PONDICHERRY UNIVERSITY

SCHOOL OF LIFE SCIENCES Centre for Bioinformatics SYLLABUS FOR M. Sc. BIOINFORMATICS
(Academic Year 2010-2011 onwards)

Course Code Semester I BINF 411 BINF 412 BINF 413 BINF 414 BINF 415 BINF 416 BINF 417 BINF 418 BINF 419 BINF 461 BINF 462 BINF 463 BINF 464 BINF 465 Semester II BINF 431 BINF 432 BINF 433 BINF 434 BINF 435 BINF 436 BINF 466 BINF 467 BINF 468 Semester III BINF 511 BINF 512 BINF 513 BINF 514 BINF 515 BINF 516 BINF 517 BINF 561 BINF 562 BINF 563 Semester IV BINF 531 BINF 532 BINF 533 BINF 534

Course Title Cell and Molecular Biology Bioinformatics Databases C and Data Structures General Physics General Chemistry General Mathematics General Biology Basics of Computer Introduction to Bioinformatics* Lab - Cell and Molecular Biology Lab - Biological Databases Lab - Basics of Computer & Operating Systems Lab - Programming in C/ C++ Lab - Bioinformatics databases and tools* Genomics and Proteomics Bioinformatics: Sequence Analysis Probability and Statistics Programming in Java Database Management System Fundamentals of Algorithms Lab - Programming in Java Lab Programming in DBMS Lab - Biosequence Analysis Structural Biology Molecular Modeling and Drug Design Programming in Perl Systems Biology Fundamentals of Spectroscopy Data Communication and Networks Finishing School Lab - Structural Biology Lab - Molecular Modeling and Drug Design Lab - Programming in Perl Analytical Biophysics Bioethics, Biodiversity and Intellectual Property Rights Scientific Presentation Project

H/S H H H S S S S S S H H H H S H H S H H S H H H H H H H S H H H H H S H H H

Credits 3 3 3 2 2 2 2 2 3 1 1 1 1 1 3 3 2 3 3 2 1 1 1 3 3 3 3 2 2 2 1 1 1 2 3 2 8

* for other department students

BINF 411 - CELL AND MOLECULAR BIOLOGY Total Credits: 3 Total: 36 Hrs.

Unit 1 6 Lectures Molecules of life - structural organization of prokaryotic and eukaryotic cells- Concept of a composite cell and Molecular composition of cells. Biomembranes- Structural organization Models of a plasma membrane, Membrane permeability - Transport across cell membranes Transmembrane signals - Artificial membranes - liposome. Unit 2 7 Lectures Mitochondrial Genome, Structure and Function Oxidative Metabolism in the Mitochondrion The Role of Mitochondria in the formation of ATP Translocation of Protons and the Establishment of a proton-motive force The Machinery for ATP formation Peroxisomes. Genome studies of Mitochondria. Unit 3 7 Lectures Chloroplast structure and function An overview of photosynthetic Metabolism The absorption of light Photosynthetic units and reaction centers Photophosphorylation Carbondioxide fixation and the synthesis of carbohydrates. Chloroplast and its genome study. Unit 4 7 Lectures Cellular Organelles Cytoskeleton components of Cytoskeleton, Microtubules, Intermediate filaments Microfilaments, Endoplasmic reticulum, Golgi complex, Types of m,\vesicles - transport and their functions, Lysosomes. Nucleus - Internal organization, Nuclear pore complex, Nucleosomes, Chromatin. Unit 5 9 Lectures DNA and Protein Synthesis - Structure of DNA - evidence for DNA as genetic material. Gene transfer in microorganisms conjugation, transformation, transduction - protoplasmic fusion. The genomes of bacteria, viruses, plasmids. DNA Structural organization - DNA replication, Transcription mRNA processing, Translation. Protein synthesis Ribosomes, enzymes, Protein processing, Introduction to the methods of DNA sequencing Text Book: 1. Cell and Molecular Biology Concepts and Experiments by Gerald Karp, 2008, Wiley International Student Version Reference Books: 1. Genes VIII (8th Ed.) by Lewin, B, 2004, Pearson Education International. 2. Cell and Molecular Biology by De Robertes and De Robertis, 2002, Saunders College, Philadelphia, USA.

BINF 412 - BIOINFORMATICS DATABASES Total Credits: 3 Total: 36 Hrs.

Unit 1 6 lectures Introduction: Aim and branches of Bioinformatics, Application of Bioinformatics, Role of internet and www in bioinformatics. Basic biomolecular concepts: Protein and amino acid, DNA & RNA, Sequence, structure and function. Forms of biological information, Types of Nucleotide Sequence: Genomic DNA, Complementary DNA (cDNA), Recombinant DNA (rDNA), Expressed sequence tags (ESTs), Genomic survey sequences (GSSs). DNA sequencing methods: Basic and Automated DNA sequencing, DNA sequencing by capillary array and electrophoresis, Gene expression data. Unit 2 8 lectures Bioinformatics Resources: NCBI, EBI, ExPASy, RCSB, DDBJ: The knowledge of databases and bioinformatics tools available at these resources, organization of databases: data contents, purpose and utility. Open access bibliographic resources and literature databases: PubMed, BioMed Central, Public Library of Sciences (PloS), CiteXplore. Bioinformatics Resources at the species level, ICTV Database, AVIS, VirGen, Viral genomes at NCBI, VBRC, VBCA, PBRC and Subviral RNA database, Species 2000, TreeBASE etc Unit 3 8 lectures Sequence databases: Nucleic acid sequence databases: GenBank, EMBL, DDBJ; Protein sequence databases: Uniprot-KB: SWISS-PROT, TrEMBL, UniParc; Repositories for high throughput genomic sequences: EST, STS GSS, etc.; Genome Databases at NCBI, EBI, TIGR, SANGER Viral Genomes; Archeal and Bacterial Genomes; Eukaryotic genomes w.r.t model organisms (Yeast, Drosophila, C. elegans, Rat, Mouse, Human, Arabidopsis thaliana, Rice, etc.). Querying and retrieval; Unit 4 8 lectures Structure and Derived Databases: Structure Databases: PDB, NDB, PubChem, ChemBank. Derived Databases: Basic concept of derived databases, sources of primary data and basic principles of the method for deriving the secondary data, organization of data, contents and formats of database entries, identification of patterns in given sequences and interpretation w.r.t the Sequence databases: InterPro, Prosite, Pfam, ProDom; Structure databases: FSSP, DSSP Unit 5 6 lectures Sequence file formats: Various file formats for bio-molecular sequences: GenBank, FASTA, GCG, MSF etc. Extraction of knowledge from resources: Immunology, Plant, animal and infectious diseases: databases and servers published in the NAR Database and Web server Issues and other Bioinformatics journals viz. BMC Bioinformatics etc. Protein and nucleic acid properties: Proteomics tools at the ExPASy server, GCG utilities and EMBOSS, Computation of various parameters Text Books: 1. Bioinformatics: Sequence and Genome Analysis by Mount D., 2004, Cold Spring Harbor Laboratory Press, New York. 2. Bioinformatics- a practical guide to the analysis of Genes and Proteins by Baxevanis, A.D. and Francis Ouellellette, B.F., 1998, John Wiley & Sons, UK. 3. Introduction to bioinformatics by Teresa K. Attwood, David J. Parry-Smith, 1999, Pearson Education.

BINF 413 C AND DATA STRUCTURES Total Credits: 3 Total: 36 Hrs.

Unit 1 6 lectures Introduction to programming languages: Introduction Programming languages Problem solving Technique: Algorithm, Flowchart, Compilation, Testing and Debugging, Documentation Data structures Array, Stack, Queue, Linked List concepts Unit 2 10 lectures Programming in C: C language Introduction Tokens Keywords, Identifier , Variables, Constants, Operators Expression Data types Operator precedence - Statement: Input statement, Output statement, Conditional and Unconditional Control Statement Looping Statement: while, do-while, for nested loop Arrays. Unit 3 7 lectures Procedural Concept: Structured Programming Built-in library function User defined functions Pointer introduction Passing pointer in a function Structure Union File handle: Read and Write character from a file Unit 4 6 lectures String Handling & Sorting: String declaration String library functions - String Manipulation - Sorting: Bubble sort, Selection sort, Insertion sort Searching: Linear search, Binary search Unit 5 7 lectures Object Oriented Programming: Programming in C++: C++ programming Object Oriented Concept: Encapsulation, Inheritance, Polymorphism Different forms of Constructor Destructor Abstract class Virtual function

Text Books: 1. Programming in ANSI C (4th Ed.) by E. Balagurusamy, 2007, Tata McGrawHill Publishing Company Limited. 2. Object Oriented Programming using C++ by Lafore, R. (4th Ed.), 2002, Sams Publishers.

