Download manonmaniam sundaranar university, tirunelveli

MANONMANIAM SUNDARANAR UNIVERSITY, TIRUNELVELI – 627 012
B.Sc. BIOINFORMATICS (CBCS)
(Effective from the Academic Year 2012 – 2013 onwards)
Course Structure
Eligibility for admission
A pass in higher secondary (10+2) or any equivalent examination with subjects in biological
sciences / computer science.
I Semester
Part
I
II
III
III
IV
Components
Tamil / Other Language
English
Core Subjects
Theory
1. Cell Biology and Genetics
2. Basics of Computer
Practical
1. Lab in Cell Biology, Genetics and Molecular Biology
Allied Subject I
Theory : 1. Programming in C
Practical : 1. Lab in Programming in C and Visual Basic
Environmental Studies
Total (6 Theory)
Hours
6
6
Credits
3
3
4
4
4
4
2
--
4
2
2
30
4
-2
20
Hours
6
6
Credits
3
3
4
4
4
4
2
2
4
2
2
30
4
2
2
24
II Semester
Part
I
II
III
III
IV
Components
Tamil / Other Language
English
Core Subjects
Theory
3. Molecular Biology
4. Biomolecular Structure
Practical
1. Lab in Cell Biology, Genetics and Molecular Biology
Allied Subject I
Theory : 2. Programming in Visual Basic
Practical : 1. Lab in Programming in C and Visual Basic
Valued Based Education
Total (6 Theory + 2 Practical)
1
III Semester
Part
I
II
III
III
IV
IV
Components
Tamil / Other Language
English
Core Subject
Theory
5. Introduction to Bioinformatics
Practical
2. Lab in Bioinformatics, Genomics and Proteomics
Allied Subject II
Theory : 3. Basic Mathematics
Practical: 2. Lab in Mathematics using SciLab and
Biostatistics using SPSS/STATA/Excel
Skill Based Subject 1
1(a) Programming in PERL (OR)
1(b) Programming in PHP
Non-Major Elective
1(a) Fundamentals of Computer and Networks (OR)
1(b) Basics of Bioinformatics
Total (6 Theory)
Hours
6
6
Credits
3
3
4
4
2
--
4
2
4
--
4
4
2
2
30
20
Hours
6
6
Credits
3
3
4
4
2
2
4
2
4
2
4
4
2
2
-30
1
25
IV Semester
Part
I
II
III
III
IV
IV
V
Components
Tamil / Other Language
English
Core Subject
Theory
6. Basics of Genomics and Proteomics
Practical
2. Lab in Bioinformatics, Genomics and Proteomics
Allied Subject II
Theory : 4. Biostatistics
Practical: 2. Lab in Mathematics using SciLab and
Biostatistics using SPSS/STATA/Excel
Skill Based Subject 2
2(a) Database Management Systems (OR)
2(b) Introduction to Algorithms
Non-Major Elective
2(a) Biological Database and Sequence Analysis (OR)
2(b) Introduction to Algorithms
Extension Activity (NCC, NSS, YRC, and YWF)
Total (6 Theory + 2 Practical)
2
V Semester
Part
III
III
III
IV
Components
Core Subjects
Theory
7. Biological Databases
8. Computational Biology
Practical
3. Lab in Biological Databases
4. Lab in Computational Biology
5. Lab in Molecular Modeling and Computer Aided
Drug Design
Major Elective 1
9(a) Structural Bioinformatics (OR)
9(b) Biophysics
Major Elective 2
10(a) Systems Biology (OR)
10(b) Introduction to Biomolecular Instrumentation
Skill Based Subject (Common)
3(a) Effective Communication (OR)
3(b) Personality Development
Total (5 Theory)
Hours
Credits
4
4
4
4
3
3
2
----
5
5
5
5
4
4
30
22
Hours
Credits
6
6
5
4
4
4
3
3
2
4
4
4
5
5
30
29
VI Semester
Part
III
III
Components
Core Subjects
Theory
11. Molecular Modeling
12. Computer Aided Drug Design
13. Free and Open Source Bioinformatics Tools
Practical
3. Lab in Biological Databases
4. Lab in Computational Biology
5. Lab in Molecular Modeling and Computer Aided
Drug Design
Major Elective 3
14(a) Applications in Bioinformatics (OR)
14(b) Introduction to Intellectual Property Rights
Total (4 Theory + 3 Practical)
Total number of courses
Total number of hours
Total number of credits
: 40 (33 Theory + 7 Practical)
: 180
: 140
Distribution of marks in theory between external and internal assessment is 75:25; for
practical 60:40; pass minimum of 40% for external and overall components.
3
Semester - I
Core 1: Cell Biology and Genetics
Unit I:
Cell as a living entity, Prokaryotic and eukaryotic cells, cell types, variation in cell size shape
and organization, An overview of Ultrastructure
Unit II:
Cellular organelles - Cell wall composition and organization, Plasma membrane properties
and functions. Mitochondria, Chloroplast & Nucleus, Lysosomes and Golgi apparatus –
Cytosol – Properties of cytoplasmic matrix, cytoskeletions, ergastic substances – cytoliths,
raphides, inulin.
Unit III:
Nucleus organization – nuclei in different forms, fine structure of DNA, Chromosomal types
– giant chromosomes – Polytene, Lambrush, cell cycle – molecular events – phases – Mitosis
and Meiosis
Unit IV:
Mendel’s experiment and Laws, Allelic and non allelic, Multiple allelism, Principles Bateson
and Punnetts experiment. Sex linkage and sex linked genes. Cytoplasmic inheritance,
crossing over Linkage groups – measurement of linkage and gene mapping.
Unit V:
Population Genetics – Hardy-Weinberg equilibrium – Significance and Factors affecting gene
frequency - DNA as the Genetic material – Properties and function.
REFERENCES:
1. De Robertis E.D.P. and De Robertis Jr, E.M.F. 1998. Cell and Molecular Biology. K. M.
Varghese Cop. Bombay.
2. Gerald Karp. 1996. Cell and Molecular Biology, Blackwell Pub. UK.
3. Benjamin Levine. 2002. Genes VI, Oxford University Press, USA.
4. Gardner, Simmons, Shustad. 1999. Principles of genetics, 8th edition. John Wiley & Sons
Inc.
4
Core 2: Basics of Computer
Unit I:
Fundamentals of computers – Block diagram of computer (input and output devices) –
History - Generations – Memory devices - Advantages and Limitations of Computers –
Comparison of different operating systems DOS, Windows NT & XP, Application Softwares.
Unit II:
Communication Technology – Networking Elements: Networking Hardware, Networking
services: Types of Networks – LAN, WAN & MAN, Intranet–Wireless communication –
Internet services, Uses of Internet
Unit III:
Fundamentals of database - Database models (Hierarchical, Network, Relational and ObjectOriented Models) – RDBMS: Relational Database Management systems - Database System
Applications and Security.
Unit IV:
Algorithm – Flowchart – Programming language – Compiling and Linking – Testing and
Debugging – Documentation – Maintenance - Utility programs.
Unit V:
Web Services – WWW, URL, Servers: Client/ Server essentials - Domain Name Server, FTP
server, E-mail server, WEB servers, Web publishing – Browsers - IP Addressing, IPV6
REFERENCES:
1. Basic Computer Skills made easy, by Sherman, J., 2001 Butterworth-Heinemann Ltd,
USA.
2. Computer Fundamentals and Applications (2nd Ed.) by Balaguruswamy, E., 1985, Tata
McGraw-Hill Publishing Co. Ltd.
3. Peter Norton, Peter Norton's Introduction to Computers, Fifth Edition Student Edition
with Electronic Workbook CD-ROM, McGraw-Hill Technology Education, 2003.
5
Allied I: 1. Programming in C
Unit I:
History of C – Character Set –Keywords and Identifiers – Constants and Variables – Data
Types – Declaration of Variables – Declaration of Storage Class – Defining Symbolic
Constants – Declaring Variables as Constant
Unit II:
Operators – arithmetic, unary, relational, logical, assignment, conditional, bitwise and
special operators - Type Conversions in Expressions - Hierarchy of operators - Input and
output statements - character, string and Formatted input and output - Arrays – one- , twoand multi- dimensional arrays - character arrays and strings comparison of strings –
mathematical and string library functions.
Unit III:
Control Statements in C – Branching Statements if-else, Switch-case, and goto - Looping
statements while, do while and for statements
Unit IV:
User Defined Functions in C - Defining and Accessing Functions - Passing Arguments –
Function prototypes – scope and visibility of variables.
Unit V:
Defining and Opening a File – Closing a File – Input/Output Operations on Files – Error
Handling During I/O Operations.
REFERENCES:
1. S. Parthasarathy, Essentials of programming in C for Life Sciences, Second Edition, Ane
Books India, New Delhi, 2011.
2. E. Balagurusamy, Programming in ANSI C, Fourth Edition, Tata McGraw-Hill
Publishing Company Limited, 2002.
3. Byron S. Gottfried, Schaum’s Outline of Programming with C, McGraw-Hill
Publications. 1996.
