m.sc. bioinformatics syllabus

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Swami Ramanand Teerth Marathwada University Nanded School of Technology Sub Centre, Latur Syllabus For the M.Sc. Bioinformatics (CGPA) School of Technology,

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Page 1: M.Sc. Bioinformatics syllabus

Swami Ramanand Teerth Marathwada University

Nanded School of Technology

Sub Centre, Latur

Syllabus For theM.Sc. Bioinformatics

(CGPA)School of Technology,

SRTMUN Sub-Centre, Latur

Page 2: M.Sc. Bioinformatics syllabus

Academic Year 2010-11

Page 3: M.Sc. Bioinformatics syllabus

M.Sc. Bioinformatics (CGPA)

School of Technology, SRTMUN Sub-Centre, Latur

M.Sc. Bioinformatics (CGPA) degree builds the student for higher studies in Bioinformatics and to be competent with the current race with the development of new computational technologies. The duration of the study is four semesters, which is normally completed in two years. The primary goal of bioinformatics is to increase our understanding of biological processes. What sets it apart from other approaches, also, it is focus on developing and applying computationally intensive techniques (e.g., computer aided drug design, systems biology, pattern recognition, data mining, machine learning algorithms, and visualization) to achieve this goal. Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association studies and the modeling of evolution.

CGPA systemPresently the School conducts M.Sc. Bioinformatics (CGPA) Post-Graduate Courses as per CGPA = CUMULATIVE GRADE POINT AVERAGEA Cumulative Grade Point Average (CGPA) is the mean Grade Point Average (GPA) from all academic terms within a given academic year, whereas the GPA may only refer to one term.

CoursesSr. No Name of the Program Duration Intake

I M. Sc. [Bioinformatics]- CGPA 2 Years 30 (Seat)

Eligibility and FeesAny science graduate is eligible for seeking admission to both of the courses. More details of admission procedure and fees structure can be seen from the prospectus of Campus Schools of the University.

Page 4: M.Sc. Bioinformatics syllabus

Feature of CGPA System

Master Degree would be of 112 Credits eachEach semester shall have five theory courses, Four practical coursesFive theory courses = 20 Credits Four practical courses= 8 Credits Total 28 credits per semesterTotal 700 marks per semesterEvery student shall complete 112 credits in a minimum of four semesters. All semester will have

28 credits each. Four semester X 28 credits = 112 creditsTotal 2800 marks for Master Degree program One Credit = 25 marksTwo Credits = 50 MarksFour Credits = 100 MarksTheory Course = 100 MarksPractical Course = 50 MarksTheory Course = 100 Marks

Internal Exam External Exam

50 Marks = 2 Credits 50 Marks = 2 Credits

Break up internal exam marks for Theory

Theory Test-1 Theory Test-2 Home Assignments Total Marks

15 marks 15 marks 20 marks 50 Marks = 2 Credits

Practical Course = 50 Marks

Internal Exam External Exam

25 Marks = 1 Credit 25 Marks = 1 Credit

Break up internal exam marks for Practical

Practical Test-1 Practical Test-2 Total Marks

10 marks 15 marks 25 Marks = 1 Credit

Page 5: M.Sc. Bioinformatics syllabus

Project Course = 200 Marks

Internal Exam External Exam

100 Marks = 4 Credits 100 Marks = 4 Credits

Break up internal exam marks for Project Synopsis Project work Total Marks

25 marks 75 marks 100 Marks = 4 Credits

Semester ICODE NO NAME OF PAPER INTERNAL EXAM /

DEPARTMENT LEVEL CREDIT

INTERNAL EXAM CREDITS

TOTAL CREDITS

BIM-101 (T) Genetics and Molecular Biology

2 2 4

BIM-102 (T) Bioinformatics 2 2 4

BIM-103 (T) Biostatistics 2 2 4

BIM-104 (T) Data Base Managements Systems Oracle

2 2 4

BIM-105 (T) Linux 2 2 4

BIM-102 (P) Bioinformatics 1 1 2

BIM-103 (P) Biostatistics 1 1 2

BIM-104 (P) Data Base Managements Systems Oracle

1 1 2

BIM-105 (P) Linux 1 1 2

14 14 28

Total Credits in I Semester = 28

Page 6: M.Sc. Bioinformatics syllabus

Semester IICODE NO NAME OF PAPER INTERNAL

EXAM / DEPARTMENT LEVEL CREDIT

INTERNAL EXAM CREDITS

TOTAL CREDITS

BIM-201 (T) Advanced Molecular Biology 2 2 4

BIM-202 (T) Computational Biology 2 2 4

BIM-203 (T) Immunoinformatics 2 2 4

BIM-204 (T) Chemoinformatics 2 2 4

BIM-205 (T) Machine Intelligence in Bioinformatics

2 2 4

BIM-203 (P) Immunoinformatics 1 1 2

BIM-204 (P) Chemoinformatics 1 1 2

BIM-205 (P) Machine Intelligence in Bioinformatics

1 1 2

BIM-206 (P) Numerical Methods and Optimization Techniques

1 1 2

14 14 28

Total Credits in II Semester = 28

Page 7: M.Sc. Bioinformatics syllabus

Semester IIICODE NO NAME OF PAPER INTERNAL

EXAM / DEPARTMENT LEVEL CREDIT

INTERNAL EXAM CREDITS

TOTAL CREDITS

BIM-301 (T) Computer Aided Drug Design 2 2 4

BIM-302 (T) Object Oriented Programming (OOPS) JAVA

2 2 4

BIM-303 (T) Microbial Genomics 2 2 4

BIM-304 (T) Principle of Drug Action 2 2 4

BIM-305 (T) Molecular Modeling 2 2 4

BIM-301 (P) Computer Aided Drug design 1 1 2

BIM-302 (P) Object oriented Programming (OOPS) JAVA

1 1 2

BIM-303 (P) Microbial Genomics 1 1 2

BIM-304 (P) Perl for Bioinformatics 1 1 2

14 14 28

Total Credits in III Semester = 28

Semester IVCODE NO NAME OF PAPER INTERNAL EXAM /

DEPARTMENT LEVEL CREDIT

INTERNAL EXAM CREDITS

TOTAL CREDITS

BIM-401 (T) Plant Genomics 2 2 4

BIM-402 (T) Metabolomics and Metabolic Engineering

2 2 4

BIM-403 (T) Oncogenomics and Cell Signaling

2 2 4

BIM-404 (T) IPR and Industrial Psychology 2 2 4

Page 8: M.Sc. Bioinformatics syllabus

BIM-405 (PJ) Project 4 4 8

BIM-401 (P) Plant Genomics 1 1 2

BIM-402 (P) Metabolomics and Metabolic Engineering

1 1 2

14 14 28

Total Credits in IV Semester = 28

Page 9: M.Sc. Bioinformatics syllabus

Swami Ramanand Teerth Marathwada University

Nanded School of Technology

Sub Centre, Latur

Syllabus For theM.Sc. Bioinformatics

(CGPA)School of Technology,

SRTMUN Sub-Centre, Latur Academic Year 2010-11

Page 10: M.Sc. Bioinformatics syllabus

Semester -I

Page 11: M.Sc. Bioinformatics syllabus

Genetics and Molecular BiologySub. Code: BIM-101 (T)

Course Objectives: To enable the students to gain knowledge about the fundamentals concepts and basic principles such as structure of DNA / RNA, transcription, translation gene regulation, and RNA splicing and also the Mendelian genetics

Total: 45L Total Credits: 4

Unit -I: Structure of Nucleic Acid (9L)Structure of DNADifferent forms of DNA and RNAIdentification of DNA as genetic material by Griffith –Avery, McLeod and McCartyFrankel and Singer Hershey and Chase Messelson and Stahl experiment

Unit -II: DNA Replication and Mutation (9L)Semi-Conservative replicationReplication of DNA in EukaryotesMolecular basis of Mutation Classification of mutation

Unit -III: Gene Expression and Regulation (9L)Genetic codeTranscription Prokaryotes and Eukaryotes Post transcriptional modification Translation in prokaryotes and Eukaryotes Post translational modification Gene Regulation Lac operon model

Unit -IV: Mendelian Genetics (9L)Mendel’s laws MonohybridDihybrid inheritanceMultiple allelesStructure and organization of chromosome in Prokaryote and Eukaryotes

Unit -V: Crossing Over and Linkage (9L)LinkageTypes of linkageCrossing over and their typesRecombination mappingTwo point and three point text cross mapping in bacteria

Page 12: M.Sc. Bioinformatics syllabus

Text Books:Molecular Genetics: Structure of Life, Virendra Gomase and Aravind Tripathi, VDM Verlag Dr.

Müller, Germany, ISBN:978-3-639-25001-5, (2010). Genetechnology, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,

ISBN: 978-3-639-13467-4, (2010). Molecular biology of the Cell, Bruce Alberts, Alexander Johnson, Alexander Johnson, Julian

Lewis, Martin Raff, keith Roberts, Peter Walter; Garland Science, Taylor & Francis group,4th Edition (2002)

Essential Cell Biology, Bruce Alberts Dennis Bray, Karen Hopkins, Alexander Johnson Julian Lewis, Martin Raff, Keith Roberts, Peter Walter; Garland Science; Taylor & Francis Group,4th Edition (2004)

Cell Molecular Biology, E. D. P. De Robertis, E. M. F. De Robertis, Jr, Lippinwt William & Wilkins (2001)

Molecular biology, David Freifelder, Narosa Publishing House, 1st Edition(2004)Genes, VIII Benjamin Lewin; Pearson Education International,8th Edition (2004)Principles of Gene Manuplation, S. B. Primrose R. M. Twyman & R. W. old, Blackwell

Science,6th Edition (2001)Advanced Molecular Biology, R. M. Twyman, 1st Edition , (2003)Instant Notes on Molecular Biology; P.C. Turner, A. G. Mclennan, A. D. Bates & M. R. H.

White, 2nd Edition (2002)Molecular Biology, David Freifelder, Narosa Publishing House,2nd edition (2004)Microbial Genetics, David Freifelder, Narosa Publishing House, 2nd edition(2004)Essential Molecular Biology (volume I & II) Practical Approach; Edited By T. A. Brown; Oxford

University Press, 2nd Edition (2001)

Page 13: M.Sc. Bioinformatics syllabus

BioinformaticsSub. Code: BIM-102 (T)

Course Objectives: To enable the students to gain knowledge about Bioinformatics.

Total: 45L Total Credits: 4

Unit -I: Biological Database Design and Management (9L)DBMS, RDBMSSources of biological dataDatabase Design and Data MiningDatabase Management Security & Architecture

Unit -II: Genomics Database (9L)Human Genome ProjectDatabase of Model Species : Drosophila melanogaster , Arabidopsis thaliana, C. elegans, Saccharomyces cerevisiae, Danio rerioPlasmodium Falsiparum Genome ProjectThe Arabidopsis Genome Project

Unit -III: Biological Databanks (9L)NCBI, DDBJ, EMBL, PDB, SRS, BRENDA, TrEMBL, UniProt, KEGG, MIAME, OMIM

Unit -IV: Bioinformatics database & repositories (9L)Protein database – GenBankNucleotide & Gene database – GenBankMicroarray Database & analysisGene Expression Profile Database – GEOMetabolic Pathway – PathDBEnzyme Database – KEGGIon Transport Database

Unit -V: Genome Analysis (9L)Genome AnalysisGenome Anatomya. Prokaryotic Genome –E coli Mycoplasmab. Eukaryotic Genome- Human, Rat, Arabidopsis, Soybean, Mungbean, RiceComparative genomics c. Proteomics analysis, horizontal gene transferFunctional classification of geneGene order on chromosome

Text Books:Bioinformatics- Theory and Practice, N.J. Chikhale and V.S. Gomase, Himalaya Publication

House, India; 1 edition, 2007, ISBN-13: 978-81-8318-831-9

Page 14: M.Sc. Bioinformatics syllabus

BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl

Leon, 2003, O'Reilly Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley & Sons Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley &

Sons Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall Proteomics- Theory and Practice, V.S. Gomase and N.J. Chikhale, Himalaya Publication House,

India,1-edition, 2009, IBSN: 978-81-8488-313-8 Introduction to Bioinformatics, Teresa Attwood, David Parry-Smith, 2001, Prentice Hall Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor

Laboratory Press Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L.

