Bioinformatics Syllabus for M.Sc

CURRICULUM FOR M.Sc. IN BIOINFORMATICS

SESSION 2005-2007Brijesh Singh Yadav([email protected])

Paper Code Nomenclature of paper Max/(Min) Marks Total

(Th./Prac.) Int. / Sess.

M.Sc. (Bioinformatics) First Semester

MBI-101 (B)* Basic Mathematics 80(29) 20(10) 100

MBI-102 (T) Introduction to Bioinformatics 80(29) 20(10) 100

MBI-103 (T) Introduction to Concept in Computing & Computer Programming

80(29) 20(10) 100

MBI-104 (T) Internet Technology & Distributed Computing 80(29) 20(10) 100

MBI-105 (T) Cell Biology & Genetics 80(29) 20(10) 100

MBI-106 (P) S/W Lab I – Problems based on MBI-103 80(40) 20(10) 100

MBI-107 (P) S/W Lab II – Problems based on MBI-104 80(40) 20(10) 100

M.Sc. (Bioinformatics) Second Semester

MBI-201 (T) Biological Database, Data Mining & Data Security Techniques

80(29) 20(10) 100

MBI-202 (T) Introduction to Database System 80(29) 20(10) 100

MBI-203 (T) Programming in Object Oriented Languages 80(29) 20(10) 100

MBI-204 (T) Pharmacology & Chemoinformatics 80(29) 20(10) 100

MBI-205 (T) Structural Biology 80(29) 20(10) 100

MBI-206 (P) S/W Lab III – Problems based on MBI-202 80(40) 20(10) 100

MBI-207 (P) S/W Lab IV – Problems based on MBI-203 80(40) 20(10) 100

MBI-208 (MP) Minor Project 80(40) 20(10) 100

M.Sc. (Bioinformatics) Third Semester

MBI-301 (T) Computer Graphics & Visualization 80(29) 20(10) 100

MBI-302 (T) Machine Learning Techniques (Advanced Computing) 80(29) 20(10) 100

MBI-303 (T) Genome to Drug & Vaccine 80(29) 20(10) 100

MBI-304 (T) Metabolomes & Metabolic Pathway 80(29) 20(10) 100

MBI-305 (T) Emerging Areas in Bioinformatics 80(29) 20(10) 100

MBI-306 (P) S/W Lab V – Problems based on MBI-301 80(40) 20(10) 100

MBI-307 (P) S/W Lab VI – Problems based on MBI-302 80(40) 20(10) 100

M.Sc. (Bioinformatics) Fourth Semester

MBI-401 (T+P) Seminars on Applications of Bioinformatics in Agriculture/ Human Health/ Environment/ Biotechnology/ Molecular Biology/ Neurobiology/ Drug Designing/ Veterinary Sciences

100(50) 100(50) 200

MBI-402 (PP) Research Paper Presentation 100(50) 100(50) 200

MBI-403 (PR) Major Project 200(100) 200(100) 400

Grand Total of Marks = 3000

* Students from mathematics/ Computer Stream will study paper MBI-101(A)* of Basic Biology, whereas students from biology/ agriculture stream will study paper MBI-101(B)* of Basic Mathematics.

Department of Computer Science, A.P.S. University, Rewa (M.P.)Syllabus for M.Sc. Bioinformatics - First Semester

(Session 2004-2006)PAPER (MBI-101(B)) BASIC MATHEMATICS.

Max.Marks. 80Time: 3 hours Min.Marks. 29

Unit I

Calculus: Limits, Complete Differentials, Partial differentials of functions with one variable and multiple variables.

Integration: Elementary Integration, Definite and Non-definite integral; Series, Logarithms.

Differential Equation: Ordinary differential equations (first order), Partial differential equations.

Unit II Vector : Addition, subtraction, dot, cross, scalar triple product, divergence, curl

of a vector, equation of normal Matrix algebra: Addition, subtraction, multiplication, transpose inverse, and

conjugate of matrix etc. Trigonometric functions: Sin, Cos, Tan, Cot, Series expansion of these

functions and other related functions

Unit III Correlation, Covariance, Calculation of covariance Correlation analysis, Types of correlation, Scatter Diagram Regression analysis, Regression coefficients Probability Terms and concepts Definition, Simple problems involving probability

Unit IV Introduction to Biostatistics Measures of central tendency, Mean, Median, Mode, Mean Deviation, Standard

Deviation Chi-Square Test, Degrees Of Freedom, Chi-Square Distribution, Properties of

Chi-Distribution

References: P.N. Arora,P.K. Malhan ,Biostatistics ,Himalaya Pub. Mohan.P. Arora,Fundamentals Of Genetics,Himalaya Pub P.N.Arora : Fundamentals Of trigonometry and Matrix Manjeet Singh: Simple approach to calculus

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four short notes (one from each unit), out of which only two are to be attempted.