4. Herbert Schidlt, The Complete Reference C, Fourth Edition, Tata McGraw-Hill
Publishing Company Limited.
6
Semester - II
Core 3: Molecular Biology
Unit I:
DNA as a genetic material: Griffith’s transformation, forms of DNA & RNA, types of
restriction enzymes. Structure, properties and function; DNA, forms; RNA: tRNA & mRNA,
Organization of Genomes – Viral, Bacterial. Eukaryotic genomes: Chromosomal
organization and structure. Euchromatin, Heterochromatin, Centromere, Telomere.
Chromatin structure (nucleosomes) – histone, non-histone proteins.
Unit II:
Definition of gene – introns/exons, Regulatory sequences, promoters, enhancers. DNA
replication. Experiments of Messelson and Stahl, Okazaki, Rollong circle model, Prokaryotic
and Eukaryotic DNA replication. Enzymes and accessory proteins involved in DNA
replication. C-value paradox.
Unit III:
Genetic Code: Characteristic features of the Genetic code. Transcription and Translation in
prokaryotes and eukaryotes. Mutations in genetic code.
Unit IV:
Regulation of gene expression: positive and negative control – operon concept, TVP. OperonControl-catabolic repression. Bacterial transformation.
Unit V:
Genetic code, Molecular events of protein synthesis in prokaryotes and Eukaryotes.
Regulation of protein synthesis. Genomics, Proteomics – Gene pool & Gene library – with
definition and concept only. Post-transnational modifications and transport of proteins.
REFERENCES:
1. Freifelder, D and Malcinski, G.M, 1993 Essentials of Molecular Biology, II ED, Jones,
Bartlett, Publishers Inc, London.
2. J.D. Watson et al., 1987 Molecular Biology of the Gene, 4th Ed, The
Benjamin/Cummings Publ. California.
3. Benjamin Lewin, 2002. Gene VII. Oxford University Press, USA; 7th edition
4. Maniatis et al., 2000. Molecular Cloning: a laboratory Manual. Cold Spring, Harlor
Laboratory Press, NY.
5. R.A. Meyers, 1995. Molecular Biology & Biotechnology – A comprehensive desk
references. VCH Publishers NY.
6. Gerald Karp, 1996. Cell and Molecular Biology. John Wiley NY.
7. Benjamin Lewin. 2003. Genes VIII. Benjamin Cummings; United States edition
8. T.A. Brown. 2002 Genome 2. Garland Science; 2nd edition
9. Watson. 1997 Molecular biology of Gene. Benjamin-Cummings Publishing Company;
4th edition
7
Core 4: Biomolecular Structure
Unit I:
Introduction to amino acids: nomenclature, structure, Properties. Property of water: vapour,
liquid and solid, important of H-bond, types of bonds, bond length, bond angle, torsion angle.
Unit II:
Peptide bond information, Structure of peptide unit, dipeptide structure, Ramachandran’s
contact criteria, Ramachandran plot, polypeptide structure, stabilizing force in Biomolecular
structure.
Unit III:
Primary structure of a protein, Secondary structure of a protein (α – helix, β - strand, β- turn),
tertiary structure of protein. Functional property of Protein with antibody as example. Protein
stability and denaturation and structural change of protein due to mutation with example of
Haemoglobin
Unit IV:
Nucleic acid structure, Structural elucidation of DNA double helix, Stabilizing force in DNA
double helix, radiation effect of DNA. Different structure of DNA.
Unit V:
Introduction to carbohydrates, basics of Monosaccharide, disaccharide, O-glycosylation and
N-glycosylation.
REFERENCES:
1. Cell & Molecular Biology 1998, Roberties and Roberties K. M. Varghese Publication.
2. Cell and Molecular Biology 1996, Gerald Karp, Blackwell Pub. UK
3. Introduction to cell biology, 1998, Sundarajan, Vikas Pub.
4. Benjamin Lewin, 2002. Gene VII. Oxford University Press, USA; 7th edition
5. Principles of genetics, 1999, Gardner/Simmons/Shustad 8th edition.
6. Biochemistry, 1993, Lehinger J. CB.S. Publications
7. Biochemistry, 1995, D.Voet and JG Voet. John Wiley & Sons. Inc 2 Ed.
8. Fundamentals of Biochemistry, 2000, Jain J.L. Chand & Co, New Delhi.
9. Biochemistry, 1999. Davidson, V.L. & Sitlmon, D.L., 4th ed. Lippincoth Wiliam &
Willeing.
8
Allied I: 2. Programming in Visual Basic
Unit I:
Getting started with Visual Basic 6.0: Introduction to Visual Basic, Visual Basic 6.0
Programming Environment. Working with Forms, Developing an Application, Variables,
Data types and Modules, Procedures and Control Structures, Arrays in Visual Basic,
Additional Examples. Working with Controls: Introduction, Creating and Using Controls,
Working with Control Arrays, Additional Examples.
Unit II:
Menus, Mouse Events and Dialog Boxes: Introduction, Mouse Events, Dialog Boxes,
Additional Examples. Graphics, MDI and Flex Grid: Introduction, Graphics for Applications,
Multiple Document Interface (MDI), Using the Flex Grid Control, Additional Examples.
Unit III:
ODBC and Data Access Objects: Evolution of Computer Architectures, Data Access Options,
Additional examples. ODBC Using Data Access Objects and Remote Data objects: Open
Database Connectivity (ODBC), Remote Data Objects, Additional examples.
Unit IV:
Data Environment and Data Report: Introduction, Data Environment Designer Data Report,
Additional Examples. Object Linking and Embedding: Introduction, OLE Fundamentals,
Using OLE container Controls, Using OLE Automation Objects, OLE Drag and Drop,
Additional Examples. Objects and classes: Introduction to Objects, Working with Objects,
Classes and Class Modules, Additional examples.
Unit V:
Built-in ActiveX Controls: Working with Built-in Active X Controls, Additional examples.
Working with Active X Data Objects: An Overview of ADO and OLE DB, ADO Object
Model, Additional examples. Files and File System Controls: Introduction, File System
Controls, Accessing Files, Interface with Windows, Additional examples.
REFERENCES:
1. Content Development Group. 2002 Visual Basic 6.0 Programming - Tata McGraw-Hill
Publishing Company Limited. (Chapters: 1-9, 13, 16, 17).
2. Michael Halvorson, 1998 “Microsoft Visual Basic 6.0 Professionals”, PHI.
3. Steve Brown, 1998 “Visual Basic 6 in Record Time”, BPB Publications.
4. Gary Cornell, 1999 “Visual Basic 6 from the Ground Up”, Tata McGraw Hill.
9
Core Practical 1: Lab in Cell Biology, Genetics and Molecular Biology
Lab in Cell Biology and Genetics:
1.
2.
3.
4.
5.
6.
7.
Light Microscopy.
Histochemical techniques – Sectioning, Staining, Mounting.
Cell Division – Mitosis and Meiosis.
Mitotic Index Calculation.
Giant Chromosome from Salivary Gland of Chironomous Larve.
Blood Cell Counting – Haemocytometer.
Squamous epithelial cells from buccal cavity.
Lab in Molecular Biology:
1. Preparation of acidic, basic and Neutral buffers.
2. Preparation of stock solutions and working solution - %, Molar, Molal, ppm, and
normality.
3. Sterilization of glassware and culture medium.
4. Agarose gel electrophoresis techniques.
5. PCR amplification – Demonstration
6. Blotting Techniques – Demonstration
7. DNA isolation – (a) Plasmid from bacteria, (b) Genomic DNA from plant and animal
tissues.
8. Preparation of Protein lysate in Non-denaturation and denaturation condition.
9. Non-denaturation and denaturation protein separation by Polyacrylamide gel.
10. Finding size of protein using SDS-PAGE.
11. Preparation of Competent Cell.
10
Allied Practical 1: Lab in Programming in C and Visual Basic
Lab in Programming in C:
1.
2.
3.
4.
5.
6.
7.
8.
Compute the area and the circumference of the circle
Compute the volume of a cylinder and cone
Convert the given Fahrenheit value to centigrade scale (or vice versa)
Find the biggest of three given numbers using if-else statement
Find the molecular weight of a DNA with n base pairs in length
Find the sum of n natural numbers
Find the factorial of a given integer number
Find the pH of a solution given the concentration of H+ (or) OH- ions. Also print the
nature of the solution based on the pH value using if-else statement.
9. Write a C Program to find sum of digits of a given number
10. Write a C program to arrange a series of numbers in ascending order
11. Arrange the given names in alphabetical order
12. Write a C Program to check whether a string is palindrome or not
13. Write a C Program to find Matrix Addition
14. Write a C Program to calculate nCr of given n and r value, using function
15. Write a C Program to copy contents from one file to another.
Lab in Programming in Visual Basic:
1.
2.
3.
4.
5.
6.
7.
Create a students database using VB.
Create a simple calculator using VB.
Write a VB program to calculate factorial of a number.
