subject Code No. of Lecture Hrs./Week Total No. of Lecture Hrs.

JAVA & J2EE : 12BBI24 : 04 : 52

IA Marks Exam Hrs Exam Marks

: 50 : 03 : 100

Introduction to Java: Java and Java applications. Java Development Kit (JDK). Byte Code, JVM; Object-oriented programming. Simple Java programs. Data types and Tokens: Boolean variables, int, long, char, operators, arrays, white spaces, literals, assigning values. Creating and destroying objects. Access specifiers. Operators and Expressions: Arithmetic Operators, Bitwise operators, Relational operators, Assignment Operator, The ? Operator; Operator Precedence. Logical expression. Type casting, Strings. Control Statements: Selection statements, iteration statements, Jump Statements. Classes, Inheritance, Exceptions: Classes. Classes in Java - Declaring a class, Class name, Super classes, Constructors. Creating instances of class. Inner classes. Inheritance: Simple, multiple, and multilevel inheritance; Overriding, overloading. Exception handling: Exception handling in Java. Multi Threaded Programming, Event Handling: Multi Programming: Extending threads; Implementing rentable. Synchronization, Changing state of the thread. Bounded buffer problems, Read-write problem, ProducerConsumer problems. Event Handling: Two event handling mechanisms, Delegation event model, Event classes; Sources of events; Event listener interfaces. Delegation event model; Adapter classes; Inner classes. Applets: The Applet Class: Two types of Applets, Applet basics, Applet Architecture, An Applet skeleton; The HTML APPLET tag; Passing parameters to Applets, Simple Applet display methods; Requesting repainting; Using the Status Window. getDocumentbase() and getCodebase(); ApletContext and showDocument(); The AudioClip Interface; The AppletStub Interface; Drawing Lines; Drawing Other Stuff; Color; Mouse Input; Keyboard Input and Output to the Console. Threads and Animation, Backbuffers, Graphics, and Painting; Clocks. Playing with text: Introduction to 2D arrays and hyperlinks, 3D Graphics - Basic classes. Java 2 Enterprise Edition Overview, Database Access: Overview of J2EE and J2SE. The Concept of JDBC; JDBC Driver Types; JDBC Packages; A Brief Overview of the JDBC process; Database Connection; Associating the JDBC/ODBC Bridge with the Database; Statement Objects; ResultSet; Transaction Processing; Metadata, Data types; Exceptions.

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Servlets: Background; The Life Cycle of a Servlet; Using Tomcat for Servlet Development; Simple Servlet; The Servlet API. The Javax.servlet Package. Reading Servlet Parameter, Javax.servlet.http package, Handling HTTP Requests and Responses. Cookies and Session Tracking. TEXT BOOKS: 1. Herbert Schildt. Java - The Complete Reference, Tata McGraw Hill, 7th Edition, 2007. 2. Jim Keogh, The Complete Reference, Tata McGraw Hill, 2007. 3. Jonathan Knudsen. Java 2D Graphics, O'Reilly, 1999. REFERENCE BOOKS: 1. Y. Daniel Liang. Introduction to Java Programming Comprehensive Version,), Pearson Prentice Hall Publisher, 7th Edition, 2010. 2. Y. Daniel Liang. Introduction to JAVA Programming, Pearson Education, 6th Edition, 2007. 3. Stephanie Bodoff et al. The J2EE Tutorial, Pearson Education, 2nd Edition, 2004.

1. 2. 3. 4.

5.

6.

7. 8. 9.

JAVA & J2EE Lab Design, Write and Execute Java Program that illustrate Constructor and Method overloading. Design, Write and Execute Java Program that implement inner class and demonstrate its Access Protections. Write a Java Program to create an interface and implement it in a class. Write a Java program that prints all real solutions to the quadratic equation ax2 + bx + c = 0. Read in a, b, c and use the quadratic formula. If the discriminant b2-4ac is negative, display a message stating that there are no real solutions. Write a JAVA program to implement Client Server(Client requests a file, Server responds to client with contents of that file which is then display on the screen by Client Socket Programming) Write a program to insert Protein information into ProteinDB database and retrieve the list of Protein sequences based on particular queries Using JDBC (Design Front end using Swings). Design, Write and Execute Java Program that illustrate Exception Handling (Using Nested try catch and finally). Write a Program to construct the phylogenetic tree using sequential clustering by reading input distance matrix. Write a Java program to Implement Dynamic Programming for sequence alignment.

