Course:MBIN101;BiomolecularstructureandfunctionI

1.ElementsofQuantumTheory
Waveparticle duality and the uncertainty principle, Schrdinger equation,
probabilisticinterpretationofthewavefunction,energylevelsinrectangular
potentialwellwithapplications,linearoscillatorandrigidrotatormodelsfor
diatomicmolecules,energylevelsofhydrogenlikeatomsandthenatureof
atomicorbitals.

2.ChemicalBondinginMolecules
Formation of chemical bonds, molecular orbital (MO) theory and linear
combination of atomic orbitals (LCAO), electronic energy levels and the
nature of molecular orbitals in a hydrogen molecule, hybridized orbitals of
carbonwithapplicationstoorganicandbiologicallyimportantmolecules.

3.StructureReactivityandMechanism
Chemicalbondbreaking:homolyticorheterolyticcleavage,factorsinfluencing
electronavailability:inductiveandresonanceeffectsandtheirtimevariable
properties, dipole moments; stereoelectronic requirement for a reaction,
structure and physicochemical properties of amino acids, peptides and
proteins,implicationofstereoelectronicrequirementsinpeptideandprotein
structuralhierarchy.

4.Energetics,KineticsandSpontaneousProcess
Covalentandnoncovalentinteractionsforstabilization,chemicalkineticsand
thermodynamicprinciples,criteriaforaromacity,reactionkineticsandenergy
profile diagram, pseudo order reaction, isotope labeling, kinetically and
thermodynamically controlled reaction, implications in peptide and protein
structuralstabilizationandfoldingpathways.

Course:MBIN102,MolecularCellBiologyandGenetics
Genetics
UnitI:BasicGenetics:Mendeliangenetics,Meiosis,Linkage&
Recombination,HardyWeinbergPrinciple.

UnitII:MolecularGenetics:DNAReplication,transcription,translation,
Mutations,Genetechnology,cloningvectors,Restrictionenzymes,PCRand
itsapplications,Northern,Southern&Westernblotting,AutomatedDNA
sequencing
UnitIII:HumanGenetics:Xlinkedandautosomaldiseases,Chromatin
structureofeukaryotes,Chromosomalandgeneticsyndromes,Genetic
markers,HumanGenomemapping,Genetherapy,CancerGenetics
Biochemistry
Lipids:
Storage lipids (fatty acids, triglycerides), membrane lipids,
glycerophopholipids, sphingolipids, sterols, Biosynthesis of fatty acids,
triglyceridesandmembranephospholipids
Water:
Summaryofitsproperties,hydrogenbonds,ionizationofwater,
weakbasesandweakacids,pHscale,buffering,HendersonHasselbach
equation,Buffersystemsinbiology
CatabolismofHexoses : Glycolysis,Fatesofpyruvateunderaerobicand
aneorobic conditions, Degradation of sugars, Regulation of carbohydrate
catabolism,TCAcycle,Gluconeogenesis,Biosynthesisofglycogen,glucose
Enzymes: Reaction rates, specificity, transition stae, Enzyme kinetics
(MichaellisMentenequation,inhibitionmechanisms)
BioenergeticsandMetabolism:
Oxidativephosphorylation(ATP
synthesisdrivenbyelectrontransferandelectronflowinmitochondria);ATP
synthesisandrespiratoryelectronflow;RegulationofATPsynthesis,
thermogeninandbrownfat,hibernation

CarbohydratesofPhysiologicalSignificance

1. Carbohydrates: Monosaccharides, Oligosaccharides, Aldoses &

Ketoes, Conversion of aldose to ketose and vice versa, D and L
sugars,Mutarotation,Conversionofpentosetohexoseandviceversa,

GlucosewithFisherprojectionformulaandHowrahpyranosestructure,
Reactionofglucose,TestofGlucose
2.Polysaccharides: Starch, Cellulose,Chitinandchitosan,Application,
Glycosamineglycans,Hexosesofphysiologicsignificance,Disaccharides
ofphysiologicsignificance
3.Glycoproteins:Classification,Typeofglycoprotein,Functionof
glycoprotein
4.Carbohydratemediatedinteraction:Fundamentalsofprotein
carbohydrateinteraction,Glycobiologyofdiseases

