Swami Ramanand Teerth Marathwada University Nanded School of Technology Sub Centre, Latur

Syllabus For the

M.Sc. Bioinformatics (CGPA)
School of Technology, SRTMUN Sub-Centre, Latur
Academic Year 2010-11

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 system Presently the School conducts M.Sc. Bioinformatics (CGPA) Post-Graduate Courses as per CGPA = CUMULATIVE GRADE POINT AVERAGE A 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. Courses
Sr. No I Name of the Program M. Sc. [Bioinformatics]- CGPA Duration 2 Years Intake 30 (Seat)

Eligibility and Fees Any 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.

Feature of CGPA System
Master Degree would be of 112 Credits each Each semester shall have five theory courses, Four practical courses Five theory courses = 20 Credits Four practical courses= 8 Credits Total 28 credits per semester Total 700 marks per semester Every student shall complete 112 credits in a minimum of four semesters. All semester will have 28 credits each. Four semester X 28 credits = 112 credits Total 2800 marks for Master Degree program One Credit = 25 marks Two Credits = 50 Marks Four Credits = 100 Marks Theory Course = 100 Marks Practical Course = 50 Marks Theory Course = 100 Marks
Internal Exam 50 Marks = 2 Credits External Exam 50 Marks = 2 Credits

Break up internal exam marks for Theory
Theory Test-1 15 marks Theory Test-2 15 marks Home Assignments 20 marks Total Marks 50 Marks = 2 Credits

Practical Course = 50 Marks
Internal Exam 25 Marks = 1 Credit External Exam 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

Project Course = 200 Marks
Internal Exam 100 Marks = 4 Credits External Exam 100 Marks = 4 Credits

Break up internal exam marks for Project
Synopsis 25 marks Project work 75 marks Total Marks 100 Marks = 4 Credits

Semester I
CODE NO NAME OF PAPER INTERNAL EXAM / DEPARTMENT LEVEL CREDIT INTERNA L EXAM CREDITS TO TA L CR EDI TS 4 4 4 4

BIM-101 (T) BIM-102 (T) BIM-103 (T) BIM-104 (T)

Genetics and Molecular Biology Bioinformatics Biostatistics Data Base Managements Systems Oracle

2 2 2 2

2 2 2 2

BIM-105 (T)

Linux

2

2

4

BIM-102 (P) BIM-103 (P) BIM-104 (P)

Bioinformatics Biostatistics Data Base Managements Systems Oracle

1 1 1

1 1 1

2 2 2

BIM-105 (P)

Linux

1 14

1 14

2 28

Total Credits in I Semester = 28

Semester II
CODE NO NAME OF PAPER INTERNAL EXAM / DEPARTMENT LEVEL CREDIT INTERNAL EXAM CREDITS TO TA L CR ED IT S

BIM-201 (T) BIM-202 (T) BIM-203 (T) BIM-204 (T) BIM-205 (T)

Advanced Molecular Biology Computational Biology Immunoinformatics Chemoinformatics Machine Intelligence in Bioinformatics

2 2 2 2 2

2 2 2 2 2

4 4 4 4 4

BIM-203 (P) BIM-204 (P) BIM-205 (P) BIM-206 (P)

Immunoinformatics Chemoinformatics Machine Intelligence in Bioinformatics Numerical Methods and Optimization Techniques

1 1 1 1

1 1 1 1

2 2 2 2

14

14

28

Total Credits in II Semester = 28

Semester III
CODE NO NAME OF PAPER INTERNAL EXAM / DEPARTMENT LEVEL CREDIT INTERNA L EXAM CREDITS TO TA L CR ED ITS

BIM-301 (T) BIM-302 (T) BIM-303 (T) BIM-304 (T) BIM-305 (T)

Computer Aided Drug Design Object Oriented Programming (OOPS) JAVA Microbial Genomics Principle of Drug Action Molecular Modeling

2 2 2 2 2

2 2 2 2 2

4 4 4 4 4

BIM-301 (P) BIM-302 (P) BIM-303 (P) BIM-304 (P)

Computer Aided Drug design Object oriented Programming (OOPS) JAVA Microbial Genomics Perl for Bioinformatics

1 1 1 1 14

1 1 1 1 14

2 2 2 2 28

Total Credits in III Semester = 28

Semester IV
CODE NO NAME OF PAPER INTERNAL EXAM / DEPARTMENT LEVEL CREDIT INTERNAL EXAM CREDITS TOTAL CREDITS

BIM-401 (T) BIM-402 (T) BIM-403 (T)

Plant Genomics Metabolomics and Metabolic Engineering Oncogenomics and Cell Signaling

2 2 2

2 2 2

4 4 4

BIM-404 (T) BIM-405 (PJ)

IPR and Industrial Psychology Project

2 4

2 4

4 8

BIM-401 (P) BIM-402 (P)

Plant Genomics Metabolomics and Metabolic Engineering

1 1

1 1

2 2

14

14

28

Total Credits in IV Semester = 28

Swami Ramanand Teerth Marathwada University Nanded School of Technology Sub Centre, Latur