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10. Write a JAVA Servlet program to implement a dynamic HTML using Servlet username and password should be accepted using HTML and displayed using a Servelet). 11. Write a Java program that correctly implements producer consumer problem using the concept of inter thread communication. 12. Develop an applet that receives an integer in one text field, and computes its factorial Value and returns it in another text field, when the button named Compute is clicked. 13. Write a java program that simulates a traffic light 14. Write a Java program using AWT to demonstrate Choice implementation. 15. Create a slideshow which has three slides. Which includes only text, program should change to the new slide after 5 seconds. After the third slide program returns to the First Slide.

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Subject Code No. of Lecture Hrs./Week Total No. of Lecture Hrs.

Chemoinformatics : 12BBI251 : 04 : 52

IA Marks Exam Hrs Exam Marks

: 50 : 03 : 100

Introduction to Chemoinformatics: Fundamental concepts - molecular descriptors and chemical spaces, chemical spaces and molecular similarity, modification and simplification of chemical spaces. Compound classification and selection cluster analysis, partitioning, support vectors machines. Predicting reactivity of biologically important molecules, combining screening and structure - 'SAR by NMR', computer storage of chemical information, data formats, OLE, XML, web design and delivery. Representing intermolecular forces: ab initio potentials, statistical potentials, force fields, molecular mechanics. Chemoinformatics Databases: Compound availability databases, SAR databases, chemical reaction databases, patent databases and other compound and drug discover databases. Database search methods: Chemical indexing, Proximity searching, 2D and 3D Structure and Substructure searching. Computational Models: Introduction, Historical Overview, Deriving a

QSAR Equation. Simple and Multiple Linear Regression. Designing a QSAR "Experiment". Principal Components
Regression, Partial Least Squares. Molecular Field Analysis and Partial Least Squares. Similarity Searching: Structural queries and Graphs, Pharmacophores, Fingerprints. Topological analysis. Machine learning methods for similarity search Generic and Neural networks. Library design Diverse libraries, Diversity estimation, Multi-objective design and Focused libraries. Quantitative Structure-Activity Relationaaship Analysis: Model building, Model evaluation, 4D-QSAR. Methods of QSAR analysis - Monte Carlo methods, Simulated annealing, Molecular dynamics and Probabilistic methods. Virtual screening and Compound filtering. Virtual Screening: Introduction. "Drug-Likeness" and Compound filters. Structure-based Virtual screening and Prediction of ADMET Properties. Combinatorial Chemistry and Library Design: Introduction. Diverse and Focussed libraries. Library enumeration. Combinatorial library design strategies.

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TEXT BOOKS: 1. Rongling Wu, Min Linen. Statistical and Computational Pharmacogenomics (Interdisciplinary Statistics) Chapman & Hall/CRC, 2008. 1. Andrew R and Valerie J. Gillet. Leach. An Introduction to Chemoinformatics, Springer, 2007. 2. Barry A. Bunin, Jrgen Bajorath, Brian Siesel, Guillermo Morales. Chemoinformatics: Theory, Practice, & Products, 2005. REFERENCE BOOKS: 1. Alexandre Varnek, Alex Tropsha. Chemoinformatics Approaches to Virtual Screening, Royal Society of Chemistry, 2008. 2. Barry A. Bunin, Jrgen Bajorath, Brian Siesel, Guillermo Morales. Chemoinformatics: Theory, Practice, & Products, Royal Society of Chemistry, 2006 3. Johann Gasteiger. Chemoinformatics: A Textbook, Wiley-VCH, 2003.

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Parallel & Distributed Computing Subject Code : 12BBI252 IA Marks No. of Lecture Hrs./Week : 04 Exam Hrs Total No. of Lecture Hrs. : 52 Exam Marks