Course:MBIN103;ComputationalMethodsinBiologyI

FileformatsGenBank,FASTA,MSF,NBRFPIR,GCG.
DefinitionoftermsOrthology,paralogy,xenologyandanalogy.Similarityand
Identity.
SubstitutionmatricesPAM,BLOSUM,principlesbasedonwhichthese
matricesarederived,ScoringSchemes,gappenalty,conceptofdistanceand
similaritymatrix
DatabasesearchesBLASTalgorithm,Significanceoftheresult,statistical
parameters,filteringDUST&SEG
Alignmentspairwisealignment,DynamicProgramming,Needleman
Wunsch&SmithWatermanalgorithms

Multiplesequencealignment,Progressivemethod,Iterativemethod,sumof
pairsmethod,ClustalW
SecondaryStructurePredictionMethodsChouFasman,GOR,Neural
Networks
Algorithmsforgenerationofsequenceprofiles:ProfileAnalysis,PSSM,PSI
BLAST
ProteinandNucleicacidpropertiesEMBOSS
Conceptofdomains,motif,repeatPfam,Prosite.CATH,SCOP
PhylogeneticTreeConstructionDistancebasedmethod,characterbased
methods.conceptofdendogramsanditsinterpretation.UPGMA,Fitch
Margoliash,NeighbourJoining,MaximumParsimony,MaximumLikelihood.
Bootstrapping,Jackknifing.
3Dstructurevisualization
ComparativeGenomicsBasicconceptsandapplications:FullGenome
alignments:basicconcepts,theneedforgenomealignments,MUMs,suffix
tree,Ukkonen'salgorithm,syntenyandgeneordercomparisons

Course:MBIN104,MathematicsandStatistics

Module 1: Recapitulation of Determinants & Matrices, Adjoint and

Determinantofamatrix,Inverseofamatrix,ElementaryTransformationsina
matrix,RowEchelonformofamatrix,InversionbyGaussJordanMethod,
EigenValuesandEigenVectors,Rankofamatrix,Solutionofasystemof
simultaneous linear equations, Cayley Hamilton Theorem, Complete set of
linearlyindependentvectors,Diagonalizationofamatrix,Powerseriesofa
matrix,likeexponential,trigonometricorhyperbolicfunctions(Onlyexpanded
expressions,withoutteachingSylvesterstheorem)
Module 2: Recapitulation of functions and their graphical representation.
Reviewofbasicfunctions.Functionsofseveralvariables.Recapitulationof
theconceptsoflimits,continuityandderivatives.Recapitulationofdifferential
calculus:derivativeoffunctionofafunction,derivativeofimplicitfunctions,
derivativeinaparametricform,higherorderdifferentiation.Recapitulationof
integral calculus:indefiniteintegrals,definiteintegrals,tangentandnormal,
maximaandminima.RecapitulationofVectoralgebra.
Module 3: Setting up of a ordinary differential equation, Initial value and
Boundary value problems, First order differential equations: separation of
variables,homogeneousequations,exactdifferentialequations;Higherorder
differential equations: homogeneous equations with constant coefficients,
nonhomogeneous equations with constant coefficients, Method of
undeterminedcoefficients,Methodofvariationofparameters;Solutionofa
system of simultaneous linear differential equations, Introduction of basic
concepts of Partial Differential Equations. Examples of application of
differentialequationsinbioinformatics.
Module 4: Numerical methods: : Solution of algebraic and transcendental
equations: NewtonRaphson, GaussJordan, Jacobis iteration; Finite
DifferencesandInterpolation:Newtonsforward&Backward,Gausssforward
& Backward; Numerical integration: Trapezoidal, Simpson; Solution of
differential equation: Taylors series, Eulers method, RungeKutta, Milne;
Finding Maxima nad Minima, Optimization problem: Single variable
optimization, Gradient descent methods (Students should practice writing
C/C++codesforallthesenumericalproblems)
Module5:Population,sample,parameter,statistic,randomsample,stratified
sample, treatment group, control group, doubleblind study, confounding
factors,crosssectionaland longitudinalstudy,population(sample)variance
andstandarddeviation,Conceptofprobability:Jointprobability,Conditional
probability. Linear Regression and Correlation : Correlation coefficient,
explainedandunexplaineddeviations,coefficientofdetermination.Probability
Distribution, Probability curve, Tossing of a coin, Binomial Distribution.
Hypothesistesting:Nullhypothesis,Alternatehypothesis,teststatistic,critical

region,levelofsignificance,TypeIerror,TypeIIerror.GaussianandPoisson
distribution, Standard Normal distribution, level of confidence, confidence
interval,pvalue.CentralLimitTheorem.
Module 6: tdistribution, checking for normality, Fdistribution, Oneway
ANOVA, twoway ANOVA. CHIsquare test for goodness of fit, Tests of
independence,ContingencyTable,TestsofHomogeneity.
Module 7: Objective and subjective views of statistics, Bayes formula,
frequentistvs.Bayesianinterpretationofprobability,simpleproblemsusing
Bayesian analysis, Nontrivial results using Bayesian Analysis. Stochastic
process, random walk, Markov Processes, Markov chain, Markov matrix,
HiddenMarkovmodel.