Raymer, Elaine Nicpon Marieb, 2002, Benjamin/Cummings Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao

Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press

Page 15: M.Sc. Bioinformatics syllabus

BiostatisticsSub. Code: BIM-103 (T)

Course Objectives: To enable the students to gain knowledge about Biostatistics.

Total: 45L Total Credits: 4

Unit -I: Introduction (9L)Methods of collection of dataClassifications and graphical representation of dataBinomial and normal probability distribution Polygon, histogram, measure of central tendencySignificance of statistical methodsProbabilityDegree of freedom, measures of variation Standard deviation, Standard error

Unit -II: Statistical Sampling (9L)Sampling, sample size and power Statistical inference and hypothesis Tests for statistical significance: student t-test Chi-square test, confidence level Null hypothesis

Unit -III: Statistical Analysis (9L)Linear regression and correlation Analysis of Variance (one way and two way) Factorial designs (including fraction factorial design)Theory of probabilityPermutation and Combination Ratios, Percentage and Proportion Two way ANOVA and Multiple comparison procedures

Unit -IV: Experimental design and trials (9L)Non-parametric tests, Experimental design in clinical trials Statistical quality control, Validation Optimization techniques and Screening design Correlation and regression, least square method Significance of coefficient of correlationNonlinear regression

Unit -V: Bioassays-calculations (9L)Bioassays-calculations of doses response relationships LD50, ED50, probit analysisApplications of software for statistical calculation viz. SPSS, foxtronApplication of computers in Pharmaceutical sciences

Page 16: M.Sc. Bioinformatics syllabus

Textbook:

The Biostatistics Cookbook: The Most User-Friendly Guide for the Bio/Medical Scientist, S. Michelson and T. Schofield, Springer; 1 edition, ISBN-13: 978-0792338840, (1996).

Intuitive Biostatistics: A Nonmathematical Guide to Statistical Thinking, Harvey Motulsky, Oxford University Press, USA, ISBN-13: 978-0199730063, (2010).

Biostatistics: The Bare Essentials 3/e (with SPSS), Norman, Geoffrey Norman, David Streiner, BC Decker Inc; 3 edition, ISBN-13: 978-1550094008, (2008).

Biostatistics, Second Edition: A Guide to Design, Analysis and Discovery. Ronald N. Forthofer, Eun Sul Lee, Mike Hernandez , Academic Press; 2 edition, ISBN-13: 978-0123694928, (2006).

Fundamentals of Biostatistics, Bernard Rosner, Duxbury Press; 6 edition, ISBN-13: 978-0534418205, (2005).

Biostatistics for the Biological and Health Sciences with Statdisk, Marc M. Triolaand and Mario F. Triola, Addison Wesley, ISBN-13: 978-0321194367, (2005).

Introduction to Biostatistics: Second Edition, Robert R. Sokal and F. James Rohlf, Dover Publications; 2 edition, ISBN-13: 978-0486469614, (2009).

Basic & Clinical Biostatistics (LANGE Basic Science), Beth Dawson, Robert Trapp, Robert Trapp , McGraw-Hill Medical; 4 edition, ISBN-13: 978-0071410175, (2004).

Biostatistics, Tarum Rawat, Samuel Devlin, Kõva köide,Kirjastus: Sarup & Son, ISBN-13: 9788176258050 (2008).

Pharmaceutical Statistics: Practical and Clinical Applications, Revised and Expanded (Drugs and the Pharmaceutical Sciences), Sanford Bolton and Charles Bon , Informa Healthcare; 4 edition, ISBN-13: 978-0824746957, (2003)

Statistical Methods in Biology , Norman T. J. and Bailey M.A., Cambridge University Press; 3 edition, ISBN-13: 978-0521469838, (1995).

Primer of Applied Regression Analysis and Analysis of Variance, 2nd edition, Glantz S.A., Slinker B.K., New York: McGraw-Hill, (2001)

Page 17: M.Sc. Bioinformatics syllabus

Data Base Managements Systems Oracle Sub. Code: BIM-104 (T)

Course Objectives: To enable the students to gain knowledge about Data Base Managements Systems Oracle.

Total: 45L Total Credits: 4

Unit -I: Basic concepts (9L)Database & database users, Characteristics of the database, database systems, Concepts and architecture, date models, schemas & instances, DBMS architecture & data independence, Database languages & interfaces, Data modeling using the entity-relationship approach. Overview of hierarchical, Network & Relational Data Base Management Systems

Unit -II: Relational model, languages & systems (9L)Relational data model & relational algebraRelational model conceptsRelational model constraints, relational algebra SQL- a relational database languageDate definition in SQL, view and queries in SQLSpecifying constraints and indexes in SQL Relational database management systemsDB2, Oracle PL/SQL Programming Language / Structure Query Language- DDL, DML Unit -III: Data Structure (9L)DB2 Architecture Logical Data Structures Physical Data Structure Instances, Table Spaces, Types of Tablespaces Internal Memory Structure Background Processes Data Types, Roles & Privileges Stored Procedures User Defined Functions Packages, Cursors, Error Handling, Triggers, collectors Unit -IV: Relational data base design (9L)Function dependencies & normalization for relational databases: Functional dependencies, Normal forms based on primary keys, (1NF, 2NF, 3NF & BCNF), Lossless join and dependency preserving decomposition Unit -V: Concurrency control & recovery techniques (9L)Concurrency control techniques

Page 18: M.Sc. Bioinformatics syllabus

Locking techniques, time stamp ordering Granularity of data items, recovery techniques Recovery concepts, database backup and recovery from catastrophic failures

Text Books:Oracle Data Guard 11g Handbook (Osborne ORACLE Press Series), Larry Carpenter, Joseph

Meeks, Charles Kim, Bill Burke, Sonya Carothers, Joydip Kundu, Mike Smith, Nitin Vengurlekar, McGraw-Hill Osborne Media; 1 edition, ISBN-13: 978-0071621113, (2009)

Oracle General Ledger Guide: Implement a Highly Automated Financial Processing System, Melanie Cameron, McGraw-Hill Osborne Media; 1 edition, ISBN-13: 978-0071622295, (2009)

Database System Concepts, Avi Silberschatz, Henry F. Korth, S. Sudarshan, McGraw-Hill, ISBN 0-07-295886-3

Database Management Systems By Raghu Ramakrishnan, Johannes Gehrke, McGraw-Hill , ISBN: 0072465638 / 9780072465631

Fundamentals of Database Management Systems by Mark L. Gillenson, John Wiley & Sons, ISBN-13: 9780471262978, 978-0471262978

Relational Database Management: A Systems Programming Approach, M. Papazoglou and W. ValderPrentice Hall, ISBN-10: 0137718667

Oracle Database 11g, A Beginner's Guide, Ian Abramson, Michael Abbey, Michael Corey, McGraw-Hill Osborne Media, ISBN-10: 0071604596

An Introduction to Database Systems, C. J. Date, Addison Wesley Longman, ISBN-10: 0201385902

Page 19: M.Sc. Bioinformatics syllabus

LinuxSub. Code: BIM-105 (T)

Course Objectives: To enable the students to gain knowledge about Linux.

Total: 45L Total Credits: 4

Unit –I: Introduction to Linux (9L)OS and Linux, History of Linux and UnixLinux SoftwareLinux Documentation, DistributionInstallation of LinuxLinux and InterfacesGenome Desktop, KDE

Unit –II: Linux Environments (9L)KDE - desktop, help system, KDE configurationGenome - Interface, file manager, Panel, Applets, configurations The shell – command line, file name, encapsulation, standards output/ input, shell variables, pipes Linux File StructureShell configuration

Unit –III: System and network Configuration (9L)System configurationDistribution administration toolsRead Hat administration toolsConfiguring usersMapping CD Rom, Floppy, CD-R/W DriversPrinter, Update toolsInstall softwares packages

Unit –IV: Client Applications and Server managements (9L)Client ApplicationsMails and News clientsWeb, FTP and JAVA clientsNetworks tools, Office applicationsDBMS, Graphic tools, editorsServer managementsFTP Servers, Web servers, Domain Name Services Mail Servers, SMTP, POP, IMAP

Unit –V: System Administration and Network administration (9L)Basic of system administrationBoot management toolsManaging usersSoftware managements

Page 20: M.Sc. Bioinformatics syllabus

File system administrationDevices and PrintersKernel AdministrationConfiguration of Network connectionNFS, NIS, Applets TableSamba, Administrating TCP / IP NetworksNetwork Security, Firewalls, and authentications

Text Books:Practical Guide to Fedora and Red Hat Enterprise Linux, A (5th Edition) by Mark G. Sobell,

( 2010).Linux Bible 2010 Edition: Boot Up to Ubuntu, Fedora, KNOPPIX, Debian, openSUSE, and 13

Other Distributions, Christopher Negus, Wiley; Pap/Dvdr/C edition, ISBN-13: 978-0470485057, (2009)

Practical Guide to Linux Commands, Editors, and Shell Programming, A (2nd Edition), Mark G. Sobell, Prentice Hall; 2 edition, ISBN-13: 978-0131367364, (2009).

Linux Administration: A Beginner's Guide, Fifth Edition , Wale Soyinka, McGraw-Hill Osborne Media; 5 edition, ISBN-13: 978-0071545884, (2008).

Linux Pocket Guide, Daniel J. Barrett, O'Reilly Media; 1st edition, ISBN-13: 978-0596006280, (2004).

Linux in a Nutshell, Ellen Siever, Stephen Figgins, Robert Love, Arnold Robbins, O'Reilly Media; 6 edition, ISBN-13: 978-0596154486, (2009).

Understanding the Linux Kernel, Third Edition, Daniel P. Bovet and Marco Cesati, O'Reilly Media; 3 edition, ISBN-13: 978-0596005658, (2005).

Linux For Dummies, 9th Edition, Richard Blum, For Dummies; 9 edition, ISBN-13: 978-0470467015, (2009).

Practical UNIX/Linux, Eugene Khmelevsky, Amazon Digital Services, ASIN: B001SERN5W.Running Linux, Matthias Kalle Dalheimer and Matt Welsh, (2005).Beginning Linux Programming by Neil Matthew and Richard Stones, (2007).

Page 21: M.Sc. Bioinformatics syllabus

Bioinformatics PracticalSub. Code: BIM-102 (P)

Course Objectives: To enable the students to gain knowledge about Bioinformatics.

Total Credits: 2List of experiments Database Searching Nucleotide Databases -NCBI, DDBJ, EMBL, PDB, BRENDA, TrEMBL, KEGG, Microarray –

MIAME. GEO Diseases -OMIM DatabaseProtein databases- PIR, UniProtSearch Engines- SRS, EntrezBLAST, PHI-PSI- BLAST, FASTASequence alignments Local AlignmentsGlobal AlignmentsDynamic Programming, Dot PlotSmith-Waterman, Needleman- Wunch Algorithms,Day Hoff Matrix, Blossum, PAM Matrices, GAP PenaltiesMultiple Sequence alignments- ClustalW, DALI

Text Books:Bioinformatics- Theory and Practice, N.J. Chikhale and V.S. Gomase, Himalaya Publication

House, India; 1 edition, 2007, ISBN-13: 978-81-8318-831-9 Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology,

Dan Gusfield, 1997, Cambridge University Press BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl

Leon, 2003, O'Reilly Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley & Sons Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley &

Sons Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall Proteomics- Theory and Practice, V.S. Gomase and N.J. Chikhale, Himalaya Publication House,

India,1-edition, 2009, IBSN: 978-81-8488-313-8 Introduction to Bioinformatics, Teresa Attwood, David Parry-Smith, 2001, Prentice Hall Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor

Laboratory Press Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L.