: 50 : 03 : 100

Parallel Algorithms and Models: Need for parallel computing, Overview of different parallel computing architectures (OpenMP, MPI and CUDA) and Parallel and Evolutionary approaches to Computational Biology. Parallel Monte Carlo Simulation of HIV Molecular evolution in response to Immune surveillance. Differential evolutionary algorithms for In Vivo Dynamic analysis of Glycolysis and Pentose Phosphate Pathway in Escherichia coli. Compute-Intensive Simulations for cellular models. Parallel Computation in Simulating diffusion and deformation in Human brain. Sequence Analysis and Microarrays: Special-Purpose Computing for Biological Sequence Analysis. Multiple Sequence Alignment in Parallel on a Cluster of Workstations. Searching sequence databases using HighPerformance BLASTs. Parallel Implementations of Local sequence alignment: Hardware and Software. Parallel Computing in the analysis of Gene expression Relationships. Assembling DNA Fragments with a Distributed Genetic Algorithm. Cooperative Genetic Algorithm for Knowledge discovery in Microarray Experiments. Phylogenetics: Parallel and Distributed computation of large Phylogenetic trees. Phylogenetic parameter estimation on COWs. High-Performance Phylogeny reconstruction under Maximum Parsimony. Protein folding: Protein folding with the Parallel Replica Exchange Molecular Dynamics Method. High-Performance alignment methods for Protein Threading. Parallel evolutionary computations in discerning Protein structures. Platforms and enabling technologies: A Brief Overview of Grid Activities for Bioinformatics and Health Applications. Parallel Algorithms for Bioinformatics. Cluster and Grid Infrastructure for Computational Chemistry and Biochemistry. Distributed Workflows in Bioinformatics. Molecular Structure Determination on a Computational systems and Data Grid. Software framework for Parallel Bioinformatics on Computational grids. FPGA Computing in Modern Bioinformatics. Virtual Microscopy: Distributed image storage, Retrieval, Analysis, and Visualization. Parallel Computing for Bioinformatics and Computational Biology: TEXT BOOKS: 1. El-Ghazali Talbi. Grid Computing for Bioinformatics and Computational Biology, Wiley-Interscience Publisher, 2008.

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2. Kim-Meow Liew, Hong Shen, Simon See, Wentong Cai, Pingzhi Fan, Susumu Horiguchi. Parallel and Distributed Computing , Published by Springer, 2004. 3. Michel Cosnard, Afonso Ferreira, Joseph Peters, Parallel and Distributed Computing, Springer Publisher, 1994. REFERENCE BOOKS: 1. Albert Y. Zomaya. Parallel Computing for Bioinformatics and Computational Biology, Published by Wiley-Interscience, 2006. 2. Lynn Arthur Steen, Math and Bio 2010, MAA, 2005. 3. Albert Y. Zomaya, Parallel and Distributed Computing Handbook, McGraw-Hill Professional Publisher, 1996. 4. Chi-hau Chen, Fuzzy logic and neural network handbook McGraw-Hill, 1996.

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Cellular Neural Networks & Visual Computing Subject Code : 12BBI253 IA Marks No. of Lecture Hrs./Week : 04 Exam Hrs Total No. of Lecture Hrs. : 52 Exam Marks

: 50 : 03 : 100

Introduction: Notations, Definitions and Mathematical foundation. Characteristics and analysis of simple CNN templates Case studies: EDGE and EDGEGRAY templates Simulation of the CNN Dynamics: Integration of the standard CNN differential equation, Software simulation, Digital hardware accelerators, Analog CNN implementations, Scaling the signals, Discrete-time CNN (DTCNN). Binary CNN Characterization via Boolean Functions: Binary and Universal truth table, Boolean and Compressed local rules, Optimizing the truth table. Uncoupled CNNs: Unified Theory and Applications: Explicit CNN output formula, CNN theorem, Primary CNN mosaic, Explisit formula for transient waveform and settling time, local Boolean functions, Designing uncoupled CNNs. Introduction to the CNN Universal Machine: Global clock and global wire, Set inclusion, translation of sets and binary images. Opening, Closing and Implementation of morphological operator. Analog-to-digital array converter. CNN Universal Machine (CNN - UM): Architecture of CNN UM). Examples of CNN UM. Language, compiler and operating system. Template Design Tools: Design techniques. Binary representation, linear separability and simple decomposition, Template optimization, Template decomposition techniques. CNNs for Linear Image Processing: Coupled CNN with Linear Synaptic Weights: Active and inactive cells, dynamic local rules. Binary activation pattern and template format, A simple propagating type example. Uncoupled Standard CNNs with Nonlinear Synaptic Weights: Dynamic equations and DP plot. Standard CNNs with Delayed Synaptic Weights and Motion Analysis: Dynamic equations, Motion analysis discrete time and continuous time image acquisition.