BINF 414 - GENERAL PHYSICS Total Credits: 2 Total: 24 Hrs.

Unit 1 4 lectures Mechanics: Motion in 1D: Position, Velocity, and Speed. Instantaneous Velocity and Speed. Acceleration. Motion Diagrams. 1D Motion with Constant Acceleration. Freely Falling Objects. Kinematic Equations Derived from Calculus. Motion in 2D: The Position, Velocity, and Acceleration Vectors. 2D Motion with Constant Acceleration. Projectile Motion. Uniform Circular Motion. Relative Velocity and Relative Acceleration. The Newton's Laws of Motion and applications: Newton's First Law and Inertial Frames. Mass. Newton's Second Law. The Gravitational Force and Weight. Newton's Third Law. Forces of Friction. Newton's Second Law Applied to Uniform Circular Motion. Nonuniform Circular Motion. Motion in Accelerated Frames. Motion in the Presence of Resistive Forces. Unit 2 5 lectures Thermodynamics: Zeroth Law of thermodynamics: Equilibrium, State functions, temperature, Equations of State, First law of thermodynamics: Work, Heat, Internal Energy, Heat Capacity, Internal Energy, First Law of thermodynamics, Concept of Enthalpy. Second law of thermodynamics: Reversible and Irreversible Processes, Heat Engines, Carnot Cycle, Second Law statements, Spontaneous change, Entropy. Free Energy and Standard States: Free Energies and Thermodynamic potentials, Equilibrium, concepts of pH, pK, Chemical Potentials, Third Law of thermodynamics, Standard States, Reaction Thermodynamics, Equilibrium constant. Unit 3 5 lectures Electricity: Electric Fields: Properties of Electric Charges. Coulomb's Law. The Electric Field. Electric Field of a Continuous Charge Distribution. Motion of Charged Particles in a Uniform Electric Field. Gauss's Law: Electric Flux. Gauss's Law and its application to various charge distributions. Conductors in Electrostatic Equilibrium. Electric Potential: Potential Difference and Electric Potential. Potential Differences in a Uniform Electric Field. Electric Potential and Potential Energy Due to Point Charges. Electric Field from the Electric Potential. Electric Potential Due to Continuous Charge Distributions, Charged Conductor. Unit 4 5 lectures Magnetism: Magnetic Fields: Magnetic Field and Forces. Magnetic Force Acting on a CurrentCarrying Conductor. Torque on a Current Loop in a Uniform Magnetic Field. Motion of a Charged Particle in a Uniform Magnetic Field. Charged Particles Moving in a Magnetic Field. The Hall Effect. Sources of Magnetic Field: The Biot-Savart Law. Magnetic Force Between Two Parallel Conductors. Ampere's Law. Magnetic Field of a Solenoid. Magnetic Flux. Gauss's Law. Displacement Current and Ampere's Law. Faraday's Law: Faraday's Law of Induction. Motional emf. Lenz's Law. Induced emf and Electric Fields. Generators and Motors/ Eddy Currents. Unit 5 5 lectures Optics: The Nature of Light: Reflection. Refraction. Huygens's Principle. Dispersion and Prisms. Total Internal Reflection. Fermat's Principle. Images Formed by Flat Mirrors, Spherical Mirrors, Refraction. Interference: Conditions for Interference. Young's Double-Slit Experiment. Intensity Distribution of the Double-Slit Interference Pattern. Phasor Addition of Waves. Change of Phase Due to Reflection. Interference in Thin Films. Diffraction Patterns and Polarization: Introduction to Diffraction Patterns. Diffraction Patterns from Narrow Slits. Resolution of Single-Slit and Circular Apertures. The Diffraction Grating. Diffraction of X-rays by Crystals. Polarization of Light Waves. Text Books: 1. Physics for Scientists and Engineers (6th Ed.) by Raymond A. Serway, John W. Jewett, 2004, Thomson Brooks/Cole. 2. Physics for Scientists and Engineers (6th Ed.) by Paul A. Tipler, Gene P. Mosca, 2007, Freeman Company 3. Fundamentals of Physics (6th Ed.), Resnick, Halliday and Walker, 2001, John Wiley and Sons, USA

BINF 415 - GENRAL CHEMISTRY Total Credits: 2 Total: 24 Hrs.

Unit 1 5 Lectures Atomic and Molecular Structure: Atomic Structure - Elements and compounds, atoms and molecules-definition, . Classical atomic models - J. J. Thomson, E. Rutherford, N. Bohr. Quantum mechanical model. Electronic configuration - aufbau principle - Pauli exclusion principle - Hund's rule Modern periodic table, periodicity. Chemical bonds - ionic bonding - covalent bonding - Coordinate covalent bonding. Overlapping of atomic orbital to form and bond with example. Meaning and Difference between and bonds hybridization, resonance. Bond properties. Molecular geometry. Intermolecular forces Unit 2 5 Lectures Symmetry and Principles: Definitions and theorems of group theory, subgroups, Classes. Molecular symmetry and symmetry groups symmetry elements and operations. Symmetry planes, reflections, inversion centre, proper/ improper axes of rotation, symmetry elements and optical isomerism, symmetry point groups, classes of symmetry operations, classification of molecular point groups. Unit 3 5 Lectures Introduction to Organic chemistry: Carbon and its compounds, Position of Carbon in periodic table, tetra covalency of carbon, catenation, functional groups, formal charge, oxidation number, aromaticity, electrophiles and nucleophiles, organic acids and bases, types of organic reactions. Unit 4 5 Lectures Stereochemistry: Concept of isomerism, types of isomerism, optical isomerism, elements of symmetry, molecular chirallity, enantiomers, stereogenic centres, optical activity, properties of enantiomers, chiral and achiral molecules with two stereogenic centres, distereoisomers, mesocompounds, resolution of enantiomers. Relative and absolute configurations, sequence rules, D & L , R & S systems of nomenclature. Unit 5 4 Lectures Heteroaromatics: Five membered and six membered hetero aromatics with one and two hetero atoms and their benannulated analogues, Nucleic acid bases, Structure, name and properties like acid base property, electron rich electron deficient heterocycles, hydrogen bonding etc. (Synthesis and reactions not necessary). Text Books: 1. Organic Chemistry (6th Ed.) by Paula Yurkanis Bruice, 2010, Prentice Hall 2. Virtual textbook of Organic chemistry, http://www.cem.msu.edu/~reusch/VirtTxtJml/intro1.htm

BINF 416 - GENERAL MATHEMATICS Total Credits: 2 Total: 24 Hrs.

Unit I 4 lectures Determinants and Matrices- Properties of Determinants, Minors and Cofactors, Multiplication of Determinants, Adjoint, Reciprocal, Symmetric Determinants, Cramers rule, Different types of matrices, Matrix Operations, Transpose of a matrix, Adjoint of a square matrix, Inverse of a matrix, Eigen values and eigen vector Unit II 4 lectures Vector Analysis: The concept of a Vector, Vector addition and subtraction, Products of two vectors-Dot product and Cross product, Products of three vectors- scalar triple product and vector triple product, Gradient, Divergence and Curl. Unit III 5 lectures Trigonometry and Analytical Geometry: Trigonometric ratios, De Moivres theorem, The general equation of a Straight line, slope of a line, intercepts of a line, Angle between two lines, Intersection of two lines, The general equation of a Circle. Unit IV 6 lectures Calculus: Differential Calculus- Derivative of a function, Concept of limit, Continuity, Differentiation, Maxima and Minima of a function, Introduction to Partial Differentiation, Integral Calculus: The Idea of the Integral, The Definite Integrals, Indefinite Integrals. Unit 5 5 lectures Numerical Methods: Solution of algebraic and transcendental equations: Bisection method, Method of false position / Regula-falsi method, Newton-Raphson method, Approximate solution of equations - Horners method Text Books: 1. Algebra (3rd Ed.) by Serge A. Lang, 2003, Pearson education. 2. Introduction to Calculus & Analysis, Vol I and II by Richard Courant & Fritz John, 1999, Springer publisher. 3. Trignometry, Algebra and Calculus (3rd Ed.) by Veerarajan, T., 2003, Tata McGraw Hill Publishing Co. Ltd, New Delhi. Reference Books: 1. Basic mathematics by Serge A. Lang, 1988, Springer publisher 2. A First Course in Calculus by Serge A. Lang, 1986, Springer publisher 3. Higher Engineering Mathematics (40th Ed), by B.S. Grewal and J.S. Grewal, 2007, Khanna Publishers, New Delhi.