Syllabus For the

M.Sc. Bioinformatics (CGPA)
School of Technology, SRTMUN Sub-Centre, Latur
Academic Year 2010-11

Semester -I

Genetics and Molecular Biology
Sub. 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 Unit -I: Structure of Nucleic Acid Structure of DNA Different forms of DNA and RNA Identification of DNA as genetic material by Griffith ±Avery, McLeod and McCarty Frankel and Singer Hershey and Chase Messelson and Stahl experiment Unit -II: DNA Replication and Mutation Semi-Conservative replication Replication of DNA in Eukaryotes Molecular basis of Mutation Classification of mutation Unit -III: Gene Expression and Regulation Genetic code Transcription Prokaryotes and Eukaryotes Post transcriptional modification Translation in prokaryotes and Eukaryotes Post translational modification Gene Regulation Lac operon model Unit -IV: Mendelian Genetics Mendel¶s laws Monohybrid Dihybrid inheritance Multiple alleles Structure and organization of chromosome in Prokaryote and Eukaryotes Unit -V: Crossing Over and Linkage Linkage Types of linkage Crossing over and their types Recombination mapping Two point and three point text cross mapping in bacteria Total Credits: 4 (9L)

(9L)

(9L)

(9L)

(9L)

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)

Bioinformatics
Sub. Code: BIM-102 (T) Course Objectives: To enable the students to gain knowledge about Bioinformatics. Total: 45L Unit -I: Biological Database Design and Management DBMS, RDBMS Sources of biological data Database Design and Data Mining Database Management Security & Architecture Total Credits: 4 (9L)

Unit -II: Genomics Database (9L) Human Genome Project Database of Model Species : Drosophila melanogaster , Arabidopsis thaliana, C. elegans, Saccharomyces cerevisiae, Danio rerio Plasmodium Falsiparum Genome Project The Arabidopsis Genome Project Unit -III: Biological Databanks NCBI, DDBJ, EMBL, PDB, SRS, BRENDA, TrEMBL, UniProt, KEGG, MIAME, OMIM Unit -IV: Bioinformatics database & repositories Protein database ± GenBank Nucleotide & Gene database ± GenBank Microarray Database & analysis Gene Expression Profile Database ± GEO Metabolic Pathway ± PathDB Enzyme Database ± KEGG Ion Transport Database Unit -V: Genome Analysis Genome Analysis Genome Anatomy a. Prokaryotic Genome ±E coli Mycoplasma b. Eukaryotic Genome- Human, Rat, Arabidopsis, Soybean, Mungbean, Rice Comparative genomics c. Proteomics analysis, horizontal gene transfer Functional classification of gene Gene order on chromosome (9L)

(9L)

(9L)

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

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

Biostatistics
Sub. Code: BIM-103 (T) Course Objectives: To enable the students to gain knowledge about Biostatistics. Total: 45L Unit -I: Introduction Methods of collection of data Classifications and graphical representation of data Binomial and normal probability distribution Polygon, histogram, measure of central tendency Significance of statistical methods Probability Degree of freedom, measures of variation Standard deviation, Standard error Unit -II: Statistical Sampling 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 Linear regression and correlation Analysis of Variance (one way and two way) Factorial designs (including fraction factorial design) Theory of probability Permutation and Combination Ratios, Percentage and Proportion Two way ANOVA and Multiple comparison procedures Unit -IV: Experimental design and trials 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 correlation Nonlinear regression Unit -V: Bioassays-calculations Bioassays-calculations of doses response relationships LD50, ED50, probit analysis Applications of software for statistical calculation viz. SPSS, foxtron Application of computers in Pharmaceutical sciences Total Credits: 4 (9L)

(9L)

(9L)

(9L)

(9L)

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: 9780534418205, (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)

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 Relational data model & relational algebra Relational model concepts Relational model constraints, relational algebra SQL- a relational database language Date definition in SQL, view and queries in SQL Specifying constraints and indexes in SQL Relational database management systems DB2, Oracle PL/SQL Programming Language / Structure Query Language- DDL, DML Unit -III: Data Structure 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 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 Concurrency control techniques (9L)

(9L)

(9L)

(9L)

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

Linux
Sub. Code: BIM-105 (T) Course Objectives: To enable the students to gain knowledge about Linux. Total: 45L Unit ±I: Introduction to Linux OS and Linux, History of Linux and Unix Linux Software Linux Documentation, Distribution Installation of Linux Linux and Interfaces Genome Desktop, KDE Total Credits: 4 (9L)

Unit ±II: Linux Environments (9L) KDE - desktop, help system, KDE configuration Genome - Interface, file manager, Panel, Applets, configurations The shell ± command line, file name, encapsulation, standards output/ input, shell variables, pipes Linux File Structure Shell configuration Unit ±III: System and network Configuration System configuration Distribution administration tools Read Hat administration tools Configuring users Mapping CD Rom, Floppy, CD-R/W Drivers Printer, Update tools Install softwares packages Unit ±IV: Client Applications and Server managements Client Applications Mails and News clients Web, FTP and JAVA clients Networks tools, Office applications DBMS, Graphic tools, editors Server managements FTP Servers, Web servers, Domain Name Services Mail Servers, SMTP, POP, IMAP Unit ±V: System Administration and Network administration Basic of system administration Boot management tools Managing users Software managements (9L)

(9L)

(9L)

File system administration Devices and Printers Kernel Administration Configuration of Network connection NFS, NIS, Applets Table Samba, Administrating TCP / IP Networks Network 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: 9780470485057, (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: 9780470467015, (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).