Course:MBIN105,ComputationalTechniques

1.BasicConceptsinComputing
1. OverviewandfunctionsofacomputerInputandOutputdevices,
Storagedevices (Harddisk,Diskette, Magnetictape,CDROM,DVD
etc.),Maincircuitboard(Chips,ports,Expansionslots,etc.),Memory
(Register,Buffers,RAM,ROM,PROM,EPROMconcepts.).
2. History of Computers Generation of Computers (I, II, III, IV, V),
Classification of computers
(Mainframe, minicomputers,
microcomputers,Workstations,Servers).
3. IntroductiontoOperatingSystemsConceptofoperatingsystems,
TypesofOperatingsystems(Realtime,Batch,Multiuser,Multitasking,
etc.).
4. Internet and its Resources World Wide Web(www), Associated
tools,servicesandterminologies.
2.TheLinuxOperatingSystem
1. BriefhistoryofLinux.
2. Overview of Linux OS Kernel, Shell, Applications, File system
organization,DesktopslikeGNOME,KDE.
3. LinuxCommandLineUtilitiesGeneralpurposeutilities,Filesystem
navigation,Fieattributesandhandling, Environmentvariables,Shell,
WildcardsandRegularExpression,Filters.
4. BashShellscripting
5. Workingwithvi/vimeditor.
6. System Administration with Reference to Linux File System
Partitions, File system organization, ext2 file system, Inodes, Super
block,Bootblock,Datablock,Mountingotherfilesystems, symbolic
linketc.
7. Usermanagementandremotelogin.
3.PerlProgramming
1. Introduction History, availability, support and use with special
referencetobioinformatics.
2. Scalar data Concept, numbers, strings, operators, variables and
functions.
3. Array and List Data Concept, literal representation, variables,
operatorsandfunctions.
4. Hashes Concept, Literal representation, variables, hash functions
ansslices,HashofHashesandHashofarrays.
5. BasicI/O

6. Regular Expressions Concept, Uses of Regex and Pattern

matching,Operatorandsubstitutions,splitandjoinfunctions.
7. Subroutines Systemanduserfunctions,localoperator,Paramater
list,parameterpassingbyvalueandbyreference.
8.Variouscontrolstructures.
9. FileHandlesansFileTests Concept,OpeningandclosingofFile
Handles,Usingpathandfilenames,Usingfilehandle,die,xFiletests.
10. ProcessManagementUsingsystem,exec,andbackquotes.
11. DataTransformationsFindingsubstring,ExtractingandReplacinga
Substring.
12. FormattingDataSortingandTransliteration.
13. ObjectingOrientedPerlIntroducingtomodules,CreatingObjects.
14. BioperlIntroduction,InstallationproceduresansusesofBioperl.
4.IntroductiontoDatabaseSystems
1.
2.
3.
4.
5.
6.

Conceptsofvarioustypesofdatabases
DataAbstraction
DataModels
InstancesandandSchemes
ERModel
BasicConceptHierarchicalDataModel

5.SQLandMySQL
1.
2.
3.
4.
5.

SelectStatements
DataDefinitionStatements
DataManipulationStatements
DataControlStatements
VariablesandProcedures.

Course:MBIN201;BiomolecularstructureandfunctionII
1.StructuralBiology&StatisticalThermodynamics
Laws ofthermodynamics, concepts ofentropy and free energy, isothermal
andadiabaticprocesses,theCarnotcycle,specificheatsatconstantpressure
andvolume,conceptsofstatisticalthermodynamics,calculationofpartition
functions, rotation about single bonds and intramolecular energy,
conformational entropy of hydrogen bonded molecules, cooperative
phenomena in proteins and DNA, zipper model for helixcoil transitions in
proteins,solutionbehaviorofmacromolecules.

2.StructuralBiology&XRayCrystallography
Translational vectors, unit cell, symmetry operations on crystals: rotation,
reflectionandinversion,pointandspacesymmetrygroups,xraydiffraction
andBragslaw,Millerindices,reciprocallattice,structurefactorsandFourier
transforms,DiffractionpatternforDNA,proteincrystallography,calculationof
bondlengths,bondanglesanddihedralanglesfromproteindatabase(PDB)
files.