(Session 2004-2006)PAPER (MBI - 102 (T) INTRODUCTION TO BIOINFORMATICS


Unit I INTRODUCTION

Overview of bioinformatics Resources Genome projects Pattern recognition and prediction

Unit II DATABASES AND DATA RETRIEVAL

DNA Sequence Databases (GenBank, EMBL) Protein Sequence Databases (SWISS-PROT, PROSITE) Data/Sequence Retrieval From Databases Genome Databases - Searching And Data Retrieval

Unit III SIMILARITY/HOMOLOGY SEARCHING

Sequence Comparison/Homology searchers BLAST How BLAST Works PSI-BLAST BLASTing Against Specific Genomes FASTA Working of FASTA

Unit IV SEQUENCE ANALYSIS

Sequence Alignment Global and Local Alignment Pair wise and Multiple sequence alignment PAM and BLOSUM CLUSTALW Molecular phylogeny Making tree

DNA/PROTEIN SEQUENCE ANALYSIS AND MANIPULATION Open Reading Frame (ORF) Identification Promoter Prediction And Analysis DNA Restriction Analysis DNA Sequence Translation To Amino Acid Sequence Codon Usage analysis General Programs Of Interest

Reference: Attwood, T.K. and Parry-Smith, D. J. Introduction to Bioinformatics, Longmans S. Sundara Rajan, R. Balaji, Introduction to Bioinformatics, Himalaya Pub.



(Session 2004-2006)PAPER (MBI-103) INTRODUCTION TO CONCEPT IN COMPUTING & COMPUTER PROGRAMMING

Time: 3 hours Max.Marks. 80 Min.Marks. 29

Unit I Introduction to computers: Characteristics & capabilities; classification; Components

of computer system with Block Diagram, CPU, only preliminary concept of Software, Hardware, Low Level Language, High Level Language, Compiler and Interpreter.

Introduction to operating Systems: WINDOWS, NT, UNIX/Linux operating systems.

Unit II C Programming Part I: Basics of C programming, Structure of a simple C program,

Simple I/o functions, Data types in C, operators & their precedence, Control Structures: if-else statements, switch statement, loops: while, do-while and for loop.Functions: User-defined functions, returning a value from a function, local & Global variables, automatic, Static Register and External Storage class. Parameters: Type, declaration of a function, functions with more than one parameters, recursion, Arrays: arryas (upto 2 dimensions), Declaration and initialization, the break structured, string and character arrays, operations with arrays, The C preprocessors.

Unit III C Programming part II: String and string functions: Pointers, the concept of pointers,

the address and indirection operators, passing pointers as parameters. Dynamic memory allocation, Arrays and pointers, Passing by value and reference, Address arithmetic. Pointer to pointers, Structures: Initializing a structure, Arrays of strucgtures, arrays within structures, structures within structures; Structures and functions, Unions, Files in C, modes for files, functions used in files (putchar, getchar, getc, putc, fopen, fclose, fscanf, fprint,fseek, ftell, fread and (write), error handling in files.

Unit IV Data structure : Introduction: Algorithm analysis for time and space requirements,

introduction to stack, queue, linked list, doubly linked lsit, circular linked list and their applications; Polynomial manipulation, multiple precision, fixed block storage allocation, dynamic storage management, first fit and best fit storage allocation, garbage collection, compaction. Sorting and searching techniques. (Use of biological database for case study).

REFERENCE: Introduction to comp. : P.K. Sinha Gottfried: Programming with C E. Balagurusamy: Programming with C Horowitz & Sahni: Fundamentals of Data Structures, Comp. Sc. Press Tanenbaum A.S.: Data Structures using C, PHI

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in each unit).. The students are expected to attempt only one question from each unit. The ninth question will normally have four parts (one from each unit), out of which only two are to be attempted.