Raymer, Elaine Nicpon Marieb, 2002, Benjamin/Cummings Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao

Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press Structural Bioinformatics, Philip E. Bourne, Helge Weissig (Editors), 2003, John Wiley & Sons

Page 22: M.Sc. Bioinformatics syllabus

Protein Structure Prediction: Bioinfomatic Approach, I.F. Tsigelny, 2002, International University Line

Introduction to Protein Architecture: The Structural Biology of Proteins, Arthur M. Lesk, 2001, Oxford University Press

Protein Structure Prediction: Methods and Protocols, David M. Webster (Editor), 2000, Humana Press

Introduction to Protein Structure, Carl-Ivar Branden, John Tooze, 1999, Garland Publishing Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding,

Alan Fersht, 1999, Freeman

Page 23: M.Sc. Bioinformatics syllabus

Biostatistics PracticalSub. Code: BIM-103 (P)

Course Objectives: To enable the students to gain knowledge about Biostatistics, or the use of numerical techniques to extract information from data and facts.

Total Credits: 2List of experiments Biostatistical Design of Medical Studies.Descriptive Statistics. Descriptive Methods for Categorical Data.Descriptive Methods for Continuous Data.Probability and Probability Models.Random Variables and DistributionsEstimation of Parameters.Introduction to Statistical Tests of Significance.Comparison of Population Proportions.Comparison of Population Means.Correlation and Regression.Logistic Regression.Methods for Count Data.Analysis of Survival Data and Data from Matched Studies.Study DesignsLikelihood Ratios, Bayesian Methods and Multiple Hypotheses

Textbook:

The Biostatistics Cookbook: The Most User-Friendly Guide for the Bio/Medical Scientist, S. Michelson and T. Schofield, Springer; 1 edition, ISBN-13: 978-0792338840, (1996).

Intuitive Biostatistics: A Nonmathematical Guide to Statistical Thinking, Harvey Motulsky, Oxford University Press, USA, ISBN-13: 978-0199730063, (2010).

Biostatistics: The Bare Essentials 3/e (with SPSS), Norman, Geoffrey Norman, David Streiner, BC Decker Inc; 3 edition, ISBN-13: 978-1550094008, (2008).

Biostatistics, Second Edition: A Guide to Design, Analysis and Discovery. Ronald N. Forthofer, Eun Sul Lee, Mike Hernandez , Academic Press; 2 edition, ISBN-13: 978-0123694928, (2006).

Fundamentals of Biostatistics, Bernard Rosner, Duxbury Press; 6 edition, ISBN-13: 978-0534418205, (2005).

Biostatistics for the Biological and Health Sciences with Statdisk, Marc M. Triolaand and Mario F. Triola, Addison Wesley, ISBN-13: 978-0321194367, (2005).

Introduction to Biostatistics: Second Edition, Robert R. Sokal and F. James Rohlf, Dover Publications; 2 edition, ISBN-13: 978-0486469614, (2009).

Basic & Clinical Biostatistics (LANGE Basic Science), Beth Dawson, Robert Trapp, Robert Trapp , McGraw-Hill Medical; 4 edition, ISBN-13: 978-0071410175, (2004).

Biostatistics, Tarum Rawat, Samuel Devlin, Kõva köide,Kirjastus: Sarup & Son, ISBN-13: 9788176258050 (2008).

Pharmaceutical Statistics: Practical and Clinical Applications, Revised and Expanded (Drugs and

Page 24: M.Sc. Bioinformatics syllabus

the Pharmaceutical Sciences), Sanford Bolton and Charles Bon , Informa Healthcare; 4 edition, ISBN-13: 978-0824746957, (2003)

Statistical Methods in Biology , Norman T. J. and Bailey M.A., Cambridge University Press; 3 edition, ISBN-13: 978-0521469838, (1995).

Primer of Applied Regression Analysis and Analysis of Variance, 2nd edition, Glantz S.A., Slinker B.K., New York: McGraw-Hill, (2001)

Page 25: M.Sc. Bioinformatics syllabus

Data Base Managements Systems Oracle PracticalSub. Code: BIM-104 (P)

Course Objectives: To enable the students to gain knowledge about Data Base Managements Systems Oracle.

Total Credits: 2

List of experiments Oracle Database Administration Installing Oracle Database SoftwareCreating and Controlling Oracle DatabasesAdministering UsersManaging Schema Objects and DataImplementing Oracle Security FeaturesMonitoring PerformancePerforming Database Backup and RecoveryBasic PL/SQL Concepts.Laying the Groundwork: PL/SQL Fundamentals.Controlling Program Flow.Handling Exceptions.Standards and Structures.Creating Naming Standards.Creating Coding Standards.PL/SQL Data Manipulations.Basic Datatypes.Advanced Datatypes.Transaction Control.Dynamic SQL and PL/SQL.

Text Books:Oracle Data Guard 11g Handbook (Osborne ORACLE Press Series), Larry Carpenter, Joseph

Meeks, Charles Kim, Bill Burke, Sonya Carothers, Joydip Kundu, Mike Smith, Nitin Vengurlekar, McGraw-Hill Osborne Media; 1 edition, ISBN-13: 978-0071621113, (2009)

Oracle General Ledger Guide: Implement a Highly Automated Financial Processing System, Melanie Cameron, McGraw-Hill Osborne Media; 1 edition, ISBN-13: 978-0071622295, (2009)

Database System Concepts, Avi Silberschatz, Henry F. Korth, S. Sudarshan, McGraw-Hill, ISBN 0-07-295886-3

Database Management Systems By Raghu Ramakrishnan, Johannes Gehrke, McGraw-Hill , ISBN: 0072465638 / 9780072465631

Fundamentals of Database Management Systems by Mark L. Gillenson, John Wiley & Sons, ISBN-13: 9780471262978, 978-0471262978

Relational Database Management: A Systems Programming Approach, M. Papazoglou and W. ValderPrentice Hall, ISBN-10: 0137718667

Oracle Database 11g, A Beginner's Guide, Ian Abramson, Michael Abbey, Michael Corey, McGraw-Hill Osborne Media, ISBN-10: 0071604596

Page 26: M.Sc. Bioinformatics syllabus

An Introduction to Database Systems, C. J. Date, Addison Wesley Longman, ISBN-10: 0201385902

Page 27: M.Sc. Bioinformatics syllabus

Linux PracticalSub. Code: BIM-105 (P)

Course Objectives: To enable the students to gain knowledge about Linux.

Total Credits: 2

List of experiments Working with Linux.Toolchains, Portability.Software Configuration Management.Network Programming.Databases.Kernel Development.Kernel Interfaces.Linux Kernel Modules. The shell – command line, file name, encapsulation, standards output/ input, shell variables,

pipes Linux File StructureShell configurationClient Applications and Server managements Basic of system administrationBoot management tools,Managing users,Software managements,File system administration,Devices and PrintersKernel Administration,Configuration of Network connectionNFS, NIS, Applets Table,Samba, Administrating TCP / IP Networks,Network Security, Firewalls, authentications

Text Books:Practical Guide to Fedora and Red Hat Enterprise Linux, A (5th Edition) by Mark G. Sobell,

( 2010).Linux Bible 2010 Edition: Boot Up to Ubuntu, Fedora, KNOPPIX, Debian, openSUSE, and 13

Other Distributions, Christopher Negus, Wiley; Pap/Dvdr/C edition, ISBN-13: 978-0470485057, (2009)

Practical Guide to Linux Commands, Editors, and Shell Programming, A (2nd Edition), Mark G. Sobell, Prentice Hall; 2 edition, ISBN-13: 978-0131367364, (2009).

Linux Administration: A Beginner's Guide, Fifth Edition , Wale Soyinka, McGraw-Hill Osborne Media; 5 edition, ISBN-13: 978-0071545884, (2008).

Linux Pocket Guide, Daniel J. Barrett, O'Reilly Media; 1st edition, ISBN-13: 978-0596006280, (2004).

Linux in a Nutshell, Ellen Siever, Stephen Figgins, Robert Love, Arnold Robbins, O'Reilly Media; 6 edition, ISBN-13: 978-0596154486, (2009).

Page 28: M.Sc. Bioinformatics syllabus

Understanding the Linux Kernel, Third Edition, Daniel P. Bovet and Marco Cesati, O'Reilly Media; 3 edition, ISBN-13: 978-0596005658, (2005).

Linux For Dummies, 9th Edition, Richard Blum, For Dummies; 9 edition, ISBN-13: 978-0470467015, (2009).

Practical UNIX/Linux, Eugene Khmelevsky, Amazon Digital Services, ASIN: B001SERN5W.Running Linux, Matthias Kalle Dalheimer and Matt Welsh, (2005).Beginning Linux Programming by Neil Matthew and Richard Stones, (2007).

Page 29: M.Sc. Bioinformatics syllabus

Swami Ramanand Teerth Marathwada University

Nanded School of Technology

Sub Centre, Latur

Syllabus For theM.Sc. Bioinformatics

(CGPA)School of Technology,

SRTMUN Sub-Centre, Latur Academic Year 2010-11

Semester -II

Page 30: M.Sc. Bioinformatics syllabus

Advanced Molecular BiologySub. Code: BIM-201 (T)

Course Objectives: To enable the students to gain knowledge about Advanced Molecular Biology and genetics.

Total: 45L Total Credits: 4

Unit -I: Central Dogma of Molecular Biology (9L)DNA, RNA, Protein Replication Transcription Translation

Unit -II: Split genes and overlapping genes (9L)Evolution of one cistron one polypeptide theory, Genetic complementation –cis-trans test of genetic functions. PlasmidsMobile elements in prokaryotes and eucaryotes-Insertion sequences, transposons, transposable, elements and their properties, detection and significance, retroposons, Shapiro’s model of replicative transposition Gene transfer in bacteriaRestriction and modification of DNA Recombination and enzymes involved.

Unit -III: Recombinant DNA Technology (9L)Debate over the technology General strategy of gene cloning Tools in rDNA technology Methods of construction of rDNAs Methods of transplantation of rDNA Screening of r DNA clones, scope and significance

Unit -IV: Techniques (9L)PCR, LCR, RFLP DNA foot and fingerprinting Chromosome walking, blotting techniques human genome project Nick translation hybrid release and arrested translation Colony hybridization, enzyme and protein engineering

Unit -V: Metabolic engineering (9L)Essence of metabolic engineering examples of pathway manipulation Metabolic engineering in practice Fluxomics, Metabolic flux analysis and its applications Synthesis low molecular wt. compounds

Page 31: M.Sc. Bioinformatics syllabus

Text Books:Molecular Genetics: Structure of Life, Virendra Gomase and Aravind Tripathi, VDM Verlag Dr.

Müller, Germany, ISBN:978-3-639-25001-5, (2010). Genetechnology, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,

ISBN: 978-3-639-13467-4, (2010). Molecular biology of the Cell, Bruce Alberts, Alexander Johnson, Alexander Johnson, Julian

Lewis, Martin Raff, keith Roberts, Peter Walter; Garland Science, Taylor & Francis group,4th Edition (2002)

Essential Cell Biology, Bruce Alberts Dennis Bray, Karen Hopkins, Alexander Johnson Julian Lewis, Martin Raff, Keith Roberts, Peter Walter; Garland Science; Taylor & Francis Group,4th Edition (2004)

Cell Molecular Biology, E. D. P. De Robertis, E. M. F. De Robertis, Jr, Lippinwt William & Wilkins (2001)

Metabolomics, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany, ISBN:978-3-639-24991-0, (2010).

Molecular biology, David Freifelder, Narosa Publishing House, 1st Edition(2004)Genes, VIII Benjamin Lewin; Pearson Education International,8th Edition (2004)Principles of Gene Manuplation, S. B. Primrose R. M. Twyman & R. W. old, Blackwell

Science,6th Edition (2001)Advanced Molecular Biology, R. M. Twyman, 1st Edition , (2003)Instant Notes on Molecular Biology; P.C. Turner, A. G. Mclennan, A. D. Bates & M. R. H.

White, 2nd Edition (2002)Molecular Biology, David Freifelder, Narosa Publishing House,2nd edition (2004)Microbial Genetics, David Freifelder, Narosa Publishing House, 2nd edition(2004)Essential Molecular Biology (volume I & II) Practical Approach; Edited By T. A. Brown; Oxford

University Press, 2nd Edition (2001)

Page 32: M.Sc. Bioinformatics syllabus

Computational BiologySub. Code: BIM-202 (T)

Course Objectives: To enable the students to gain knowledge about Computational Biology.