Bioinformatics Practical
Sub. Code: BIM-102 (P) Course Objectives: To enable the students to gain knowledge about Bioinformatics. Total Credits: 2 List of experiments Database Searching Nucleotide Databases -NCBI, DDBJ, EMBL, PDB, BRENDA, TrEMBL, KEGG, Microarray ± MIAME. GEO Diseases -OMIM Database Protein databases- PIR, UniProt Search Engines- SRS, Entrez BLAST, PHI-PSI- BLAST, FASTA Sequence alignments Local Alignments Global Alignments Dynamic Programming, Dot Plot Smith-Waterman, Needleman- Wunch Algorithms, Day Hoff Matrix, Blossum, PAM Matrices, GAP Penalties Multiple 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

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

Biostatistics Practical
Sub. 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: 2

List 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 Distributions Estimation 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 Designs Likelihood 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: 9780534418205, (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)

Data Base Managements Systems Oracle Practical
Sub. 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 Software Creating and Controlling Oracle Databases Administering Users Managing Schema Objects and Data Implementing Oracle Security Features Monitoring Performance Performing Database Backup and Recovery Basic 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 An Introduction to Database Systems, C. J. Date, Addison Wesley Longman, ISBN-10: 0201385902

Linux Practical
Sub. 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 Structure Shell configuration Client Applications and Server managements Basic of system administration Boot management tools, Managing users, Software managements, File system administration, Devices and Printers Kernel Administration, Configuration of Network connection NFS, 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: 9780470485057, (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: 9780470467015, (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).

Swami Ramanand Teerth Marathwada University Nanded School of Technology Sub Centre, Latur

Syllabus For the

M.Sc. Bioinformatics (CGPA)
School of Technology, SRTMUN Sub-Centre, Latur
Academic Year 2010-11

Semester -II

Advanced Molecular Biology
Sub. Code: BIM-201 (T) Course Objectives: To enable the students to gain knowledge about Advanced Molecular Biology and genetics. Total: 45L Unit -I: Central Dogma of Molecular Biology DNA, RNA, Protein Replication Transcription Translation Total Credits: 4 (9L)

Unit -II: Split genes and overlapping genes (9L) Evolution of one cistron one polypeptide theory, Genetic complementation ±cis-trans test of genetic functions. Plasmids Mobile 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 bacteria Restriction and modification of DNA Recombination and enzymes involved. Unit -III: Recombinant DNA Technology 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 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 Essence of metabolic engineering examples of pathway manipulation Metabolic engineering in practice Fluxomics, Metabolic flux analysis and its applications Synthesis low molecular wt. compounds (9L)

(9L)

(9L)

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)

Computational Biology
Sub. 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 Database Protein databases- PIR, UniProt Search Engines- SRS, Entrez BLAST, PHI-PSI- BLAST, FASTA Unit -II: Sequence alignments Local Alignments Global Alignments Dynamic Programming, Dot Plot Smith-Waterman, Needleman- Wunch Algorithms, Day Hoff Matrix, Blossum, PAM Matrices, GAP Penalties Multiple Sequence alignments ClustalW, DALI Unit -III: Pattern identification Pattern matching function, Repeat analysis Invert repeats Domain Motif Restriction enzyme cleavage sites Unit -IV: Protein analysis Primary structure analysis ±Protparam, COILS Topology Prediction -TMHMM Secondary structure prediction -GOR, SOPMA, PHD Tertiary structure prediction-CPHModels Antigenic predictions Isoelectric points Unit -V: Phylogenic tree constructions General-purpose packages Parsimony programs Distance matrix methods Computation of distances (9L)

(9L)

(9L)

(9L)

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

Immunoinformatics
Sub. 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 (9L)

Unit -I: Introduction to Immunoinformatics Introduction Immunity Immune 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 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 Defining HLA Supertypes supertypes of GRID/CPCA Hierarchical clustering methods Hla-Ad supertypes MHC supertypes, and Class I Hla Alleles Unit -IV: Immunoinformatics databases IMGT/HLA IPD SYEPEITHI MHCBN database JenPep database Unit -V: Immunoinformatics Methods MHC Prediction Predicting Peptide-MCH Binding MCH binders

(9L)

(9L)

(9L)

(9L)