(Session 2004-2006)PAPER (MBI-104) INTERNET TECHNOLOGY & DISTRIBUTED COMPUTING


Unit I

Internet: History and evolution of Internet. Internet and intranet, Basic concept of www, HTTP, FTP, URL, domain name, IP address, web browser, web server, web page, web site, portals, email, chatting, usenet, telnet, newsgroup, fax, telephony, telecommuting, conferencing, searching, downloading, uploading, files on internet, search engines. Email (reading, ending, deleting, replying), voice and video conferencing. Internet protocol: TCP/IP, dialup access, direct access, three levels of internet connectivity, ISPs, Introduction to DNS.

Unit II Internet Security & HTML: Overview of internet security, access security,

transaction security, security zones, digital IDS, sending / receiving signed and encrypted emails. Introduction to firewalls. Web page design: static and dynamic web pages. Introduction to HTML, HTML elements and tags, formatting with HTML tags, physical, logical HTML styles, setting fonts, colors and headings, displaying plain, presenting and arranging text using <DIV>, <SPAN>, <LAYERS> tags.

Unit III Advance HTML: Working with images, links and lists, creating tables, working

with frames, creating horizontal, vertical frames, named frames, opening new browser window, creating HTML forms, adding controls on forms, submitting data from forms, working with multimedia, multimedia sound, video, 3D using multimedia files, inline sound and videos. Style sheets: types, creating and using style sheets.

Unit IV Java Script and XML: Introduction to client and server side scripting.

Introduction to Java script, data types, operators, conditional statement, loops in Java script, functions, arrays, objects and elements in Java script, Form validation using Java script. Introduction to XML, creating XML, documents, specifying attributes in DTDs, accessing XML data with XML Data Island, documents. Handling events while loading XML documents.

References: The Internet: Christian Crumlish HTML Complete: BPB Publication Internet Complete: BPB Publication Teach yourself Internet in 24 hours: Techmedia.



(Session 2004-2006)PAPER (MBI-105) CELL BIOLOGY & GENETICS


Unit I

Cell Biology Prokaryotic and eukaryotic cells; membranes and cellular compartmentation; An

overview of organelles, (mitochondria, chloroplasts, ER, Golgi, lysosomes and peroxisomes; nucleus and nucleolus) and organelle genetic systems.

Cellular membranes : Structure, transport, channels, carriers, receptors, endocytois, membrane potentials.

Cell motility and shape : cytoskeletal elements, cilia and flagella; motor proteins. Unit II

Cell-cell interactions and signal transduction: Intercellular junctions, signaling by hormones and neurotransmitters; receptors, G-proteins, protein kinases and second messengers.

Protein traffic in cells : Protein sorting and signal sequences; protein translocation in ER and vesicular transport to Golgi, lysosmes and plasma membrane; protein import into nuclei, mitochondria, chloroplasts and peroxisomes.

Cell cycle and its regulation; events during mitosis and meiosis Unit III

Genetics Science of genetics – objectives, terminologies, methods. Mendelian principles of inheritance, sex linked inheritance. Concept of linkage, linkage maps and recombination. Mutations – molecular, gene/point and chromosomal.

Unit IV Phenotype and genotype relationships, role of environment, from gene to phenotype,

gene interactions Study of quantitative traits. Genetics of populations, genetics and evolution. Genetics and diseases, cancer.

References1. The world of the cell, 4th edition. Becker, Kleinsmith & Hardin. 2. Cell, A Molecular Approach,2nd edition, GM Cooper3. Fundamentals of Genetics, Mohan P Arora



(Session 2004-2006)PAPER (MBI-106) : S/W LAB I – PROBLEMS BASED ON MBI-103

Max.Marks. 80 Min.Marks.40

Part-A

1. Write a C program to create a doubly linked list and arrange the list in ascending sorted order of information. Information field is of type integer.

2. Write INSERT and DELETE functions in C language, simulating insertion and deletion operations of a queue, which is implemented by singly linked list. Make necessary assumptions.

3. Write a general, non-recursive C program for postorder traversal of a binary tree.4. Write a C program for selection and bubble sort.5. Write a C program to evaluate the postfix expression P using stack. Explain the

execution of the program with the exampleP: 562 + * 124/- (5 # 6 # 2 # + # * # 12 # / # -) (# stands for a blank space)

6. Write PUSH and POP functions in C language, simulating push and pop operations of a stack, which is implemented by a singly linked list. Make necessary assumption.