Total: 45L Total Credits: 4

Unit -I: Database Searching (9L)Nucleotide Databases -NCBI, DDBJ, EMBL, PDB, BRENDA, TrEMBL, KEGG Microarray –MIAME, GEO Diseases -OMIM DatabaseProtein databases- PIR, UniProtSearch Engines- SRS, EntrezBLAST, PHI-PSI- BLAST, FASTA

Unit -II: Sequence alignments (9L)Local AlignmentsGlobal AlignmentsDynamic Programming, Dot PlotSmith-Waterman, Needleman- Wunch Algorithms,Day Hoff Matrix, Blossum, PAM Matrices, GAP PenaltiesMultiple Sequence alignmentsClustalW, DALI

Unit -III: Pattern identification (9L)Pattern matching function, Repeat analysisInvert repeatsDomain MotifRestriction enzyme cleavage sites

Unit -IV: Protein analysis (9L)Primary structure analysis –Protparam, COILSTopology Prediction -TMHMMSecondary structure prediction -GOR, SOPMA, PHDTertiary structure prediction-CPHModels Antigenic predictionsIsoelectric points

Unit -V: Phylogenic tree constructions (9L)General-purpose packages Parsimony programs Distance matrix methods Computation of distances

Page 33: M.Sc. Bioinformatics syllabus

Maximum likelihood and Bayesian methods Artificial-intelligence and genetic algorithms methods Invariants (or Evolutionary Parsimony) methods Consensus trees, subtrees, supertrees, distances between trees Tree-based alignment Description or prediction of data from trees

Text Books:Bioinformatics- Theory and Practice, N.J. Chikhale and V.S. Gomase, Himalaya Publication

House, India; 1 edition, 2007, ISBN-13: 978-81-8318-831-9 Proteomics- Theory and Practice, V.S. Gomase and N.J. Chikhale, Himalaya Publication House,

India,1-edition, 2009, IBSN: 978-81-8488-313-8 BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl

Leon, 2003, O'Reilly Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley & Sons Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley &

Sons Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall Introduction to Bioinformatics, Teresa Attwood, David Parry-Smith, 2001, Prentice Hall Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor

Laboratory Press Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L.

Raymer, Elaine Nicpon Marieb, 2002, Benjamin/Cummings Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao

Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press

Page 34: M.Sc. Bioinformatics syllabus

ImmunoinformaticsSub. Code: BIM-203 (T)

Course Objectives: To enable the students to gain knowledge about Immunoinformatics is an emerging sub discipline of bioinformatics.

Total: 45L Total Credits: 4

Unit -I: Introduction to Immunoinformatics (9L)IntroductionImmunityImmune system Immunoinformatics is an emerging sub discipline of bioinformatics Immunology and informatics Genomics immunological methods Proteomics and immunological methods Networks regulating the immune system

Unit -II: Applied data-driven strategies (9L)MHC TCR Peptide-MHC and allergen research Epitope prediction De-immunization of therapeutic proteins Host-pathogen interactions Modeling of immune responses to pathogens Large-scale chemical mutagenesis-driven genetic analyses systems

Unit -III: Immunological Supertypes (9L)Defining HLA Supertypes supertypes of GRID/CPCA Hierarchical clustering methods Hla-Ad supertypes MHC supertypes, and Class I Hla Alleles

Unit -IV: Immunoinformatics databases (9L)IMGT/HLA IPD SYEPEITHIMHCBN databaseJenPep database

Unit -V: Immunoinformatics Methods (9L)MHC PredictionPredicting Peptide-MCH Binding MCH binders

Page 35: M.Sc. Bioinformatics syllabus

TAP bindingMHC similarities, and predicting virulence factors B-cell epitopes T-Cell epitopes Class I and II MHC HLA-peptide binding

Text Books:Immunobiotechnology, Virendra Gomase and Sunilkumar Dwivedi, VDM Verlag Dr. Müller,

Germany, ISBN: 978-3-639-25017-6, (2010). Immunoinformatics: Shoba Ranganathan, Vladimir Brusic, Christian Schonbach, ISBN:

0387729674, Springer, (2007).Immunoinformatics: Darren R Flower, ISBN: 1588296997, Humana Press, (2007).Immunology: Richard A. Goldsby, Thomas J. Kindth, Barbara A, Osborne, Janis Kuby, W. H.

Freeman & Company, 5th Edition (2003).Roitt’s Essential Immunology: Ivan M. Roitt, Peter J. Delves Blackwell Science Ltd., 10th

Edition (2001)An Introduction to Immunology: C.V. Rao; Narosa Publishing House,1st Edition (2004)Instant Notes in Immunology; P.M. Lydyard, A. Whelan, M.W. Fanger BIOS Scientific

Publishers Ltd, 1st Edition (2003)Textbook of Microbiology: R. Ananthnarayan, C. K. J. Panicker, Orient Longman , 6th Edition

(2003)Immunology: Introductory Textbook; Nandini Shetty, New Age International pvt. Ltd. 1st

Edition (2003)

Page 36: M.Sc. Bioinformatics syllabus

ChemoinformaticsSub. Code: BIM-204 (T)

Course Objectives: To enable the students to gain knowledge about Computers in Chemical Research.

Total: 45L Total Credits: 4

Unit -I: Introduction to Chemoinformatics (9L)Introduction to ChemoinformaticsComputers in Chemical Research Data analysis and data management tools in preclinical development Impact of bioinformatics on preclinical drug and vaccine discovery Statistical modeling in pharmaceutical research Drug discovery from Medicinal Plants

Unit –II: Pharmaceutical Information (9L)Pharmaceutical Information ManagementStrategies for using information effectively in early stage drug discovery Pharmacophore Modeling Computer aided drug designLigand Libraries and ScreeningHigh Throughput Screening for Pharmacogenetics Clinical data collection and management New paradigm for analyzing adverse drug events

Unit –III: Drug Databases and Data Banks (9L)Drug information data basesType of Drug DataDatabases of Chemical StructuresDatabases on Chemical ReactionsSpectroscopic DatabasesChemistry in the InternetComputers and protein crystallography Protein-ligand free energy predictions for drug discovery Molecule libraries for synthesis

Unit –IV: Data Collection and Simulation Strategies (9L)Pharmacogenomics and Pharmacoproteomics Computer methods for predicting drug metabolism Toxicogenomics and Toxicoinformatics Computational optimization of biopharmaceutical properties Computer simulations in pharmacokinetics and pharmacodynamicsMicroRNA, RNAinterference for Drug targets Computational Biology of microRNAs

Page 37: M.Sc. Bioinformatics syllabus

Unit –V: Legal and Ethical Aspects (9L)Legal and Ethical Aspects of ChemoinformaticsChemical formulation informatics The ethics of computing in pharmaceutical and chemical research An expert system for contextual hyper linking in knowledge management Intellectual property protection, Copyright and CopyleftInformation infrastructure regulations

Text Books:Encyclopedia of Drug Design (11 Volumes), Virendra Gomase and Shruti Gomase, ISBN:978-9-

380-02632-9, IK International Publishing House Pvt. LtdComputer Applications in Pharmaceutical Research and Development, Wang, Binghe, ISBN-10:

0-471-73779-8, John Wiley and Sons India Pvt. Ltd. Quantitative molecular pharmacology and informatics in drug discovery, Michael Lutz and Jerry

Kenatin, ISBN-10: 0471988618, John Wiley and Sons India Pvt. Ltd. RNA Interference Technology- From Basic Science to Drug Development, Krishnarao Appasani,

ISBN: 13:9780521836777, Cambridge University Press India Private LimitedmicroRNAs: From Basic Science to Disease Biology, Krishnarao Appasani, ISBN-13:

9780521865982, Cambridge University Press India Private LimitedMicroarray Bioinformatics, Dov Stekel, ISBN:13:9780521525879, Cambridge University Press

India Private LimitedMedical Informatics & Telemedicine: Recent Advances, J Mukhopadhyay,

ISBN:9780230630185, Macmillan India Limited Nanotechnology in Biology and Medicine Methods, Devices, and Applications, Tuan Vo-Dinh,

ISBN: 0849329494, I.K. International Publishing House Pvt. LtdMolecular pharmacology a short course, Jerry Kenatin, ISBN-10: 086542540X, John Wiley and

Sons India Pvt. Ltd. Pharmaceutical Drug Analysis, Ashutosh Kar, ISBN:9788122415827, New Age International (P)

Ltd., PublishersStereochemistry of Organic Compounds, Ernest L. Eliel, Samuel H. Wilen, ISBN: 978-0-471-

01670-0, John Wiley and Sons India Pvt. Ltd.Organic Chemistry, T. W. Graham Solomons, Craig B. Fryhle, ISBN: 978-0-471-68496-1, John

Wiley and Sons India Pvt. Ltd.Stereochemistry, David G. Morris, ISBN: 978-0-471-22477-8, John Wiley and Sons India Pvt.

Ltd.

Page 38: M.Sc. Bioinformatics syllabus

Machine Intelligence in Bioinformatics Sub. Code: BIM-205 (T)

Course Objectives: To enable the students to gain knowledge about Machine Intelligence.

Total: 45L Total Credits: 4

Unit -I: Introduction to Biological Data Mining (9L)Data Mining in GenomicsGene Expression Data MiningData Mining in ProteomicsData Mining Preparatory ActivitiesData cleaning, data preprocessing, and semantic integration of heterogeneous, distributed biomedical databasesRNA Data Mining

Unit -II: 3. Optimization Techniques (9L)Steepest descent Conjugate gradient Newton RaphsonSimulated annealing and biomolecular structure optimizationGenetic algorithms

Unit -III: Machine Learning Techniques (9L)Neural Network based biological applicationsHMM based biological applicationsDynamic programming and biological applicationsSequences alignmentsStructure alignments

Unit -IV: Monte Carlo and Bayesian approaches in data mining (9L)Data mining models and data streamsBayesian techniques and current biological researchStatistical alignment MCMC workbench Models of computational analysisMarkov Chain Monte CarloBayesian phylogenetics RNA substitution model and early mammalian evolutionAdvantages of Bayesian applications

Unit -V: Clustering algorithms and applications (9L)Hierarchical and non-hierarchical clusteringGrid Based clustering, Microarray analysisMicroarray and automatic segmentation Protein array data analysis Text Books:

Page 39: M.Sc. Bioinformatics syllabus

Bioinformatics- Theory and Practice, N.J. Chikhale and V.S. Gomase, Himalaya Publication House, India; 1 edition, 2007, ISBN-13: 978-81-8318-831-9

Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Dan Gusfield, 1997, Cambridge University Press

BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl

Leon, 2003, O'Reilly Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley & Sons Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley &

Sons Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall Proteomics- Theory and Practice, V.S. Gomase and N.J. Chikhale, Himalaya Publication House,

India,1-edition, 2009, IBSN: 978-81-8488-313-8 Introduction to Bioinformatics, Teresa Attwood, David Parry-Smith, 2001, Prentice Hall Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor

Laboratory Press Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L.

Raymer, Elaine Nicpon Marieb, 2002, Benjamin/Cummings Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao

Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press Structural Bioinformatics, Philip E. Bourne, Helge Weissig (Editors), 2003, John Wiley & Sons Protein Structure Prediction: Bioinfomatic Approach, I.F. Tsigelny, 2002, International

University Line Introduction to Protein Architecture: The Structural Biology of Proteins, Arthur M. Lesk, 2001,

Oxford University Press Protein Structure Prediction: Methods and Protocols, David M. Webster (Editor), 2000, Humana

Press Introduction to Protein Structure, Carl-Ivar Branden, John Tooze, 1999, Garland Publishing Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding,

Alan Fersht, 1999, Freeman

Page 40: M.Sc. Bioinformatics syllabus

Immunoinformatics PracticalSub. Code: BIM-203 (P)

Course Objectives: To enable the students to gain knowledge about Immunoinformatics is an emerging sub discipline of bioinformatics.