TAP binding MHC 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)

Chemoinformatics
Sub. Code: BIM-204 (T) Course Objectives: To enable the students to gain knowledge about Computers in Chemical Research. Total: 45L Total Credits: 4 (9L)

Unit -I: Introduction to Chemoinformatics Introduction to Chemoinformatics Computers 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 Management Strategies for using information effectively in early stage drug discovery Pharmacophore Modeling Computer aided drug design Ligand Libraries and Screening High Throughput Screening for Pharmacogenetics Clinical data collection and management New paradigm for analyzing adverse drug events Unit ±III: Drug Databases and Data Banks Drug information data bases Type of Drug Data Databases of Chemical Structures Databases on Chemical Reactions Spectroscopic Databases Chemistry in the Internet Computers and protein crystallography Protein-ligand free energy predictions for drug discovery Molecule libraries for synthesis Unit ±IV: Data Collection and Simulation Strategies Pharmacogenomics and Pharmacoproteomics Computer methods for predicting drug metabolism Toxicogenomics and Toxicoinformatics Computational optimization of biopharmaceutical properties Computer simulations in pharmacokinetics and pharmacodynamics MicroRNA, RNAinterference for Drug targets Computational Biology of microRNAs (9L)

(9L)

Unit ±V: Legal and Ethical Aspects (9L) Legal and Ethical Aspects of Chemoinformatics Chemical 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 Copyleft Information infrastructure regulations

Text Books: Encyclopedia of Drug Design (11 Volumes), Virendra Gomase and Shruti Gomase, ISBN:978-9380-02632-9, IK International Publishing House Pvt. Ltd 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 Limited microRNAs: From Basic Science to Disease Biology, Krishnarao Appasani, ISBN-13: 9780521865982, Cambridge University Press India Private Limited Microarray Bioinformatics, Dov Stekel, ISBN:13:9780521525879, Cambridge University Press India Private Limited Medical 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. Ltd Molecular 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., Publishers Stereochemistry of Organic Compounds, Ernest L. Eliel, Samuel H. Wilen, ISBN: 978-0-47101670-0, 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.

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 Genomics Gene Expression Data Mining Data Mining in Proteomics Data Mining Preparatory Activities Data cleaning, data preprocessing, and semantic integration of heterogeneous, distributed biomedical databases RNA Data Mining Unit -II: 3. Optimization Techniques Steepest descent Conjugate gradient Newton Raphson Simulated annealing and biomolecular structure optimization Genetic algorithms Unit -III: Machine Learning Techniques Neural Network based biological applications HMM based biological applications Dynamic programming and biological applications Sequences alignments Structure alignments Unit -IV: Monte Carlo and Bayesian approaches in data mining Data mining models and data streams Bayesian techniques and current biological research Statistical alignment MCMC workbench Models of computational analysis Markov Chain Monte Carlo Bayesian phylogenetics RNA substitution model and early mammalian evolution Advantages of Bayesian applications Unit -V: Clustering algorithms and applications Hierarchical and non-hierarchical clustering Grid Based clustering, Microarray analysis Microarray and automatic segmentation Protein array data analysis Text Books: (9L)

(9L)

(9L)

(9L)

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

Immunoinformatics Practical
Sub. 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, SYEPEITHI Information retrieval and analysis of database i.e. MHCBN, JenPep Immunoinformatics Methods MHC Prediction Predicting Peptide-MCH Binding MCH binders prediction TAP binders prediction MHC 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)

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 Plants Pharmacophore Modeling Ligand Libraries and Screening High Throughput Screening for Pharmacogenetics Clinical data collection and management Databases of Chemical Structures Databases on Chemical Reactions Protein-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: 0-47173779-8, 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 Limited microRNAs: From Basic Science to Disease Biology, Krishnarao Appasani, ISBN-13: 9780521865982, Cambridge University Press India Private Limited Microarray Bioinformatics, Dov Stekel, ISBN:13:9780521525879, Cambridge University Press India Private Limited Medical 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. Ltd Molecular 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., Publishers Stereochemistry 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.

Machine Intelligence in Bioinformatics Practical
Sub. Code: BIM-205 (P) Course Objectives: To enable the students to gain knowledge about Machine Intelligence techniques, algorithms in bioinformatics. Total Credits: 2 List of experiments Data mining in genomics Gene expression data mining Data mining in proteomics RNA secondary structure comparison and alignment Minimum free-energy method for RNA secondary structure prediction Gene mapping by pattern discovery Data mining: predicting protein folding pathways Data mining methods for a systematic of protein subcellular location Sequence homology Sequences alignments Structure alignments Motif involve in protein targeting Ab 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,1edition, 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

Numerical Methods and Optimization Techniques Practical
Sub. 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 Principles Optimization and Programming Optimization Techniques Numerical Analysis Application of Optimization Techniques Numerical Methods & Optimization Coordinate descent and subgradient method Optimization and Cutting Plane Methods Babylonian, Restricted step methods and Non linear equations Linearly 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