7. Write a C program to print the information, from each node in reverse order in a doubly linked list, in which pointer to last node is TAIL.

8. Write a C program thata) counts the number of nodes in a liked listb) will concatenate two linked lists. The function should have two parameters, pointers

to the beginning of the list, and the function should link the end of first list to the beginning of the second.

9. Write a program that will split a linked list into two linked lists, so that successive nodes go to different lists (the 1st, 3rd and all odd numbered nodes go to the first list and the 2nd,4th and all even numbered nodes go to the second).

10. Write a C program to carry out Binary Search on a tree.

Part-B

1. Write a C function to insert an item into a hash table with open addressing and linear probing.

2. Write a C program to find the shortest path in a given weighted graph.3. Write a program to correct rudimentary syntax errors like unbalanced parenthesis, brackets

and braces. Don’t forget about single and double quotes, escape sequences and comments.

4. Write a program to implement a circular queue as a linked list.5. Design the algorithm and generate a program to perform an in-fix to post-fix conversion.6. Design a function to obtain the mirror image of binary tree and demonstrate its functioning

with a C program.7. Write a program, which will convert a singly linked list into a binary tree.8. Write a program, which will convert binary tree into a binary search tree.9. Write a program to search a given numbers in a linked list and print the output a found or not

and no. of occurrences (if so).10. Write a program for indenting of a C program.

Department of Computer Science, A.P.S. University, Rewa (M.P.)Syllabus for M.Sc. Bioinformatics - Second Semester

(Session 2004-2006)MBI - 201 (T) BIOLOGICAL DATABANKS, DATA SECURITY AND DATA MINING TECHNIQUES


Unit I Data warehousing, data capture, data analysis Introduction to Nucleic Acid and Protein Sequence Data Banks Nucleic acid sequence data banks: Genbank, EMBL nucleotide sequence data

bank, AIDS Virus sequence data bank, rRNA data bank Protein sequence data banks: NBRF-PIR, SWISSPROT, Signal peptide data

bank

Unit II Database Similarity Searches: BLAST, FASTA, PSI-BLAST algorithms Pair wise sequence alignment - NEEDLEMAN and Wunsch, Smith Waterman

algorithms Multiple sequence alignments - CLUSTAL, PRAS

Unit III Patterns, motifs and Profiles in sequences:

Derivation and searching, Derived Databases of patterns, motifs and profiles: Prosite, Blocks,

Prints-S, Pfam, etc. Primer Design

Unit IV Data Security

Science and study of methods of protecting data: Discretionary and mandatory access controls, secure database design, data integrity, secure architectures, secure transaction processing, information flow controls, inference controls, and auditing. Security models for relational and object-oriented databases. Security of databases in a distributed environment. Statistical database security.

References : Baxevanis, A.D. & Ouellettee, B.F.F.: Bioinformatics: a practical guide to the analysis

of genes and proteins. (2nd. Ed.) New York. Wiley Interscience, 2001. Mount, D. W.: Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor.

CSHL Press, 2001. Marshall D. Abrams, Sushil Jajodia, and Harold J. Podell, eds. Information Security:

An Integrated Collection of Essays, IEEE Computer Society Press, 1995.



(Session 2004-2006)MBI - 202 (T) INTRODUCTION TO DATABASE SYSTEMS


UNIT I Basic Concept: An Introduction to database System, Basic Data System

Terminology, Purpose of DBMS, Data Independence, An Architecture of DBMS: Schema, Subschema, mapping, Physical & Logical Data, Basic File Systems, File Organization: Sequential, Index Sequential, Hosting, B-Tree based index, File Organisation based on Dynamic Hashing with immediate splitting, Model of Real World, Details of E-R Model.

UNIT II Three Data Models: An Overview of three Main Data Models i.e.

Hierarchical Model, Network Model, Relational Model and their Inter comparison, Concept of Relation, Relational Algebra: Basic Operation like Union, Intersection, Difference, Product Join, The relational Calculus: Domain & Tuple Calculus, Relational Database Design: Integrity Constraints, Functional Dependency: Single Value and Multi Value Functional dependency, Normal Forms: I, II, III, Boycee Codd, & IVth Normal forms; Join Dependency.