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Visual Microprocessors - Analog and Digital VLSI Implementation of the CNN Universal Machine: Analog CNN core, Analogic CNN UM cell, Emulated digital implementation, Visual microprocessor. CNN Models in the Visual Pathway and The bionic eye: Receptive field organization, synaptic weights and Cloning templates, CNN models of visual pathway, CNN model of Vertebrate retina, Bionic Eye implemented on a CNN UM. TEXT BOOKS: 1. Angela Slavova, Valeri Mladenov. Cellular Neural Networks: Theory and Applications , Nova Publishers, 2004. 2. Leon O. Chua, Tamas Roska, Cellular Neural Networks and Visual Computing, Cambridge University Press, 2002. REFERENCE BOOKS: 1. Klaus Mainzer. Thinking in Complexity, Springer Publisher, 2007. 2. Angela Slavova. Cellular Neural Networks: dynamics and modeling, Springer Publisher, 2003.

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Seminar Subject Code Field work/Assignment Hrs./Week Seminar Mechanism 1. 2. 3. 4. 5. 6. 7. A list of contemporary topics will be offered by the faculty members of the department. Student can opt for a topic of their own choice and indicate their option to the department at the beginning of the semester. Students have to do a literature survey of the selected topic from journals and web resources. A draft copy of the report should be submitted one week before the presentation, to the seminar coordinator. Students have to give a presentation in power point for about 30 minutes followed by the Q/A session. The Evaluation will be done by committee constituted by the department. The final copy of the report should be submitted after incorporating any modifications suggested by the evaluation committee. : 12BBI27 : 03 IA Marks : 50

Guidelines for Evaluation The following are the weightages given for the various stages of the seminar: 1. Selection of the topic. 05 Marks. (20%) 2. Literature survey. 05 Marks. (20%) 3. Understanding and presentation of the given topic. 05 Marks. (20%) 4. Reporting and Documentation. 10 Marks. (40%)

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Subject Code No. of Lecture Hrs./Week Total No. of Lecture Hrs.

Artificial Intelligence : 12BBI321 : 04 : 52

IA Marks Exam Hrs Exam Marks

: 50 : 03 : 100

Introduction to Artificial Intelligence: Introduction to Artificial Intelligence, Problems, Approaches and tools for Artificial Intelligence. Introduction to search, Search algorithms, Heuristic search methods, Optimal search strategies. Use of graphs in Bioinformatics. Grammers, Languages and Automata. Current Techniques of Artificial Intelligence: Probabilistic approaches: Introduction to probability, Bayes theorem, Bayesian networks and Markov networks. Nearst Neighbour and Clustering Approaches: Nearst Neighbour method, Nearst Neighbour approach for secondary structure protein folding prediction, Clustering and Advanced clustering techniques. Identification Trees - Gain criterion, Over fitting and Pruning. Nearst Neighbour and Clustering Approaches for Bioinformatics. Neural Networks: Methods and Applications. Application of Neural Networks to Bioinformatics. Genetic algorithms and Genetic programming: Single-Objective Genetic algorithm, Multi-Objective Genetic algorithm. Applications of Genetic algorithms to Bioinformatics. Genetic programming Method, Applications, Guidelines and Bioinformatics applications. Applications of Artificial Intelligence: Genetic programming Neural Networks for the study of Gene-Gene interactions. Artificial neural networks for reducing the dimensionality of expression data. Cancer classification with Microarray data using Support Vector Mechanics. Prototype based recognition of splice sites. Analysis of Large-Scale mRNA expression data sets by genetic algorithms. Artificial Immune Systems in Bioinformatics. Evolutionary algorithms for the protein folding problem. Considering StemLoops as sequence signals for finding Ribosomal RNA genes. Assisting cancer diagnosis Inferring Gene Regulatory Networks from Expression Data: Introduction, Modeling gene regulatory networks. Boolean Networks and Bayesian Networks and Fuzzy Neural Networks. TEXT BOOKS: 1. Werner Dubitzky, Francisco Azuaje. Artificial Intelligence Methods and Tools for Systems Biology Published by Springer, 2005.

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2. Edward Keedwell, Ajit Narayanan, Intelligent Bioinformatics: The Application of Artificial Intelligence Techniques to Bioinformatics Problems, published by John Wiley and Sons, 2005. REFERENCE BOOKS: 1. Arpad Kelemen, Ajith Abraham, Yuehui Chen. Computational Intelligence in Bioinformatics, SpringerLink (Online service) Published by Springer, 2008. 2. Tomasz G. Smolinski, Mariofanna G. Milanova, Aboul Ella Hassanien. Computational Intelligence in Biomedicine and Bioinformatics: Current Trends and Applications, Published by Springer, 2008. 3. Stuart Jonathan Russell, Peter Norvig, John F. Canny, Artificial Intelligence: A Modern Approach, Published by Prentice Hall, 2003.