Swami Ramanand Teerth Marathwada University Nanded School of Technology Sub Centre, Latur

Syllabus For the

M.Sc. Bioinformatics (CGPA)
School of Technology, SRTMUN Sub-Centre, Latur
Academic Year 2010-11

Semester -III

Computer Aided Drug Design
Sub. Code: BIM-301 (T) Course Objectives: To enable the students to gain knowledge about Computer Aided Drug Design Total: 45L Unit-I: Introduction to CADD Introduction to CADD, SBDD Representation of Molecular Structures Chemical Nomenclature and Structure Representation Processing Constitutional Information Representation of 3D Structures Molecular Shape Analysis Representation of Chemical Reactions Unit-II: Virtual Screening Virtual Screening Chemoinformatics in Lead Discovery Computational Chemistry, Molecular Complexity and Screening Set Design Algorithmic Engines in Virtual Screening Strengths and Limitations of Pharmacophore-Based Virtual Screening Unit-III: Lead Discovery High Throughput Screening Hit and Lead Discovery Enhancing Hit Quality and Diversity within Assay Throughput Constraints Molecular Graphics, Molecular Dynamics and Simulation of Lead Molecular Diversity in Lead Discovery: From Quantity to Quality In Silico Lead Optimization Total Credits: 4 (9L)

(9L)

(9L)

Unit-IV: Databases and Libraries (9L) Databases and Libraries PubChem, PubEchm-BioAssay, Pharma Project, DrugBank WOMBAT: World of Molecular Bioactivity Cabinet - Chemical and Biological Informatics Network Structure Modification in Chemical Databases Rational Design of GPCR-specific Combinational Libraries Based on the Concept of Privileged Substructures Unit-V: CADD Applications CADD Applications A Practical Strategy for Directed Compound Acquisition Efficient Strategies for Lead Optimization Chemoinformatics Tools for Library Design Hit-to-Lead Process: A User's Perspective (9L)

Application of Predictive 3DQSAR Models to Database Mining Drug 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. Ltd Quantum Chemistry and Spectroscopy, Engel, ISBN: 9788131712856, Pearson Education Quantum Chemistry, Ira N. Levine, ISBN: 8120330641, Prentice-Hall of India An Introduction to Drug Design, S.N. Pandeya, New Age International (P) Ltd., Publishers Pharmaceutical Organic Chemistry, Rama Rao Nadendla, ISBN: 9781403924957, Macmillan India Limited Virtual Screening in Drug Discovery, Juan Alvarez and Brian Shoichet, ISBN-13: 9780824754792, CRC Press Biological Thermodynamics, Donald T. Haynie, ISBN:9780521704045, Cambridge University Press India Private Limited Stereochemistry of Organic Compounds, Ernest L. Eliel, Samuel H. Wilen, ISBN: 978-0-47101670-0, 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: 978-3-52730680-0, 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.

Object oriented Programming (OOPS) JAVA
Sub. Code: BIM-302 (T) Course Objectives: To enable the students to gain knowledge about Object oriented Programming (OOPS) JAVA. Total: 45L Total Credits: 4 (9L)

Unit-I: Introduction to Computing 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 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

(9L)

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 Class Exception Handling, I/O & JDBC Exception 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 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 (9L)

Delegation Event Model, Event Classes Event Listener Interfaces, Adapter and Inner Classes Unit-V: Multithreading & Communication Java Thread Model: Priorities, Synchronization Messaging, Life Cycle of Thread, Thread class Runnable interface, Interthread Communication Suspending, Resuming and Stopping threads Multithreading, 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: 0074625425 Java 2: The Complete Reference, Herbert Schildt, McGraw-Hill Osborne Media, ISBN-10: 0070495432 Mastering Java 2, J2se 1.4 by Zukowski, BPB Publication, ISBN: 8176566187 (9L)

Microbial Genomics
Sub. Code: BIM-303 (T) Course Objectives: To enable the students to gain knowledge about Microbial Genomics. Total: 45L Unit-I: Introduction History- Bioinformatics and microbial pathogenesis Bacteriophage Bioinformatics New methods of gene sequencing Unit-II: Genome Analysis Comparative Microbial Metabolism Genomic Analysis of Membrane Transport Analysis of the Bacterial Cell Cycle Unit-III: Bacterial Biodiversity Concepts of Bacterial Biodiversity for the age of Genomics Coevolution of symbionts and pathogens with their hosts Unit-IV: Pathogenic Genomes Plant pathogen genomes Parasite genomics Genomes of pathogenic enterobacteria and thermophiles Unit-V: Application Application of Genomics to Biocatalysis and Biodegradation Microbial proteomics Total Credits: 4 (9L)

(9L)

(9L)

(9L)

(9L)

