(Any revisions to the syllabus will be informed to the students from time to time.

)
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SEMESTER I
Course title L-T-P-C
1 Cell and Molecular Biology 4-0-0-4 H 4
2 Biochemistry of Macromolecules 3-1-0-4 H 4
3 Genetics 4-0-0-4 H 4
4 Mathematics for Biologists 3-1-0-4 H 4
5 Basic Bioinformatics 1-1-0-2 H 2
6 Computer Programming and Operating System - Python, C and Linux 2-0-0-2 H 2
7 Cell and Molecular Biology, and Genetics – Laboratory 0-0-4-4 P 4
8 Computer
Programming and Operating System - Python, C and Linux – 0-0-4-4 P 4
Laboratory
TOTAL 28

Unit 1: Basic structure and function of cells and their organelles (8 hours)
Differences in the basic structure and composition of prokaryotic cells and eukaryotic animal and
plant cells; structure and function of eukaryotic (plant and animal) cell organelles.

Unit 2: Diversity in structure and function across tissues/species (8 hours)

Diversity in the size and shape of cells depending on functions within different tissues; variations
in the number and structure of organelles depending on the type of cells (e.g., rich smooth
endoplasmic reticulum in lipid secreting cells).

Unit 3: Cell cycle and divisions (12 hours)

Introduction to cell cycle, cell division and types: mitosis and meiosis; typical phases of mitosis and
meiosis; brief discussions on the molecular mechanisms, relationship with growth, differentiation
and reproduction.

Unit 4: The Central Dogma of biology (4 hours)

DNA as a universal genetic material in cells across species and the flow of genetic information
from DNA to RNA to proteins.
The concept of ‘gene expression’: molecular basis of biochemical events and phenotypes.
Significance of proteins, non-coding RNAs and other biomolecules in cellular functions in complex
species.

Unit 5: DNA replication and repair (8 hours)

Characteristics and functions of bacterial DNA polymerases
Mechanism of prokaryotic DNA replications: replication bubbles, replication forks, the role of
topoisomerases, SSBs and helicases. Mechanism and significance of telomerases
Types of DNA damages and major types of repair systems: DNA damage alkylation, deamination,
oxidation, UV radiation. Repair mechanisms photo reactivation, excision repair, post replication
repair, mismatch repair and SOS repair.
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Relevance of DNA replication and repair to mitosis, meiosis, growth, reproduction, cancer and
evolution.

Unit 6: RNA synthesis and processing (8 hours) Gene organization: promoters, exons and introns.
Mechanism of transcription. Molecular control of transcription initiation: transcription factors,
core promoters and RNA polymerases; Types of (rRNA, tRNA, mRNA coding) genes and their
promoter features post-transcriptional processing; 5'-capping and poly-adenylation of transcripts;
types of alternative splicing and significance of splicing in cell functions. An overview of splicing
mechanism.

Unit 7: Protein synthesis and processing (8 hours) Reading frames, codons and the Wobble
hypothesis.
Structure and function of ribosomes
Mechanism of translation: amino acid activation, ribosome assembly with initiator tRNA,
elongation and termination process.
Common types of post-translational modifications of proteins. Role of microRNAs and RNA
interference in eukaryotes.

Unit 8: Gene expression regulation (8 hours)

Prokaryotic operon models: inducible and repressible systems, lac and trp operon Eukaryotic core
and distal promoters, cis elements, enhancers and insulators.
Transcription factors and their binding sites
An overview of DNA-protein interactions in the context of transcriptional regulation. Comparison
of prokaryotic vs. eukaryotic gene expression mechanisms and regulations:
relationship of gene-expression-control with cellular and physiological events; role of hormones
and signal transduction systems
A brief discussion on other stages at which gene expression can be regulated.

Textbooks:
1. B. Alberts et. al.; Molecular biology of the cell; Taylor & Francis Publishers, 2008; 5 th edition.
2. H. Lodish, A. Berk, S. L. Zipursky, P. Matsudaira, D. Baltimore and J. Darnell; Molecular Cell
Biology; W. H. Freeman & Comp., 2007; 6th edition
3. G. M. Cooper and R. E. Hausman; The cell: A molecular approach; ASM Press, 2009; 5 th edition.

Reference books:
1. B. Alberts et. al.; Molecular biology of the cell; Taylor & Francis Publishers, 2014.; 6th edition.
2. T. A. Brown; Genomes 3; Oxford: Wiley-Liss, 2007; 3rd edition
3. J. E. Krebs, E. S. Goldstein and S. T. Kilpatrick, Lewin's Genes XII; Jones & Bartlett Publishers,
Inc., 2017; 12th edition.