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Subject Code No. of Lecture Hrs./Week Total No. of Lecture Hrs.

Neuroinformatics : 12BBI322 : 04 : 52

IA Marks Exam Hrs Exam Marks

: 50 : 03 : 100

Introduction: Introduction to Neuroinformatics, Scope, Applications, Brief introduction about Neuron, Glial Cells, Neurophysiology - action potential, resting potential, Chemical control of Brain, Learning and Memory. Linear Response Theory and Single Neuron Models: Properties of a linear system, Convolution and Fourier transforms. Neuron models - Integrate and Fire model, Multi compartment models and Network Models. Neural Encoding: Introduction; Spike Trains and Firing rates, Spike Train Statistics, Neural encoding and decoding - Neural Code, Estimating Firing Rates, Introduction to Receptive Fields, Neural Decoding and Information theory. Entropy, Mutual Information, Bayers Theorem: Adaptation and learning. Synaptic plasticity rules. Supervised and unsupervised learning. Classical conditioning and Reinforcement learning. Neuroscience Knowledge Management: Managing knowledge in Neuroscience, Interoperability across Neuroscience databases. Database architectures for Neuroscience applications, XML for data representation and Data model specification. Computational Neuronal Modeling and Simulation: Tools and methods for simulation of Neurons and Neural Circuits - Model structure analysis in NEURON, Constructing realistic Neural simulations with GENESIS, Simulators for Neural Networks and Action potentials. Data mining through simulation. Computational exploration of Neuron and Neural Network models in Neurobiology. Neuroinforamtics Applications and Infrastructure: Neuroinformatics in Genetics and Neurodegenerative Disorders: Information approach to Systems Neurogenetics. Computational models of dementia and Neurological problems, Application of Systems biology approach to the neuroscience (application to schizophrenia). Brain Image construction, Analysis and Morphometric tools - Brain image Atlases, Databases and Repositories. Tools and databases for Mapping Neural structure and Connectivity Pattern. Neuroinforamtics Applications and Models for Neuropsychology: General Neuropsychological assessment - Visuospatial processing, Visual attention and Spatial neglect, Speech, Language and Aphasia, Phenomics and

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Neuropsychology. Human Brain Project: Microscale and Macroscale characterization; Basis of Brain mapping; Functional and Cognitive Brain atlas; Interoperable and Federated Brain Map databases. TEXT BOOKS: 1. Vinoth Jagaroo. Neuroinformatics for Neuropsychology, Springer, 2009. 2. Dayan and Abbot. Theoretical Neuroscience Computational and Mathematical Modeling of Neural System, The MIT Press, 1st Edition, 2001. REFERENCE BOOKS: 1. Chiquito Joaquim Crasto. Neuroinformatics, Humana Press, 2007. 2. Stephen H. Koslow, Michael F. Huerta. Neuroinformatics: an overview of the Human Brain Project, Routledge, 1997.

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Java for Bioinformatics & Biomedical Application Subject Code : 12BBI323 IA Marks No. of Lecture Hrs./Week : 04 Exam Hrs Total No. of Lecture Hrs. : 52 Exam Marks