BINF 417 - GENERAL BIOLOGY Total Credits: 2 Total: 24 Hrs.

Unit 1 4 Lectures Diversity in Living World: Diversity of living organisms-Classification of the living organisms (five kingdom classification, major groups and principles of classification within each kingdom). Systematics and binomial System of nomenclature - Salient features of animal (non-chordates up to phylum level and chordates up to class level) and plant (major groups; Angiosperms up to class) classification, viruses, viroids, lichens Botanical gardens, herbaria, zoological parks and museums. Unit 2 4 Lectures Structural Organisation in Animals and Plants : Tissues in animals and plants. Morphology, anatomy and functions of different parts of flowering plants: Root, stem, leaf, inflorescence, flower, fruit and seed. Morphology, anatomy and functions of different systems of an annelid (earthworm), an insect (cockroach) and an amphibian (frog). Unit 3 5 Lectures Cell: Structure and Function: Cell: Discovery of the cells - Cell theory; Prokaryotic and eukaryotic cell, cell wall, cell membrane and cell organelles' (plastids, mitochondria, endoplasmic reticulum, Golgi bodies/dictyosomes, ribosomes, lysosomes, vacuoles, centrioles) and nuclear organization. Mitosis, meiosis, cell cycle.Basic chemical constituents of living bodies.Structure and functions of carbohydrates, proteins, lipids and nucleic acids.Enzymes: types, properties and function. Unit 4 6 Lectures Genetics and Evolution: Mendelian inheritance. Chromosome theory of inheritance, deviations from Mendelian ratio (gene interaction- incomplete dominance, co-dominance, multiple alleles). Sex determination in human beings: XX, XY. Linkage and crossing over. Inheritance pattern : Mendelian disorders and chromosomal disorders in humans. DNA and RNA, search for genetic material, replication, transcription, genetic code, translation. Gene expression and regulation. Genome and Human Genome Project. DNA fingerprinting. Evolution: Origin of life, theories and evidences, adaptive radiation, mechanism of Evolution, origin and evolution of man. Unit 5 5 Lectures Methods in Biology: Light Microscope Transmission Electron Microscopy Scanning Electron and Atomic Force Microscopy Fractionation of Cell contents by Differential Centrifugation Purification of Nucleic Acids Enzymatic amplification of DNA by PCR DNA Sequencing. Text Book: 1. Molecular Biology of the cell (4th Ed.) by Bruce Alberts, 2002, Garland publishing Inc. Reference Books: 1. Cell - A molecular approach (2nd Ed.) by Cooper. G. M., 2000, Oxford University Press 2. Cell and Molecular Biology by De Robertes and De Robertis, 2002 Saunders College, Philadelphia, USA.

BINF 418 - BASICS OF COMPUTER Total Credits: 2 Total: 24 Hrs.

Unit 1 5 Lectures Computer Organization Fundamentals of computers Block diagram of computer (input and output devices) History - Generations Memory devices - Advantages and Limitations of Computers Comparision of different operating systems DOS, Windows NT & XP, Application Softwares. Unit 2 5 Lectures Network Basics Communication Technology Networking Elements: Networking Hardware, Networking services: Types of Networks LAN, WAN & MAN, IntranetWireless communication Internet services, Uses of Internet Unit 3 4 Lectures Introduction to Database systems Fundamentals of database - Database models (Hierarchical, Network, Relational and ObjectOriented Models) RDBMS: Relational Database Management systems - Database System Applications and Security. Unit 4 5 Lectures Programming Language Algorithm Flowchart Programming language Compiling and Linking Testing and Debugging Documentation Maintenance - Utility programs. Unit 5 5 Lectures Internet Technologies Web Services WWW, URL, Servers: Client/ Server essentials - Domain Name Server, FTP server, E-mail server, WEB servers, Web publishing-Browsers-IP Addressing, IPV6 Text Books: 1. Basic Computer Skills made easy, by Sherman, J., 2001 Butterworth-Heinemann Ltd, USA 2. Computer Fundamentals and Applications (2nd Ed.) by Balaguruswamy, E., 1985, Tata McGraw-Hill Publishing Co. Ltd., India. 3. Microsoft Office Manual

BINF 419 - INTRODUCTION TO BIOINFORMATICS Total Credits: 3 Total: 36 Hrs.

Unit 1 6 lectures Introduction: Aim and branches of Bioinformatics, Application of Bioinformatics, Role of internet and www in bioinformatics. Basic biomolecular concepts: Protein and amino acid, DNA & RNA, Sequence, structure and function. Forms of biological information, Types of Nucleotide Sequence: Genomic DNA, Complementary DNA (cDNA), Recombinant DNA (rDNA), Expressed sequence tags (ESTs), Genomic survey sequences (GSSs). DNA sequencing methods: Basic and Automated DNA sequencing, DNA sequencing by capillary array and electrophoresis, Gene expression data. Unit 2 7 lectures Bioinformatics Resources: NCBI, EBI, ExPASy, RCSB, DDBJ: The knowledge of databases and bioinformatics tools available at these resources, organization of databases: data contents, purpose and utility. Open access bibliographic resources and literature databases: PubMed, BioMed Central, Public Library of Sciences (PloS), CiteXplore. Unit 3 7 lectures Sequence databases: Nucleic acid sequence databases: GenBank, EMBL, DDBJ; Protein sequence databases: Uniprot-KB: SWISS-PROT, TrEMBL, UniParc; Structure Databases: PDB, NDB, PubChem, ChemBank. Sequence file formats: Various file formats for biomolecular sequences: GenBank, FASTA, GCG, MSF etc. Protein and nucleic acid properties: Proteomics tools at the ExPASy server, GCG utilities and EMBOSS, Computation of various parameters Unit 4 8 lectures Sequence Analysis: Basic concepts of sequence similarity, identity and homology, definitions of homologues, orthologues, paralogues and xenologues Scoring matrices: basic concept of a scoring matrix, Matrices for nucleic acid and proteins sequences, PAM and BLOSUM series, matrix derivation methods and principles. Unit 5 8 lectures Sequence alignment: Measurement of sequence similarity; Similarity and homology. Pairwise sequence alignment: Basic concepts of sequence alignment, Needleman and Wunsch, Smith and Waterman algorithms for pairwise alignments, gap penalties, use of pairwise alignments for analysis of Nucleic acid and protein sequences and interpretation of results. Text Books: 1. Bioinformatics: Sequence and Genome Analysis by Mount D., 2004 Cold Spring Harbor Laboratory Press, New York. 2. Bioinformatics- a practical guide to the analysis of Genes and Proteins by Baxevanis, A.D. and Francis Ouellellette, B.F., 1998, John Wiley & Sons, UK. Reference Book: 1. Introduction to bioinformatics by Teresa K. Attwood, David J. Parry-Smith, 1999, Pearson Education.

BINF 461 - LAB - CELL AND MOLECULAR BIOLOGY Total Credits: 1 Exercises in Cell Biology Paper Chromatography of Chlorophyll pigments Estimation of Chlorophyll Ascorbic acid estimation in different tissues of plants and animals. Growth curve of Bacteria. Estimation of cell mass of bacteria. Exercises in Molecular Biology Isolation & Purification of genomic DNA from bacteria Isolation & Purification of plasmid DNA Agarose gel electrophoresis of chromosomal & plasmid DNA Restriction Digestion of chromosomal & plasmid DNA Isolation of DNA fragment from agarose gel

BINF 462 - LAB - BIOLOGICAL DATABASES Total Credits: 1 Exercises: 1. Bioinformatics Resources : NCBI, EBI, DDBJ, RCSB, ExPASy 2. Open access bibliographic resources and literature databases a. PubMed b. BioMed Central c. Public Library of Sciences (PloS) d. CiteXplore. 3. Bioinformatics Resources at the species level a. ICTV Database b. AVIS c. VirGen d. Viral genomes at NCBI, VBRC, VBCA, PBRC and Subviral RNA database, Species 2000, TreeBASE etc 4. Sequence databases: a. Nucleic acid sequence databases: GenBank, EMBL, DDBJ; b. Protein sequence databases: Uniprot-KB: SWISS-PROT, TrEMBL, UniParc; c. Repositories for high throughput genomic sequences: EST, STS GSS, etc.; d. Genome Databases at NCBI, EBI, TIGR, SANGER 5. Structure Databases: PDB, NDB, PubChem, ChemBank, FSSP, DSSP 6. Derived Databases: InterPro, Prosite, Pfam, ProDom 7. Sequence file formats: GenBank, FASTA, GCG, MSF etc. 8. Protein and nucleic acid properties: Proteomics tools at the ExPASy server, GCG utilities and EMBOSS