Unit 1: Fundamental chemistry (17 hours)

Atomic structure, classification of elements and periodic trends, chemical bonding, valence bond
and molecular orbital theory, geometric shapes of molecules. Elements of stereochemistry -
different kinds of stereoisomerism, single bond rotation and torsion angle concept, intermolecular
interactions ­ van der Waal radius of an atom, nonbonded interactions, van der Waal’s, hydrogen
bond and electrostatic interactions. Acids and bases – definitions, chemical equilibrium, ionic
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product of water, pH, pKa, acid titration curves and buffer solutions. Introduction to
thermochemistry – energy, enthalpy and entropy, different types of systems, laws of
thermodynamics, spontaneous reactions.

Unit 2: Structure and function of DNA (12 hours)

Structures and conformations of nucleosides, nucleotides and dinucleosides, base pairs, base
triples and base quartets; Unique properties of Watson and Crick pairs and duplex DNA structure,
NonWatson and Crick base pairs, DNA structural polymorphism BDNA, ADNA, ZDNA, triplex, G
quadruplex, i-motif, cruciforms; Interactions of intercalating and groove binding drugs with DNA;
examples of a few protein structural motifs that interact with DNA; DNA methylation and
epigenetics, nucleosome, chromatin and higher order structures.

Unit 3: Structure and function of RNA (5 hours)

Structure of duplex RNA, Structure of yeast tRNAPhe; RNA structural motifs U-turn, hairpins,
pseudoknot; structure of hammerhead ribozyme, anti-sense oligonucleotides and small
interferingRNA.

Unit 4: Structure and function of proteins (13 hours)

Structure, properties and classification of amino acids, peptide conformation and Ramachandran
map, secondary structural motifs, super secondary structural motifs and domains, tertiary and
quaternary structures of proteins. Structure-function correlation of a few globular, fibril proteins,
membrane proteins and transporters. Protein engineering concepts.

Unit 5: Protein folding and stability (4 hours)

What is the protein folding problem? Anfinsen’s experiments, Levinthal paradox and free energy
funnel, folding intermediates, protein misfolding, roles of chaperones and chaperonins.

Unit 6: Structure and function of carbohydrates (13 hours)

Overview of chemical structures of aldoses and ketoses, stereochemistry of sugars, open and
closed forms of sugars. Disaccharides – linkages and structural features. Structural diversity of
polysaccharides – hydrogen bonding schemes in disaccharides and polysaccharides. Overview of
bacterial cell wall polysaccharides, glycoconjugates, proteoglycans, glycoproteins, glycolipids.
Structural features of glycosaminoglycans in the extra cellular matrix.

Textbooks:
1. D. W. Oxtoby, H. P. Gillis and L. J. Butler; Principles of Modern Chemistry; 8 th edition,
CENGAGE, 2016.
2. D.L. Nelson and M.M. Cox; Principles of Biochemistry; 5th edition, Freeman & Co. NY, 2008. 3.
C. Branden and J. Tooze; Introduction to Protein Structure; Garland Publishing, NY, 1991. 4.
W. Saenger; Principles of Nucleic Acid Structure; Springer-Verlag, NY, 1984.

Reference books:
1. R. Myers; Basics of Chemistry; Greenwood Press, USA, 2003.
2. L. Stryer; Biochemistry, 5th edition, W H Freeman & Co, 2002.
3. L. Jones and P. Atkins; Chemistry: Molecules, matter and change; W.H. Freeman and
Company, 4th edition, 2000.
4. D. Voet, J. G. Voet and C. W. Pratt; Principles of Biochemistry; John Wiley, 2007.
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5. C. R. Calladine, H. R. Drew, B. F. Luisi and A. A. Travers; Understanding DNA: The molecule and
how it works; 3rd edition, Elsevier Press, 2004.
6. S. Neidle, Principles of Nucleic Acid Structure; Elsevier Press, 2008.
7. T. E. Creighton, Proteins: Structure and Molecular Properties; W.H. Freeman and Co. San
Francisco, 1992.
8. M. E. Taylor and K. Drickamer; Introduction to Glycobiology; 3rd edition, Oxford University
Press, 2011.
9. V. S. R Rao, P.K. Qasba, P.V. Balaji and R. Chandrasekaran; Conformation of carboyhydrates;
CRC Press, 1998.

Online Contents and video lectures https://ocw.mit.edu/courses/chemistry/5-111sc-principles-of-

chemical-science-fall-2014/
https://ocw.mit.edu/courses/chemistry/5-112-principles-of-chemical-science-fall-2005/

Unit 1: Physical basis of heredity (10 hours)

Introduction, concepts and theories of Mendelian genetics, chromosome theory of inheritance,
Non-Mendelian Inheritance, gene interaction, linkage and crossing over, two-point and three point
mapping, linkage map

Unit 2: Cytogenetics (6 hours)

Chromosome structure, organization, and classification, normal karyotype, chromosomal
abnormalities, idiogram, robertsonian translocation, imprinting, mutations and repair

Unit 3: Biochemical and clinical genetics (11 hours)

Deciphering pathways for metabolic disorders, signatures in the genome used for generating
haplotypes, single-gene inheritance, pedigree analysis, Human Genome Project, identification of the
gene involved in rare monogenic disorders, mapping genomes.