: 50 : 03 : 100

Introduction to Java: Basics, Introduction to Java Applications, The Java Programming Environment, Fundamental Programming Structures in Java, Objects and Classes in Java, Polymorphism and Abstract Classes, Inheritance, Interfaces and Inner Classes, Program Design & Considerations , Graphical Components & Visual Design ,Java Utilities , Exception Handling, Exception Handling, File I/O, Applets, Linked Data Structures, Multithreading. Bioinformatics and Java: Current state of biomedical research. Cancer biomedical informatics and Grid program. caBIG organization and architecture. Model-View-Controller framework. Web services and service oriented architecture, caGrid. Sequence Search: Peforming BLAST analysis, Developing SwingBlast application. Designing SwingBlast Java application - adding events to applications, Designing SwingBlast GUI, Coding SwingBlast GUI. Description of Blast Classes, Implementing JQBlast. Enhacing SwingBlast application Retrieving sequence from GenBank using BioJava and without using BioJava. Facilitating PubMed Searches: JavaServer pages and Java Servelets HTTP and CGI, HTTP Protocol, GET and POST methods. Servelets and JavaServer pages technologies - Java API for Servelets and JSPs, JavaServer pages Standard Tag Library (JSTL), Apache Tomcat server. The NCBI PubMed literature search and retrieval service. Accessing biomedical literature through Entrez. Development of web application with Servelets and JSPs. Creating a Gene Prediction and BLAST Analysis Pipeline: Gene prediction programs. Performing Gene prediction with Genscan - Running genscan analysis, Analyzing Genscan output. Craeting SwingGenscan, Coding for SwingGenScan, SwingGenScan user Iunterface and Running SwingGenScan. Cancer Biomedical Informatics Grid (caBIG): Cancer Biomedical informatics Grid: Structure and Organisation of caBIG, Data Integration and ETL, Cancer Common Ontology Representation Environment (caCORE). Cancer Bioinformatics and Infrastructure Object (caBIO). Downloading and configuring caBIO. Creating JcaBIO application - JcaBIO classes and Application, Coding the SwingCaBIO application and Running JcaBIO application.

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TEXT BOOKS: 1. Harshawardhan Bal, Johnny Hujol. Java for Bioinformatics, Published by Pearson Education, Limited, 2007. 2. Harshawardhan Bal, Johnny Hujol. Java for Bioinformatics and Biomedical Applications, Published by Springer, 2007. 3. Cay S. Horstmann, Gary Cornell. Java 2: Fundamentals: Fundamentals, Published by Prentice Hall PTR, 2001. REFERENCE BOOKS: 1. Harshawardhan Bal, Johnny Hujol. Java for Bioinformatics, Published by Pearson Education Limited, 2007. 2. Cynthia Gibas, Per Jambeck. Developing bioinformatics computer skills, Published by O'Reilly, 2001.

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Database Management & Grid Computing Subject Code : 12BBI331 IA Marks No. of Lecture Hrs./Week : 04 Exam Hrs Total No. of Lecture Hrs. : 52 Exam Marks

: 50 : 03 : 100

Introduction to Biological Databases: Nucleic acid and Protein sequence data banks: Genbank, EMBL, DDBJ, cDNA databanks, AIDS Virus sequence data bank, rRNA data bank, Protein sequence data banks: NBRFPIR, SWISSPROT, Signal peptide data bank, TrEMBL, GenPept, PRINTS, CATH, SCOPE, BLOCKS. Structural databases PDB, exPDB, MMDB and PDBsum, Data Base Management System: Data Abstraction and Data Models. Basic concepts of database: Data Independence DML, DCL, DDL and Architecture of DBMS. Entity Relationship diagram. Application of ER diagram in designing database system. Relational Algebra and Tuple Relational Calculus. Database Design Issues: Normalization 1NF, 2NF, 3NF, 4NF, BCNF and 5NF and database design problem. Security and Integrity: Use of SQL for specifying Security and integrity. Authorization, View, Encryption. Storage structure indexing and hashing. Different type of file organization. Transaction & Concurrency control - Schedules, Testing, Serializability, Protocols - Lock based Protocol, Time Stamp protocol. Validation technique - Multiple granularity, Multi-version scheme Insert and delete operation, Crash recovery, Log based recovery, Buffer management checkpoints, Shadow paging. Object oriented databases. Distributed Database Structure: Design transparency and Autonomy. Distributed Query Processing Recovery - Commit protocol Deadlock handling, Multidatabase system. Parallel database concept and related issues, Web interface to database and Database System Architecture. Distributed Database Structure Implementation: Implementation of networks, Programme Environment. Implementation of Hierarchical database - Hierarchical Data Manipulation Language. Relational database model Basic principles in relational algebra, Relational Calculus, Domain relational calculus. Introduction, ISBL, SQUARE, SEQUEL, Query by Example, Commercial database systems. Grid Computing: Introduction. Grid computing concepts: Exploiting underutilized resources, Parallel CPU Capacity, Virtual resources and Virtual organizations for collaboration. Resource management - Access to additional resources, Resource balancing and resource reliability.