3.StructuralBiology&MolecularSpectroscopy
UVvisiblespectroscopyformolecularelectronicspectra:signaltonoiseratio,
inherent line broadening, transition probability and population difference,
Fouriertransformation
Circular dichroism (CD) and optical rotatory dispersion (ORD), the Cotton
effectandtheirapplicationsinstructuralbiology
Nuclear Magnetic Resonance (NMR), chemical shifts, coupling constant,
applicationsof2DNMRinstructuralbiology.
IR & Raman spectroscopy for molecular vibrations and rotations and its
applicationsindeterminationofmacromolecularstructure
Fluorescencespectroscopyanditsapplicationsinstructuralbiology

Course:MBIN203;ComputationalMethodsinBiologyII

NucleicAcidStructure:

WatsonCrickBasePairs.
DoubleHelix.
TripleHelix.
QuadrupletHelix.
DNALigandInteraction.
StructuralfeaturesofADNA,BDNA,ZDNA.
Sequencedirectedstructure[CalldinesRule].
Basepairparameters.

MacromolecularInteraction:

Vanderwaalsforce.
ColumbicForces.
ReceptorLigandinteraction.
MonteCarlosimulation.
GeneticAlgorithm.
Molecularmechanicsforcefield.
Energyminimization(SteepestDescent,Conjugategradient,NR)

DrugDesign
1. Basicconcept
2. DrugDevelopment:Leadmodification
1. Identificationofthetheactivepart:ThePharmacophore
2. Functionalgroupmodification
3. StructureActivityRelationships
4. Structuremodificationtoincreasepotency
Homologation
Chainbranching
RingChaintransformation
Bioisosterism
5.QuantitativeStructureActivityRelationships
Physicochemicalparameters
Electroniceffects:TheHammettEquation
Lipophilicityeffects:ThebasisfortheHanschequation
Stericeffect
Correlationbetweenphysicochemicalparametersandbiological
activity:Hanschequation.

AdvancedStatistics
1.Stochasticprocess,Markovproperties,Markovchains,Markovmatri
ces.HiddenMarkovmodel.Forwardalgorithm,Viterbialgorithm,Baum
Welchalgorithm.
2.MaximumLikelihoodTest;Likelihoodratiotest.MLEestimationfor
univariateGaussiandistribution,PoissondistributionandBinomialdistri
bution.
3.ClusterAnalysis:Hierarchialclustering.Computingmetric,comput
inglinkage.Singlelinkage,completelinkageandaveragelinkageclustering.
4.ClusterAnalysis:kmeansclustering.Convergenceofthealgorithm.
Weaknessofkmeansclustering.
5.PrincipalComponentAnalysis:Changeofbasis;Varianceofnoisy
data,Reductionofdimension;Diagonalizationofcovariancematrix.
6.SingularValueDecomposition:Fullsingularvaluedecomposition;
Reducedsingularvaluedecomposition.

Course:MBIN204;ProteomicsandGenomics
Modern concepts of metabolomics, genomics, proteomics, functional
genomics, systems biology. Wholistic concepts of Omics. Overview of
technologies,drivingworkintheseareas.
ProblemsrelatedtogenomesinBiology:Cvaluepradox,genomeassembly,
genome evolution, comparative genomics synteny, gene detection,
conservation, gene volatility, linkage, SNP, alternate splicing. General
applicationusingNeuralNetworks.
Regulatory signals on genome: promoters, attenuators, terminators,
riboswitches.
Functionalsignaturesingenomes:repeates,epigenetics
Transcriptomics: basic concepts and technology, data normalization,
clustering (Hierarchical, kmeans, SOM), detection of over expression and
underexpression(PCA).ModelingusingBooleanNetworks.EST,Unigene.
Proteomics: limitations and advantages over transcriptomics, outline of a
typical proteome experiment, example applications of proteomics
technologies, mass spectrometry different instrumental configuration,
its advantages in terms of accuracy and sensitivity, spectra
deconvolution, tandem mass spectrometry peptide sequencing using de
novo
and database search (different ion nomenclatures, scoring), outline of
quantitativeproteomicsexperiment
Structural proteomics: fundamentals of protein/peptide structure,
energetics (including Poisson Boltzmann Equation). Molecular mechanical
energy functions and force fields, Monte Carlo, Simulated Annealing,
GeneticAlgorithm,Introductiontomoleculardynamicssimulation.