Write a VB program to calculate nCr of n and r.
Write a VB program to check the given string is palindrome or not.
Write a VB program to draw a circle, square, and polygon.
Write a VB program to find sum of digits of a number.
11
Semester - III
Core 5: Introduction to Bioinformatics
Unit I:
Introduction to Bioinformatics: Definition and Scope of Bioinformatics, Applications of
Bioinformatics in various areas, Overview of available Bioinformatics Resources on the
Web, Proteome and Genome; Information Resources and Analysis Tools; Established
Techniques and Methods; Sequence File Formats FASTA, GenBank and Structured File
Formats.
Unit II:
Biological Databases: Protein Sequence and Structural Databases, Nucleotide Sequence
Databases; NCBI, PubMed, Protein Data Bank (PDB), PIR, SwissProt, EMBL. GenBank,
DDBJ, UniGene, SGD and EMI Genomes. Specialized Databases: Pfam, SCOP, GO,
GenBank, Genome Net, EST, SNP, Metabolic Pathways Databases, EMBL, Similar
Sequence Search BLAST, Gene/Protein Sequences and its Implications. Sequence
Alignment: Pair-wise Alignments, Scoring Matrix, PAM, BLOSUM and Gap Penalty.
Unit III:
Secondary Structure Analysis Tools/Server: Sequence Motif Databases, Pfam, PROSITE,
Protein Structure Classification; SCOP, CATH, Other Relevant Databases, KEGG, PQS,
PMDB, MPDB. Protein Structure Alignments; Structure Superposition, RMSD, Different
Structure Alignment Algorithms, DALI, and TM-align.
Unit IV:
Methods of Sequence Analysis: Heuristic Methods; FASTA, Statistics of Sequence
Alignment Score; E-Value, P-Value, Multiple Sequence Alignments; ClustalW, Profile,
Profile-Sequence Alignment, Profile-Profile Alignment, PSI-BLAST, Hidden Markov
Models, Viterbi Algorithm and HMM Based Multiple-Sequence Alignment.
Unit V:
Phylogenetic Analysis: Distance and Character Based Methods and Software, Computing
Tools for Phylogenetic Analysis, Distances, GROWTREE, PAUP, PHYLIP and MEGA;
Construction and Visualization of Phylogenetic Tree; and Application of Phyolgenetic
Analysis.
REFERENCES:
1. Anna Tramontano, 2007; “Introduction to Bioinformatics”, Chapman and Hall Series.
2. Jason T.L .Wang, Mohammed J. Zaki, Hannu T.T. Toivonene and Dennis Shasha, 2005;
“Data Mining in Bioinformatics”, Springer International Edition.
3. Yi-Ping Phoebe Chen, 2007; “Bioinformatics Technologies”, Springer International
Edition.
4. Mount, D.W., 2001; “Bioinformatics: Sequence and Genome analysis”, Cold Spring
Harbour Laboratory Press.
12
Allied II: 3. Basic Mathematics
Unit I:
Matrices: Matrix algebra – Types of matrices – determinant – inverse, rank of matrix –
existence and uniqueness of solution of simultaneous equations – Eigenvalues and
Eigenvectors – Cayley Hamilton’s Theorem (statement only) – Symmetric, Skew Symmetric,
Orthogonal, Hermitian, Skew Hermitian, & Unitary Matrices - Diagonalisation of matrix –
Applications
Unit II:
Vectors: Vector algebra - addition and subtraction of vectors – product of vectors, dot &
cross products - scalar triple product.
Unit III:
Vector differentiation – velocity & acceleration - Vector & scalar fields – Gradient of a
vector- Directional derivative – divergence & curl of a vector solenoidal & irrotational
vectors – Laplacian double operator – simple problems
Unit IV:
Basic differentiation of algebraic and trigonometric functions – Maxima and Minima Integration of simple functions - Integration by parts – definite integrals - reduction formula –
Table of integrals
Unit V:
Differential equations – First order differential equations – Second order differential
equations with constant coefficients – Application to simple harmonic oscillator.
REFERENCES:
1. T.K.Manicavachagam Pillai & others, Differential Calculus, S.V Publications, Chennai,
1985 Revised Edition.
2. S.Arumugam & A.Thangapandi Issac, Modern Algebra, New Gamma Publishing House,
2000.
3. M.L. Khanna, Vector Calculus, Jai Prakash Nath and Co., 8th Edition, 1986.
4. T.K.Manickavasagam Pillai & others, Integral Calculus, SV Publications.
5. S.Narayanan, Differential Equations, S. Viswanathan Publishers, 1996.
13
Skill Based Subject 1: 1(a). Programming in PERL
Unit I:
Introduction: History of Perl, Availability, Support, Versions, Installation. Basic Concepts,
Significance of Perl in Bioinformatics.
Unit II:
Basics Constructs: Scalar Data, Numbers, Strings, Scalar Operators, Scalar Variables, Scalar
Operators and Functions. Arrays and List Data: What is a List or Array? Literal
Representation, Variables, Array Operators and Functions, Scalar and List Context. Hashes:
What is a Hash? Hash Variables, Literal Representation of a Hash, Hash Functions, Hash
Slices. Control Structures: Statement blocks, Loops and conditions. Basic Input / Output.
Unit III:
Advance Constructs and Features: Regular Expressions: Concepts about Regular
Expressions, Simple Uses of Regular Expressions, Patterns, Matching Operator,
Substitutions, The split and join functions, Subroutines: System and User Functions, The
local Operator, Variable-length, Parameter Lists, Lexical Variables, File handles and File
Tests: File Handle, Opening and Closing a File handle, Using Pathnames and Filenames, die,
Using File handles.
Unit IV:
Object-Oriented Perl: Introduction to Modules, Creating Objects and References. CGI
Programming: The CGI.pm Module, CGI Program in Context, Simple CGI Programs,
Passing Parameters via CGI, Perl and the Web.
Unit V:
BioPerl: BioPerl Overview and Installation Procedures; Fundamental Constructs and Special
Features; BioPerl Modules, Creating BioPerl Objects. Applications of BioPerl, Utility and its
Applications.
REFERENCES:
1. James D. Tisdall, 2001; "Beginning Perl for Bioinformatics", O’Rilley and Association.
2. Cynthi Gibas & Per Jamesbeck, 2000; "Developing Bioinformatics Computer Skills",
O’Rilley & Association.
3. Harshawardhan P Bal, 2003; "Perl Programming for Bioinformatics", Tata McGraw Hill.
4. Randal L. Schwartz and Tom Phoenix, 2005; "Learning Perl", 3rd Edition, O’Rilley.
14
Skill Based Subject 1: 1(b). Programming in PHP
Unit I:
What is PHP? History of web programming; how PHP fits into the web environment;
installation and configuration; "Hello World"; syntax, variables, operators, flow control
structures; More language basics; using GET and POST input, working with HTML forms;
built-in and user-defined functions; variable scope; using the PHP manual, getting help
Unit II:
Input validation, string manipulation and regular expression functions; Date and time
functions code re-use, require(), include(), and the include_path; filesystem
functions and file input and output; file uploads; error handling and logging; sending mail
Unit III:
HTTP headers and output control functions; HTTP cookies; maintaining state with HTTP
sessions; writing simple web clients Introducing MySQL; database design concepts; the
Structured Query Language (SQL); communicating with a MySQL backend via the PHP
MySQL API
Unit IV:
More MySQL database access; graphic manipulation with the GD library; Introduction to
Object Oriented Programming; OOPs Instance Method; CakePHP
Unit V:
Using PEAR packages; More PEAR packages; the Smarty template engine; parsing XML;
PHP 5-specific feature; PHP AJAX - XML, JSON
REFERENCES:
1. PHP 6/MySQL Programming for the Absolute Beginner by Andrew B. Harris.
2. http://www.php.net/
15
Non Major Elective 1: 1(a). Fundamentals of Computer and Networks
Unit I:
Fundamentals of computers – Block diagram of computer (input and output devices) –
History - Generations – Memory devices - Advantages and Limitations of Computers –
Comparison of different operating systems DOS, Windows NT & XP, Application Softwares.
Unit II:
Communication Technology – Networking Elements: Networking Hardware, Networking
services: Types of Networks – LAN, WAN & MAN, Intranet – Wireless communication –
Internet services, Uses of Internet
Unit III:
Fundamentals of database - Database models (Hierarchical, Network, Relational and ObjectOriented Models) – RDBMS: Relational Database Management systems - Database System
Applications and Security.
Unit IV:
Algorithm – Flowchart – Programming language – Compiling and Linking – Testing and
Debugging – Documentation – Maintenance - Utility programs.
Unit V:
Web Services – WWW, URL, Servers: Client / Server essentials - Domain Name Server, FTP
server, E-mail server, WEB servers, Web publishing – Browsers - IP Addressing, IPv6.
REFERENCES:
1. Basic Computer Skills Made Easy, by Sherman, J., 2001 Butterworth-Heinemann Ltd,
USA
2. Computer Fundamentals and Applications (2nd Ed.) by Balaguruswamy, E., 1985, Tata
McGraw-Hill Publishing Co. Ltd.