UNIT III Query Processing & Database Software: Query Interpretation, Equivalence

of Expression, Estimation of Query Processing Cost, Query Optimization by Algebraic Manipulation, Join Algorithms, Types of Data Base Languages: Procedural and Non-procedural Language, Relational Commercial Query languages,QBE, SQL: Introduction, Basic Structure, the Power of SQL (Creation, Insertion, Deletion, Indexing & Modification of Databases in SQL), query optimization strategies.

UNIT IV Management Considerations & Future Trends: Security & Integrity:

Introduction, Access Control, Crypto Systems, Statistical DataBase Security; Concurrency Control: Transaction, Database System Architecture, Serializability, Locking, Database Recovery: Kinds of Failure, Recovery Techniques, Object, An Overview of Oriented Model, Distributed database: Structure, Tradeoffs, Design, Client Server Database, Knowledge databases.

Text Books:1. Henry F. Korth & A. Silbershatz: Data Base System Concepts, MGH2. Arun K. Majumdar & P. Bhattacharya: Data Base Management System, TMH

Reference Books1. Jeffrey O. Ullman : Principles of Database Systems, Galgotia Pub. Co. Ltd.2. Bipin C. Desai: An Introduction to Database Systems, Galgotia Pub. Co. Ltd.3. James Martin: Principles of Database Management, PHI4. James Martin, Computer Database organization, PHI



(Session 2004-2006)MBI - 203 (T) PROGRAMMING IN OBJECT ORIENTED LANGUAGES


Unit IJAVA

An introduction to JAVA programming Object oriented programming and Java Java Basics, Working with objects, Arrays, Conditionals and Loops Creating Classes and Applications in Java, More about methods Java Applets Basics, Graphics, Fonts and Color. Simple Animation and Threads, Advanced Animation, Images and Sound Managing Simple Events and Interactivity Creating User Interfaces with AWT

Unit II Windows, Networking and other Tidbits, Modifiers, Access Control and Class

Design. Packages and Interfaces, Exception, Multithreading, Streams and I/O. Using Native Methods and Libraries, Under the Hood, Java Programming

Tools. Working with Data Structures and Java Image Filters

Unit III

Programming Visual Basic

Introduction to Application Development using Visual Basic Working with Code and Forms Variables, Procedures and Controlling Program Executor Standard Controls

Unit IV Data Access Using Data Control Connecting to Oracle Database using Visual Basic

References: Java by dissestion , Ira Pohl and Charlie Mc Dowell, Addison Wesley. Java Software Solutions , John Lewis and William Loftus, Addison Wesley

Java for Computer Information Systems , Andrew Stangaard , Prentice Hall. Data Structures and Algorithms in Java (Edition ), Michael T. Goodrich, Roberto

Tamassia, John Wiley. VB6 Unleashed – Techmedia. Using Visual Basic 6, Que.



(Session 2004-2006)MBI 204 (T) BIODIVERSITY INFORMATICS AND CHEMOINFORMATICS


Unit I Introduction: Biological information, biological diversity of life, species

diversity: taxonomic information on plants, animals, microbes and viruses. Genetic diversity, Ecological/ Ecosystem diversity, Urban biodiversity, methods for species identification and classification, biodiversity databases and software for identification.

Unit II

Immunology : Overview of immune system, innate and acquired immune system, Characteristics of B Cell and T Cell antigens, Autoimmunity, Ligand- receptor interaction in the light of protein structure in immune system, Use of bioinformatics in immunology and vaccine development

Unit III Chemoinformatics: History, current activities and challenges in the

chemoinformatics, Chemical information and sources, Major chemical databases and information retrieval, Chemical Structure drawing tools.

Unit IV Pharmacology and drug discovery, Pharmacodynamics and pharmacokinetics, Drug

potency and Efficacy, Docking, Active site, Pharmacophore identification, Absorption, Development of a drug: Classical steps, Chemical Parameters in drug design, Structure based drug discovery, Quantitative Structure Activity Relationships.

Reference:

PANKHURST, R.J.: Practical taxonomic computing. 1991.