Total Credits: 2

List of experiments Information retrieval and analysis of database i.e. IMGT/HLA IPD, SYEPEITHIInformation retrieval and analysis of database i.e. MHCBN, JenPep Immunoinformatics Methods MHC PredictionPredicting Peptide-MCH Binding MCH binders prediction TAP binders predictionMHC similarities, and predicting virulence factors B-cell epitopes prediction T-Cell epitopes prediction Class I and II MHC prediction methods HLA-peptide binding

Text Books:Immunobiotechnology, Virendra Gomase and Sunilkumar Dwivedi, VDM Verlag Dr. Müller,

Germany, ISBN: 978-3-639-25017-6, (2010).Immunoinformatics: Shoba Ranganathan, Vladimir Brusic, Christian Schonbach, ISBN:

0387729674, Springer, (2007).Immunoinformatics: Darren R Flower, ISBN: 1588296997, Humana Press, (2007).Immunology: Richard A. Goldsby, Thomas J. Kindth, Barbara A, Osborne, Janis Kuby, W. H.

Freeman & Company, 5th Edition (2003).Roitt’s Essential Immunology: Ivan M. Roitt, Peter J. Delves Blackwell Science Ltd., 10th

Edition (2001)An Introduction to Immunology: C.V. Rao; Narosa Publishing House,1st Edition (2004)Instant Notes in Immunology; P.M. Lydyard, A. Whelan, M.W. Fanger BIOS Scientific

Publishers Ltd, 1st Edition (2003)Textbook of Microbiology: R. Ananthnarayan, C. K. J. Panicker, Orient Longman , 6th Edition

(2003) Immunology: Introductory Textbook; Nandini Shetty, New Age International pvt. Ltd. 1st

Edition (2003)

Page 41: M.Sc. Bioinformatics syllabus

Chemoinformatics Practical Sub. Code: BIM -204 (P)

Course Objectives: To enable the students to gain knowledge about Chemoinformatics is an emerging sub discipline of bioinformatics.

Total Credits: 2

List of experiments

Data analysis and data management tools in preclinical development Statistical modeling in chemical research Study of Secondary metabolites from Medicinal PlantsPharmacophore Modeling Ligand Libraries and ScreeningHigh Throughput Screening for Pharmacogenetics Clinical data collection and managementDatabases of Chemical StructuresDatabases on Chemical ReactionsProtein-ligand free energy predictions for drug discovery Molecular libraries for synthesis Computational optimization of biopharmaceutical properties Computer simulations in pharmacokinetics and pharmacodynamics Molecular analysis for drug design

Text Books:Computer Applications in Pharmaceutical Research and Development, Wang, Binghe, ISBN-10: 0-471-

73779-8, John Wiley and Sons India Pvt. Ltd. Quantitative molecular pharmacology and informatics in drug discovery, Michael Lutz and Jerry Kenatin,

ISBN-10: 0471988618, John Wiley and Sons India Pvt. Ltd. RNA Interference Technology- From Basic Science to Drug Development, Krishnarao Appasani, ISBN:

13:9780521836777, Cambridge University Press India Private LimitedmicroRNAs: From Basic Science to Disease Biology, Krishnarao Appasani, ISBN-13: 9780521865982,

Cambridge University Press India Private LimitedMicroarray Bioinformatics, Dov Stekel, ISBN:13:9780521525879, Cambridge University Press India

Private LimitedMedical Informatics & Telemedicine: Recent Advances, J Mukhopadhyay, ISBN:9780230630185,

Macmillan India Limited Nanotechnology in Biology and Medicine Methods, Devices, and Applications, Tuan Vo-Dinh, ISBN:

0849329494, I.K. International Publishing House Pvt. LtdMolecular pharmacology a short course, Jerry Kenatin, ISBN-10: 086542540X, John Wiley and Sons

India Pvt. Ltd. Pharmaceutical Drug Analysis, Ashutosh Kar, ISBN:9788122415827, New Age International (P) Ltd.,

PublishersStereochemistry of Organic Compounds, Ernest L. Eliel, Samuel H. Wilen, ISBN: 978-0-471-01670-0,

John Wiley and Sons India Pvt. Ltd.Organic Chemistry, T. W. Graham Solomons, Craig B. Fryhle, ISBN: 978-0-471-68496-1, John Wiley and

Sons India Pvt. Ltd.

Page 42: M.Sc. Bioinformatics syllabus

Machine Intelligence in Bioinformatics PracticalSub. Code: BIM-205 (P)

Course Objectives: To enable the students to gain knowledge about Machine Intelligence techniques, algorithms in bioinformatics.

Total Credits: 2List of experiments Data mining in genomicsGene expression data miningData mining in proteomicsRNA secondary structure comparison and alignmentMinimum free-energy method for RNA secondary structure predictionGene mapping by pattern discoveryData mining: predicting protein folding pathwaysData mining methods for a systematic of protein subcellular locationSequence homologySequences alignmentsStructure alignmentsMotif involve in protein targetingAb initio method prediction from sequence Mining chemical compounds

Text Books:Bioinformatics- Theory and Practice, N.J. Chikhale and V.S. Gomase, Himalaya Publication House, India;

1 edition, 2007, ISBN-13: 978-81-8318-831-9 Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Dan

Gusfield, 1997, Cambridge University Press BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl Leon,

2003, O'Reilly Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley & Sons Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley & Sons Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall Proteomics- Theory and Practice, V.S. Gomase and N.J. Chikhale, Himalaya Publication House, India,1-

edition, 2009, IBSN: 978-81-8488-313-8 Introduction to Bioinformatics, Teresa Attwood, David Parry-Smith, 2001, Prentice Hall Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor Laboratory

Press Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L. Raymer, Elaine

Nicpon Marieb, 2002, Benjamin/Cummings Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao Jiang,

Ying Xu, Michael Zhang (Editors), 2002, MIT Press

Page 43: M.Sc. Bioinformatics syllabus

Numerical Methods and Optimization Techniques PracticalSub. Code: BIM -206 (P)

Course Objectives: To enable the students to gain knowledge about Numerical Methods and Optimization Techniques Practical, algorithms in bioinformatics.

Total Credits: 2

List of experiments Engineering Optimization Methods and PrinciplesOptimization and ProgrammingOptimization TechniquesNumerical AnalysisApplication of Optimization TechniquesNumerical Methods & OptimizationCoordinate descent and subgradient methodOptimization and Cutting Plane MethodsBabylonian, Restricted step methods and Non linear equationsLinearly Constrained Optimization Techniques

Text Books:Gilat Amos (2004) MATLAB: An Introduction with Applications (2nd edition ed.). John Wiley

& Sons. ISBN 0-471-69420-7. Hildebrand F. B. (1974) Introduction to Numerical Analysis (2nd edition ed.). McGraw-Hill.

ISBN 0-070-28761-9. Leader Jeffery J. (2004) Numerical Analysis and Scientific Computation. Addison Wesley. ISBN

0-201-73499-0. Trefethen Lloyd N. (2006) "Numerical analysis", 20 pages. In: Timothy Gowers and June

Barrow-Green (editors), Princeton Companion of Mathematics, Princeton University Press

Marti K. (2002) Stochastic Optimization Techniques: Numerical Methods And Technical Applications, ISBN: 3540428895, Springer

Emmanuel Le Tallec Patrick, Numerical Methods In Sensitivity Analysis And Shape Optimization, {with Cd-rom}, ISBN: 0817643222, (2003), Birkhauser

Page 44: M.Sc. Bioinformatics syllabus

Swami Ramanand Teerth Marathwada University

Nanded School of Technology

Sub Centre, Latur

Syllabus For theM.Sc. Bioinformatics

(CGPA)School of Technology,

SRTMUN Sub-Centre, Latur Academic Year 2010-11

Semester -III

Page 45: M.Sc. Bioinformatics syllabus

Computer Aided Drug DesignSub. Code: BIM-301 (T)

Course Objectives: To enable the students to gain knowledge about Computer Aided Drug Design

Total: 45L Total Credits: 4

Unit-I: Introduction to CADD (9L)Introduction to CADD, SBDDRepresentation of Molecular Structures Chemical Nomenclature and Structure RepresentationProcessing Constitutional InformationRepresentation of 3D StructuresMolecular Shape AnalysisRepresentation of Chemical Reactions

Unit-II: Virtual Screening (9L)Virtual ScreeningChemoinformatics in Lead DiscoveryComputational Chemistry, Molecular Complexity and Screening Set DesignAlgorithmic Engines in Virtual ScreeningStrengths and Limitations of Pharmacophore-Based Virtual Screening

Unit-III: Lead Discovery (9L)High Throughput Screening Hit and Lead DiscoveryEnhancing Hit Quality and Diversity within Assay Throughput ConstraintsMolecular Graphics, Molecular Dynamics and Simulation of LeadMolecular Diversity in Lead Discovery: From Quantity to QualityIn Silico Lead Optimization

Unit-IV: Databases and Libraries (9L)Databases and Libraries PubChem, PubEchm-BioAssay, Pharma Project, DrugBankWOMBAT: World of Molecular BioactivityCabinet - Chemical and Biological Informatics NetworkStructure Modification in Chemical DatabasesRational Design of GPCR-specific Combinational Libraries Based on the Concept of Privileged Substructures

Unit-V: CADD Applications (9L)CADD ApplicationsA Practical Strategy for Directed Compound AcquisitionEfficient Strategies for Lead OptimizationChemoinformatics Tools for Library Design Hit-to-Lead Process: A User's Perspective

Page 46: M.Sc. Bioinformatics syllabus

Application of Predictive 3DQSAR Models to Database MiningDrug Discovery - Case Study

Text Book:Computer Applications in Pharmaceutical Research and Development, Wang, Binghe, ISBN-10:

0-471-73779-8, John Wiley & Sons India Pte. Ltd. Engineering Chemistry, R.V. Gadag and A. Nityananda Shetty, ISBN: 8188237833, I.K.

International Publishing House Pvt. LtdQuantum Chemistry and Spectroscopy, Engel, ISBN: 9788131712856, Pearson EducationQuantum Chemistry, Ira N. Levine, ISBN: 8120330641, Prentice-Hall of India An Introduction to Drug Design, S.N. Pandeya, New Age International (P) Ltd., PublishersPharmaceutical Organic Chemistry, Rama Rao Nadendla, ISBN: 9781403924957, Macmillan

India Limited Virtual Screening in Drug Discovery, Juan Alvarez and Brian Shoichet, ISBN-13: 978-

0824754792, CRC PressBiological Thermodynamics, Donald T. Haynie, ISBN:9780521704045, Cambridge University

Press India Private LimitedStereochemistry of Organic Compounds, Ernest L. Eliel, Samuel H. Wilen, ISBN: 978-0-471-

01670-0, John Wiley and Sons India Pvt. Ltd.Organic Chemistry, T. W. Graham Solomons, Craig B. Fryhle, ISBN: 978-0-471-68496-1, John

Wiley and Sons India Pvt. Ltd.Chemoinformatics, Gasteiger, Johann / Engel, Thomas (eds.), ISBN-13: 978-3-527-30681-7,

John Wiley & Sons India Pte. Ltd. Chemoinformatics in Drug Discovery, Tudor I. Oprea, Raimund Mannhold, Hugo Kubinyi, Gerd

Folkers, ISBN: 978-3-527-30753-1, John Wiley & Sons India Pte. Ltd. Handbook of Chemoinformatics: From Data to Knowledge, Johann Gasteiger, ISBN: 978-3-527-

30680-0, John Wiley & Sons India Pte. Ltd.An Introduction to Computational Biochemistry, C. Stan Tsai, ISBN: 978-0-471-40120-9, John

Wiley & Sons India Pte. Ltd.

Page 47: M.Sc. Bioinformatics syllabus

Object oriented Programming (OOPS) JAVASub. Code: BIM-302 (T)

Course Objectives: To enable the students to gain knowledge about Object oriented Programming (OOPS) JAVA.

