BIOINFO SYlubs

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
Duration of
Exam in Hours
Marks for
Total
Marks Lecture
Practical/
Field Work/
Assignment/
Tutorials
I.A. Exam
12BBI11B
12BBI11C
$Data Structures in C & C++ /
$$ Biomolecules, Molecular Biology and
Genetic Engineering
4 2# 3 50 100 150
12BBI12
Statistical & Probabilistic methods for
Bioinformatics
4 2# 3 50 100 150
12BBI13 Essential Bioinformatics 4 2* 3 50 100 150
12BBI14 Biomolecular Modeling & Simulation 4 2* 3 50 100 150
12BBI15X Elective I 4 2 3 50 100 150
12BBI16 Seminar -- 3 -- 50 -- 50
Total 20 13 15 300 500 800

Elective I
12BBI151 DNA Chips & Microarray Data Analysis
12BBI152 Computational Biology
12BBI153 Health Informatics
$ Not for CSE & ISE students $$ Not for Biotechnology Students
M.Tech Full Time Scheme [New] Page 1
II Semester
Subject
Code
Name of the Subject
Teaching hours/week
Duration of
Exam in Hours
Marks for
Total
Marks Lecture
Practical/
Field Work/
Assignment/
Tutorials
I.A. Exam
12BBI21 Genomics & Proteomics 4 2* 3 50 100 150
12BBI22 Systems Biology 4 2# 3 50 100 150
12BBI23 Data Warehousing & Data Mining 4 2# 3 50 100 150
12BBI24 JAVA & J2EE 4 2* 3 50 100 150
12BBI25X Elective II 4 2 3 50 100 150
12BBI26 **Project Phase-I(6 week Duration)
12BBI27 Seminar -- 3 -- 50 -- 50
Total 20 13 15 300 500 800

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.
III Semester
Subject
Code
Name of the Subject
Teaching hours/week
Duration of
Exam in Hours
Marks for
Total
Marks Lecture
Practical/
Field Work/
Assignment/
Tutorials
I.A. Exam
12BBI31 Research Methodology 4 -- 3 50 100 150
12BBI32X Elective-III 4 2 3 50 100 150
12BBI33X Elective-IV 4 2 3 50 100 150
12BBI34 Project Phase II $
12BBI35 Evaluation of Project Phase I -- 3 -- 50 -- 150
Total 12 07 09 200 300 500

Elective III Elective - IV
12BBI321 Artificial Intelligence 12BBI331 Database Management & Grid Computing
12BBI322 Neuroinformatics 12BBI332 BioPerl, BioPython & NCBI C++ Toolkit
12BBI323 Java for Bioinformatics & Biomedical Application 12BBI333Bioinformatics in Drug Design & Discovery
$ 3 Days Course work and 3 days for Project work

IV Semester
Subject
Code
Name of the Subject
Teaching hours/week
Duration of
Exam in Hours
Marks for
Total
Marks Lecture
Practical/
Field Work/
Assignment/
Tutorials
I.A. Exam
12BBI41 Evaluation of Project Phase II -- -- 3 50 -- 50
12BBI42 Evaluation of Project work III -- -- 3 50 -- 50
12BBI43
Project work evaluation and
Viva-voce
-- 3 3 -- 100+100 200
Total -- 03 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.

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).
1

Data Structures in C & C++
Subject Code : 12BBI11B IA Marks : 50
No. of Lecture Hrs./Week : 04 Exam Hrs : 03
Total No. of Lecture Hrs. : 52 Exam Marks : 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
2

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.

3

Biomolecules, Molecular Biology & Genetic Engineering
Subject Code : 12BBI11C IA Marks : 50
No. of Lecture Hrs./ Week : 04 Exam Hrs : 03
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 non-
homologous, 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,
4

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, 6
th

Edition, 2001.
2. Lewin B. Genes IX, Jones and Bartlett Publications, 2008.
3. Lodish et al. Molecular Cell Biology, ? 6
th
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.

5

Statistical & Probabilistic Methods for Bioinformatics
Subject Code : 12BBI12 IA Marks : 50
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, r-
Scans. 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,
6

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.

7

Essential Bioinformatics
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
8

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. Sequence retrieval from nucleic acid and protein databases.
2. Retrieval of information about structure, bioassay, physical and
Chemical properties of chemical compounds (such as Drugs and
naturally occurring compounds).
3. Gene sequence assembly and contig mapping and identification of
Gene.
4. Sequence searches using FASTA and BLAST.
5. Phylogenetic analysis.
6. Prediction of secondary structure for given protein and RNA
sequences.
9

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

10

Biomolecular Modeling & Simulation
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
11

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, Self-
Assembly 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.

12

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

13

DNA Chips & Microarray Data Analysis
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 agro-
industry; 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 large-
scale structures. Strand algebras for DNA computing Introduction, Strand
14

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.

15

Computational Biology
Introduction to Computational biology: Introduction, scope and
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
16

- 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 IMGT-
GENE-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.
17

Health Informatics
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:
18

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.

19

Seminar
Field work/Assignment
Hrs./Week
: 03

Seminar Mechanism

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

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%)
20

Genomics & Proteomics
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, Mass-
Spectroscopy 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.
21

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 R-
SNP 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.
22

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. Virtual sequencing (base calling, Sequence assembly, Mapping
assembly, Contig mapping)
2. Analysis of next generation sequencing data
3. Genome annotation.
4. Structure and sequence detection.
5. Study of vector and virtual subcloning
6. Chromatographic data analysis.
7. Chromatogram sequence alignment and editing.
8. CGH and Genotype Array Analysis.
9. 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.
23

Systems Biology
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.

24

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.

25

Data Warehousing & Data Mining
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.

26

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.
27

JAVA & J2EE
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, Producer-
Consumer 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.
28

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.

JAVA & J2EE Lab
1. Design, Write and Execute Java Program that illustrate Constructor
and Method overloading.
2. Design, Write and Execute Java Program that implement inner class
and demonstrate its Access Protections.
3. Write a Java Program to create an interface and implement it in a
class.
4. 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.
5. 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)
6. 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).
7. Design, Write and Execute Java Program that illustrate Exception
Handling (Using Nested try catch and finally).
8. Write a Program to construct the phylogenetic tree using sequential
clustering by reading input distance matrix.
9. Write a Java program to Implement Dynamic Programming for
sequence alignment.
29

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.

30

Chemoinformatics
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.

31

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.

32

Parallel & Distributed Computing
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 High-
Performance 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.
33

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.
34

Cellular Neural Networks & Visual Computing
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.
35

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.

36

Seminar
Field work/Assignment
Hrs./Week
: 03

Seminar Mechanism

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

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%)
37

Artificial Intelligence
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 Stem-
Loops 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.
38

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.

39

Neuroinformatics
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
40

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.

41

Java for Bioinformatics & Biomedical Application
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.
42

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.

43

Database Management & Grid Computing
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: NBRF-
PIR, 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.
44

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.

45

BioPerl, Biopython & NCBI C++ Toolkit
BioPerl:
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, goto
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.
46

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

47

Bioinformatics in Drug Design & Discovery
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, Non-
Enumerative 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
48

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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