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

Sub. Code: BIM-304 (T) Course Objectives: To enable the students to gain knowledge about Principle of Drug Action. Total: 45L Unit-I: Principle of Drug Action Basic Principles Drug Action, Drug Interactions Pharmacodynamics 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 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 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 Agents Used in Anemia and Hematopoietic Growth Factors Drugs Used in Coagulation Disorders Drugs Used in the Treatment of Hyperlipidemias Nonsteroidal Anti-Inflammatory Drugs Total Credits: 4 (9L)

(9L)

(9L)

(9L)

Hypothalamic and Pituitary Hormones 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 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: 978-3-52732343-2, John Wiley and Sons India Pvt. Ltd. Essentials of Pharmacotherapeutics, Barar FSK, ISBN: 8121904447, S Chand & Company Ltd Current Trends in Pharmacology, Arunabha Ray and Kavita Gulati, ISBN:8188237779, I.K. International Publishing House Pvt. Ltd The Textbook of Pharmaceutical Medicine, John P. Griffin, New Age International (P) Ltd., Publishers An Introduction to Drug Design, S.N. Pandeya, ISBN : 978-81-224-0943-7, New Age International (P) Ltd., Publishers Medical Pharmacology at a Glance, M.J. Neal, New Age International (P) Ltd., Publishers Katzung and Trevor's Review of Pharmacology, Anthony Trevor, Bertram Katzung, Susan Masters, ISBN13: 9780071488693, McGraw-Hill Modern Pharmacology with Clinical Applications, Charles R Craig and Robert E Stitzel, ISBN13: 978-0-7817-3762-3, Lippincott Williams & Wilkins Lippincott's Illustrated Reviews: Pharmacology, ISBN-10: 0-7817-7155-2, Lippincott Williams & Wilkins (9L)

Molecular Modeling
Sub. Code: BIM-305 (T) Course Objectives: To enable the students to gain knowledge about Molecular Modeling. Total: 45L Unit-I: Introduction Molecular Structure Molecules Electronic States and Coordinates patterns Rotation, Vibration, and Potential Curves of Diatomic Molecules Spectra of Diatomic Molecules Molecule Symmetries and Group Theory Rotation and Vibrations of Polyatomic Molecules Electronic States of Polyatomic Molecules Spectra of Polyatomic Molecules Molecules in External Fields Van der Waals Molecules and Clusters Unit-II: Molecular Mechanics 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 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 Molecular Dynamics Methodology Algorithms for time dependence Introduction to quantum modeling The Schrödinger equation Total Credits: 4 (9L)

(9L)

(9L)

(9L)

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 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, ZINDO The 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: 97881-8318-865-4, 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 Education Physical Chemistry, Peter Atkins and Julio De Paula, ISBN: 9780195685220, Oxford University Press (9L)

Computer Aided Drug Design
Sub. Code: BIM-301 (P) Course Objectives: To enable the students to gain knowledge about Computer Aided Drug Design. Total Credits: 2 List of experiments Representation of Molecular Structures, Molecular Shape Analysis Chemical Nomenclature and Structure Representation Virtual Screening, 3DQSAR Models Molecular Dynamics and Simulation of Lead Molecular Diversity in Lead Discovery: In Silico Lead Optimization Databases and Libraries Combinational Libraries Based on the Concept of Privileged Substructures Hit-to-Lead Process: A User's Perspective 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. Ltd Quantum Chemistry and Spectroscopy, Engel, ISBN: 9788131712856, Pearson Education Quantum Chemistry, Ira N. Levine, ISBN: 8120330641, Prentice-Hall of India An Introduction to Drug Design, S.N. Pandeya, New Age International (P) Ltd., Publishers Pharmaceutical Organic Chemistry, Rama Rao Nadendla, ISBN: 9781403924957, Macmillan India Limited Virtual Screening in Drug Discovery, Juan Alvarez and Brian Shoichet, ISBN-13: 9780824754792, CRC Press Biological Thermodynamics, Donald T. Haynie, ISBN:9780521704045, Cambridge University Press India Private Limited Stereochemistry of Organic Compounds, Ernest L. Eliel, Samuel H. Wilen, ISBN: 978-0-47101670-0, 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: 978-3-52730680-0, 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.

Object oriented Programming (OOPS) JAVA
Sub. Code: BIM-302 (P) Course Objectives: To enable the students to gain knowledge about Object oriented Programming (OOPS) JAVA. Total Credits: 2 List 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: 0074625425 Java 2: The Complete Reference, Herbert Schildt, McGraw-Hill Osborne Media, ISBN-10: 0070495432 Mastering Java 2, J2se 1.4 by Zukowski, BPB Publication, ISBN: 8176566187 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 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

Sub. Code: BIM-303 (P) Course Objectives: To enable the students to gain knowledge about Microbial Genomics . Total Credits: 2

List of experiments Microbial Bioinformatics Microbial metabolism Genomics-Based Analysis of the Bacterial Cell Cycle Plant pathogens Comparative Microbial Metabolism Microbial Genomic Analysis of Membrane Transport Analysis of the Bacterial Cell Plant -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).