Total: 45L Total Credits: 4

Unit-I: Introduction to Computing (9L)Introduction to Programming, Computer Organization Evolution of Operating Systems Personal – Distributed and Client/Server Computing Machine Languages – Assembly Languages and High level Languages Structured Programming, Object Technology Unit-II: Backbone of OOPS (9L)Abstract Data Type (ADT), Encapsulation Object, Message, Method, Class, Inheritance Late Binding Polymorphism, Virtual Functions Abstract Classes, Interface, Generic Classes and Interfaces Constructors & Destructors, Overloading & Overriding, Copy Constructor

Unit-III: JAVA Basics (9L)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, Object ClassException Handling, I/O & JDBCException Handling: Fundamentals exception types, uncaught exceptions, throw, throw final, 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, Data Compression, Using Standard Java Packages (lang, util, io, net)Database: JDBC Architecture, JDBC Basics, JDBC Drivers, Connecting to Database and accessing databases

Unit-IV: AWT & Event Handling (9L)Creating User interface with AWT Applets, Applet Life Cycle Simple Graphics, Fonts and Colors Events, Listeners, Components Containers, Working with Layouts Image Processing, AWT Exceptions

Page 48: M.Sc. Bioinformatics syllabus

Delegation Event Model, Event Classes Event Listener Interfaces, Adapter and Inner Classes

Unit-V: Multithreading & Communication (9L)Java Thread Model: Priorities, Synchronization Messaging, Life Cycle of Thread, Thread class Runnable interface, Interthread Communication Suspending, Resuming and Stopping threadsMultithreading, Synchronization Scheduling and Priority of Threads Sockets, Types of Sockets Working with URLs, Web browsers and Handlers Text Books:

Java How to Program (How to Program (Deitel), Harvey & Paul, Deitel & Deitel, Prentice Hall, ISBN-10: 0131483986

Java In A Nutshell, David Flanagan, O'Reilly Media; ISBN-10: 0596007736 Programming With Java A Primer by Balagurusamy, TMH, ISBN: 0074625425Java 2: The Complete Reference, Herbert Schildt, McGraw-Hill Osborne Media, ISBN-10:

0070495432Mastering Java 2, J2se 1.4 by Zukowski, BPB Publication, ISBN: 8176566187

Page 49: M.Sc. Bioinformatics syllabus

Microbial GenomicsSub. Code: BIM-303 (T)

Course Objectives: To enable the students to gain knowledge about Microbial Genomics.

Total: 45L Total Credits: 4

Unit-I: Introduction (9L)History- Bioinformatics and microbial pathogenesisBacteriophage BioinformaticsNew methods of gene sequencing

Unit-II: Genome Analysis (9L)Comparative Microbial MetabolismGenomic Analysis of Membrane TransportAnalysis of the Bacterial Cell Cycle

Unit-III: Bacterial Biodiversity (9L)Concepts of Bacterial Biodiversity for the age of GenomicsCoevolution of symbionts and pathogens with their hosts

Unit-IV: Pathogenic Genomes (9L)Plant pathogen genomesParasite genomicsGenomes of pathogenic enterobacteria and thermophiles

Unit-V: Application (9L)Application of Genomics to Biocatalysis and BiodegradationMicrobial proteomics

Text Books:Microbial Genomes, Fraser, Claire M, Read, Timothy, Nelson, Karen E., Humana Press, (2004).Microbial Genome Methods, Kenneth W. Adolph, CRC Press, (1996).Microbial Functional Genomics, Jizhong Zhou, Wiley-IEEE, (2004).Microbial Genomics and Drug Discovery, Thomas John Dougherty, Steven J. Projan, CRC Press,

(2003). Microbial Biodegradation: Genomics and Molecular Biology, Eduardo Diaz, Caister Academic

Press; 1 edition, ISBN:978-1904455172 (2008).Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists

(Computational Biology), David W. Ussery, Trudy M. Wassenaar, Stefano Borini, Springer; 1 edition, ISBN:978-1848002548, (2008).

Functional Microbial Genomics, Volume 33 (Methods in Microbiology), Brendan Wren, Nick Dorrell, Academic Press; 1 edition, ISBN:978-0125215336, (2002).

Microbial Genomics and Drug Discovery, Thomas J. Dougherty, Steven J. Projan, CRC Press; 1 edition, ISBN:978-0824740412, (2003).

Principle of Drug Action

Page 50: M.Sc. Bioinformatics syllabus

Sub. Code: BIM-304 (T)Course Objectives: To enable the students to gain knowledge about Principle of Drug Action.

Total: 45L Total Credits: 4

Unit-I: Principle of Drug Action (9L)Basic Principles Drug Action, Drug InteractionsPharmacodynamics Pharmacokinetics Drug Metabolism Drug Evaluation and Regulation Introduction to Autonomic Pharmacology Cholinoceptor-Activating and Cholinesterase-Inhibiting Drugs Cholinoceptor Blockers and Cholinesterase Regenerators Sympathomimetics, Adrenoceptor Blockers

Unit-II: Cardiovascular and Bronchodilators (9L)Cardiovascular Drugs Drugs Used in Hypertension Vasocilators & the Treatment of Angina Drugs Used in Congestive Heart Failure Antiarrhythmic Drugs Diuretic Agents Histamine, Serotonin, and the Ergot Alkaloids Vasoactive Peptides Prostaglandins and Eicosanoids Nitric Oxide, Donors, and Inhibitors Bronchodilators

Unit-III: CNS (9L)Drugs That Act in the Central Nervous System Sedative-Hypnotic Drugs, Alcohols Antiseizure Drugs General Anesthetics, Local Anesthetics Skeletal Muscle Relaxants Drugs Used in Parkinsonism & Other Movement Disorders Antipsychotic Drugs & Lithium, Antidepressants Opioid Analgesics & Antagonists Drugs of Abuse

Unit-IV: NSAIDS and Hormones (9L)Agents Used in Anemia and Hematopoietic Growth Factors Drugs Used in Coagulation Disorders Drugs Used in the Treatment of Hyperlipidemias Nonsteroidal Anti-Inflammatory Drugs Hypothalamic and Pituitary Hormones

Page 51: M.Sc. Bioinformatics syllabus

Thyroid and Antithyroid Drugs Corticosteroids and Antagonists Gonadal Hormones and Inhibitors Pancreatic Hormones, Antidiabetic Agents and Hyperglycemic Drugs Drugs that Affect Bone Mineral Homeostasis

Unit-V: Chemotherapeutic Agents (9L)Beta-Lactam Antibiotics and Cell Wall Synthesis Inhibitors Aminoglycosides Antimycobacterial Drugs, Antifungal Agents Antiviral Chemotherapy and Prophylaxis Antiparasitic Chemotherapy, Antiprotozoal Drugs Anthelmintic Drugs Cancer Chemotherapy Immunopharmacology Vaccines, Immune Globulins, and Complex Biologic Products Vitamins, Heavy Metals and Chelating Agents

Text Books

Medical Pharmacology at a Glance, Michael J. Neal, ISBN: 978-1-4051-3360-9, John Wiley and Sons India Pvt. Ltd.

Pharmacology: From Drug Development to Gene Therapy, Robert A. Meyers, ISBN: 978-3-527-32343-2, John Wiley and Sons India Pvt. Ltd.

Essentials of Pharmacotherapeutics, Barar FSK, ISBN: 8121904447, S Chand & Company LtdCurrent Trends in Pharmacology, Arunabha Ray and Kavita Gulati, ISBN:8188237779, I.K.

International Publishing House Pvt. LtdThe Textbook of Pharmaceutical Medicine, John P. Griffin, New Age International (P) Ltd.,

PublishersAn Introduction to Drug Design, S.N. Pandeya, ISBN : 978-81-224-0943-7, New Age

International (P) Ltd., PublishersMedical Pharmacology at a Glance, M.J. Neal, New Age International (P) Ltd., PublishersKatzung and Trevor's Review of Pharmacology, Anthony Trevor, Bertram Katzung, Susan

Masters, ISBN13: 9780071488693, McGraw-HillModern Pharmacology with Clinical Applications, Charles R Craig and Robert E Stitzel, ISBN-

13: 978-0-7817-3762-3, Lippincott Williams & WilkinsLippincott's Illustrated Reviews: Pharmacology, ISBN-10: 0-7817-7155-2, Lippincott Williams

& Wilkins

Page 52: M.Sc. Bioinformatics syllabus

Molecular Modeling Sub. Code: BIM-305 (T)

Course Objectives: To enable the students to gain knowledge about Molecular Modeling.

Total: 45L Total Credits: 4

Unit-I: Introduction Molecular Structure (9L)Molecules Electronic States and Coordinates patterns Rotation, Vibration, and Potential Curves of Diatomic MoleculesSpectra of Diatomic MoleculesMolecule Symmetries and Group TheoryRotation and Vibrations of Polyatomic MoleculesElectronic States of Polyatomic MoleculesSpectra of Polyatomic MoleculesMolecules in External FieldsVan der Waals Molecules and Clusters

Unit-II: Molecular Mechanics (9L)Electric charges and their properties The Forces between Molecules The dipole-dipole interaction Balls on Springs Modeling the solvent Modern Force Fields The Molecular Potential Energy Surface (PES) Order Methods Geometry Optimization Conformation Searches Flexible Molecules QSAR

Unit-III: The energy Sharing (9L)The Boltzmann Probability A two-level quantum system Lindemann's Theory of Melting Statistical Thermodynamics The Internal Energy Uth Equation of state and pressure The Virial of Clausius Monte Carlo Simulations MC Simulation of Rigid Molecules

Unit-IV: Molecular Dynamics (9L)Molecular Dynamics Methodology Algorithms for time dependence Introduction to quantum modeling The Schrödinger equation

Page 53: M.Sc. Bioinformatics syllabus

Particles in potential wells Vibrational Motion The Maxwell Boltzmann distribution of atomic kinetic energies Fermions and Bosons The Pauli Exclusion Principle

Unit-V: Quantum modeling (9L)The orbital model The LCAO model The HF-LCAO model The Unrestricted Hartree Fock (UHF) model Hückel ã-electron Theory All Valence Electron ZDO models CNDO, INDO, MINDO AM1, PM3, SAM1, ZINDOThe Kohn-Sham LCAO equations IMOMM, IMOMO, ONIOM

Text Book

Molecular Modelling for Beginners, Alan Hinchliffe, ISBN: 978-0-470-51313-2, John Wiley and Sons India Pvt. Ltd.

Molecular Physics: Theoretical Principles and Experimental Methods, Wolfgang Demtröder, ISBN: 978-3-527-40566-4, John Wiley and Sons India Pvt. Ltd.

Biophysical Chemistry -Principles and Techniques, Upadhyay, Upadhyay and Nath, ISBN: 978-81-8318-865-4, Himalaya Publication House

Perspective In Structural Biology , Vijayan, ISBN:978-81-7371-254-8, Orient Blackswan Private Limited (University Press)

Fundamental of Crystal Chemistry, Tarren, ISBN:978-81-7371-297-5, Orient Blackswan Private Limited (University Press)

Electrostatic of Atoms and Molecules, Gadre, ISBN:978-81-7371-296-8, Orient Blackswan Private Limited (University Press)

Organic Chemistry of Natural Products-I, Gurdeep R. Chatwal, ISBN:81-8318-307-7, Himalaya Publication House

The Art of Molecular Dynamics Simulation, 2nd Edition, D. C. Rapaport, ISBN:13:9780521825689, Cambridge University Press India Private Limited

Molecular Reaction Dynamics, Raphael D. Levine, ISBN:9780521842761, Cambridge University Press India Private Limited

Molecular Structure and Spectroscopy, G. Aruldhas, ISBN:9788120332157, Prentice-Hall of India

Molecular Spectroscopy, Jeanne L. McHale, ISBN: 9788131720592, Pearson EducationPhysical Chemistry, Peter Atkins and Julio De Paula, ISBN: 9780195685220, Oxford University

Press

Page 54: M.Sc. Bioinformatics syllabus

Computer Aided Drug DesignSub. Code: BIM-301 (P)

Course Objectives: To enable the students to gain knowledge about Computer Aided Drug Design.

Total Credits: 2List of experiments Representation of Molecular Structures, Molecular Shape Analysis Chemical Nomenclature and Structure RepresentationVirtual Screening, 3DQSAR ModelsMolecular Dynamics and Simulation of LeadMolecular Diversity in Lead Discovery: In Silico Lead OptimizationDatabases and Libraries Combinational Libraries Based on the Concept of Privileged SubstructuresHit-to-Lead Process: A User's Perspective

Text BookComputer Applications in Pharmaceutical Research and Development, Wang, Binghe, ISBN-10:

0-471-73779-8, John Wiley & Sons India Pte. Ltd. Engineering Chemistry, R.V. Gadag and A. Nityananda Shetty, ISBN: 8188237833, I.K.