BINF 463 - LAB BASICS OF COMPUTER & OPERATING SYSTEMS Total Credits: 1 Exercises: 1. DOS Commands - Internal Commands: Viewing a directory, Changing Directory, Renaming a Directory - File operations: Creating files, removing a file, renaming files, viewing a file - External commands: Copying a disk, Comparing disks Overview of different versions of Windows Working with Windows- Desktop Basic Layout, Icons, Opening Windows, Window Characteristics, Window Controls, Resize Windows, Arrange Windows, Taskbar. Working with Programs: Basic Program Layout, WordPad Program, Scrolling in Documents, Moving Insertion Point, Delete & Insert Key, Selecting Text, Cut, Copy & Paste, Working with Multiple Programs. Files & Folders: Organization, View Folder Structure, Working with Folders Search for Files, Organizing Workspace - Personal Desktop, Shortcuts, Start Menu, Start Properties, Display as Menu, Taskbar, Quick Launch. Windows Properties - Navigating Control Panel, Changing Theme, Desktop Settings, Screen Saver Settings, Appearance Settings, Display Settings, Mouse Settings Working with documents: Creating a document, Manage files and folders for documents, working with icons, editing documents - Text formatting and alignment, Indentation. Paragraph formatting - Margins, tabs and page numbering. Working with tables and borders and replace text - Mail merge. Printing - Working with Images and Text - Find

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Creating and formatting a presentation Creation of a new Presentation, Adding Slides and Text to a Presentation, Editing Slide Text, Saving a Presentation, and Running a Slide Show- Adding Tables and charting data Modifying objects and adding Images, Preparing to deliver a presentation. Creating and modifying a worksheet- Formatting Worksheets Working with multiple worksheets Performing Calculations Surfing information using Search Engines, Saving web pages to a disk, Composing Email, Sending E-mail.

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BINF 464 - LAB - PROGRAMMING IN C/ C++

Total Credits: 1 LINUX Operating System: Overview of Linux Architecture, Installation, Booting and Shutdown Process, System Processes(an overview), User Management- Types of users, Creating Users, Granting Rights, File System management C 1. Working with the Escape sequence 2. Program that illustrate operator precedence 3. working with Switch case construct 4. Working with looping construct (print n sequences) 5. Program for character manipulation ( count the number of codons ) 6. Matrix manipulation 7. Program for pointer manipulation in a function 8. Program for String Handling ( Find the longest sequence among the n sequences) 9. Sorting and Binary search (Check the presence of sequence in the list) 10. Read and write a sequence in a file C++ 1. 2. 3. 4. 5. Create a class which shows the various form of constructors Inheritance implementation Function overloading example Operator overloading example Dynamic polymorphism implementation

BINF 465 - LAB - BIOINFORMATICS DATABASES AND TOOLS Total Credits: 1 Exercises: 1. Entrez and Literature Searches. a. PubMed b. PubMed central c. OMIM / OMIA d. Citation matcher 2. SRS of Biological Databases a. Nucleotide/ Genome Databases. b. Protein Sequence Database. c. Structure databases. d. Protein Pattern Databases 3. File format conversion a. FmtSeq b. ReadSeq c. Sequence manipulation Suite 4. Sequence Analysis a. Dot Plot b. Pairwise alignment c. Multiple Sequence Alignment 5. Softwares a. BioEdit. b. GeneDoc c. ClustalW / X, MEGA, MEME 6. Visualization Tool a. RasMol b. Cn3D c. MolMol

BINF 431 - GENOMICS AND PROTEOMICS Total Credits: 3 Total: 36 Hrs.

Unit 1 8 Lectures Genomics and Metagenomics: Large scale genome sequencing strategies. Genome assembly and annotation. Genome databases of Plants, animals and pathogens. Metagenomics: Gene networks: basic concepts, computational model such as Lambda receptor and lac operon. Prediction of genes, promoters, splice sites, regulatory regions: basic principles, application of methods to prokaryotic and eukaryotic genomes and interpretation of results. Basic concepts on identification of disease genes, role of bioinformatics-OMIM database, reference genome sequence, integrated genomic maps, gene expression profiling; identification of SNPs, SNP database (DbSNP). Role of SNP in Pharmacogenomics, SNP arrays. Basic concepts in identification of Drought stress response genes, insect resistant genes, nutrition enhancing genes Unit 2 7 Lectures Epigenetics: DNA microarray: database and basic tools, Gene Expression Omnibus (GEO), ArrayExpress, SAGE databases DNA microarray: understanding of microarray data, normalizing microarray data, detecting differential gene expression, correlation of gene expression data to biological process and computational analysis tools (especially clustering approaches) Unit 3 7 Lectures Comparative genomics: Basic concepts and applications, whole genome alignments: understanding the significance; Artemis, BLAST2, MegaBlast algorithms, PipMaker, AVID, Vista, MUMmer, applications of suffix tree in comparative genomics, synteny and gene order comparisons Comparative genomics databases: COG, VOG Unit 4 7 Lectures Functional genomics: Application of sequence based and structure-based approaches to assignment of gene functions e.g. sequence comparison, structure analysis (especially active sites, binding sites) and comparison, pattern identification, etc. Use of various derived databases in function assignment, use of SNPs for identification of genetic traits. Gene/Protein function prediction using Machine learning tools viz. Neural network, SVM etc Unit 5 7 Lectures Proteomics: Protein arrays: basic principles. Computational methods for identification of polypeptides from mass spectrometry. Protein arrays: bioinformatics-based tools for analysis of proteomics data (Tools available at ExPASy Proteomics server); databases (such as InterPro) and analysis tools. Protein-protein interactions: databases such as DIP, PPI server and tools for analysis of protein-protein interactions Text Books: 1. Principles of Genome Analysis and Genomics (3rd Ed.) by Primrose, S.B. and Twyman, R.M., 2003, Blackwell Publishing Company, Oxford, UK. 2. Introduction to proteomics Tools for the new biology (1st Ed.) by Liebler, D.C., 2002, Human Press Inc., New Jersey, USA. 3. Bioinformatics and Functional Genomics by Pevsner, J., 2003, John Wiley and Sons, New Jersey, USA. 4. Bioinformatics: Sequence and Genome Analysis by Mount, D., 2004, Cold Spring Harbor Laboratory Press, New York.

BINF 432 - BIOINFORMATICS: SEQUENCE ANALYSIS Total Credits: 3 Total: 36 Hrs.

Unit 1 7 Lectures Sequence Analysis: Basic concepts of sequence similarity, identity and homology, definitions of homologues, orthologues, paralogues and xenologues Scoring matrices: basic concept of a scoring matrix, Matrices for nucleic acid and proteins sequences, PAM and BLOSUM series, matrix derivation methods and principles. Database Searches: Keyword-based Entrez and SRS; Sequence-based: BLAST & FASTA; Use of these methods for sequence analysis including the on-line use of the tools and interpretation of results from various sequence and structural as well as bibliographic databases Unit 2 6 Lectures Pairwise sequence alignment: Basic concepts of sequence alignment, Needleman and Wunsch, Smith and Waterman algorithms for pairwise alignments, gap penalties, use of pairwise alignments for analysis of Nucleic acid and protein sequences and interpretation of results Unit 3 7 Lectures Multiple sequence alignments (MSA) : The need for MSA, basic concepts of various approaches for MSA (e.g. progressive, hierarchical etc.). Algorithm of CLUSTALW and PileUp and their application for sequence analysis (including interpretation of results), concept of dendrogram and its interpretation, Use of HMM-based Algorithm for MSA (e.g. SAM method) Unit 4 8 Lectures Sequence patterns and profiles: Basic concept and definition of sequence patterns, motifs and profiles, various types of pattern representations viz. consensus, regular expression (Prositetype) and sequence profiles; profile-based database searches using PSI-BLAST, analysis and interpretation of profile-based searches. Algorithms for derivation and searching sequence patterns: MeMe, PHI-BLAST, SCanProsite and PRATT. Algorithms for generation of sequence profiles: Profile Analysis method of Gribskov, HMMer, PSI-BLAST Unit 5 8 Lectures Taxonomy and phylogeny: Basic concepts in systematics, taxonomy and phylogeny; molecular evolution; nature of data used in Taxonomy and Phylogeny, Definition and description of phylogenetic trees and various types of trees, Phylogenetic analysis algorithms such as maximum Parsimony, UPGMA, Transformed Distance, Neighbors-Relation, NeighborJoining, Probabilistic models and associated algorithms such as Probabilistic models of evolution and maximum likelihood algorithm, Bootstrapping methods, use of tools such as Phylip, Mega, PAUP Text Books: 1. Bioinformatics: Sequence and Genome Analysis by Mount D., 2004 Cold Spring Harbor Laboratory Press, New York. 2. Bioinformatics- a practical guide to the analysis of Genes and Proteins by Baxevanis, A.D. and Francis Ouellellette, B.F., 1998, John Wiley & Sons, UK.