Perl for Bioinformatics
Sub. Code: BIM-304 (P) Course Objectives: To enable the students to gain knowledge about Perl for Bioinformatics. Total Credits: 2 List of experiments Installing Perl on Your Computer Text Editors, Individual Approaches to Programming Sequences and Strings, Representing Sequence Data A Program to Store a DNA Sequence Concatenating DNA Fragments Transcription: DNA to RNA Using the Perl Documentation Calculating the Reverse Complement in Perl Proteins, Files, and Arrays Reading Proteins in Files Motifs and Loops, Finding Motifs Counting Nucleotides Exploding Strings into Arrays Command-Line Arguments and Arrays Mutations and Randomization Program Using Randomization Program to Simulate DNA Mutation, Generating Random DNA Data Structures and Algorithms for Biology Translating DNA into Proteins Reading DNA from Files in FASTA Format Restriction Maps and Restriction Enzymes GenBank Files Parsing PDB Files Obtaining BLAST String Matching and Homology, Web Programming Algorithms and Sequence Alignment Microarrays and XML Graphics 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.

Swami Ramanand Teerth Marathwada University Nanded School of Technology Sub Centre, Latur

Syllabus For the

M.Sc. Bioinformatics (CGPA)
School of Technology, SRTMUN Sub-Centre, Latur
Academic Year 2010-11

Semester -IV

Plant Genomics
Sub. Code: BIM-401 (T) Course Objectives: To enable the students to gain knowledge about Plant Genomics Total: 45L Unit-I: Plant Genome Databases Nucleotide database- NCBI (GenBank), DDBJ, EMBL, Protein structure Databank - PDB, Search Engine - SRS, Entrez Enzyme databases- BRENDA, , KEGG Protein database - TrEMBL, UniProt, PIR Index to Plant Chromosome Numbers database - IPCN Total Credits: 4 (9L)

Unit-II: The Arabidopsis Genome Project (9L) History of Plant, Arabidopsis Genome study, Entrez Records, Phylogenetic relationship, Model Plant Arabidopsis Thaliana, TAIR, TIGR Cytogenetics - 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 gene Repeat Sequences- RNA Advantages as a model organism Unit-III: Genome organization and evolution (9L) Plant genomics and Proteomics Transmission of genetic information ± Mapping, High resolution maps, Horizontal gene transfer Genome Analysis Eukaryotic 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

Unit-V: Application of Plant Genomics Transgenic Plants Metabolomics Functional genomics- Arabidopsis thaliana Metabolic profiling and fingerprinting New drug developments Phylogenetic analysis Gene expression analysis Microarray techniques

(9L)

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).

Metabolomics and Metabolic Engineering
Sub. 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 Unit-I: Introduction to Metabolomics Overview of Metabolomics Metabolomics in Arabidopsis thaliana Metabolic pathway databases EcoCyc, MetaCyc, LIGAND, ENZYME, BRENDA, KEGG Unit-II: Metabolome Informatics Introduction to the ARM Database The Genome-Based E-CELL Modeling (GEM) System Large-Scale Simulation of Metabolism Metabolomics and Medical Sciences Unit-III: Introduction to Metabolic Engineering Importance of metabolic engineering Comprehensive models for cellular reactions Material balances & Data Consistency Metabolic pathway synthesis Metabolic pathway and disease interaction Secondary metabolites and new drug approach System Biology approach Network Engineering Unit-IV: Metabolic Flux Analysis and its Application Theory-determination of flux by isotope labeling Metabolic control analysis Control coefficients and summation theorems, FCC determination Grouping of reactions, gFCC, identification of independent pathways Unit-V: Flux Analysis of Metabolic Networks Bottom up and Top down approaches Case study-optimization of flux amplification Consistency tests and experiment validation Supervised and unsupervised approach Machine learning techniques Cluster analysis for pathways Total Credits: 4 (9L)

(9L)

(9L)

(9L)

(9L)

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).

Oncogenomics and Cell Signaling
Sub. 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 Basic Cancer Genetics Protooncogene and Viral Oncogene, Tumor Suppressor Genes Genome-wide Search for Mutations in Human Cancers Expression Profiling and Model System of Cancer Identification and validation of oncogenes Molecularly Targeted Drugs Comparative Oncogenomics, and functional genomics Development, Progression, Conceptual & Clinical implications of melanoma Unit- II: Current Cancer Targets Implications for viral therapy of cancer Toxicokinetics, Nanomedicines Molecular Approaches to Cancer, Molecular Profiling in Cancer Hereditary Cancers and Model Systems Review of Basic Cancer Genetics and Molecularly Targeted Drugs Array based genomic hybridization NCI-60 and Tissue Analysis in Cancer Proteomics and Model Systems in Cancer Current Cancer Drug Targets Genetic Engineering ± A New Era for Cancer Immunotherapy Epigenomics Unit- III: Monitor signaling activity in cells Basics of Signaling Pathways Signaling by Nuclear Receptors G-Protein Coupled Signal Transmission Pathways Secondary Messengers Serine Threonine Protein Kinases and Protein phosphatase Tyrosine Specific Protein Kinases Signal Transmission via Ras Proteins (9L)