(Session 2004-2006)MBI 205 (T) STRUCTURAL BIOLOGY / MOLECULAR BIOLOGY


Unit I Internal and external co-ordinate system Generation of co-ordinates of biopolymers in Cartesian and cylindrical polar co-

ordinate system Methods of single crystal X-ray Diffraction of macromolecules: molecular replacement

method and direct method Fiber diffraction Analysis of structures and correctness of structures Submission of data to PDB: atomic coordinates and electron density maps

Unit II Anatomy of Proteins

Ramachandran plot Secondary structures Motifs Domains Tertiary and quaternary structures

Anatomy of DNA: A, B, Z DNA, DNA bending etc. RNA structure Structure of Ribosome Principles of Protein Folding Structural data banks - Protein Data Bank, Cambridge small molecular crystal structure

data bank Calculation of conformational energy for bio-macromolecules

Unit III Methods for Prediction of Secondary and Tertiary structures of Proteins

Knowledge- based structure prediction Fold recognition Ab initio methods for structure prediction

Methods for comparison of 3D structures of proteins Methods to predict three dimensional structures of nucleic acids, rRNA Electrostatic energy surface generation

Unit IV Molecular Mechanics & Molecular Dynamics of Oligopeptides, Proteins, Nucleotides,

& small Molecules Mechanics and dynamics of bio-macromolecules Simulation of molecular mechanics and dynamics Simulations of Free Energy changes Force fields

Molecular interactions of Protein – Protein Protein – DNA Protein – carbohydrate DNA – small molecules etc.

Docking of Molecules Molecular Design

References Creighton, T. E. Ed.: Protein Structure: A Practical Approach. 1989. Creighton, T.E.: Proteins: Structure And Molecular Properties. Second Edition. New York. W.

H. Freeman And Company, 1993. Creighton,T.: Protein Folding, 1992. Sternberg, M.J.E.: Protein structure prediction: a practical approach, 1996 Pain, R.G.: Mechanisms of protein folding, 1994 Leach.A.R: Molecular modelling: principles and applications


Department of Computer Science, A.P.S. University, Rewa (M.P.)Syllabus for M.Sc. Bioinformatics - Third Semester

(Session 2004-2006)MBI - 301 (T) COMPUTER GRAPHICS AND VISUALIZATION


UNIT I Overview of Graphics Systems and 2D Transformation: Display Devices, Hardcopy devices, Interactive Input Devices, Display processors, Graphics Software. Output Primitives: Points and lines, Line drawing algorithms, Circle generating algorithms Basic Transformations, Matrix Representations and Homogeneous Coordinates, Composite Transformations, Reflection, Shear, Raster methods for transformations. Windowing and Clipping : Windowing concepts, Clipping algorithms, Window-to-Viewport transformation.

UNIT II 3D Transformation , Viewing and Modeling: Three Dimensional Transformations : Basic transformations, Rotation about an arbitrary axis, Reflections, Shears, Transformations of coordinate system. Projections, Viewing transformations, Software implementation, Hardware implementation. Hidden surface & Hidden line removal : Classification, Back face removal, Depth Buffer method, Scan line method, Hidden line elimination, Curved surfaces. Shading and color models : Modeling light intensities, Displaying light intensities, Surface shading methods, Color models. Modeling methods : Basic concept, Master coordinates and modeling transformation structured display files, symbol operations.

UNIT – IIIOverview of Multimedia: Introduction, Application of multimedia, terminology, multimedia enabling technologies in digital representation, Hardware & Software requirement, multimedia standard, hypertext; History, nature, links, navigation & structure. The nature of sound, digitizing sound, processing sound, compression format, MIDI, Combining, source & picture, Video & image processing: Digitizing video, video standards video compression, digital video editing and post production, streamed video and video conferencing.

UNIT – IVAnimation: Captured animation and image sequences, digital cel and sprite animation, key frame animation, 3D animation, Combining media: synchronization based presentation: SMIL (synchronize multimedia integration language), synchronize presentation (HTML + TIME), accessibility. knowledge base multimedia, future direction. ECMAScript syntax outline, Multimedia and network: network and transport protocols, multicasting, application protocols for multimedia: HTTP, caching; Quality of service, server side computation.