Unit 4: Population genetics (7 hours)

Gene pools, allele frequencies, Hardy Weinberg equation, non random breeding, genetic drift, gene
flow, selection, speciation. Protein and DNA sequence polymorphism, molecular basis of evolution
in Homo sapiens, basic methods for DNA analysis: mutation detection, indirect mutant gene
tracking, analysis of DNA length polymorphism, analysis of single-nucleotide polymorphisms.

Unit 5: Cancer genetics (8 hours)

The genetic basis of cancer, oncogenes, tumor suppressor genes, genetic instability and cancer,
cancer gene pathways, genetic alterations in common cancers, cancer genetics in the clinic.
Unit 6: Developmental genetics (22 hours)
Determination and embryonic patterning, how genes regulate embryonic development and
patterning in Drosophila and mouse, genes regulating neural tube formation and heart, genes
regulating stem cell potency, modeling human diseases in mouse: techniques to study
developmental disorders, congenital defects. Mechanisms of sex determination, sex determination
in D. melanogaster and C. elegans, sex determination in mammals, clinical implications of sexual
determination and dimorphism
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References:
1. D. L. Hartl and M. Ruvolo; Genetics: Analysis of Genes and Genomes, Jones & Bartlett
Learning, 8th edition, 2011.
2. M. J. Simmons, D. P. Snustad and E. J. Gardner; Principles of Genetics, John Wiley and Sons
Inc, 8th edition; 1991.
3. T. A. Brown; Introduction to Genetics: A Molecular Approach, Garland Science, 2011.
4. E. S. Tobias, M. Connor, M. Ferguson-Smith; Essential Medical Genetics, Wiley-Blackwell,
6th edition, 2001
5. D. L Hartl and E. W. Jones; Genetics: Analysis of genes and genomes, Jones and Bartlett
Publishers; 4th edition; 1998.
6. S Moody; Principles of Developmental Genetics; Academic Press, 2nd edition; 2014.
7. F Bunz; Principles of Cancer Genetics; Springer; 2008.

Unit 1: Basic concepts (11 hours)

Co-ordinates: Cartesian and polar coordinate systems.
Functions, domain and range, plotting of functions and inequalities. Linear, polynomial,
exponential, logarithmic, trigonometric functions and their properties.
Concept of limit, rules followed by limits, methods of finding the limits of polynomials and rational
functions, one-sided and two-sided limits. Continuity and differentiability, continuity at a point,
continuous extension to a point, continuity on intervals, the intermediate value theorem.

Unit 2: Derivatives (11 hours)

Derivative of a function, differentiation, second and higher order derivatives, L'Hospital's rule for
finding limits, implicit differentiation, partial derivatives. The tangent and normal lines to a curve
at a point. Finding extreme values of functions, local and global extrema. Linear approximations to
functions at a point. Differentials, computing absolute, relative and percentage changes in
formulas. The mean value theorem for derivatives.

Unit 3: Integration (11 hours)

Indefinite integrals, integration methods. Summation of series, Riemann sums and definite
integral, evaluation of definite integrals. Area under the curve, average values of continuous
functions. First order differential equations and their solutions, variable-separable method,
general form and solution of first order linear differential equations, use of differential equations
in biology with examples.

Unit 4: Linear algebra (11 hours)

Concept of a vector, vector addition and scalar multiplication, magnitude and direction of a vector,
unit vector, vectors in cartesian coordinates, dot product and cross product of vectors, vector and
scalar triple products, vector and scalar functions and fields, derivatives.

Matrix algebra: Concept of vector spaces, determinants, matrix as a linear transformation, matrix
addition and multiplication, matrix properties, simultaneous equations, Cramer's rule and the
solution of homogeneous and inhomogeneous linear algebraic equations, Eigen values, Eigen
vectors and their applications.
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Unit 5: Sequence and series (10 hours)
Fundamental concepts, convergence tests, alternating series, series of a function and Taylor
expansion.

Unit 6: Biological applications of the above concepts (10 hours)

Graphical representations of experimental results, extraction of information from experimental
curves by finding derivatives and area under the curve. Exponential growth and decay curves,
logarithmic plots of data, applications of periodic functions, first order time derivatives and
enzyme kinetics. Modeling metabolic networks with ordinary differential equations, eigen value
problems in principal component analysis.