BINF 433 - PROBABILITY AND STATISTICS Total Credits: 2 Unit 1 Total: 24 Hrs. 5 Lectures

Numerical descriptive techniques: Measures of central tendency: mean, median, mode, relation between mean, median and mode. Partition values: quartiles, deciles, percentiles; Measures of dispersion: Absolute and Relative Measures, Moments, skewness and kurtosis Unit 2 5 Lectures Correlation and Regression: Principles of least squares, scatter diagram, correlation, covariance, correlation coefficient, properties of correlation coefficient, regression, properties of linear regression, rank correlation, multiple correlation Unit 3 5 Lectures

Probability Theory: Concept of probability: sample space and events, independent events, mutually exclusive events. axioms of probability, conditional probability, additional and multiplication theorem of probability, Baye's theorem, Bernoulli trials, binomial distribution, normal distributions, Poisson distribution Unit 4 4 Lectures Sampling Theory: Meaning and objective of sampling, Sampling Error, Types of Sampling, Sampling Distribution, Sampling Distribution of Sample Mean and Sample Proportion, Standard Error

Unit 5 5 Lectures Test of Hypothesis of Small and Large Samples: Standard Normal distribution, Chi-square distribution, Students t distribution, F distribution, Analysis of Variance Text Books: 1. Biostatistics (9 Ed.) by Wayne W. Daniel, Wiley 2004 ISBN: 978-0-471-45654-4 2. Schaums Outlines - Introduction to Probability and Statistics by Seymour Lipschutz and John Schiller, 1998, TATA McGraw-Hill edition. Reference Books: 1. Statistical Methods by N. G. Das, Vol: I and II, 2009, The McGraw-Hill Companies 2. Fundamentals of Biostatistics (6th Ed.), Bernard Rosner, 2006, Thomson Brooks/Cole ISBN: 0-534-41820-1

BINF 434 - PROGRAMMING IN JAVA Total Credits: 3 Total: 36 Hrs.

Unit 1 6 Lectures Java Basics - Importance and features of java, Modifiers, Access Controls, Data types, Expressions, Declarations, Statements & Control Structures, Program Structures, String handling, Packages, Interfaces, Working with java util Package, Garbage Collection Unit 2 8 Lectures Exception Handling, I/O & JDBC Exception Handling: built in exception, creating your own exceptions, Input Stream & Output Stream: Streams, Byte and Character stream, Predefined streams, Reading and Writing from Console and Files, Buffered Reader & Writer, Serialization, Database: JDBC Basics Unit 3 7 Lectures Multithreading and Communication Java Thread Model: Life Cycle of Thread, Thread class, Runnable interface, Interthread Communication, Suspending, Resuming and Stopping threads, Synchronization, Scheduling and Priority of Threads. Unit 4 7 Lectures AWT & Event Handling Creating User interface with AWT, Applets, Applet Life Cycle, Simple Graphics, Fonts and Colors, Events, Listeners, Components, Containers, Working with Layouts, Image Processing, Delegation Event Model, Event Classes, Event Listener Interfaces, Adapter and Inner Classes Unit 5 8 Lectures BioJava - Installing BioJava, Symbols, Basic Sequence Manipulation (DNA to RNA, Reverse Complement, motif as regular expression), Translation (DNA to Protein, Codon to amino acid, Six frame translation), Proteomics (Calculate the mass and pI of a peptide), Sequence I/O (File Formats conversions), Locations and Features (PointLocation, RangeLocation, Feature modifications), BLAST and FASTA (Blast and FastA Parser, extract information from parsed results), Counts and Distributions, Weight Matrices and Dynamic Programming, User Interfaces. Text Books: 1. Herbert Schildt,Java- A Beginners Guide (4th Ed.), 2007, Tata Mc-Graw-Hill publication Reference Books: 1. Computing Concepts with Java 2 Essentials (2nd Ed.) by Horstmann, C.S., 2000, John Wiley Publishers. 2. Object Oriented Design and Applications (2nd Ed.) by Benjamin, Cummings and Booch, G., 1994, Addison Wesley Publishers.

BINF 435 - DATABASE MANAGEMENT SYSTEM Total Credits: 3 Unit 1 Total: 36 Hrs.

7 Lectures Introduction , Database System Versus File Systems, Characteristics of Database, Database Concepts, Schemas & Instances, DBMS architecture and Data Independence, Data Models, Database Languages & Interfaces, View of Data, Database users and Administrators, Database System Structure, Database System Applications

Unit 2 7 Lectures Data models ER Model: Keys, Constraints, Design Issues, Extended ER features, Reductions of ER Schema to Tables. Relational Model: Structure, Relational Algebra; Hierarchical Model, Network Model, Object Oriented Model Unit 3 6 Lectures Structured Query Language Basic Structure, Set Operations, Aggregate Functions, Null Values, Nested Sub queries, Views, Integrity: Domain constraints, Joined Relations, DataDefinition Language Unit 4 8 Lectures Relational Database and Storage Pitfalls in Relational Design Database, Functional dependencies, Decomposition Normal Forms 1NF, 2NF, 3NF & Boyce-Codd NF, Data Storage Ordered indices, Hashing concepts - Security and Authorization. Unit 5 8 Lectures Concurrency control techniques & Information retrieval Transactions: Properties of transactions: Concurrency problems, Serialisability and Locking techniques, Granularity of Data Items Database System Architecture and Information retrieval: Centralized and ClientServer Architecture Text Books: 1. Database system Concepts (4th Ed.) by Silberschatz, A., Korth, H.F. and Sudarshan, S., 2002, McGraw Hill Publishers. Text Books: 1. An introduction to Database systems (7th Ed.) by Date, C.J., 2000, Addison Wesley Publishers. 2. Fundamentals of Database systems (4th Ed.) by Elmasri and Navathe, 2004, Addison Wesley Publishers. 3. Principles of Database systems (2nd Ed.) by Ullman, J. D., 2001, Galgotia Publications.

BINF 436 - FUNDAMENTALS OF ALGORITHMS Total Credits: 2 Total: 24 Hrs.

Unit 1 Computing Algorithms 4 lectures Algorithms in Computing, Analyzing algorithms, Designing algorithms, Asymptotic notation, Standard notations, Big O notations, Time and space complexity of algorithms and common functions. Unit 2 Sorting, Searching & Strings Matching 5 lectures Sorting: Bubble sort, Insertion sort, Selection sort, Merge Sort, Quick Sort, External sort: Kway mergesort, balanced mergesort, Searching: Binary Search, Fibonacci Search. String Matching: Nave algorithm, Boyer Moore algorithm. Unit 3 Graphs 5 lectures Representation of Graphs, Breadth First Search, Depth First Search, Topological Sort, Connected Components, Minimum Spanning Tree, Single-Source Shortest Path: Dijkstras Algorithm, All-Pairs Shortest Paths, Coloring of Graphs Unit 4 Trees 5 lectures Forests, DAGs, Ancestors, and Descendants, Binary Search Trees, Querying a Binary search tree, Insertion and Deletion, Tree Traversals, AVL-Trees, Rotations, Insertion, Deletion, Btrees. Unit 5 Algorithm Design and Analysis 5 lectures The substitution method, The iteration method, Divide and Conquer, Greedy Algorithms, Dynamic Programming: Traveling Sales Person Problem Backtracking Algorithms: 8-queens Problem. Text Books: 1. Fundamentals of Algorithms by E. Horowitz and S. Sahani, 1999, Galgotia Book source Pvt. Ltd. 2. Data Structures by Seymour Lipschutz, 2007, Tata Mc-Graw-Hill publication 3. Introduction to Algorithms (3rd Ed.) by T .H. Cormen, C. E. Leiserson, R .L. Rivest, 2007, The MIT Press

BINF 466 - LAB - PROGRAMMING IN JAVA

Total Credits: 1 Exercise in JAVA 1. Working with Objects, Arrays, Conditionals and Loops. 2. Creating Classes and Applications in Java. 3. Java Exception handling 4. Streams and I/O, Using Native Methods and Libraries 5. Simple Animation and Threads, Advanced Animation, Images and Sound. 6. Managing Simple Events and Interactivity. 7. Local and global alignment of sequences 8. Creating User Interfaces with AWT, Modifiers. 9. Multithreading example 10. Java Programming Tools, Working with Data Structures.