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Grid Architecture: Application Considerations; CPU considerations; Data considerations. Design Building Grid architecture, Solution objectives, Grid architecture models: Computational Grid and Data grid. Grid Topologies Intragrid, Extragrid. Conceptual Architecture Infrastructure, Conceptual Components. Schedulers; Condor. Data sharing; Distributed File Systems: Security. Service Oriented Architecture Web Services, Convergence of Web Services and Grid Services. Introduction to Globus Toolkit (Open Standards based). Case Studies on Grid Implementation for Life Sciences projects. TEXT BOOKS: 1. Abraham Silberschatz, Henry F. Korth, S. Sudarshan. Database System Concept, McGraw-Hill, 2010. 2. Database Systems: A Practical Approach To Design, Implementation And Management, 4/E, Pearson Education India , 2008. 3. C. J. Date, An introduction to database systems, Addison-Wesley, 2000. REFERENCE BOOKS: 1. Peter Rob, Carlos Coronel. Database systems: design, implementation, and management, Cengage Learning, 2009. 2. Lizhe Wang, Wei Jie, Jinjun Chen. Grid computing: infrastructure, service, and applications, CRC Press, 2009. 3. Brajesh Goyal, Shilpa Lawande. Enterprise grid computing with Oracle, McGraw-Hill Professional, 2006.

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BioPerl, Biopython & NCBI C++ Toolkit : 12BBI332 Subject Code IA Marks No. of Lecture Hrs./Week : 04 Exam Hrs Total No. of Lecture Hrs. : 52 Exam Marks BioPerl:

: 50 : 03 : 100

Perl - Introduction to Perl, writing and executing a Perl program. Data Types Scalar, Arrays and Associative arrays. Operators, Variables and Special variables. Regular expressions, Subroutines. Packages writing and calling packages. Modules writing and calling modules. Programming Applications: Motifs and Loops - Finding Motifs, Counting Nucleotides, Exploding Strings into Arrays, Operating on Strings, Writing to Files. Mutations and Randomizations - A program to simulate DNA mutation, Generating random DNA, Analyzing DNA. The Genetic Code - Hashes, Data Structures and Algorithms for Biology, Translating DNA into Proteins, Reading DNA from Files in FASTA format, Reading Frames. Restriction Maps and Regular Expressions - Restriction Maps and Restriction Enzymes, Generation of Restriction maps of Nucleic acid sequence. Database access and searching: GenBank Files, GenBank Libraries, Separating Sequence and Annotation, Parsing Annotations, Indexing GenBank with DBM. Protein Data Bank - PDB Files, Parsing PDB Files. BLAST - Obtaining BLAST, String Matching and Homology, Parsing BLAST Output. BioPerl: Introduction to BioPerl, BioPerl Modules, Applications of BioPerl Sequence retrieval and Sequence submission, Pair wise and Multiple sequence alignment, Parsing BLAST/FASTA results, Phylogenetic analysis. Retrieval and Parsing PDB Files. Creating graphics for Sequence display and Annotation. BioPython: Introduction to python: Python basics Variables, Operators, Data types and Assignments. Statements Input/output statements, flow control IFTHEN.ELSE, SWITCH, FOR, MAP, FILTER and WHILE, go to statements. Names, Functions and Modules. Object Oriented Programming in Python: Introduction to object oriented programming in python. Classes and objects. Inheritance, Polymorphism. Constructors and Destructors. Exception handling.

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Biopython and Bioinformatics: Parsing DNA data files, Image manipulation, Sequence analysis - Sequence alignment, Dynamic Programming, Detecting tandem repeats and generating Hidden Marko Models, Simulation of EST Clustering. Data mining - Text mining, Simulating Genetic algorithm. Analysis of Microarray data Spot finding and Measurement. NCBI C++ Toolkit: Introduction: Introduction, Applications and Feutures of NCBI C++ Tool kit. Introduction to C++ modules - CORELIB, ALGORITHM, CGI, CONNECT, CTOOL, DBAPI, GUI, HTML, OBJECT MANAGER, SERIAL and UTIL module. C++ Toolkit Library Reference - CORELIB Module Writing simple applications. Working with diagnostic streams - Debug Macros, Handling exceptions. Working with files and directories. TEXT BOOKS: 1. John Lewis, Peter Joseph DePasquale, Joseph Chase, Joe Chase. Java Foundations, Addison-Wesley, 2010. 2. Mitchell L Model. Bioinformatics Programming Using Python , O'Reilly Media, Inc., 2009. 3. D. Curtis Jamison. Perl Programming for Biologists, Wiley-IEEE, 2003. REFERENCES/REFERENCE BOOKS: 1. Todd Greanier, Jason M. Kinser, Jones & Bartlett Learning. Python for bioinformatics , 2009. 2. Java foundations, John Wiley and Sons, 2004 3. http://www.bioperl.org 4. http://biojava.org/ 5. http://biojava.org/wiki/BioJava:BioJavaInside