Textbooks:
1. G. B. Thomas, J. R. Hass and M. D. Weir; Thomas' Calculus; Pearson 2010, 12 th edition.
2. M. R. Spiegel, S. Lipschutz and D. Spellman; Schaum's Outline: Vector Analysis; McGraw-Hill
2009, 2nd edition.
3. R. A. Horn and C. R. Johnson; Matrix Analysis; Cambridge 2016, 2nd edition.
4. G. B. Arfken and H. J. Weber; Mathematical Methods for Physicist; Elsevier 2011, 6 th edition.

Unit 1: Biological sequences (6 hours)

DNA and protein sequences, genome and transcriptome, open reading frames, gene structure in
prokaryotes and eukaryotes, coding and non-coding genes, extracting, collecting and storing
sequences; various file formats for bio-molecular sequences: GenBank, FASTA, GCG, MSF, NBRF-
PIR.

Unit 2: Database resources (6 hours)

EMBL, NCBI, OMIM, UCSC browser and other resources – comparisons of formats and volumes;
utilities of metadata across GEO, TCGA, Array Express, 1000 genome, dbSNPs, COSMIC; Pfam,
SCOP, KEGG and UNIPROT databases for protein sequence analysis.

Unit 3: Sequence analysis (10 hours)

Dot plot, basic concepts of sequence similarity, identity and homology, definitions of homologues,
orthologues, paralogues, concepts behind scoring matrices, database searching: using BLAST,
FASTA and other sequence analysis online tools to assign homology. Gene-id conversions,
specialized primer-designing, PCR.
Unit 4: Structural bioinformatics (10 hours)
Molecular structures – visualizing and graphical representations. Calculation of geometric
parameters (bond distance, bond angle, dihedral angle). Identifying intramolecular and inter
molecular interactions from crystal structures (using GUI).

Reference books:
1. N. Gautham; Bioinformatics: Databases and Algorithms; Alpha Science, 2006.
2. D. W. Mount; Bioinformatics Sequence and Genome Analysis; Cold Spring Laboratory Press,
2001.
3. F. J Burkowski; Structural Bioinformatics An Algorithmic Approach; CRC Press, 2009.
4. A. M Lesk; Introduction to Bioinformatics; Oxford University Press, 2002.
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5. J. Bedell, I. Korf and M. Yandell; BLAST; O’Reilly Press, 2003.
6. J. M. Keith; Bioinformatics Vol. 1, Data, sequence analysis & evolution; Humana Press, 2008.
7. R. Durbin; Biological sequence analysis; Cambridge University Press, 1998.
8. R. M. Holmes; A cell biologists’ guide to modeling and bioinformatics; Wiley Interscience,
2007.

Online courses and materials https://www.coursera.org/learn/python

http://www.pythonlearn.com/ http://www.pythonlearn.com/book_007.pdf
https://www.coursera.org/learn/bioinformatics-pku#

6. Computer Programming and Operating System - Python, C and Linux H2

Python (10 hours) Unit 1:

Why Python?; brief history; introduction to Python programming; environment and environment
setup; basic syntax.

Unit 2:
Variables; operators; decision making; loops.

Numbers, lists, strings, tuples, dictionary; functions in Python; modules in Python; files and file
operations in Python.

Unit 3:
Classes and objects; regular expressions; CGI programming; multi threading; dxception handling;
XML processing; GUI programming.

Textbooks and Reference books:

1. A. Martelli, A. Ravenscroft and S. Holden; Python in a Nutshell; O’Reilly Publication, 3 rd edition,
2017.
2. D. Beazley and B. K. Jones; Python Cookbook ­ Recipes for Mastering Python; O’Reilly
Publication, 3rd edition, 2013.
3. J. Jose and S P. Lal; Introduction to Computing and Problem Solving with Python; Khanna
Publishers, 1st edition, 2015.

C-Programming (11 hours) Unit

4:
Role of hardware, OS in successful programming; compiler and its role; compiler vs interpreter;
linker and loader; importance of C-standards and coding standards
Why C and Linux is an outstanding combination?; introduction to GNU C compiler; prerequisites to
start C-programming (OS, C-compiler, editor etc).

Unit 5:
What is structured programming; How C language supports structured style of programming;
skeletal C code; What is a pre processor and a pre processor directive?; analysis of #include
directive and header files in C; analysis of C as a function oriented language; analysis of main()
function, the important starting point of C code; how C library functions make our life easy;
important C library functions.
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Unit 6:
Data, data types and data structures - an introduction; basic data types in C language; difference
between short, long, signed, unsigned data types; size of different data types; user defined data
types - what are these?; arithmetic and logical operations; different operators.

Arrays - single and multi dimensional; control/condition statements; iterations and looping.