BINF 467 - LAB PROGRAMMING IN DBMS Total Credits: 1 Exercise in DBMS (MYSQL) Data Definition Language (DDL) statements: Creating database, Selecting database, Deleting database, Creating table, Modifying Table, Deleting table Data Manipulation statements: Inserting, updating and deleting records Retrieving Records Retrieving specific rows and columns Use of MySQL operators Arithmetic operators, Comparison Operators, Logical operators Math functions, Aggregate functions String operations Limiting, Sorting and grouping query results Handling null values Renaming or aliasing table and column names Using subqueries Using Joins joining a table to itself, joining multiple tables Use of Indexes Security Management Granting and Revoking rights on tables

BINF 468 - LAB - BIOSEQUENCE ANALYSIS Total Credits: 1 Exercices: 1. Sequence Analysis Packages: EMBOSS, NCBI ToolKit, SMS 2. Database search engines: Entrez, SRS, DBGET 3. Pair wise alignment: a. Search tools against Databases: i. BLAST ii. FASTA 4. Multiple sequence alignment: a. Clustal b. Dialign c. Multalign 5. Sequence patterns and profiles: a. generation of sequence profiles i. PSI-BLAST b. derivation of and searching sequence patterns: i. MeMe, ii. PHI-BLAST iii. SCanProsite iv. PRATT 6. Protein motif and domain analysis: a. MEME/MAST b. eMotif c. InterproScan d. ProSite e. ProDom f. Pfam 7. Phylogenetic analysis MEGA, PAUP, PHYLIP 8. Genome annotation Artemis. 9. Hypothetical Protein analysis 10. Genome Comparison

BINF 511 - STRUCTURAL BIOLOGY Total Credits: 3 Total: 36 Hrs.

Unit 1 5 Lectures DNA and RNA: types of base pairing Watson-Crick and Hoogstein; types of double helices A, B, Z and their geometrical as well as structural features; structural and geometrical parameters of each form and their comparison; various types of interactions of DNA with proteins, small molecules. RNA secondary and tertiary structures, t-RNA tertiary structure Unit 2 6 Lectures Proteins: Principles of protein structure; anatomy of proteins Hierarchical organization of protein structure Primary. Secondary, Super secondary, Tertiary and Quaternary structure; Hydrophobicity of amino acids, Pacing of protein structure, van der Waal and Solvent accessible surface, Internal coordinates of proteins; Derivation, significance and applications of Ramachandran Map. Unit 3 6 Lectures Carbohydrates: The various building blocks (monosaccharides), configurations and conformations of the building blocks; formations of polysaccharides and structural diversity due to the different types of linkages. Glyco-conjugates: various types of glycolipids and glycoproteins Unit 4 7 Lectures Structure Prediction Strategies: Secondary structure prediction: Algorithms viz. Chou Fasman, GOR methods; analysis of results and measuring the accuracy of predictions using Q3, Segment overlap, Mathews correlation coefficient Identification/assignment of secondary structural elements from the knowledge of 3-D structure of macromolecule using DSSP and STRIDE methods Unit 5 6 Lectures Tertiary Structure prediction: Fundamentals of the methods for 3D structure prediction (sequence similarity/identity of target proteins of known structure, fundamental principles of protein folding etc.) Homology Modeling, fold recognition, threading approaches, and ab-initio structure prediction methods - protocols/algorithms. Prediction of protein structure: PHD and PSI-PRED methods Unit 6 6 Lectures Classification and comparison of protein 3D structures: Purpose of 3-D structure comparison and concepts; Algorithms such as FSSP, CE, VAST and DALI, Fold Classes. Databases of structure-based classification: CATH and SCOP. Structures of oligomeric proteins and study of interaction interfaces Text Books: 1. Molecular Modeling Principles and Applications (2nd Ed.) by Andrew R. Leach, 2001, Prentice Hall, USA. 2. Principles of Protein Structure by G. E. Schulz, 2009, Springer 3. Lehninger Principles of Biochemistry by David L. Nelson and Michael M. Cox, 2005, W. H. Freeman

BINF 512 MOLECULAR MODELING AND DRUG DESIGN Total Credits: 3 Total: 36 Hrs.

Unit 1 4 lectures Introduction to molecular force fields: General features- bond stretching, angle bending, improper torsions, out of plane bending, cross terms, non-bonded interactions, point charges, calculation of atomic charges, polarization, van der waals interactions, hydrogen bond interactions, Water models. Types of force field - all atoms force field , united atom force field, etc. Unit 2 5 lectures Molecular Energy minization: Steepest descent, conjugate gradient Derivatives, First order steepest decent and conjugate gradients. Second order derivatices Newton-Raphson, Minima, maxima saddle points and convergence criteria.-non derivatives minimization methods, the simplex, sequential univariative. Unit 3 10 Lectures Molecular Dynamics Simulation methods: Classical Molecular Dynamics: Newtonian dynamics, Integration algorithm, Periodic boundary conditions and minimum image convention, Potential truncation and shifted-force potentials, Neighbor list, Force calculations, Long range interactions, MD code for liquid Argon. Classical Monte Carlo: Random numbers, Evaluating integrals using random numbers, Importance sampling, Metropolis algorithm, Smart MC techniques. Analysis of simulated trajectories: Radial distribution functions, Self diffusion coefficient, Time correlation functions Unit 4 10 Lectures Drug and Vaccine design: Drug discovery process. Role of Bioinformatics in drug design. Target identification and validation, lead optimization and validation. Structure-based drug design and ligand based drug design. Modeling of target-small molecule interactions. Fundamentals of docking small and macromolecules to proteins and nucleic acids. Vaccine design: Reverse vaccinology and immunoinformatics. Databases in Immunology. B-cell epitope prediction methods. T-cell epitope prediction methods. Resources to study antibodies, antigen-antibody interactions Unit 5 7 Lectures Structure Activity Relationship: QSARs and QSPRs, QSAR Methodology, Various Descriptors used in QSARs: Electronics; Topology; Quantum Chemical based Descriptors. Use of Genetic Algorithms, Neural Networks and Principle Components Analysis in the QSAR equations Text Books: 1. Molecular Modeling Principles and Applications (2nd Ed.) by Andrew R. Leach, 2001, Prentice Hall, USA. 2. Molecular Modeling and Simulation An interdisciplinary Guide by Tamar Schlick, 2000, Springer-verlag 3. Computational medicinal chemistry for drug discovery edited by Patrick Bultinck, 2004, Marcel Dekker Inc.

BINF 513 - PROGRAMMING IN PERL

Total Credit: 3

Total hrs: 36

Unit 1 7 lectures Data Structure : Scalar Variables, Scalar Operations and Functions, Array Variables Literal Representation of Array, Array Operations and Functions, Scalar and List Context, Hash Variables, Literal Representation of a Hash, Hash Functions, Using Hashes for the Genetic Code, Gene Expression Data Using Hashes

Unit 2 7 lectures Modular Programming: Subroutines, Advantage of Subroutines, Scoping and Subroutines, Arguments, Passing Data to Subroutines, Modules and Libraries of Subroutines, Concept about File handle, Opening and Closing a File handle, Opening and Closing a Directory Handle, Reading a Directory Handle, File and Directory Manipulation. Unit 3 7 lectures Regular Expression and Pattern Matching: Concepts about Regular Expressions, Simple uses of Regular Expressions, Patterns, Matching Operator, Substitutions, Split and Join functions. Unit 4 7 lectures Common Gateway Interface (CGI) Programming: The CGI.pm Module, CGI program in Context, Simple CGI programs, Passing Parameters via CGI, Perl and the Web Unit 5 8 lectures Bioperl: Introduction to Bioperl, Installing procedures, Architectures, General Bioperl Classes, Sequences (Bio::Seq Class, Sequence Manipulation), Features and Location Classes (Extracting CDS), Alignments (AlignIO), Analysis (Blast, Genscan), Databases (Database Classes, Accessing a local database), Implementing REBASE Text Books: 1. Beginning Perl for Bioinformatics (1st Edition) by Tisdall, J., 2004, OReilly Publishers. 2. Learning Perl (5th Edition) by Randal L. Schwartz, Tom Phoenix and Brain d Foy, 2008, OReilly Publishers. 3. Programming Perl (3rd Edition) by Wall, W., Christiansen, T. and Orwant, J., 2000, OReilly Publishers.