Course:MBIN205;

IntellectualPropertyRightsLaw
Module1:GeneralOverviewofIntellectualPropertyIntroductioninrem:
NatureandObjectivesofIntellectualpropertyAGeneralOverview,
JustificationsforProtectionandHistoricalPerspectives,BasicPrinciplesand
AcquisitionofIPRs
Module2:IndustrialProperty:Patents,Designs
Module3:IndustrialProperty:Trademarks,GeographicalIndications,Trade
SecretsandRoleofUnfairCompetitionwithpracticalexamples
Module4:ProtectionofCopyrightsandRelatedRights(National&
InternationalRegimes)
Module5:SemiconductorsIntegratedCircuitsLayoutDesignsandLayout
DesignsTopography
Module6:ContemporaryIntellectualPropertyIssues
Module7:OwnershipandEnforcementofIntellectualPropertyRights
Module8:Nanotechnology&IPRs:ACorporateOverviewintheIndian
PerspectivethroughPrimarySourceMaterials
CasesandStatutes:

Course:MBIN292;

Computerlanguage
ProcedureorientedProgrammingusingC

Cbasics
o Variables,Constant,Datatypes,Keywords

Logicalordecisionmakingblock
o If
o Ifelse
o Nestedifelse
o Ifelseladder
o Switchcase

Repetitionofsameprocess:Loops
o Whileloops
o DoWhileloops
o Forloops

Array
o Typeofarray,Declarationofarray,creationofarray
o Onedimensionalarray
o Twodimensionalarray
o Matrixcreationandmanipulationandcalculationusingarray

Functions
o Types,need,features
o Libraryfunction
o Userdefinedfunction
o Returnableandnonreturnablefunction

Structures
o Creation,Declaration
o DifferencebetweenArrayandStructure
o ArrayofStructure

Pointers
o Importanceanduses
o Differencebetweenpointerandarray
o Structureusingpointer
o Memoryhandling

ObjectorientedProgrammingusingJAVA

JavaBasics
o

AnIntroductiontoJavaProgramming

ObjectOrientedProgrammingandJava

Arrays,Conditionals,andLoops

CreatingClassesandApplicationsinJava
o

MoreAboutMethods
o MainMethod
o

Userdefined

AbstractMethod

Packages
o Whatispackages
o

WorkingwithObjects

TypesofPackages

Inheritance
o WhatisInheritance
o

TypesofInheritance

Extendskeyword

Interfaces
o

WhyInterface

WhatisInterface

Implementskeyword

ExceptionHandling
o

ErrorandException

TypesofExceptions

Try,Catch,Finallyblock

Multithreading
o WhatisThreading
o

NeedandPurposeofThreading

CreatingThreads

ThreadLifeCycle

ManagingThreadsfromonestatetoanother

Applet
o AppletLifeCycle
o

Graphics,Fonts,andColor

SimpleAnimationandThreads

ImagesandThreads

PHP
1. BasicHTML
Introduction,HTMLTags,HTMLdocuments/WebPages,Elements,
ElementSyntax,Attributes,Headings,Paragraphs,Lines,Comments,
Line break, Text Formatting bold, italics, font, color, size etc.,
Background,HTMLlinks,hyperlinks,Images,Tables,Lists,Forms
variousobjects/elementsandtheirattributesinformsliketext,text
area,radio,checkbox,buttonsubmit,optionetc.
2. Brief Overview of Web servers, Web Browsers and Apache HTTP
server.
3. IntroductiontoPHP
What is PHP?, requirements, Why PHP? Basic PHP syntax, tag,
Comments in PHP, variables, different operators(arithmetic,
assignment,comparison,logicalandconcatenation).
4. PHPConditionalStatements
if,if...else,if...elseif...else,Nestedif...else,SwitchStatement.
5. PHParray
Numeric,Associative,Multidimensionalarray.Creation,Assignvalues,
retrievevaluesandDynamiccreation.

6. PHPLoops
while,do...while,for,foreach
7. PHPformhandling.
8. PHPfunctions
Declaringfunctions,Addingparameters,Returningvalues.
9. WorkingwithPHP$_GET,$_POST,$_SELF.
10. Usingvariousbuiltinfunctions
array_pop(), array_push(), array_reverse(),
array_unshift(),sort,print,printf,split,join,strlen,substr.
11. PHPMySQL
Connect,Create,Insert,Selectetc.

array_shift(),