Unit 7:
Introduction to pointers; different types of pointers - basic type pointers, user defined data type
pointers; void pointers vs null pointers vs dangling pointers; struct and union; struct pointers, self
referential structures.

Unit 8:
Functions and their role in C; function definition vs function prototype vs function call; how stack
is related to a function; normal function vs recursive function; function signature(s); parameter
passing to a function - call by value vs call by reference.

File and file operations; important C library functions related to file operations.

Textbooks and Reference books:

1. B. W. Kernighan and D. Ritchie; The C Programming Language; Pearson Education India, 2nd
edition, 2015.
2. Balagurusamy; Programming in ANSI C; McGraw Hill Education India Private Ltd, 7 th edition,
2017.
3. H. Schildt; C- The Complete Reference; McGraw Hill, 4th edition, 2017.

Linux (11 hours) Unit 9:

Introduction to Unix/Linux; Advantages of going for Linux; different flavours of Linux – An insight;
why Linux and C language is powerful?

Important features of Linux: file management, process management, memory management, IO

management, scheduling, security, how its a multiuser, multitasking, multi process and
multiprocessing OS, Linux on a single CPU system, makefile.

Unit 10:
Shell: importance of a shell, role of a shell, multiple shells on a single Linux system, basic
commands of a shell, internal vs external commands, shell programming – basics.

Unit 11:
File management: file and file system, disk formatting and file system relationship, important
blocks of Linux file system, file handle, inode and incore inode, hierarchical file system, important
system folders of Linux, root user vs normal user, file permissions and how to manipulate the
same, file descriptors, file system related system calls.

Unit 12:
process management: process and its creation, role of process ID, relation between a process and
a file, process life cycle, process states, process context and context wwitching, HWP vs LWP, -
process system related system calls, importance of /proc folder, fork() and exec() calls - two of the
most critical calls, background vs foreground process, zombie vs daemon process.
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Unit 13:
Memory Management: basics
IO Management: basics
Scheduling: Importance, single CPU vs multi CPU systems, schedulers, scheduling algorithms.

Textbooks and Reference books:

1. E. Siever; Linux in a Nutshell; O’Reilly Publication, 6th edition, 2009.
2. L. Robert; Linux System Programming; Shroff Publishers and Distributors Private Ltd, 2 nd
revised edition, 2014.
3. M. J. Bach; The Design of the UNIX Operating System; Pearson Education India, 1 st edition,
2015.

7. Cell and Molecular Biology, and Genetics – Laboratory P4

1. Experiments in accuracy and precision (pipetting weighing balance, pH meter)

2. Cleanliness, sterilization, and safety (autoclaving, reagent, and media preparation)
3. Estimation of protein concentration using Lowry and Bradford methods
4. Separation of plant pigments by thin layer chromatography
5. Isolation and analysis of nucleic acids by agarose gel electrophoresis
6. Separation of proteins by SDS-PAGE, followed by commassie and silver staining
7. Karyotyping and G and C banding of chromosomes using normal and cancerous cell lines of
humans.
8. Dissection and mounting of salivary glands and imaginal discs of Drosophila.
9. Demonstration of polytene chromosomes in Drosophila.
10. Preparation of sample and identification of various stages of mitosis and meiosis
11. Isolation of nucleus, mitochondria and chloroplasts by centrifugation
12. Mammalian cell culturing and viability testing by MTT, LDH and trypan blue exclusion assay
13. Transfection of mammalian cells.
14. Splitting and cryopreservation of mammalian cells.

Textbooks and Reference books:

1. D. R. Randall; Molecular Biology Laboratory Manual; Available online
(available free of cost at https://archive.org/details/MolecularBiologyLaboratoryManual_456).
2. S. Surzycki; Human Molecular Biology Laboratory Manual; Wiley-Blackwell, 2003.
3. K. V. Chaitanya; Cell and Molecular Biology: A Lab Manual; PHI Learning Press, 2013.
4. Practising Safe Science video https://www.youtube.com/watch?v=sTzW6XENAXQ 5. Cell
Fractionation and Organelle Isolation
https://www.thermofisher.com/us/en/home/lifescience/protein-biology/protein-biology-
learningcenter/protein-biology-resource-library/pierceprotein-methods/cell-fractionation-
organelle-isolati on.html
6. http://www.biology.arizona.edu/cell_bio/cell_bio.html
7. R. I. Freshney; Culture of Animal Cells: A Manual of Basic Technique; 4th Ed. Wiley Liss; New
York, 2000.
8. J. M. Davis; Basic Cell Culture; Oxford University Press, New York, 93–134, 1996.
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8. Computer Programming and Operating System - Python, C and Linux – Laboratory P4