BINF 514 - SYSTEMS BIOLOGY Total Credits: 3 Total: 24 Hrs.

Unit 1 5 lectures Introduction: Systems Biology Networks- basics of computer networks, Biological uses and Integration. Micro array definition, Applications of Micro Arrays in systems biology. Selforganizing maps and Connectivity maps - definition and its uses. Networks and Pathways Types and methods. Metabolic networks. Unit 2 5 lectures Simulation of pathways: Whole cell: Principle and levels of simulation Virtual Erythrocytes. Pathological analysis. Flux Balance Analysis. Biochemical metabolic pathways, Metabolomics and enzymes. Interconnection of pathways, metabolic regulation. Translating biochemical networks into linear algebra. Cellular models. Networks and Motifs: Gene Networks: basic concepts, computational models. Lambda receptor and lac operon as an example. All types of networks and its uses. Unit 3 5 lectures Signalling & Experimental methods in systems biology: slow and autoregulation The coherent FFL- temporal order, FIFO, DOR, Global, Development, memory and irreversibilitysignaling networks and neuron circuits-robust adaptationany model. Robustness and optimality in Biology: model and integral feedback-signaling/bifunctional enzymes. Perfect robustness- Role and its measurement. Linking models and measurement, concepts, calibration and identification, data Vs metadata Unit 4 4 lectures Design of Circuits and Databases: Introduction- databases KEGG, EMP, MetaCyc, AraCyc etc., Expression databases and various databases related to systems biology. Optional design of gene circuits I- cost and benefit: gene circuits II- selection of regulation. Stochasticity in gene expression. Unit 5 5 lectures Synthetic Biology: Introduction, definition and Basics, Synthetic Oligonucleotide/DNA-based, RNA-based, Peptide-based and polyketide Technologies and Applications, Technologies and Applications of Directed Evolution and Microbial Engineering, Potential Hazards of Synthetic Biology Text Books: 1. Systems Biology: Definitions and perspectives by L.Alberghina H.V.westerhoff, 2005 Springer 2. Synthetic Biology, A New Paradigm for Biological Discovery, a report by Beachhead Consulting, Feb 2006 Reference Books: 1. Computational systems biology by A.Kriete, R.Eils, 2005, Academic press. 2. Systems Biology in practice: Concepts, Implementation and applications by E.Klipp R.Herwig, A.Kowlad, C.Wierling and H.Lehrach, 2005, Wiley InterScience 3. Systems Biology and Synthetic Biology by Pengcheng Fu, Sven Panke, 2009, Wiley InterScience

BINF 515 - FUNDAMENTALS OF SPECTROSCOPY Total Credits: 2 Total: 24 Hrs.

Unit 1 5 lectures UV- Visible spectroscopy - Absorption laws - calculations involving Beer - lambert's law instrumentation - photocolonmeter and spectrophotometer - block diagrams with description of components - theory - types of electronic transitions - chromophore and auxochromes absorption bands and intensity - factors governing absorption maximum and intensity. Unit 2 5 lectures Infrared spectroscopy - principle - types of stretching and bending vibrations - vibrational frequencies - instrumentation - block diagram - source - monochromator - cell sampling techniques - detector and recorders - identification of organic molecules from characteristic absorption bands. FTIR and its advantages Unit 3 4 lectures Raman spectroscopy - Raleigh and Raman scattering - stoke's and anti stokes lines instrumentation block diagram - differences between IR and Raman spectroscopy - mutual exclusion principle - applications - structural diagnosis. Unit 4 5 lectures Magnetic Resonance Spectroscopy: Nuclear Magnetic Resonance Spectroscopy Nuclear spin magnetic moment, Interaction of nuclear magnet with external magnetic field, NMR spectrometer, relaxation and dynamic processes, chemical shift, Heteronuclear NMR experiments, Electron Spin Resonance Spectroscopy: Electron spin and Magnetic moment, Resonance condition in ESR and significance of 'g' value, applications of ESR. Unit 5 5 lectures X-ray Spectroscopy: Production and properties of X-rays. The Bragg Law X-ray Spectroscopy Diffraction Directions Diffraction Methods Powder Method Particle size Calculation X-ray scattering by electrons. Reference Books: 1. Atomic spectra & atomic structure by Gerhard Hertzberg, 1944, Dover publication, New york Recent edition. 2. Fundamentals of molecular spectroscopy by C. N. Banwell, 1983, McGraw-Hill 3. Physical chemistry by P. W. Atkins. ELBS. 1986 4. Introduction to molecular spectroscopy by G. M. Barrow, 1962, McGraw-Hill 5. Molecular spectroscopy by I. N. Levins, 1975, Wiley interscience. 6. Nuclear magnetic Resonance by J. D. Roberts, McGraw-Hill. 7. Introduction to Magnetic resonance by A. Carrrington and A. D. McLachlan. Harper and Row, 1967 8. Electron Spin Resonance , Elemenatry theory and practical applications by J. E. Wetz and J. R. Boulton , 1972, McGrew Hill . 9. Introduction to Magnetochemistry by Earnst Shaw., 1968, Academic Press 10. Electrical and optical properties of molecular behavior by M. Davies, pergman press.

BINF 516 DATA COMMUNICATION AND NETWORKS Total Credits: 2 Total: 24 Hrs.

Unit 1 5 Lectures Nuts & Bolts in Networks Reference Model, Network Topologies and Protocols, Types of Networks: Local Area Network (LAN), Wide Area Network (WAN), Metropolitan Area Network (MAN), Network Security (Firewall, Packet Filtering, VPN), Uses of Computer Networks Unit 2 6 Lectures Network Architecture OSI & Internet Architecture, IEEE 802 standards, Physical Layer - Transmission Media, Switching. Data Link Layer - Design Issues, Example Data Link Protocols, Data Link layer in the Internet, Media Access Sub layer: Static and Dynamic channel allocation ALOHA CSMA CSMA / CD. Unit 3 4 Lectures Network Layer Network Layer - Design Issues, Routing Algorithms, Congestion Control algorithm, Router Operation, Router Configuration, Internetworking, IP Addressing, IP Subnet Mask, IPv6 (an overview) Unit 4 4 Lectures Transport Layer Transport Layer Transport Service, Elements of Transport protocols Internet Transport Protocols (UDP) - Internet Transport Protocols (TCP) Related issues Unit 5 5 Lectures Application Layer Design Issues, Conventional Encryption, Classical and Modern Techniques, Encryption and Decryption Algorithms (RSA), Confidentiality, DNS, SNMP, RMON, WWW, E-mail, Digital Signatures Text Book: 1. Computer Networks (3rd Ed.) by Tananbaum A.S., 1999, PHI Reference Books: 1. Computer Networks-Protocols, Standards and Interfaces by Black U., 1996, PHI 2. Distributed Systems Concepts & Design (3rd Ed) by George Coulouris, Jean Dollimore, Tim Kindsberg, 2000, Addison Wesley

BINF 517 FINISHING SCHOOL Total Credits: 2 Total: 24 Hrs.

Unit 1 5 Lectures Organizations- their meaning, formations, establishments- individuals and organizations- their inter connections- elements of recruitment, selection, interview techniques, induction, training and development, promotions, transfers, retirement, retrenchment, rehabilitation. Teams- team works- need for inter personal and intra-personal interactions human behavior at workpersonnel issues- human resources management issues. Unit 2 5 Lectures Personality Development role of health in personality development a healthy mind and a healthy body for greater productivity- role of productivity for the individual and organizationgoals setting for individuals and organizations Unit 3 Human behavior in organizations- elementary aspects Unit 4 Time management- planning and scheduling, stress in work- work-life balance 4 Lectures

5 Lectures

Unit 5 5 Lectures Ethics and values, Indian culture and cultural ethos- cultural diversity-diversity in organizations

BINF 561 LAB: STRUCTURAL BIOLOGY

Total Credits: 1 1. Advanced Visualization Software and 3D representations. 2. Coordinate generations and inter-conversions. 3. Secondary Structure Prediction 4. Fold Recognition, ab initio (Rosetta Server) 5. Homology based comparative protein modeling. 6. Energy minimizations. 7. Validation of models. PDB Goodies, Procheck, ProsaII, PDBsum, WHATIF, VERIFY 3D 8. Protein 3D Structure Alignment. 9. Modeller 10. Geno-3D 11. Discovery Studio Server.