(9L)

(9L)

Unit- III: Signaling Pathways IntraCellular Signal Transduction MAP Kinase Pathways Membrane Receptors with Associated Tyrosine Kinase activity Malfunctioning of Signaling Pathways and Tumorigenesis Ion Channels and Signal Transduction Biomarkers Stem Cell & Development Toxicology & Drug ADME

(9L)

Text Book Oncogenomics: 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 House Structure 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 House Cell 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 Press Molecular And Cellular Physiology Of Neurons, Fain Gordon L., ISBN :81-203-2734-9, Prentice-Hall of India Cancer Bioinformatics: From Therapy Design to Treatment, Sylvia Nagl, ISBN: 978-0-47086304-6, John Wiley & Sons India Pte. Ltd. Lung Cancer, Sujal Desai, ISBN: 9780521872027, Cambridge University Press India Private Limited

IPR and Industrial Psychology
Sub. Code: BIM-404 (T) Course Objectives: To enable the students to gain knowledge about IPR and Industrial Psychology. Total: 45L Unit- I: Intellectual Property Protection 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 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 Principles, Practices, and Problems Techniques, Tools, and Tactics The Development of Human Resources Employee Selection Principles and Techniques Psychological Testing Performance Appraisal Raining and Development Unit- IV: Organizational Psychology Research Methods Attraction and socialization Productive behaviour or organisation Job satisfaction and organisational commitment Counterproductive behaviour in organizations Occupational Stress Theories of motivation Total Credits: 4 (9L)

(9L)

(9L)

(9L)

Engineering Psychology Consumer Psychology Unit- V: Psychology and Leadership Traits Leadership and Influence processes Group behaviour Organisational Culture Interpersonal Skills - Delegation, Humour, Trust, Expectations, Value, Status and Compatibility Positive Thinking - Attitudes and Beliefs Positive Thinking Martin Seligman¶s Theory of Learned Helplessness Positive Thinking- Martin Seligman¶s Theory of Learned Optimism Psychology and Leadership Traits (9L)

Text Book High Performance Leadership, Dr. G. Vijayaragavan, ISBN-978-81-8318-901-9, Himalaya Publication House Intellectual Property Law for Engineers and Scientists, Howard B. Rockman, ISBN: 978-0-47144998-0, 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 House Business Law For Management, P. Saravanavel & S. Sumathi, ISBN-81-8318-069-8, Himalaya Publication House Managing Intellectual Property, Vinod V. Sople, ISBN :81-203-3061-7, Prentice-Hall of India Psychology, Baron Robert A., ISBN :978-81-203-2335-3, Prentice-Hall of India Organizational Behavior 1: Essential Theories Of Motivation And Leadership, Miner John B., ISBN :81-203-2951-1, Prentice-Hall of India

Project
Sub. Code: BIM-405 (T) Course Objectives: Project carried out for the partial fulfillment of the M.Sc.Bioinformatics. Total Credits: 8

Area for the projects
Sequence Analysis Evolution and Phylogeny Genomic Proteomics Metabolomics: NMR base genetic diversity Immunogenomics: recent discoveries Machine intelligence Phosphoproteomics Immunoinformatics and its role in microbes and vaccines Cellunomics: the interaction analysis of cells Phylogenomics: evolution and genomics intersection microRNA: human disease and development Interactomics: Chemical interaction analysis Pathogenomics RNomics: functional RNA analysis Immunoproteomics Phospho-onco-proteomics Nutrigenomics Fluxomics Glycomics Lipidomics Vaccinomics Transgenomics Oncogenomics Pharmacogenomics Proteomics: Technologies for Protein Analysis Microarray: An Approach for Current Drug Targets Epigenomics Transcriptomics Toxicogenomics Kinomics Physiomics Cytomics Metabolomics Metabolic Pathways Networks and Systems Biology Structural Bio-informatics Neuro-informatics Bio-Ontologies Biomedical Text Mining Biological Data Modeling and Integration

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

Plant Genomics
Sub. Code: BIM-401 (P) Course Objectives: To enable the students to gain knowledge about Plant Genomics Total Credits: 2 List of Experiments: Plant Genome organization and evolution Plant Functional genomics Plant Transgenomics approach Plant Metabolomics Plant Comparative genomics Molecular modeling & Docking Plant Micro array data analysis Plant Primer design Phylogenetic analysis Molecular Evolution Metabolic pathways analysis Secondary 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).

Metabolomics and Metabolic Engineering
Sub. 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 engineering Comprehensive models cellular reactions Metabolic flux analysis and its applications Metabolome and its study Applications of metabolomics Molecular Evolution Metabolic pathways analysis Secondary metabolites and new drug approach System Biology approach Network Engineering Metabolic pathway and disease interaction Supervised and unsupervised approach Machine learning techniques Cluster 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).

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