Python:
1. Environment and environment setup (python setup with correct parameterisation).
2. Basic syntax; variables; operators (basic python programming)
3. Decision making; loops (selection and iterations in python programming) 4. Numbers, lists,
strings, tuples, dictionary (advanced data structures in python programming). 5. Functions in
python; modules in python (function and module orientation in python programming)
6. Files and file operations in python (data storage and retrieval using files in python).
7. Classes and objects (object oriented programming in python)
8. Regular expressions; CGI programming; multi threading; exception handling; XML processing;
GUI programming (advanced python programming)

C-Programming:
9. Skeletal C code (understanding the syntax/style of C code)
10. Pre processor and a pre processor directive;
#include directive and header files in C (basic pre processing and directives involving header
files) 11. main() function, the important starting point of C code (understanding of function
orientation and the main function’s importance)
12. Important C library functions (working with important pre compiled functions of C)
13. Data, data types and data structures - an introduction; basic data types in C language;
difference between short, long, signed, unsigned data types; size of different data types; user
defined data types (hands on assignments on the building blocks in terms of data types and
data structures, most essential ingredients in C programming)
14. Arithmetic and logical operations; different operators. (basic C programming - Part1)
15. Arrays - single and multi dimensional; control/condition statements; iterations and looping
(basic C programming - Part 2)
16. Pointers; different types of pointers – basic type pointers, user defined data type pointers;
void pointers vs null pointers vs dangling pointers; struct and union; struct pointers, self
referential structures (working on power of pointers in C language)
17. Functions and their utility in C (Hands on assignments on built in functions and user created
functions in C language)
18. File and file operations; important C library functions related to file operations (data storage
andretrieval – core concept of files are worked on) Linux:
19. Shell: Basic commands of a shell, internal vs external commands (working on multiple shell
commands and understanding of how it interacts with Linux)
20. Shell programming (working on core shell programming in sync with Linux)
21. Linux file management: file and file system , file system related system calls (programming
exercises on core Linux file system and file system related calls)
22. Linux process management: creation of a process to process system management
(assignments on core Linux process management, life cycle, context and state, /proc system) 23.
Make utility and makefile (understanding the practical importance of make utility)
 14/40
Textbooks and Reference books:
1. A. Martelli, A. Ravenscroft and S. Holden; Python in a Nutshell; O’Reilly Publication, 3 rd edition,
2017.
2. D. Beazley and B. K. Jones; Python Cookbook – Recipes for Mastering Python; O’Reilly
Publication, 3rd edition, 2013.
3. J. Jose and S P. Lal; Introduction to Computing and Problem Solving with Python; Khanna
Publishers, 1st edition, 2015.
4. B. W. Kernighan and D. Ritchie; The C Programming Language; Pearson Education India, 2 nd
edition, 2015.
5. Balagurusamy; Programming in ANSI C; McGraw Hill Education India Private Ltd, 7 th edition,
2017.
6. H. Schildt; C – The Complete Reference; McGraw Hill, 4th edition, 2017.
7. E. Siever; Linux in a Nutshell; O’Reilly Publication, 6th edition, 2009.
8. L. Robert; Linux System Programming; Shroff Publishers and Distributors Private Ltd, 2 nd
revised edition, 2014.
9. M. J. Bach; The Design of the UNIX Operating System; Pearson Education India, 1 st edition,
2015.
SEMESTER II

Course title L-T-P-C

1 Advanced Biochemistry and Physiology 4-0-0-4 H 4
2 Microbiology and Immunology 4-0-0-4 H 4
3 Advanced Bioinformatics 2-0-0-2 H 2
4 Biostatistics and R Programming 2-0-0-2 H 2
5 Advanced C, C++ and Introduction to JAVA Programming 2-0-0-2 S 2
6 Immunology, Microbiology and Biochemistry – Laboratory 0-0-0-4 P 4
7 Advanced Bioinformatics – Laboratory 0-0-2-2 P 2
8 Biostatistics and R Programming – Laboratory 0-0-0-2 P 2
9 Advanced C, C++, JAVA – Laboratory 0-0-0-4 P 4
TOTAL 26

1. Advanced Biochemistry and Physiology

Unit 1: Metabolism (8 hours)

Organic reaction mechanisms, experimental approaches to study metabolism, oxidation-reduction
reactions, glycolysis, glycogen metabolism, glycogen storage disease, Citric acid cycle, Pentose
Phosphate pathway, Fatty acid metabolism, amino acid biosynthesis, Nitrogen fixation. respiration
in plants and photosynthesis, Calvin cycle and oxidative phosphorylation.