International Publishing House Pvt. LtdQuantum Chemistry and Spectroscopy, Engel, ISBN: 9788131712856, Pearson EducationQuantum Chemistry, Ira N. Levine, ISBN: 8120330641, Prentice-Hall of India An Introduction to Drug Design, S.N. Pandeya, New Age International (P) Ltd., PublishersPharmaceutical Organic Chemistry, Rama Rao Nadendla, ISBN: 9781403924957, Macmillan

India Limited Virtual Screening in Drug Discovery, Juan Alvarez and Brian Shoichet, ISBN-13: 978-

0824754792, CRC PressBiological Thermodynamics, Donald T. Haynie, ISBN:9780521704045, Cambridge University

Press India Private LimitedStereochemistry of Organic Compounds, Ernest L. Eliel, Samuel H. Wilen, ISBN: 978-0-471-

01670-0, John Wiley and Sons India Pvt. Ltd.Organic Chemistry, T. W. Graham Solomons, Craig B. Fryhle, ISBN: 978-0-471-68496-1, John

Wiley and Sons India Pvt. Ltd.Chemoinformatics, Gasteiger, Johann / Engel, Thomas (eds.), ISBN-13: 978-3-527-30681-7,

John Wiley & Sons India Pte. Ltd. Chemoinformatics in Drug Discovery, Tudor I. Oprea, Raimund Mannhold, Hugo Kubinyi, Gerd

Folkers, ISBN: 978-3-527-30753-1, John Wiley & Sons India Pte. Ltd. Handbook of Chemoinformatics: From Data to Knowledge, Johann Gasteiger, ISBN: 978-3-527-

30680-0, John Wiley & Sons India Pte. Ltd.An Introduction to Computational Biochemistry, C. Stan Tsai, ISBN: 978-0-471-40120-9, John

Wiley & Sons India Pte. Ltd.

Page 55: M.Sc. Bioinformatics syllabus

Object oriented Programming (OOPS) JAVASub. Code: BIM-302 (P)

Course Objectives: To enable the students to gain knowledge about Object oriented Programming (OOPS) JAVA.

Total Credits: 2List of experiments 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:

Java How to Program (How to Program (Deitel), Harvey & Paul, Deitel & Deitel, Prentice Hall, ISBN-10: 0131483986

Java In A Nutshell, David Flanagan, O'Reilly Media; ISBN-10: 0596007736 Programming With Java A Primer by Balagurusamy, TMH, ISBN: 0074625425Java 2: The Complete Reference, Herbert Schildt, McGraw-Hill Osborne Media, ISBN-10:

0070495432Mastering Java 2, J2se 1.4 by Zukowski, BPB Publication, ISBN: 8176566187Bioinformatics- Theory and Practice, N.J. Chikhale and V.S. Gomase, Himalaya Publication

House, India; 1 edition, 2007, ISBN-13: 978-81-8318-831-9 Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology,

Dan Gusfield, 1997, Cambridge University Press Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall Proteomics- Theory and Practice, V.S. Gomase and N.J. Chikhale, Himalaya Publication House,

India,1-edition, 2009, IBSN: 978-81-8488-313-8 Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor

Laboratory Press Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao

Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press

Microbial Genomics

Page 56: M.Sc. Bioinformatics syllabus

Sub. Code: BIM-303 (P)Course Objectives: To enable the students to gain knowledge about Microbial Genomics .

Total Credits: 2

List of experiments Microbial BioinformaticsMicrobial metabolismGenomics-Based Analysis of the Bacterial Cell CyclePlant pathogensComparative Microbial MetabolismMicrobial Genomic Analysis of Membrane TransportAnalysis of the Bacterial CellPlant -Microbial interaction

Text Books:Microbial Genomes, Fraser, Claire M, Read, Timothy, Nelson, Karen E., Humana Press, (2004).Microbial Genome Methods, Kenneth W. Adolph, CRC Press, (1996).Microbial Functional Genomics, Jizhong Zhou, Wiley-IEEE, (2004).Microbial Genomics and Drug Discovery, Thomas John Dougherty, Steven J. Projan, CRC Press,

(2003). Microbial Biodegradation: Genomics and Molecular Biology, Eduardo Diaz, Caister Academic

Press; 1 edition, ISBN:978-1904455172 (2008).Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists

(Computational Biology), David W. Ussery, Trudy M. Wassenaar, Stefano Borini, Springer; 1 edition, ISBN:978-1848002548, (2008).

Functional Microbial Genomics, Volume 33 (Methods in Microbiology), Brendan Wren, Nick Dorrell, Academic Press; 1 edition, ISBN:978-0125215336, (2002).

Microbial Genomics and Drug Discovery, Thomas J. Dougherty, Steven J. Projan, CRC Press; 1 edition, ISBN:978-0824740412, (2003).

Page 57: M.Sc. Bioinformatics syllabus

Perl for BioinformaticsSub. Code: BIM-304 (P)

Course Objectives: To enable the students to gain knowledge about Perl for Bioinformatics.

Total Credits: 2List of experiments Installing Perl on Your ComputerText Editors, Individual Approaches to ProgrammingSequences and Strings, Representing Sequence DataA Program to Store a DNA SequenceConcatenating DNA FragmentsTranscription: DNA to RNAUsing the Perl DocumentationCalculating the Reverse Complement in PerlProteins, Files, and ArraysReading Proteins in FilesMotifs and Loops, Finding MotifsCounting NucleotidesExploding Strings into ArraysCommand-Line Arguments and ArraysMutations and RandomizationProgram Using RandomizationProgram to Simulate DNA Mutation, Generating Random DNAData Structures and Algorithms for BiologyTranslating DNA into ProteinsReading DNA from Files in FASTA FormatRestriction Maps and Restriction EnzymesGenBank FilesParsing PDB FilesObtaining BLASTString Matching and Homology, Web ProgrammingAlgorithms and Sequence AlignmentMicroarrays and XMLGraphics Programming

Text Books:Perl Programming for Bioinformatics & Biologists, Lab Manual D. Curtis Jamison, John Wiley

& Sons, INC., 2004. Perl Programming for Bioinformatics, Harshawardhan P Bal, Tata McGraw Hill, 2003. James Tisdall, Mastering Perl for Bioinformatics, O’Reilly, 2003. Perl Programming for Bioinformatics & Biologists, D. Curtis Jamison, John Wiley & Sons,

INC., 2004. Bioinformatics Biocomputing and Perl, Michael Moorhouse, Paul Barry, Wiley, 2004.

Page 58: M.Sc. Bioinformatics syllabus

Swami Ramanand Teerth Marathwada University

Nanded School of Technology

Sub Centre, Latur

Syllabus For theM.Sc. Bioinformatics

(CGPA)School of Technology,

SRTMUN Sub-Centre, Latur Academic Year 2010-11

Page 59: M.Sc. Bioinformatics syllabus

Semester -IV

Page 60: M.Sc. Bioinformatics syllabus

Plant GenomicsSub. Code: BIM-401 (T)

Course Objectives: To enable the students to gain knowledge about Plant Genomics

Total: 45L Total Credits: 4

Unit-I: Plant Genome Databases (9L)Nucleotide database- NCBI (GenBank), DDBJ, EMBL, Protein structure Databank - PDB, Search Engine - SRS, EntrezEnzyme databases- BRENDA, , KEGGProtein database - TrEMBL, UniProt, PIRIndex to Plant Chromosome Numbers database - IPCN

Unit-II: The Arabidopsis Genome Project (9L)History of Plant, Arabidopsis Genome study, Entrez Records, Phylogenetic relationship, Model Plant Arabidopsis Thaliana, TAIR, TIGRCytogenetics - A cytogenetic resource of FISH-mapped, sequence-tagged clones; dbSNP- Database of SNPs and other genetic variation; Entrez- Gene Focal point for genes and associated information; RefSeq - Reference Sequence collection: genomic DNA, transcripts, and proteins; UniGene -Non-redundant gene-oriented clusters; UniSTS- STS markers; Protein coding geneRepeat Sequences- RNAAdvantages as a model organism

Unit-III: Genome organization and evolution (9L)Plant genomics and ProteomicsTransmission of genetic information – Mapping, High resolution maps, Horizontal gene transferGenome AnalysisEukaryotic Genome- Arabidopsis, Soybean, Mungbean, Rice, Cotton, Withania, Maize,Plant viruses study – Coat protein study, TMV, PMV, PAMV

Unit-IV: Protein function and biochemical pathways (9L)BRITE- Biomolecular Relations in Information Transmission and Expression EcoCyc/MetaCyc- Encyclopedia of E. coli genes and metabolism; Metabolic encyclopedia EMP- Metabolic pathways KEGG -Kyoto encyclopedia of genes and genomes Biochemical Pathways -Enzyme database and link to biochemical pathway map Metabolic Pathway- Metabolic pathways of biochemistry aMAZE- Protein function and biochemical pathways project at EBI PathDB- Metabolic pathway information Secondary metabolites,Pathway analysis,Phytochemicals

Page 61: M.Sc. Bioinformatics syllabus

Unit-V: Application of Plant Genomics (9L)Transgenic PlantsMetabolomicsFunctional genomics- Arabidopsis thalianaMetabolic profiling and fingerprintingNew drug developmentsPhylogenetic analysisGene expression analysisMicroarray techniques

Text Books:Plant Biotechnology: Green Revolution, Virendra Gomase and Anant Sherkhane, VDM Verlag

Dr. Müller, Germany, ISBN:978-3-639-03208-6, (2010). Encyclopedia of Agricultural Sciences (5 Vol. Set), Virendra Gomase, Shruti Gomase, Serial

Publication, India, ISBN:978-8-183-87339-0, (2010).Toxicogenomics, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,

ISBN:978-3639249958, (2010).Plant Genomics: Methods and Protocols (Methods in Molecular Biology), Daryl J. Somers, Peter

Langridge, J.P. Gustafson, Humana Press; 1 edition, ISBN-13: 978-1588299970, (2009).Principles and Practices of Plant Genomics, Volume 3: Advanced Genomics, Chittaranjan Kole,

Albert G. Abbott, Science Publishers; 1 edition, ISBN-13: 978-1578086832, (2010).Plant Stress Biology: From Genomics to Systems Biology, Heribert Hirt, Wiley-VCH, ISBN-13:

978-3527322909, (2009).Genetics and Genomics of Soybean (Plant Genetics and Genomics: Crops and Models), Gary

Stacey, B. Goldberg, Springer; 1 edition, ISBN-13: 978-0387722986, (2008).Plant Pathogenic Bacteria: Genomics and Molecular Biology, Robert W. Jackson, Caister

Academic Press; illustrated edition edition, ISBN-13: 978-1904455370, (2009).

Page 62: M.Sc. Bioinformatics syllabus

Metabolomics and Metabolic EngineeringSub. Code: BIM-402 (T)

Course Objectives: To enable the students to gain knowledge about metabolomics and the metabolic engineering in post genomic era.

Total: 45L Total Credits: 4

Unit-I: Introduction to Metabolomics (9L)Overview of MetabolomicsMetabolomics in Arabidopsis thalianaMetabolic pathway databasesEcoCyc, MetaCyc, LIGAND, ENZYME, BRENDA, KEGG

Unit-II: Metabolome Informatics (9L)Introduction to the ARM DatabaseThe Genome-Based E-CELL Modeling (GEM) SystemLarge-Scale Simulation of MetabolismMetabolomics and Medical Sciences

Unit-III: Introduction to Metabolic Engineering (9L)Importance of metabolic engineeringComprehensive models for cellular reactionsMaterial balances & Data ConsistencyMetabolic pathway synthesisMetabolic pathway and disease interaction Secondary metabolites and new drug approachSystem Biology approachNetwork Engineering

Unit-IV: Metabolic Flux Analysis and its Application (9L)Theory-determination of flux by isotope labelingMetabolic control analysisControl coefficients and summation theorems, FCC determinationGrouping of reactions, gFCC, identification of independent pathways

Unit-V: Flux Analysis of Metabolic Networks (9L)Bottom up and Top down approachesCase study-optimization of flux amplificationConsistency tests and experiment validationSupervised and unsupervised approachMachine learning techniquesCluster analysis for pathways

Page 63: M.Sc. Bioinformatics syllabus

Textbooks:Metabolomics, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,

ISBN:978-3-639-24991-0, (2010). Metabolomics- The Frontier of Systems Biology, M. Tomita, T. Nishioka, Springer Publications,

(2003).Metabolic Engineering- Principles and Methodologies, Gregory N. Stephanopoulos, Academic

press, First Edition, (1998).An Introduction to Metabolic and Cellular Engineering, S. Cortassa, World scientific public

company Ltd., (2002).Metabolomics: Methods And Protocols, Wolfram Weckwerth, Humana Press, (2007).