3. Peter Norton, Peter Norton's Introduction to Computers, Fifth Edition Student Edition
with Electronic Workbook CD-ROM, McGraw-Hill Technology Education, 2003.
16
Non Major Elective 1: 1(b). Basics of Bioinformatics
Unit I:
Bioinformatics – An overview, Definition & History; Information Networks – Internet in
Bioinformatics – Bioinformatics databases & tools on the Internet.
Unit II:
Biological Sequence analysis – Pairwise sequence comparison – Sequence queries against
biological databases – BLAST and FASTA algorithm - Multiple sequence alignments Phylogenetic alignment.
Unit III:
Introduction to –omics, Genomics and Proteomics – Sequencing genomes – Genome
databases on the web.
Unit IV:
Proteins – Amino acids – Peptide bond – Levels of protein structure – α-helix, β-sheet and βturns – Ramachandran Map – Super secondary structures – Domains – quaternary structure –
DNA and RNA structure – Watson and Crick model – A, B and Z forms of DNA – RNA
secondary structure.
Unit V:
Protein structure visualization tools – RasMol, Swiss PDB Viewer, PyMol – Protein structure
prediction tools, Molecular modeling and docking tools.
REFERENCES:
1. T.K. Attwood and D.J. Parry-Smith, Introduction to Bioinformatics, Pearson Education
Ltd., New Delhi (2004).
2. D.R. Westhead, J.H. Paris and R.M. Twyman, Instant Notes: Bioinformatics – Viva
Books Private Ltd, New Delhi (2003).
3. Arthur M. Lesk, Introduction to Bioinformatics, Oxford University Press, New Delhi
(2003).
4. D. Higgins and W. Taylor (Eds), Bioinformatics - Sequence, structure and databanks,
Oxford University Press, New Delhi (2000).
17
Semester - IV
Core 6: Basics of Genomics and Proteomics
Unit I:
Human genome-physical structure and genetic content-Genome structure and anatomy of
prokaryotic and eukaryotic genome-nuclear genomes-organelle genomes
Unit II:
Repetitive DNA - sequence repeats - transposable elements - pseudo genes - Comparative
genome analysis - genome databases – organisms - specific databases - Genome analysis and
annotation
Unit III:
Genomes of model organisms - E.coli - Saccharomyces cerevisiae - Arabidopsis thalianaCaenorhabditis elegans - Drosophilla melanogaster – Human – SNP Evolution of genomesBioinformatics approaches for metabolic pathways
Unit IV:
Proteomics introduction - Protein sequencing - 2D gel electrophoresis and Mass spectra Tools for proteome technology - Protein identification from 2D gel, mass spectra and
sequence data - Protein identification programs - Muscot - PeptIdent
Unit V:
Proteome databases and Resources - Comparative proteomics methods - 2D gel databases Protein interaction data bases - Metabolic pathway databases
REFERENCES:
1. A. Baxevanis and B.F. Ouellette. Bioinformatics: A practical Guide to the Analysis of
Genes and Proteins, 2nd & 3rd Editions, Wiley- Interscience, Hoboken, NJ, 2002 & 2005.
2. T. A. Brown, Genomes, 2nd Edition, BIOS Scientific Publishers, Ltd., Oxford, UK, 2002.
3. David W. Mount, Bioinformatics – Sequence and Genome analysis, Cold Spring Harbor
Laboratory Press, New York, 2001.
4. C.W.Sensen, Essentials of Genomics and Bioinformatics, Wiley-VCH, 2002
5. S.R.Pennington and M.J.Dunn, Proteomics, Viva Books Pvt. Ltd., New Delhi, 2002.
18
Allied II: 4. Biostatistics
Unit I:
Nature of biological and clinical experiments – collection of experimental data – Frequency
distribution and Graphical representation of data – Descriptive statistics - Measures of central
tendency – mean (AM, GM, HM) - median – mode – percentiles – Box plot.
Unit II:
Measures of dispersion - range, mean deviation, variance, standard deviation, coefficient of
variance – skewness – kurtosis – Using statistical packages (Microsoft Excel or SPSS).
Unit III:
Correlation analysis: Types of correlation- Methods of studying correlation: Karl Pearson’s
coefficient of correlation and Rank correlation coefficient; Regression analysis: Regression
line and equations – Simple problems based on biological data.
Unit IV:
Tests of Significance: Small sample tests – Student t test for mean, difference of two means
and test for Correlation – Chi Square test for goodness of fit – F test for equality of variance.
Unit V:
Basic concepts of Probability – Sample space and events – Addition and Multiplication
theorem – Theoretical distribution: Binomial, Normal and Poison.
REFERENCES:
1. Sokal R.J. and Roflf. S.J., Introduction to Biostatistics, W.H.Freeman, London, 1981.
2. Zar, J.H., Biostatistical Analysis, McGraw Hill, London, 1983.
3. S.C. Gupta, and V.K.Kapoor, Fundamentals of mathematical Statistics, S. Chand and
Sons, New Delhi, 2002.
19
Skill Based Subject 2: 2(a). Database Management Systems
Unit I: Introduction
Purpose of Database System – Views of data – Data Models – Database Languages –
Database System Architecture – Database users and Administrator – Entity-Relationship
model (E-R model ) – E-R Diagrams – Introduction to relational databases
Unit II: Relational Model
The relational Model – The catalog- Types – Keys - Relational Algebra – Domain Relational
Calculus – Tuple Relational Calculus - Fundamental operations – Additional Operations
Unit III: SQL Concepts
SQL fundamentals - Integrity – Triggers - Security – Advanced SQL features – Embedded
SQL– Dynamic SQL- Missing Information – Views – Introduction to Distributed Databases
and Client/Server Databases
Unit IV: Transactions
Transaction Concepts - Transaction Recovery – ACID Properties – System Recovery –
Media Recovery – Two Phase Commit - Save Points – SQL Facilities for recovery –
Concurrency – Need for Concurrency – Locking Protocols – Two Phase Locking – Intent
Locking – Deadlock- Serializability – Recovery Isolation Levels – SQL Facilities for
Concurrency
Unit V: Database Design
Functional Dependencies – Non-loss Decomposition – Functional Dependencies – First,
Second, Third Normal Forms, Dependency Preservation – Boyce/Codd Normal Form Multi-valued Dependencies and Fourth Normal Form – Join Dependencies and Fifth Normal
Form
TEXT BOOKS:
1. Abraham Silberschatz, Henry F. Korth, S. Sudharshan, “Database System Concepts”,
Fifth Edition, Tata McGraw Hill, 2006. (Unit I)
2. C. J. Date, A. Kannan, S. Swamynathan, “An Introduction to Database Systems”, Eighth
Edition, Pearson Education, 2006. (Unit II, III, IV and V)
REFERENCES:
1. Ramez Elmasri, Shamkant B. Navathe, “Fundamentals of Database Systems”, Fourth
Edition, Pearson / Addision Wesley, 2007.
2. Raghu Ramakrishnan, “Database Management Systems”, Third Edition, McGraw Hill,
2003.
3. S. K. Singh, “Database Systems Concepts, Design and Applications”, First Edition,
Pearson Education, 2006.
20
Skill Based Subject 2: 2(b). Introduction to Algorithms
Unit I: Algorithmic problems
Sorting and searching; Graph algorithms: Graph traversal (DFS, BFS) and applications –
Connectivity, strong connectivity, bi-connectivity – Minimum spanning tree – Shortest path –
Matchings - Network flow
Unit II: Hard Algorthmic problems
Hard problems: Traveling salesman problem – Longest path, Hamilton cycle – Boolean
circuit satisfiability – Clique – Vertex cover
Unit III: Algorithm design
Divide-and-conquer; Graph traversal; Greedy; Dynamic Programming; Reductions; Use of
advanced data structures
Unit IV: Algorithm correctness
Proofs and proof techniques (assumptions, basic logic inference and induction); Tree and
graph properties that make graph algorithms work; When does the greedy algorithm work?
Unit V: Algorithm analysis
Time and space complexity; Asymptotic analysis: Big Oh – Little oh – Theta; Worst case and
average case analysis; Lower bounds
TEXT BOOKS:
1. Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest, Clifford Stein. Introduction
to Algorithms. 3rd Edition. The MIT Press Cambridge, Massachusetts. 2009.
21
Core Practical 2: Bioinformatics, Genomics and Proteomics
Lab in Bioinformatics
1. Search on NCBI – PubMed bibliographic search – different options – author name,
keyword in title, abstract, title and/or abstract, related articles – different display options
2. Search on EMBL for nucleic acid sequences
3. Perform a similarity search of PIR & SwissProt database for the given protein sequence
4. Pairwise sequence alignment by LALIGN tool
5. Sequence similarity search using NCBI-BLAST tool
6. Computation of protein sequence features using PROTPARAM tool
7. Retrieving genomic information using GOLD database
8. Structure exploration using PDB
9. Structure visualization using RASMOL & PYMOL software
10. To list SCOP lineages and CATH architecture description for a set of proteins
11. Perform multiple sequence alignment using ClustalW, and display the phylogenetic
relationship of sequences in NJplot
Lab in Genomics and Proteomics
1.