Unit 2: Thermodynamics and bioenergetics (6 hours)

Review of thermochemistry and energetics. Order of reactions and rate constant. ATP-ADP cycle,
energy charge (phosphate potential) and its retention to metabolic regulation. Substrate level
phosphorylation. Electron-transport chain, uncouplers, inhibitors and ionophores.
 15/40
Unit 3: Methods in biochemistry (12 hours)

Salting, dialysis, gel filtration chromatography, ion-exchange chromatography, affinity

chromatography, HPLC, Gel electrophoresis, protein sequencing, production of monoclonal and
polyclonal antibodies, ELISA, western blotting, MALDI-TOF, mass spectroscopy, NMR.

Unit 4: Enzymology (12 hours)

Principles of catalysis, enzymes and enzyme kinetics, enzyme regulation, mechanism of enzyme
catalysis, isozymes; enzyme immobilization; examples of quantitative studies; Michaelis-Menten
equation, LWB plot, enzyme inhibition: competitive, non-competitive and uncompetitive.
Allosteric modulation. Ribozymes and abzymes.

Unit 5: General and membrane physiology (4 hours)

The cell and general physiology, functional organization of the human body and control of the
'internal environment' 'homeostatic' mechanisms of the major functional systems, homeostasis,
regulation of body functions, control systems of the body, examples of feedback control
mechanisms.
Membrane physiology: membrane transport, resting membrane potential, action potential and
their measurement, neuromuscular junction, secretion of acetylcholine at the nerve terminals,
molecular biology of acetylcholine production and release, drugs that enhance or block their
transmission at the neuromuscular junction, Myasthenia gravis.
Mechanisms of hormone action, pituitary gland, adrenal glands, thyroid and parathyroid glands,
pancreas and other endocrine glands, autocrine and paracrine regulation.

Unit 6: Circulatory and muscle systems (6 hours)

Heart as a pump, function of the heart valves, cardiac cycle, diastole and systole, relationship of
the electrocardiogram to the cardiac cycle, cardiac output, conduction by the cardiac nerves:
sympathetic and parasympathetic nerves, normal electrocardiogram, cardiac arrhythmias and
electrocardiographic interpretation, heart sounds; heart defects, blood pressure, arteries, veins,
lymphatic system, clotting cascade.

Muscle system: Physiological anatomy of skeletal and heart muscle, types skeletal muscle fibers,
molecular mechanism of muscle contraction, sources of energy for muscle contraction,
characteristics of whole muscle contraction, excitation of skeletal muscle, contraction and
excitation of smooth muscle.

Unit 7: Digestive, excretory, respiratory and nervous systems (10 hours)

Digestive system: esophagus and stomach, small intestine, large intestine, liver, gall bladder, and
pancreas, neural and endocrine regulation of the digestive system/digestion and absorption of
carbohydrates, lipids, and proteins.

Excretory system: General organization of the kidneys and urinary tract, the nephron, urine
Formation by the kidneys, multiple functions of the kidneys in homeostasis, GFR and its control,
renin-angiotensin, ADH control of blood volume and blood pressure.

Respiratory system: physical aspects of ventilation, mechanics of breathing, gas exchange in the
lungs, regulation of breathing, hemoglobin and oxygen transport, carbon dioxide transport and
acidbase balance, effect of exercise and high altitude on respiratory function/interactions.
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Organization of the nervous system, basic functions of synapses, transmitter substances, action
potential, seneral design of the nervous system, central nervous system, brain, learning and
memory, measuring brain activity by EEG, diseases of the nervous system.

Unit 8: Cell signalling (6 hours)

Principles of signal transduction; classification of signaling mechanisms; examples of quantitative
studies; hormones and their receptors classes; signaling through G-protein coupled receptors and
their effectors; tyrosine kinases and Ras, MAP Kinase pathways; second messengers; steroid
hormone receptors, interaction and regulation of signaling pathways; bacterial and plant
twocomponent signaling systems; bacterial chemotaxis and quorum sensing.

Textbooks:
1. T. Palmer; Enzymes: Biochemistry, biotechnology, clinical chemistry; Affiliated East-West Press
Private Limited, 2004.
2. L. Stryer; Biochemistry; W H Freeman & Co, 2002, 5th edition.
3. D. L. Nelson and M. M. Cox; Lehninger - Principles of Biochemistry; Freeman & Co., 2008, 5th
edition.
4. D. Voet and J. G. Voet; Biochemistry; Wiley, 2008, 3rd edition.
5. B. Rupp; Biomolecular crystallography; Garland Science, 2009.
6. G.G. Hammes; Spectroscopy for biological sciences; Wiley, 2005.
7. J. R. Lakowicz; Principles of fluorescence spectroscopy; Springer, 2008, 3rd edition.
8. D. M. Blow; Outline of crystallography for biologists; Oxford University Press, 2002.
9. J. M. Miller; Chromatography: Concepts and contrasts; Wiley, 2009, 2nd edition.
10. R. K. Scopes; Protein purification – principles and practice; Springer Verlag, 1994.
11. G. J. Tortora and B. H. Derrickson; Principles of anatomy and physiology; Wiley
HigherEducation, 11th edition, 2006.
12. S. S. Nussey and S. A. Whitehead; Endocrinology: An Integrated Approach; London: Taylor
&Francis; 2001.
13. A.Waugh, A. Grant; Ross and Wilson Anatomy and Physiology in Health and Illness, Churchill
Livingstone, 12th edition, 2014.
14. J. Hall, A. Guyton; Textbook of Medical Physiology; Saunders, 11th edition, 2005.
15. E. N. Marieb and K N. Hoehn; Human Anatomy and Physiology; Pearson, 9th edition, 2012.