Text Books :1. D. Hearn and Baker : Computer Graphics, Prentice Hall of India Pvt. Ltd.2. Steven Harrington : Computer Graphics, MGH.3. Chapman,Wiley; Digital Multimedia,4. J.D.Foley, A.Van Dam - Fundamentals of Interactive Computer Graphics.5. David F. Rogers. - Procedural Elements for Computer Graphics6. David F. Rogers, J.A.Adams - Mathematical Elements for Computer Graphics

Reference Book:1. Newman and R.F. Sprouli : Principles on Interactive Computer Graphics, MGH.2. W.K. Giloi : Interactive Computer Graphics, PHI.3. R.A. Piastock and G. Kalley : Theory and Problems of Computer Graphics, MGH4 John F. Kloegel Buford; Multimedia System



(Session 2004-2006)MBI - 302 (T) MACHINE LEARNING TECHNIQUES IN BIOINFORMATICS


Unit I - IntroductionBiological data in digital symbol sequences, genomes – Diversity, size and structure, proteins and preteomes, on the information content of biological sequences, prediction of molecular function and structure.Machine-Learning Foundations: The probabilistic framework, Introduction: Bayesian Modeling, the cox jaynes axioms, Bayesian inference and induction, model structures: graphical models and other tricks, summary.Probabilistic Modeling and Inference: Examples, the simplest sequence models, statistical mechanics.

Unit II – Machine Learning AlgorithmsIntroduction, dynamic programming, gradient descent, EM/GEM algorithms, Markov-Chain Monte-Carlo methods, simulated annealing, evolutionary and genetic algorithms, learning algorithms: miscellaneous aspects.Neural Networks: The theory, introduction, universal approximation properties, priors and likelihoods, learning algorithms: backpropagation.Neural Networks: Applications, sequence encoding and output interpretation, sequence correlations and neural networks, prediction of protein secondary structure, prediction of signal peptides and their cleavage sites, applications for DNA and RNA nucleotide sequences, prediction performance evaluation, different performance measures.

Unit III Introduction, Prior information and initialization, likelihood and basic algorithms, learning algorithms, applications of HMMs: General aspects.Hidden Markov Models: Applications, Protein applications, DNA and RNA Applications, Advantages and limitations of HMMs.Probabilistic Graphical Models in Bioinformatics: The Zoo of graphical models in bioinformatics, Markov Models and DNA symmetries, Markov Models and Gene finders, Hybrid models and neural network parameterization of graphical models, the single-model case, Bidirectional Recurrent neural networks for protein secondary structure prediction.

Unit IV Probabilistic Models of Evolution: Phylogenetic Trees, Introduction to probabilistic Models of evolution, substitution probabilities and evolutionary rates, rates of evolution, data likelihood, optimal trees and learning, parsimony, extensions.Stochastic grammars and linguistics: Introduction to formal grammars, formal grammars and the Chomsky hieararchy, applications of grammars to biological sequences, prior information and initialization, likelihood, learning algorithms, applications of SCFGs, experiments, future directions.Microarrays and Gene expression: Introduction to Microarray data, probabilistic modeling of Array Data, clustering, gene regulation.

Reference:



(Session 2004-2006)MBI - 303 (T) FROM GENOME TO DRUGS


Unit IFrom Genomes to Drugs with Bioinformatics: The molecular basis of disease, the molecular approach to curing diseases, finding protein targets, genomics vs preteomics, developing drugs, a bioinformatics landscape, the intrinsic view, the extrinsic view, drug screening, scenario 3: genetic variability. Database searching : single sequence heuristic algorithms, alignment and search statistics, multiple sequence alignment, multiple alignment and database searching, protein families and protein domains, conclusion.Structure, properties and computer identification of Eukaryotic genes: Structural characteristics of eukaryotic genes, classification of splice sites in mammalian genomes, methods for the recognition of function signals, search for nonrandom similarity with consensus sequences, position-specific sensors, accuracy measures, prediction of donor and acceptor splice junctions, recognition of promoter regions in human DNA, prediction of poly-A sites, gene identification approaches, annotation of sequences from genome sequencing projects, functional analysis and verification of predicted genes, internet sites for gene finding and functional site prediction.Unit IIFrom Genomes to Drugs with Bioinformatics: General features of Regulatory regions in eukaryotic genomes, general functions of regulatory regions, transcription factor binding sites (TF-sites), sequence features, structural features, structural elements, organizational principles of regulatory regions, bioinformatics models for the analysis and detection of regulatory regions, detection of transcription factor binding sites, detection of structural elements, statistical and biological significance, methods for detection of regulatory regions, regulatory sequences.Unit IIIHomology modeling in Biology and Medicine: Introduction, the concept of homology modeling, input data, methods, modeling at different levels of complexity, range of targets, strengths and limitations, validation, side-chain prediction accuracy, protein health, availability, backbone conformations, side-chain conformational analysisProtein structure prediction: Overview, definition of terms, structure comparison and classification, 3D structure prediction, results, remote homology detection, structural genomics, sequence to structure to function paradigm, validation of predictions, strengths and limitations, threading, strengths, limitations, accessibility.Unit IVProtein-Ligand Docking in Drug Design: Introduction, A taxonomy of docking problems, application scenarios in structure-based drug design, methods for protein-ligand docking, docking of combinatorial libraries, molecular docking in practice, preparing input data, analyzing docking results, software accessibilityModeling protein-protein and protein-DNA Docking: Introduction, the need for protein-protein and protein-DNA docking, overview of the computational approach, structural studies of protein complexes, methodology of a protein-protein docking strategy, Modeling protein - DNA complexes, method, results, strategies for protein-protein docking, Fourier correlation methods, other rigid body docking approaches, flexible protein-protein docking, blind trials of protein-protein docking, energy landscape for protein docking, conclusions. CADD and modeling using QSAR.