2.
3.
4.
5.
6.
7.
8.
9.
Bacterial operon prediction by OperonDB tools
Gene prediction by WebGene, ORF finder and COG database and GenoCluster software
Promoter and regulan prediction by Virtual FootPrint
Identification of coding region by CRITICA and CodanDB tools
Identification of mutations in genes by GeneSNP-VISTA software
Recombination frequency analysis by MEGA, RAS and RAT software
Metabolic pathway prediction by UB-BBD and Pathway Hunter Tool
Protein bulk properties prediction by WinGene/WinPep software
Protein modification site prediction by GlyMod, PhosMod, AceMod tools and WinPep
software
10. 2D gel data analysis by SWISS-2D GEL DB and NCI Flicker web server/software
22
Allied Practical 2: Lab in Mathematics using SciLab and Biostatistics using
SPSS/STATA/Excel
Lab in Mathematics using SciLab
1.
2.
3.
4.
5.
6.
7.
8.
Perform all matrix operations.
Compute Eigen values and Eigen vectors of a given matrix.
Verify Cayley-Hamilton Theorem for a given matrix.
Perform vector addition, subtraction, dot and cross products.
Compute angle between two vectors.
Perform differentiation of simple functions.
Compute maxima and minima.
Perform integration of simple functions.
Lab in Biostatistics using SPSS / STATA / Excel
1.
2.
3.
4.
5.
6.
7.
8.
Measures of central tendency – mean (AM, GM, HM) - median – mode.
Measures of dispersion - range, variance, standard deviation, coefficient of variance.
Karl Pearson’s coefficient of correlation.
Regression line and equations.
Student ‘t’ test.
Chi square test.
F-test.
Plotting curves.
23
Non Major Elective 2: 2(a). Biological Database and Sequence Analysis
Unit I:
Literature Databases:
PubMed, BioMed, Google Scholar, PMC, Quertle
Unit II:
Sequence Databases:
Nucleic acid sequence databases: GenBank, EMBL, DDBJ, UniGene,
Protein sequence databases: Uniprot-KB: SWISS-PROT, TrEMBL, PIR-PSD
Repositories for high throughput genomic sequences: EST, STS GSS, etc.
Genome Databases at NCBI, EBI, TIGR, SANGER
Viral Genomes
Archeal and Bacterial Genomes;
Unit III:
Structural Databases:
3D Structure Database: PDB, NDB, CSD, MMDB,
Chemical Structure database: PubChem, DrugBank, ChemSpider,
Gene Expression database: GEO, SAGE,
Unit IV:
Derived Databases:
Sequence: InterPro, Prosite, Pfam, ProDom, Gene Ontology
Structure classification database: CATH, SCOP, FSSP, DSSP, HSSP
Protein-Protein interaction database: STRING
Unit V:
Database Access & Analysis Tools:
Keyword-based searches using tools like ENTREZ and SRS
Sequence-based searches: BLAST and FASTA
Structure-based searches: BLAST with PDB.
REFERENCES:
1. T.K. Attwood and D.J. Parry-Smith, Introduction to Bioinformatics, Pearson Education
Ltd., New Delhi (2004).
2. D.R. Westhead, J.H. Paris and R.M. Twyman, Instant Notes: Bioinformatics – Viva
Books Private Ltd, New Delhi (2003).
24
Non Major Elective 2: 2(b). Applied Bioinformatics
Unit I:
Commercial bioinformatics – Survey of bioinformatics companies in India and abroad –
Economics prospects – pharma-informatics – combinatorial chemistry – HT screening – in
silico screening - from lead to commercialization.
Unit II:
Sequence assembly and Finishing methods - Sequence assemblers – finishing and
visualization programmes - SNP – Types - SNP discovery methods.
Unit III:
Application of genomics to agriculture - gene discovery and gene function - model systems –
technologies – methods to introduce novel genes – Pharmaceutical bioinformatics and drug
discovery – Introduction - novel gene discovery - methods for identifying novel targets protein classification and functional assignments – Disease - target gene relationship.
Unit IV:
Intellectual Property Rights(IPR): IPR - Importance of IPR, Organization - WIPO & WTO Agreements and Treaties - GATT-TRIPS - Types of IPR – patents – copyrights - trademarks
and trade secrets - IPR in India - IPR impacts on Biotechnology Research in India significance biotechnological patents in India..
Unit V:
Biosafety & Bioethics: Biosafety - Topics of concern - Hazards of Genetically Engineered
Microorganisms – Bioremediation - Framework of biosafety regulations in India – Bioethics The ethical and social impacts of biotechnology and bioinformatics.
REFERENCES:
1. T. A. Brown, Genomes, 2nd Edition, BIOS Scientific Publishers, Ltd., Oxford, UK, 2002.
2. S. R. Pennington and M. J. Dunn, Proteomics, Viva Books Pvt. Ltd., New Delhi, 2002.
3. N. R. Subbaram, What everyone should know about patents?, 2nd Edition, Pharma Book
Syndicate, Hyderabad, 2006.
4. Philip W. Grubb, Patents for Chemicals, Pharmaceuticals and BiotechnologyFundamentals of Global Law practices and strategy, 4th Edition, Oxford University Press,
2006.
5. R.C. Dubey, A Textbook of Biotechnology, S. Chand & Company, 1993.
6. Ben Mepham, Bioethics-an Introduction for the biosciences, Oxford University Press,
2005
25
Semester - V
Core 7: Biological Databases
Unit I: Introduction to Bioinformatics data and Databases
Introduction to database – Database models – Database languages – Types of databases: Flat
file, Relational databases and Object oriented databases – Types of biological databases –
Pitfalls of biological databases – Types of Biological data: Genomic DNA, Complementary
DNA (cDNA), Recombinant DNA (rDNA), Expressed sequence tags (ESTs), Genomic
survey sequences (GSSs) – Primary Databases: GenBank, EMBL, DDBJ – Composite
Databases: NRDB, UniProt – Literature Databases: Open access and open sources, PubMed,
PLoS, Biomed Central.
Unit II: Genome Databases
Viral genome database: ICTVdb – Bacterial Genomes database: Genomes OnLine Database
(GOLD), Microbial Genome Database (MBGD) – Organism specific Genome database:
OMIM / OMIA, SGD, WormBase, PlasmoDB, FlyBase, TAIR – Genome Browsers:
Ensembl, VEGA genome browser, NCBI map viewer, KEGG, MIPS, UCSC Genome
Browser.
Unit III: Sequence Databases
Nucleotide sequence Databases: GenBank, EMBL, DDBJ – Protein sequences Databases:
SwissProt, TrEMBL, UniProt, UniProt Knowledgebase (UniProtKB), UniProt Archive
(UniParc), UniProt Reference Clusters (UniRef), UniProt Metagenomic and Environmental
Sequences (UniMES) – Sequence motifs Databases: Prosite, ProDom, Pfam, InterPro –
Sequence file formats: GenBank, FASTA, PIR, ALN/ClustalW2, GCG/MSF.
Unit IV: Structure and Derived Databases
The primary structure databases: Protein Data Bank (PDB), Cambridge Structural Database
(CSD), Molecular Modeling Database (MMDB) – The secondary structure databases:
Structural Classification of Proteins (SCOP), Class Architecture Topology Homology
(CATH), Families of Structurally Similar Proteins (FSSP), Catalytic Site Atlas (CSA) –
Molecular functions/Enzymatic catalysis databases: KEGG, BRENDA.
Unit V: Bioinformatics Database Search Engines
Text-based search engines: Entrez, SRS, DBGET / LinkDB – Sequence similarity based
search engines: BLAST and FASTA – Motif-based search engines: ScanProsite and eMOTIF
– Structure similarity based search engines: VAST and DALI.
REFERENCES:
1. Bioinformatics: Sequence and Genome Analysis by Mount D., Cold Spring Harbor
Laboratory Press, New York. 2004
2. Bioinformatics- a Practical Guide to the Analysis of Genes and Proteins by Baxevanis,
A.D. and Francis Ouellette, B.F., Wiley India Pvt Ltd. 2009
3. Introduction to bioinformatics by Teresa K. Attwood, David J. Parry-Smith. Pearson
Education. 1999
26
Core 8: Computational Biology
Unit I: Strings and Graphs
Strings and Sequences – Graphs and Trees – Algorithm basics – Comparing two sequence:
Global, Local and Semi-global comparison – Linear and affine gap penalty functions –
Comparing multiple sequences – PAM – BLOSUM – BLAST – FAST – Similarity and
distance.
Unit II: Fragment Assembly of DNA
Fragment assembly of DNA – Alternative methods for DNA sequencing – Shortest common
superstring – Reconstruction – Multicontig – Algorithms for fragment assembly of DNA:
Shortest superstrings as paths, Acyclic subgraphs and Greedy – Heuristics: Fragment
assembly in practice.