Page 64: M.Sc. Bioinformatics syllabus

Oncogenomics and Cell SignalingSub. Code: BIM-403 (T)

Course Objectives: To enable the students to gain knowledge about Oncogenomics and Cell Signaling.

Total: 45L Total Credits: 4

Unit- I: Introduction to Oncology and Chemotherapy (9L)Cancer: Terminology and classification Introduction to anti-cancer drugs Side effects of chemotherapy and radiotherapy New developments in cancer therapy Introduction to: Breast, lung, upper GI, colorectal, ovarian, prostate and skin cancers Clinical trial issues in oncology

Unit- II: Oncogenomics (9L)Basic Cancer GeneticsProtooncogene and Viral Oncogene, Tumor Suppressor GenesGenome-wide Search for Mutations in Human CancersExpression Profiling and Model System of CancerIdentification and validation of oncogenesMolecularly Targeted DrugsComparative Oncogenomics, and functional genomicsDevelopment, Progression, Conceptual & Clinical implications of melanoma

Unit- II: Current Cancer Targets (9L)Implications for viral therapy of cancerToxicokinetics, NanomedicinesMolecular Approaches to Cancer, Molecular Profiling in CancerHereditary Cancers and Model SystemsReview of Basic Cancer Genetics and Molecularly Targeted DrugsArray based genomic hybridizationNCI-60 and Tissue Analysis in CancerProteomics and Model Systems in CancerCurrent Cancer Drug TargetsGenetic Engineering – A New Era for Cancer ImmunotherapyEpigenomics

Unit- III: Monitor signaling activity in cells (9L)Basics of Signaling Pathways Signaling by Nuclear ReceptorsG-Protein Coupled Signal Transmission PathwaysSecondary MessengersSerine Threonine Protein Kinases and Protein phosphataseTyrosine Specific Protein KinasesSignal Transmission via Ras Proteins

Page 65: M.Sc. Bioinformatics syllabus

Unit- III: Signaling Pathways (9L)IntraCellular Signal TransductionMAP Kinase PathwaysMembrane Receptors with Associated Tyrosine Kinase activityMalfunctioning of Signaling Pathways and TumorigenesisIon Channels and Signal TransductionBiomarkers Stem Cell & Development Toxicology & Drug ADME

Text BookOncogenomics: Molecular Approaches to Cancer, Charles Brenner and David Duggan, ISBN:

978-0-471-22592-8, John Wiley & Sons India Pte. Ltd. Biomarkers, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,

ISBN:978-3639170306, (2010). Transcriptomics: Expression Pattern Analysis, Virendra Gomase and Somnath Tagore, VDM

Verlag Dr. Müller, Germany, ISBN:978-3639214864, (2009). Toxicogenomics, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,

ISBN:978-3639249958, (2010). Molecular Genetics Of Cancer, C.B. Powar, ISBN-81-7866-680-4, Himalaya Publication HouseStructure and Function in Cell Signalling, John Nelson, ISBN: 978-0-470-02551-2, John Wiley

& Sons India Pte. Ltd. Cell Signalling, C.B. Powar, ISBN-81-8318-365-4, Himalaya Publication HouseCell Signalling, John Hancock, ISBN : 0199264678, I.K. International Publishing House Pvt. Ltd The Biochemistry of Cell Signaling, Ernst J.M. Helmreich, ISBN:9780195673845, Oxford

University PressMolecular And Cellular Physiology Of Neurons, Fain Gordon L., ISBN :81-203-2734-9,

Prentice-Hall of IndiaCancer Bioinformatics: From Therapy Design to Treatment, Sylvia Nagl, ISBN: 978-0-470-

86304-6, John Wiley & Sons India Pte. Ltd. Lung Cancer, Sujal Desai, ISBN: 9780521872027, Cambridge University Press India Private

Limited

Page 66: M.Sc. Bioinformatics syllabus

IPR and Industrial PsychologySub. Code: BIM-404 (T)

Course Objectives: To enable the students to gain knowledge about IPR and Industrial Psychology.

Total: 45L Total Credits: 4

Unit- I: Intellectual Property Protection (9L)Overview of Intellectual Property Law The Use of Intellectual Property in Business How to Read and Obtain Information from a Modern Patent Introduction to Patents Patentable Subject Matter and Utility Novelty of the Invention Requirement of Non-Obviousness for Patentability The Patenting Process Claims, Patent Application and Prosecution

Unit- II: Patentability and Inventions (9L)Protection of Computer-Related Inventions Patentability of Biotechnology Inventions Business Method Protection Foreign Patent Protection Enforcement of the Patent Right Ownership and Transfer of Patent Rights The Engineer and Scientist as Expert Witness; and Ethics Copyrights as a Vehicle for Technology Protection Mask Work Protection Trade Secrets, Trademarks

Unit- III: The Practice of Industrial-Organizational Psychology (9L)Principles, Practices, and ProblemsTechniques, Tools, and TacticsThe Development of Human ResourcesEmployee Selection Principles and TechniquesPsychological TestingPerformance AppraisalRaining and Development

Unit- IV: Organizational Psychology (9L)Research MethodsAttraction and socialization Productive behaviour or organisationJob satisfaction and organisational commitment Counterproductive behaviour in organizationsOccupational StressTheories of motivation

Page 67: M.Sc. Bioinformatics syllabus

Engineering PsychologyConsumer Psychology

Unit- V: Psychology and Leadership Traits (9L)Leadership and Influence processesGroup behaviourOrganisational Culture Interpersonal Skills - Delegation, Humour,Trust, Expectations, Value, Status and CompatibilityPositive Thinking - Attitudes and BeliefsPositive Thinking Martin Seligman’s Theory of Learned HelplessnessPositive Thinking- Martin Seligman’s Theory of Learned OptimismPsychology and Leadership Traits

Text BookHigh Performance Leadership, Dr. G. Vijayaragavan, ISBN-978-81-8318-901-9, Himalaya

Publication HouseIntellectual Property Law for Engineers and Scientists, Howard B. Rockman, ISBN: 978-0-471-

44998-0, John Wiley & Sons India Pte. Ltd.Organisational Psychology, Steve M. Jex, ISBN:9812532307, John Wiley & Sons India Pte. Ltd.Industrial and Organizational Psychology: Linking Theory with Practice, Cary L. Cooper, ISBN:

978-0-631-20992-8, John Wiley & Sons India Pte. Ltd.Business Ethics, C.S.V. Murthy, ISBN-81-8318-148-1, Himalaya Publication HouseBusiness Law For Management, P. Saravanavel & S. Sumathi, ISBN-81-8318-069-8, Himalaya

Publication HouseManaging Intellectual Property, Vinod V. Sople, ISBN :81-203-3061-7, Prentice-Hall of IndiaPsychology, Baron Robert A., ISBN :978-81-203-2335-3, Prentice-Hall of IndiaOrganizational Behavior 1: Essential Theories Of Motivation And Leadership, Miner John B.,

ISBN :81-203-2951-1, Prentice-Hall of India

Page 68: M.Sc. Bioinformatics syllabus

Project Sub. Code: BIM-405 (T)

Course Objectives: Project carried out for the partial fulfillment of the M.Sc.Bioinformatics.

Total Credits: 8Area for the projectsSequence Analysis Evolution and Phylogeny Genomic Proteomics Metabolomics: NMR base genetic diversityImmunogenomics: recent discoveriesMachine intelligence PhosphoproteomicsImmunoinformatics and its role in microbes and vaccinesCellunomics: the interaction analysis of cellsPhylogenomics: evolution and genomics intersectionmicroRNA: human disease and developmentInteractomics: Chemical interaction analysisPathogenomicsRNomics: functional RNA analysisImmunoproteomics Phospho-onco-proteomicsNutrigenomicsFluxomicsGlycomicsLipidomicsVaccinomicsTransgenomicsOncogenomicsPharmacogenomics Proteomics: Technologies for Protein AnalysisMicroarray: An Approach for Current Drug TargetsEpigenomicsTranscriptomicsToxicogenomicsKinomicsPhysiomicsCytomics MetabolomicsMetabolic Pathways Networks and Systems Biology Structural Bio-informatics Neuro-informatics Bio-Ontologies Biomedical Text Mining Biological Data Modeling and Integration

Page 69: M.Sc. Bioinformatics syllabus

LIMS, SIMS and Other Tools to Support Experimental Biology Applications of Bio-informatics to Biomedicine Agriculture and Drug Discovery Information TechnologyComputer application in Bioinformatics, Pharmacoinformatics Databases and Software tools for analysis Life Sciences ApplicationDrug Design and DiscoveryComputational NeurosciencesMedical Informatics New Trends in Computer Technology

Page 70: M.Sc. Bioinformatics syllabus

Plant GenomicsSub. Code: BIM-401 (P)

Course Objectives: To enable the students to gain knowledge about Plant Genomics

Total Credits: 2List of Experiments:Plant Genome organization and evolution Plant Functional genomicsPlant Transgenomics approach Plant MetabolomicsPlant Comparative genomicsMolecular modeling & DockingPlant Micro array data analysisPlant Primer designPhylogenetic analysisMolecular EvolutionMetabolic pathways analysisSecondary metabolites and new drug approach

Text Books:Plant Biotechnology: Green Revolution, Virendra Gomase and Anant Sherkhane, VDM Verlag

Dr. Müller, Germany, ISBN:978-3-639-03208-6, (2010). Encyclopedia of Agricultural Sciences (5 Vol. Set), Virendra Gomase, Shruti Gomase, Serial

Publication, India, ISBN:978-8-183-87339-0, (2010).Toxicogenomics, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,

ISBN:978-3639249958, (2010).Plant Genomics: Methods and Protocols (Methods in Molecular Biology), Daryl J. Somers, Peter

Langridge, J.P. Gustafson, Humana Press; 1 edition, ISBN-13: 978-1588299970, (2009).Principles and Practices of Plant Genomics, Volume 3: Advanced Genomics, Chittaranjan Kole,

Albert G. Abbott, Science Publishers; 1 edition, ISBN-13: 978-1578086832, (2010).Plant Stress Biology: From Genomics to Systems Biology, Heribert Hirt, Wiley-VCH, ISBN-13:

978-3527322909, (2009).Genetics and Genomics of Soybean (Plant Genetics and Genomics: Crops and Models), Gary

Stacey, B. Goldberg, Springer; 1 edition, ISBN-13: 978-0387722986, (2008).Plant Pathogenic Bacteria: Genomics and Molecular Biology, Robert W. Jackson, Caister

Academic Press; illustrated edition edition, ISBN-13: 978-1904455370, (2009).

Page 71: M.Sc. Bioinformatics syllabus

Metabolomics and Metabolic EngineeringSub. Code: BIM-402 (P)

Course Objectives: To enable the students to gain knowledge about Metabolomics and Metabolic Engineering

Total Credits: 2

List of Experiments:Metabolic engineeringComprehensive models cellular reactionsMetabolic flux analysis and its applicationsMetabolome and its studyApplications of metabolomicsMolecular EvolutionMetabolic pathways analysisSecondary metabolites and new drug approachSystem Biology approachNetwork EngineeringMetabolic pathway and disease interaction Supervised and unsupervised approachMachine learning techniquesCluster analysis for pathways

Textbooks:Metabolomics, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,

ISBN:978-3-639-24991-0, (2010). Metabolomics- The Frontier of Systems Biology, M. Tomita, T. Nishioka, Springer Publications,

(2003).Metabolic Engineering- Principles and Methodologies, Gregory N. Stephanopoulos, Academic

press, First Edition, (1998).An Introduction to Metabolic and Cellular Engineering, S. Cortassa, World scientific public

company Ltd., (2002).Metabolomics: Methods And Protocols, Wolfram Weckwerth, Humana Press, (2007).