REFERENCE: 1. Bioinformatics-From Genome to Drugs by R . MANNHOLD,H.KUBINYI,2. H. TIMMERMANN(Thomas lengauer edition)



(Session 2004-2006)MBI - 304 (T) METABOLOMES AND METABOLIC PATHWAYS


Unit I Carbonydrates and lipids, their importance in cells. Proteins: Amino acids and peptides; primary, secondary, tertiary and quaternary

structures; protein – protein interactions; sequence homology, functional and evolutionary relationships of proteins.

Unit II Nucleic acids: Bases, nucleotides, RNA and DNA. Different structural forms of DNA,

denaturation and renaturation of DNA, protein-nucleic acid interactions. Enzymes: Units of activity, coenzymes and metal cofactors, temperature and pH effects,

Michaelis-Menten kinetics, inhibitors and activators, active site and mechanism of enzyme action, isoenzymes, allosteric enzymes, regulation by covalent modification.

Unit III Organization of metabolic systems: enzyme chains, multienzyme complexes and

multifunctional enzymes, regulatory enzymes and feedback control of metabolic pathways, energy charge.

Carbohydrate metabolism: Glycolysis, gluconeogenesis, glycogenolysis, glycogenesis and pentose phosphate pathway; hormonal control.

Unit IV TCA cycle and oxidative phosphorylation -oxidation and biosynthesis of fatty acids. Transamination and deamination of amino acids, ketogenic and glucogenic amino acids,

urea cyclePurine and pyrimidine biosynthesis



(Session 2004-2006)MBI - 305 (T) EMERGING AREAS IN BIOINFORMATICS


Unit-IQuestions based on Micro-array technology and system biology

Unit-IIQuestions based on Bioinformatics in Drug designating

Unit-IIIQuestions based on ANN and pattern recognition technique applied for bioinformatics

Unit-IVQuestions based on Nano technology and other tools / technology used in Bioinformatics, and Challenges associated with it.

References:Internet and recent research papers including the books already mention in various papers related to topic mention.



(Session 2004-2006)PAPER (MBI-103) INTRODUCTION TO CONCEPT IN COMPUTING & COMPUTER PROGRAMMING


Unit I

Fundamentals of Computing Introduction to operating Systems: WINDOWS, NT, UNIX/Linux operating

systems Comparative Advantages of Security (hacking, cracking) Installation,

Portability and Programming of these operating systems Computer Viruses

Unit II Elements of Programming in ‘C’ - Pointers, Pointers to the functions, Macros

and Programming in C, Graphs, Data structure - Linked List; stack; Queue, Binary Trees, Threaded Binary trees; File handling in C; Exception handling in C

Unit III Use of INTERNET & WWW LAN, WAN, MODEM Optical Vs. Electronic Networking Security of the network, Fire-walls Searches on MEDLINE, CD, bibliographic databases.

Unit IV

Network Goals Applications Network Network structure Network architecture Hierarchical networks Ethernet and TCP/IP family of protocols Transport protocol design

Reference: Andrew S. Tanenbaum: Computer Networks


Documents

Bioinformatics Syllabus for M.Sc