Unit III: Phylogeny
Phylogenetic trees – Character states and Perfect phylogeny problem – Binary character
states – Parsimony and compatibility in phylogenies – Algorithm for distance matrices:
Additive trees and Ultrametric trees.
Unit IV: Genome Rearrangements
Genome rearrangements: Introduction – Oriented blocks: Diagram of reality and desire,
Interleaving graphs and Bad components – Unoriented blocks – Applications of genome
rearrangements.
Unit V: Sequence to Structure Prediction
RNA secondary structure prediction – Protein folding problem – Protein threading –
Computing with DNA: Hamiltonian path problem, Satisfiability, Problems and promises.
REFERENCES:
1. Waterman, M. Introduction to Computational Biology: Maps, Sequences and Genomes.
1995. CRC Press, ISBN: 0412993910
2. Setubal, J. and Meidanis, J. 1997. Introduction to Computational Molecular Biology.
Brooks Cole Publishing, ISBN: 0534952623
3. Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. 1998. Biological Sequence Analysis:
Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, ISBN
0521629713
4. Venter et al. 2001. The Sequence of the Human Genome. Science 291: 1304-1351
5. Eisen MB, Spellman, PT, Brown, PO, and Botstein, D. 1999. Cluster analysis and display
of genome-wide expression patterns. PNAS 95(25): 14863
6. Schena M, Shalon D, Davis RW, and Brown PO. 1995. Quantitative monitoring of gene
expression patterns with a complementary DNA microarray. Science 270: 467-70.
7. Gusfield, D. 1997. Algorithms on strings, trees, and sequences: computer science and
computational biology. Cambridge University Press, ISBN: 0521585198
8. Mount, D. Bioinformatics: Sequence and Genome Analysis. 2001. Cold Spring Harbor
Laboratory Press, ISBN 0879696087
27
Major Elective 1: 9(a). Structural Bioinformatics
Unit I: Basics and Structure Visualization
Introduction to structural bioinformatics: Structural basis of biological phenomena,
Challenges in computing with structural data. Fundamental principles of protein/DNA/RNA
structure: Chemical structure of proteins, Protein secondary and tertiary structure, Protein
domains and folds, Sequence-to-structure-to-function paradigm, Chemical structure of
nucleic acids, Structure of nucleic acids. Molecular visualization: Visualization styles and
software.
Unit II: Structure Determination and Databases
Experimental methods for structure determination: Basic principles of X-ray crystallography,
Basic principles of NMR spectroscopy, Other methods for direct and indirect determination
of structure of biopolymers, Structural/functional genomics initiative and high-throughput
techniques, Structural quality assurance. Structure-based databases: Protein Data Bank,
SCOP and CATH classifications, RNABase, Other sources.
Unit III: Structure Comparison and Prediction
Structure comparison and alignment: Automated assignment of secondary structure,
Structural similarity measures, Structural alignment algorithms. Prediction of structure of
biopolymers: Prediction of protein structure (prediction of secondary structure, homology
modeling, fold recognition and ab initio methods), Membrane proteins, Prediction and
Energy minimization of RNA structure, Prediction of DNA curvature.
Unit IV: Function Prediction and Docking
Prediction of protein function from structure and other types of data: Definition of protein
function and gene ontology, Enzyme classification and functional site identification,
Relationship between structure and function, Prediction of protein-ligand interactions.
Principles of molecular recognition and docking: Protein-small molecule interactions,
Macromolecular docking and protein-protein interactions, Structural bioinformatics in drug
discovery.
Unit V: Applications of Structural Bioinformatics
Intrinsically disordered (unstructured) proteins: Sequence-to-disordered ensemble-tofunction paradigm, Functional characterization of disordered proteins, Prediction of
disordered proteins. Types of tools for Homology modeling, Threading/fold recognition, Ab
initio structure prediction, Secondary structure prediction, Transmembrane helix prediction
and Signal peptide prediction.
REFERENCES:
1. P.E. Bourne and H. Weissig (Eds.) Structural Bioinformatics, John-Wiley and Sons, 2003
2. C. Branden and J. Tooze, Introduction to Protein Structure, Garland Publishing Inc., New
York, 1999.
3. Chris Calladine, Horace Drew, Ben Luisi, and Andrew Travers, Understanding DNA, 3rd
Edition, Elsevier Academic Press, USA, 2004.
28
Major Elective 1: 9(b). Biophysics
Unit I: Atomic & Molecular structure
Structure of atom, Schrödinger’s theory, Quantum numbers, Pauli’s exclusion principle,
Hund’s rule, Concept of bonding, Atomic and molecular orbitals, Hybridization of orbitals, σ
and π bonds, Polar and non-polar molecules, Inductive effect, Resonance, Structural
isomerism; Geometrical isomerism; Optical isomerism & Optical activity.
Unit II: Acid & Bases
Mole concept, Molarity & Normality, Weak acids, Ampholyte, pH, Calculations of pH from
H & OH concentrations, Measurements of pH, Henderson – Hasselbalch equation, Buffers,
Redox potential, Nernst equation, Oxidation-Reduction reactions.
Unit III: Thermodynamics and Bioenergetics
Laws of thermodynamics, Concept of free energy, Unavailable energy and Entropy,
Enthalpy, Negative entropy change in living system, Heat content of food, Endergonic and
exergonic, Molecularity of reactions, Energy of activation, Metabolism pathways, High
energy compounds, Metabolism of glucose, Formation of ATP, Glycolysis, Kreb’s cycle,
Electron transport chain.
Unit IV: Biomembranes and Kinetics
Membrane structure – Composition; Function; Membrane transport, Simple diffusion,
Passive transport, Active transport, Reactions - 0th, 1st, 2nd and 3rd order reactions, Diffusion,
Osmosis, Osmotic pressure, Osmoregulation, Surface tension, Dialysis, Adsorption,
Viscosity, Thermal conduction, Collides, Sedimentation.
Unit V: Macromolecular Interactions
Receptor-ligand kinetics, Scatchard plot, Interaction between binding sites, MWC model,
KNF model, Oxygen-hemoglobin binding, Binding of two different ligands, Cooperative
binding, Anti-cooperative binding, Excluded site binding, Energetics and dynamics of
binding, Structures of protein ligand complexes, free radicals in biology and medicine.
REFERENCES:
1. Ackerman E.A. Ellis, L.E.E. & Williams L.E. (1979), Biophysical Science, Prentice-Hall
Inc.
2. Barrow. C. (1974), Physical Chemistry for Life Sciences, McGraw-Hill.
3. Bloomfield V.A. and Harrington R.E. (1975), Biophysical chemistry, W.A.Freeman and
CO.
4. Bulter l.A.V. And Noble D.Eds. (1976), Progress in Biophysics and Molecular Biology
(all volumes) pergamon, Oxford.
5. Cantor C.R. and Schimmel P.R. (1980), Biophysical chemistry, W.A.Fremman and Co.
6. Casey E.J. (1967), Biophysics, concepts and mechanisms. Affiliated East west press.
7. Chang R. (1971), Basic principles of spectroscopy, McGraw-Hill.
8. De Robertis E.D.P. and De Robertis E.M.P. (1981), Essentials of cell and molecular
Biology, Holt sounders International Editions.
9. Dickerson R.E. & Geis I. (1972), Proteins: structure, function and evaluation, Benjamin.
10. Dugas H. and Penney C. (1981), Bioorganic chemistry, Springer-Verlag.
11. Fleischer S. Hatefi Y. McLennan D.H. and Tzagoloff A. (1977), The molecular biology
of Membranes, Plenum press.
12. Haschemyer R.N. and Haschemyer A.E.B.V. (1973), Proteins, John Wiley and sons.
29
13. Hughes W. (1979), Aspects of Biophysics, John Wiley and sons.
14. Jain M.K. and Wanger R.C. (1980), Introduction to Biological Membranes, John Wiley
and sons.
15. Lehninger A. (1981), Biochemistry, Butter Worth Publication.
30
Major Elective 2: 10(a). Systems Biology
Unit 1: Introduction to Systems Biology
Introduction to Systems Biology. Need for System Analysis in Biology. Basic Concepts in
System Biology: Component vs System, Links and Functional States, Links to Networks,
Hierarchical Organization in Biology.
Unit 2: Metabolic Networks and Models in System Biology
Basic Features of Metabolic Networks. Reconstruction Methods of Metabolic Networks.
Models as Dynamical Systems. Parameter Problem. Meanings of Robustness.
Unit 3: Systems Biology Databases
KEGG (Kyoto Encyclopedia of Genes and Genomes). BRENDA (BRaunschweig ENzyme
DAtabase). BioSilico. EMP (Embden-Meyerhof-Parnas). MetaCyc and AraCyc. SABIO-RK
(System for the Analysis of Biochemical Pathways - Reaction Kinetics). BioModels.