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Bioinformatics in Drug Design & Discovery Subject Code : 12BBI333 IA Marks No. of Lecture Hrs./Week : 04 Exam Hrs Total No. of Lecture Hrs. : 52 Exam Marks

: 50 : 03 : 100

Drug Design Process: Drug design - Compound searching, Target Identification, Target characterisation, Study of molecular interactions between target and compound (docking), ADMET Studies and Study of drug resistance. Drug design process for a known protein target Structure based drug design process, Finding initial hits, Compound refinement, ADMET Studies and Study of drug resistance. Drug design process for unknown protein target Ligand based drug design process, Finding initial hits, Compound refinement, ADMET Studies and Study of drug resistance. Case studies. Compound Library Design: Target library vs Diverse libraries, NonEnumerative techniques, Drug likeliness and Synthetic accessibility, Analysing diversity and Spanning known chemistries. Compound selection techniques. Homology Modeling and Drug Design: Structure Generation, Retrieval, Structure Visualization. Homology modeling - Constructing an initial model, Refining the model, Manipulating the model, Navigation of the model. Model evaluation Model evaluation techniques, Concept of energy minimization and Energy minimization techniques. Conformation generation, Deriving bioactive conformations, Molecular superposition and alignment, Deriving the Pharmacophoric pattern, Receptor mapping and estimating biological activities. Structural similarities and Superimposition techniques. Rational Drug Design and Chemical Intuition, Important Key and the Role of the Molecular Model, Limitations of Chemical Intuition. Molecular Mechanics: Introduction to Molecular mechanics, Force fields for drug design. Study of protein folding: Algorithms, Conformation analysis. Docking: Introduction, Search algorithms, Scoring functions, Docking Process Protein Preparation, Building the ligand, Setting the bounding box, Running the docking calculations. Building the Pharmacophore Models: Components of Pharmacophore model, Creating a Pharmacophore model from active compounds, Creating Pharmacophore model from Active site and Searching compound databases. QSAR: Conventional QSAR vs 3D-QSAR, QSAR Process, Molecular descriptors, Automated QSAR Programs. 3D-QSAR 3D-QSAR Process. Quantum Mechanics in Drug Design: Quantum Mechanics algorithms in Drug design - Modeling Systems with metal atoms, Computing reaction

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paths and Computing spectra. ADMET Studies: Oral bioavailability of compound, Finding Drug Half life in the Blood stream, Blood- Brain Barrier permeability and Toxicity studies, Computer - Assisted Drug Discovery: Drug Discovery and Development process, New Lead Discovery Strategies. Composition of Drug Discovery teams, Current Practice of CADD in the Pharmaceutical industry, Management structures of CADD groups, Contributions and achievements of CADD groups, Limitations of CADD support, Inherent Limitations of CADD support. State of Current Computational Models, Software and Hardware constraints TEXT BOOKS: 1. D. C. Young. Computational Drug Design: A Guide for Computational and Medicinal Chemists, Wiley-Interscience, 2009. 2. Stephen Neidle. Cancer Drug Design and Discovery , Academic Press Publisher, 2008. 3. Yi-Ping Phoebe Chen. Bioinformatics Technologies , Springer Publisher, 2005. 4. Povl Krogsgaard-Larsen, Tommy Liljefors, Ulf Madsen. Textbook of drug design and discovery, Published by Taylor & Francis, 2002. REFERENCE BOOKS: 1. Charles Owens Wilson, John H. Block, Ole Gisvold, John Marlowe Beale Lippincott . Wilson and Gisvold's Textbook of Organic Medicinal and Pharmaceutical Chemistry, Williams & Wilkins, 2010. 2. Alexandros Makriyannis, Diane Biegel, Marcel Dekker. Drug Discovery Strategies and Methods, 2004. 3. Alexander Hillisch, Rolf Hilgenfeld, Birkhuser. Modern Methods of Drug Discovery, 2003. 4. Hugo Kubinyi, Gerd Folkers, Yvonne C. Martin. 3D QSAR in Drug Design: Ligand-protein interactions and molecular similarity, Springer, 1998 5. Veerapandian, Pandi Veerapandian, Marcel Dekker. Structure-based drug design 1997.

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