BINF 562 - LAB MOLECULAR MODELING AND DRUG DESIGN Total Credits: 1 Exercise: Software packages: 1. Discovery Studio 2. Gold 3. Autodock 4. Schrodinger maestro 5. Sybyl CoMFA 6. Gromacs 7. VMD The above tools are to be used for the following analysis 1. Conformational Analysis 2. BABEL,MOPAC 3. Binding Site Identification. 4. Pharmacophore Identification 5. Receptor and Ligand Optimization 6. Docking 7. QSAR 8. Molecular dynamics simulations 9. Molecular Dynamics Visualization

BINF 563 - LAB - PROGRAMMING IN PERL

Total Credits: 1 1. 2. 3. 4. 5. 6. 7. 8. Uses of Scalar and Array Variables to manipulate DNA/RNA/Protein sequence data Concatenation DNA fragments, Transcribing DNA into RNA Calculating the Reverse complement of a DNA strand Uses of common Array Operators Uses of Do-Until Loops Uses of substr function to look into the string Reading a sequence data from a file and writing the results to a file Opening and closing a Directory Handle, Reading a Directory and other directory manipulation functions. 9. Uses of Subroutines 10. Uses of Hashes for the genetic code: translating codons into amino acids 11. Uses of subroutine to read FASTA files 12. Translate a DNA sequence in all six reading frames 13. Uses of Regular Expressions 14. Extract annotation and sequence from GenBank file 15. Parsing GenBank annotation using arrays 16. Extract sequence chains from PDB file 17. Uses of CGI.pm Module and Passing Parameters via CGI, Debugging CGI programs 18. Installing Bioperl, Uses of Bioperl modules for sequence manipulation, accessing local database

BINF 531- ANALYTICAL BIOPHYSICS Total Credits: 2 Total: 24 Hrs.

Unit 1 5 lectures Electrophoresis: Theory and types; moving boundary electrophoresis, zone electrophoresis, paper, cellulose acetate gel electrophoresis, Native PAGE, disc PAGE, Gradient PAGE, SDS PAGE, DNA agarose gel electrophoresis, Southern, Northern, Western blotting techniques, Isoelectric focusing, finger printing, DNA sequencing, Pulsed - field Electrophoresis, Capillary Electrophoresis. Unit 2 4 lectures Chromatography: Principles, methodology and applications of chromatography using paper, thin layer, column (gel filtration, ion exchange, affinity), gas and types of HPLC Unit 3 5 lectures Centrifugation: Principles, types and applications. Ultracentrifugation- types, optical methods used and applications of preparative and analytical ultracentrifuges. Unit 4 4 lectures Enzyme kinetics: Membrane potential, Active site, Cofactors, apo-enzymes, Enzyme specificity, Factor affecting enzyme activity, Michaelis-Menten equation, LB Plot, Determination of Km, Types of inhibition, Allosteric enzymes,. Unit 5 6 lectures Various Biophsical techniques to study interactions caused by the macromolecules: Isothermal Titration Calorimetry- instrumentation. Protocol and application in the study of Proteinligand interactions. Optical and magnetic tweezers- principle, Instrumentation and modern developments. Role of Optical tweezers in studying the molecular motors and the properties of DNA. Fluorescence Resonance Energy Transfer: Principle, Instrumentation, Protocol and application in analyzing the macromolecular interactions. Dual Polarisation Interferometry [DPI]- Principle, Instrumentation and protocol. Application of DPI in one dimensional determination of protein structures and in studying the interactions and activity of biomolecules. Text Books: 1. Principles and Techniques of Practical Biochemistry (5th Ed) by Keith Wilson and John Walker, 2001, Cambridge University Press Reference Books: 1. Physical Biochemistry (2nd Ed) by D. Freifelder, 1982, Freeman 2. Biochemical calculation (5th Ed.) by I.H. Segal, 2000, Cambridge University Press. 3. Protein Purification - Principles & Practices (3rd Ed.) by R. Scopes, 1994, Springer Verlag. 4. Biophysical Chemistry: Techniques for the study of biological structure and functions by Charles C. R. & Paul. S. R., 2004, W.H. Freeman & Co. New York.

BINF 532 BIOETHICS, BIODIVERSITY AND INTELLECTUAL PROPERTY RIGHTS Total Credits: 3 Total: 36 Hrs.

Unit 1 8 Lectures Regulatory Procedures: Good laboratory practice, Good manufacturing practice and FDA regulations - Regulations for recombinant DNA research and manufacturing process - Biosafety and Bioethics - Regulations for clinical trials, Documentation and Compliance, in India and selected countries - Rules for import and export of biological materials. Unit 2 8 Lectures Biotechnology Processes and Products : Techniques used in Biotechnology, with special emphasis on molecular and recombinant DNA techniques - Cloning Strategies and Tissue culture procedures for plant cells, animal and stem cells - Transgenic plants, animals, genetically modified organisms (GMO) and GM food etc. - Large scale production of recombinant proteins, Processes for separation and purification - Medical Biotechnology: gene therapy, tissue engineering and xeno-transplantations - Biotechnology Products: Health care products Vaccines Diagnostics - Recombinant therapeutic proteins - Agricultural : Hybrid and modified seeds - Bio-pesticides - Bio-fertilizers Unit 3 IPR - Definition - WTO - Definition - Functions - Forms of IPR Protection 6 Lectures

Unit 4 7 Lectures Patents - Definition - conditions for patentablity - test of novelty of patents composition of a patent - Patenting of Biotechnological discoveries Unit 5 7 Lectures Other forms of IPR - Copyright - Trademark - Designs - Importance in Indian Scenario & forthcoming laws in India. Reference Books: 1. The Indian Environmental Protection Act (EPA), 1986 2. Rules for manufacture, use/import/export and storage of hazardous microorganisms or cells Act, 1989 3. Food Safety and Standards act (Government of India), 2006 4. Bioethics and Biosafety in Biotechnology by Sree Krishna V., 2007, New Age International (P) Ltd., Publ., Mumbai (ISBN: 81-224-2085-0) 5. Intellectual Property Rights on Biotechnology by Singh, KC, BCIL, New Delhi

BINF 533 SCIENTIFIC PRESENTATION Total Credits: 2 Total: 24 Hrs.

Unit 1 6 Lectures Scientific writing - Reasons to publish - being a good writer - Making it happen - Achieving creativity -Thought, structure and style - Getting started - Forming a plan - Choosing a journal Uniform requirements - Instructions to authors - Standardised reporting guidelines - Authorship Contributions - Writing your paper - Abstract - Introduction - Methods - Results - Discussion Finishing your paper - Choosing a title - Title page - References and citations - Peer review. Unit 2 6 Lectures Post-graduate theses - Writing style - Plain English - Topic sentences - Subjects, verbs and objects -Eliminating fog - Say what you mean - Word order - Creating flow - Tight writing Chopping up snakes - Parallel structures - Style matters - Grammar - Nouns - Adjectives Verbs - Adverbs - Pronouns and determiners - Conjunctions and prepositions - Phrases Clauses - Which and that - Grammar matters - Word choice - Label consistently. Unit 3 5 Lectures Readings, writing exercises and in-class discussion - Students (in small groups) will lead inclass discussions on assigned readings and writing exercises. Unit 4 4 Lectures Individual oral presentation - Students select a research project/topic and present results as an oral presentation followed by a Q&A session. Unit 5 3 Lectures Individual Poster presentation - Students select a research project/topic and present results as a poster followed by a Q&A session Text Books: 1. Scientific Writing Easy when you know how by Jennifer Peat, 2002, BMJ books 2. Successful Scientific Writing: A step-by-step Guide for Biomedical Scientists (2nd Ed.) by Mathews, 2001, Cambridge University Press Reference Book: 1. From Research to Manuscript: A Guide to Scientific Writing by MICHAEL JAY KATZ, 2006, Published by Springer.

BINF 534 - PROJECT

Total Credits: 8 The course is designed to result in the satisfactory completion and defense of the Masters dissertation. This process includes a) the conceptualization of the independent research that will comprise the dissertation, b) the preparation of and satisfactory defense of the dissertation proposal, c) the collection, analysis, and interpretation of data, d) presentation of findings in the dissertation format, and e) oral defense of the dissertation.

Dissertation activity must be completed within prescribed time frame for the semester.