Unit 4: Tools for System Biology
CellDesigner. Ali Baba. CellProfiler. JDesigner. Bio-SPICE (Biological Simulation Program
for Intra and Inter Cellular Evaluation). SBML (Systems Biology Markup Language). SBGN
(Systems Biology Graphical Notation). SBML-SAT (SBML based Sensitivity Analysis
Tool).
Unit 5: Premises & Promises of Systems Biology
Premise of Systems Biology. Promise of Systems Biology. Challenges of Systems Biology.
Applications of Systems Biology.
REFERENCES:
1. Bernhard O. Palsson (2006). Systems Biology: Properties of Reconstructed Networks.
Cambridge University Press, New York.
2. Björn H. Junker, Falk Schreiber (2008). Analysis of Biological Networks. John Wiley &
Sons, Inc., Hoboken, New Jersey.
3. Huma M. Lodhi, Stephen H. Muggleton. Elements of Computational Systems Biology.
John Wiley & Sons, Inc., Hoboken, New Jersey.
4. M. Cánovas, J.L. Iborra and A. Manjón (2006). Understanding and Exploiting Systems
Biology in Biomedicine and Bioprocesses. CajaMurcia Foundation, Spain.
5. http://www.systemsbiology.org
6. http://www.systems-biology.org
31
Major Elective 2: 10(b). Introduction to Biomolecular Instrumentation
Unit I: Spectroscopy
Basic principles of spectroscopy; Nature of electromagnetic radiation; Interaction of light
with matter; Absorption and emission of radiation; Electronic, vibrational and rotational
spectroscopy of molecules; Principle, Instrument design, Methods and applications of UV visible spectroscopy, IR spectroscopy, Raman spectroscopy, Fluorescence spectroscopy,
Atomic absorption spectroscopy, Inductively coupled plasma atomic emission
spectrophotometry, NMR spectroscopy, Nuclear quadrupole resonance spectroscopy, ESR
spectroscopy, Mass spectroscopy, Photoacoustic spectroscopy.
Unit II: Electrophoresis and Chromatography
Electrophoresis: Principle; Electrophoretic mobility (EPM) estimation; Factors affecting
EPM; Principle, Instrument design, Methods and applications of 2D electrophoresis and zone
electrophoresis techniques (Paper, Cellulose acetate, Agarose, Starch gel, Pulsed-field,
PAGE, SDS-PAGE, Capillary).
Chromatography: Basic concepts of adsorption and partition chromatography; Principle,
Instrument design, Methods and applications of all types of adsorption and partition
chromatography methods – Paper, Thin layer, Gas, HPLC and Ion chromatography.
Unit III: Microscopy and Hydrodynamic Techniques
Microscope: Principle, Instrumentation and Application of microscopy; Image formation;
Magnification; Resolving power; Different types of Microscopy – Dark field, Phase contrast,
Polarization, Fluorescence and Electron microscopy.
Hydrodynamics: Fundamental, principles and applications of Centrifugation,
Ultracentrifugation, Viscometry, Haemocytometer, Osmosis and Diffusion.
Unit IV: X-ray Crystallography
X-ray: Principle and applications, Unit cell, Crystal symmetry, Bravais lattices, Symmetry
elements and operations, Point groups and space groups, Bragg’s law, Diffraction, Atomic
scattering factors, Structure factors, Fourier transformation, Amplitude and Phase, Protein
crystallization, Electron density map.
Structure Determination: Different techniques of crystallization, Diffractometer, Imaging
plates, Phase determination, Patterson method, Direct methods, Molecular replacement
methods, Isomorphous replacement method, Anomalous dispersion, Structure refinement,
Software for visualization and refinement, R- factor, Validation of the structures.
Unit V: Microarray
Principle, Instrumentation and Application of DNA microarray and protein array; Sequence
databases for microarrays; Image processing; Normalisation; Analysis of relationships
between genes, tissues or treatments; Validation tools: GoMiner, qPCR, and TM4-MeV;
Emerging applications of microarray and next generation sequencing.
REFERENCES:
1. Wilson K. and Walker J., Principles and Techniques of Biochemistry and Molecular
Biology (6th Edition, Cambridge University Press, 2008).
2. Freifielder D., Physical Biochemistry, (2nd Edition, W.H. Freeman and Co., New York
1982).
3. Ghosal S. and Srivastav A.K., Fundamentals of Bioanalytical Techniques and
Instrumentation, (PHI Learning Private Limited, New Delhi, 2009).
32
4. Wang, Junbai; Tan, Aik Choon; Tian, Tianhai (Eds.). Next Generation Microarray
Bioinformatics (Methods and Protocols). Humana Press. 2012.
5. Dov Stekel, Microarray Bioinformatics. Cambridge University Press. 2003.
33
Semester - VI
Core 11: Molecular Modeling
Unit I: Molecular Modeling
Introduction to molecular modeling, Quantum chemistry, Schrödinger equation, Potential
energy functions, Energy minimization, Local and global minima, Saddle point, Grid search,
Various approximations; LCAO, HF, Semi-empirical calculations; Single point calculations,
Full-geometry optimization methods, ZDO, MNDO, CNDO, NDDO, AM1, PM3, RM1,
Conformational search, Z-matrix, Docking, Molecular modeling packages, Molecular
Graphics.
Unit II: Molecular Mechanics
Introduction to molecular mechanics, Balls and springs, Force fields, Bond-stretching, Bondbending, Dihedral motions, Out of plane angle potential, Non-bonded interaction, Coulomb
interactions, Conformational search, United atoms and cut-offs, Derivative methods; Firstorder methods; Steepest descent, Conjugate gradient, Second order methods; NewtonRaphson method.
Unit III: Molecular Dynamics
Introduction to molecular dynamics, Newton’s equation of motion, Equilibrium point, Radial
distribution function, Pair correlation functions, MD methodology, Periodic box, Algorithm
for time dependence; Leapfrog algorithm, Verlet algorithm, Boltzman velocity, Time steps,
Duration of the MD run. Starting structure, Analysis of MD job, Uses in drug designing,
Ligand protein interactions.
Unit IV: Quantum Mechanics
Introduction to quantum mechanics; Postulates of quantum mechanics; Electronic structure
calculations; Semi-empirical and density functional theory calculations; Molecular size
versus accuracy; Approximate molecular orbital theories; Monte Carlo Simulations:
Calculating properties by integration, Metropolis methods.
Unit V: Protein Structure Prediction
Protein Structure Prediction; Homology modeling; Threading and ab initio modeling;
Prediction of protein structure from sequences; Functional sites; Protein folding problem;
Protein folding classes; Protein identification and characterization: AACompIdent, TagIdent,
PepIdent and MultiIdent, PROSEARCH, PepSea, PepMAPPER, FindPept; Predicting
transmembrane helices; Primary structure analysis and prediction; Secondary structure
analysis and prediction: motifs, profiles, patterns and fingerprints search; Levinthal's paradox
and the kinetics of protein folding.
REFERENCES:
1. C. Stan Tsai, An Introduction to Computational Biochemistry, Wiley-Liss Inc., New
York, 2002.
2. Cynthia Gibas and Per Jambeck, Developing Bioinformatics Computer Skills, O’Reilly,
2001
3. Andrew Leach, Molecular Modelling: Principles and Applications, 2nd Edn, Pearson
Education, UK, 2010.
4. Höltje, Hans-Dieter Sippl, Wolfgang Rognan, Didier Folkers and Gerd, Molecular
Modeling: Basic Principles and Applications, Wiley-VCH, Weinheim. 2008.
5. Alan Hinchliffe, Molecular Modelling for Beginners, John Wiley, UK, 2003
34
Core 12: Computer Aided Drug Design
Unit I: Introduction to Cheminformatics
Introduction to cheminformatics, History of cheminformatics, Applications of
cheminformatics, Evolution of cheminformatics, Future scope of cheminformatics, Data and
data source in chemistry, Searching chemical structures, Chemical structure file formats.
Unit II: Representation of Chemical Compounds
Representation of chemical compounds, Manipulations in 2D and 3D structures of chemical
compounds, Representation of chemical reactions, Molecular descriptors, Calculations of
physical and chemical data, Calculations of structural deciphers.
Unit III: Drug Development
Drugs, Development of drug, Source of drugs, Structural effects on drug action, Drug life
cycle, Drug development time lines, Stages of drug discovery, Strategic issues in drug
discovery, Emerging approaches to drug design and discovery, Drug metabolism, Drug
design physicochemical properties: Hansch π; Hammett σ; Es, MR, Pharmacokinetic action
of drug on human body, Prodrug design and applications.
Unit IV: Computer Aided Drug Design
Computer Aided Drug Design, Methods of computer aided drug design, Ligand design
methods, Docking algorithms and programs, Drug design approaches, Strategy for target
identification and validation, Lead compound identification and optimization, High
throughput screening for lead discovery, Receptor theory, Receptor models and
nomenclature.
Unit V: Virtual Screening and ADMET properties
Combinatorial Chemistry and Library Design, Virtual screening, Drug likeliness and
Compound filters. ADMET (Absorption, Distribution, Metabolism, Excretion and toxicity)
property prediction, Computer based tools for drug design.
REFERENCES:
1. Andrew R. Leach, Valerie J. Gillet, Introduction to Chemoinformatics, Springer,
Netherlands, 2007.
2. Frank Jensen, Introduction to Computational Chemistry, Wiley, 1999.
3. S.P.Vyas and R.K.Khar, Targeted and Controlled Drug Discovery, CBS Publishers, 2012.
4. Johann Gasteiger and Thomas Engel, Cheminformatics, Wiley-VCH, 2003.
5. Thomas Lengauer (Ed.), Bioinformatics from Genome to Drug, Wiley-VCH, 2002.
6. Kerns, E.H.; Di, L. Drug-Like Properties: Concepts, Structure Design and Methods: from
ADME to Toxicity Optimization, Academic Press, Oxford, 2008
7. Burger’s Medicinal Chemistry and Drug Discovery, 5th Edition, Vol. 1. Principles and
Practice, edited by M. E. Wolff, John Wiley & Sons: New York, 1995.
8. Principles of Medicinal Chemistry, 4th Edition, edited by W.O. Foye, T.L. Lemke, and D.
A. Williams, Williams and Wilkins: Philadelphia, 1995.
9. Medicinal Chemistry: Principles and Practice, edited by F.D. King, Royal Society of
Chemistry: Cambridge, 1994.
10. A Practical Guide to Combinatorial Chemistry, edited by A. W. Czarnik and S. H.
DeWitt, American Chemical Society: Washington DC, 1997.
35
Core 13: Free and Open Source Bioinformatics Tools
Unit I: Introduction to Free and open-source software
Introduction to Free and open-source software (FOSS), Open Bioinformatics Foundation
(O|B|F), Software license, Types of software, Types of software licenses, Software
categories, Benefits and challenges, Bioinformatics Linux distributions (BioBrew, Bio-Linux,
BioLand, Vlinux, Vigyaan, Bioknoppix, Dnalinux, and Quantian).
Unit II: Free and open-source software Tools I
.NET Bio, AMPHORA, Anduril, Armadillo workflow platform, AutoDock, Biochemical
Algorithms Library (BALL), caCORE, caArray, LabKey Server, OpenClinica, PromKappa,
MeV: Multi-Experiment Viewer, PathVisio, REDCRAFT
Unit III: Free and open-source software Tools II
EMBOSS, Gaggle, Galaxy, GenePattern, GeWorkbench, GMOD, GeneTalk, GenGIS,
GenomeSpace, GENtle, Integrated Genome Browser, Argo Genome Browser, Integrative
Genomics Viewer (IGV), IntAct, InterMine, Java Treeview.
Unit IV: Free and open-source software Tools III
SAM Tools, Staden Package, STAMP, Taverna workbench, TGAC Browser, T-REX
WebServer, Unipro UGENE, Visomics, Genome Analysis Toolkit 1.0 (GATK 1.0).
Unit V: Bio Tools Projects
Bio4j, Bioclipse, Bioconductor, BioHaskell, BioJava, BioMOBY, BioPerl, BioPHP,
Biopython, BioRails, BioRuby, BioSmalltalk, BioUno.
REFERENCES:
1. Edwards, David; Stajich, Jason; Hansen, David (Eds.), Bioinformatics: Tools and
Applications, Springer, 2009.
2. World Wide Web
36
Major Elective 3: 14(a). Applications in Bioinformatics
Unit I: Eukaryotic Genome applications
Sequencing of Complete Genomes – Characterization of Genomes using STS and EST
Sequences – Sequence Tagged Sites are Landmarks in the Human Genome – Expressed
Sequence Tags – Implementation of an EST Project – Identification of Unknown Genes –
Discovery of Splice Variants – Genetic Causes for Individual Differences –
Pharmacogenetics and Individual Medicine.
Unit II: Functional analysis of genomes
Identification of the Cellular Functions of Gene Products – Basic concepts of
Transcriptomics, Proteomics, Metabolomics, Phenomics, Systems Biology.
Unit III: Medical and forensic applications of gene manipulation
Diagnosis and characterization of medical conditions – Treatment using rDNA technology –
gene therapy – DNA profiling.
Unit IV: Transgenic plants and animals
Transgenic plants – Why transgenic plants? – Ti plasmids as vectors for plant cells – Making
transgenic plants – Putting the technology to work – Transgenic animals – Why transgenic
animals? – Producing transgenic animals – Applications of transgenic animal technology.
Unit V: Patenting of Biological Materials
Product patents and its Importance to investors – Conditions for patenting – Patenting of
Liveforms – Significance of Patents in India – Some example cases of patenting.
REFERENCES:
1. P.M. Selzer, R.J. Marhöfe and A. Rohwer, Applied Bioinformatics, Springer-Verlag,
Heidelberg, 2008.
2. Desmond S. T. Nicholl, Introduction to Genetic Engineering, Cambridge Univ. Press,
UK, 2002.
3. R.C. Dubey, A Textbook of Biotechnology, Rev. Edn., S.Chand & Company, New Delhi,
2006.
37
Major Elective 3: 14(b). Introduction to Intellectual Property Rights
Unit I: Bioethics
Bioethics – Definition – Goals – History – Principles – Approaches – Need – Problem and
Solution – Environmental Ethics
Unit II: Ethical Issues in Biotechnology
Ethical Issues in Health and Biomedical Innovation – Organ Transplant – Stem Cells –
Ethical Implication in Human Genome Project – Gene Therapy – Ethical Concern on Cloning
–Biodiversity – Genetic Engineering
Unit III: Introduction to Intellectual Property Rights
Introduction to Intellectual Property Rights (IPR) – Patent and Confidential Information –
Patent System – Need of Granting Patent – International Patent System – Patentability –
Novelty – Publication – Application – Future of Patent
Unit IV: IPR components
Trademarks – Registration – Protection – Passing off – Ownership – Copyright and Moral
Rights – Duration – Dealing – Design – Registered – Unregistered – Community
Unit V: BioSafety and Regulatory Agencies
Bio-Safety – International Agreement – Regulation – IPR – GATT– WTO – TRIPS – WIPO
– Patent Status – International scenario – UPOV – PCT – EPC – Budapest Treaty – OECD –
Biological Material – Significance
REFERENCES
1. Tina Hart and Linda Fazzani, “Intellectual Property Rights”, 3rd edition, Palgrave
Macmillan, UK, 2004
2. S. Ignacimuthu, S. J., “Bioethics”, Narosa Publishing House, New Delhi, 2009
3. R. C. Dubey “A Textbook of Biotechnology”, S. Chand & Company Ltd, New Delhi,
2006
38
Core Practical 3: Lab in Biological Databases
1. Search a nucleotide sequence of your interest in GenBank database, and download the
sequence in GenBank file format.
2. Search a protein sequence of your interest in SwissProt database, and download the
sequence in FASTA file format.
3. Search a nucleotide sequence of your interest in EMBL database, and download the
sequence in EMBL file format.
4. Gather information about a disease/protein from Biomed Central.
5. Collect disease/disorder genome sequence data from OMIM database, and explore its
genome assembly using UCSC genome browser.
6. Search a drug compound and pathway of a disease protein from KEGG database.
7. Find the protein families, domains and functional sites, amino acid patterns and profiles
of a protein sequence using PROSITE.
8. Align protein sequences using ClustalX/W and construct amino acid patterns from the
aligned protein sequences using PRATT.
9. Download a protein structure from PDB and visualize it using RasMol.
10. Search similar structures using VAST, and download the result and visualize it using
Cn3D.
39
Core Practical 4: Lab in Computational Biology
1.
2.
3.
4.
Global and local alignment using EMBOSS.
Dotplot using EMBOSS.
Protein properties prediction using ProtScale.
Multiple sequence alignment using Clustal Omega / T-Coffee / MUSCLE / Kalign /
ClustalX/W.
5. Phylogenetic tree construction using MEGA/Phylip/MrBayes.
6. DNA sequence assembly using Phrap/Staden/DNA Baser Sequence Assembler.
7. RNA secondary structure prediction using mfold/RNA123/RNAComposer.
8. Protein secondary structure prediction using CFSSP/GOR/NNPREDICT/SOPMA.
9. Protein sequence to structure/function prediction using ProFunc.
10. Protein threading server LOMETS/THREADER/PSIPRED.
40
Core Practical 5: Lab in Molecular Modeling and Computer Aided Drug Design
1. Homology modeling using Swiss-Model/MODELLER.
2. Protein structure and function predictions using I-TASSER/Phyre2.
3. Automatic fold recognition server for predicting the structure and/or function of your
protein sequence.
4. ab initio protein folding and protein structure prediction using QUARK.
5. Protein side chain modeling using YASARA.
6. Protein ligand binding site prediction using COACH.
7. Search and download drug compounds using ZINC/ChEMBL/DrugBank.
8. Ligand binding site prediction using 3DLigandSite.
9. Docking using AutoDock/ZDOCK/PatchDock.
10. Protein-Ligand interaction plotting using LigPlot.
41