Unit 1: Prokaryotes (10 hours)

Introduction to the microbial world (bacteria, yeasts/fungi, and algae); bacterial structure, growth,
and metabolism; endospores and exospores; taxonomic principles (cell wall components,
isoprenoid quinones, amino acid sequence of proteins, protein profiles, cytochrome composition);
molecular genetic methods in taxonomy (ribosomal RNA/DNA, PCR, and DNA fingerprinting, DNA
base composition, rDNA sequencing etc); phylogeny of living organisms; archaebacteria:
taxonomic position (extremophiles, relatedness to eukaryotes and prokaryotes, unique molecular
and biochemical features); bacteriophages (lysogenic and lytic cycles).
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Unit 2: Fungi (8 hours)

Introduction to the fungi; fungal cell structure and morphology; classification of fungi and their
relationship to other organisms; diversity of fungi; Ascomycetes and Basidiomycetes; fungal
physiology, nutrition, and growth; fungal ecology.

Unit 3: Viruses (8 hours)

History and principles of virology; viruses as acellular entities; virus structure and morphology;
virus taxonomy; hierarchical classification; introduction to replication strategies; Baltimore
classification.

Unit 4: Pathogenic microbes (4 hours)

Characteristics of major bacterial, fungal, and viral pathogens; concepts of pathogenicity and
virulence; microbes of medical importance (E. coli, B. anthracis, Salmonella, Influenza virus, Ebola
virus, Rabies virus, Candida albicans, Histoplasma capsulatum, etc.)

Unit 5: Introduction to immunology (8 hours)

Innate and acquired immunity, structure and functions of immune cells. Components and organs of
the immune system (primary and secondary lymphoid organs). Primary and secondary immune
responses; clonal selection theory; antigens and antibodies – structure determination; classes of
immunoglobulins, CDRs, generation of polyclonal and monoclonal antibodies, haptens, adjuvants,
CD and immunnophenotyping, complement system – components, properties and functions;
complement pathways and their biological significance, inflammation, TLRs, cross talk of innate and
adaptive immune responses.

Unit 6: Immunological diversity (8 hours)

Genetic control of immune response (VDJ recombination); antigen processing and presentation-
major histocompatibility complex (structure and functions of MHC and HLA); B cell maturation and
lymphocyte activation, tissue and organ transplantation (allo and xenograft, host reaction, and
rejection); immunosuppressive therapy.

Unit 7: Immune system in diseases (6 hours)

Host-parasite interaction; allergy and types of hypersensitivity; lymphokines and cytokines
(interleukins and interferons, their production, biological functions and assay methods);
immunological tolerance. Autoimmunity (Hashimoto's disease, systemic lupus erythematosus,
multiple sclerosis, myasthenia gravis) and its treatment; immunotherapy (immunosupression and
immunostimulation).

Unit 8: Immunological methods/techniques, vaccines and other immunotherapies (12 hours)

Immunodiagnosis; antigen-antibody based techniques (ELISA, dot blotting, RIA, western blotting,
immunofluorescence).

Conventional, peptide vaccines, subunit, DNA vaccines. Toxoids, antisera, edible vaccines,
plantibodies, ISCOMs, recombinant antibodies.
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Textbooks:
1. M. J. Pelczar, E. C. S Chan, and N. R. Krieg; Microbiology; Tata McGraw Hill, 2001, 5 th edition.
2. C. J. Alexopoulos, C. W. Mims and M. Blackwell; Introductory Mycology; Wiley, 1996, 4th
edition.
3. S. J. Flint, L.W. Enquist, V. R. Racaniello, and A. M. Skalka; Principles of Virology: Molecular
Biology, Pathogenesis, and Control of Animal Viruses; ASM Press, 2004, 2nd edition.
4. J. G. Black; Microbiology: Principles and Explorations, John Wiley and Sons, 2008, 7 th edition.
5. M. T. Madigan, J. M. Martinko, P. V. Dunlap and D. P. Clark; Brock Biology of
Microorganisms; Pearson Education, 2009, 12th edition.
6. J. Willey, L. Sherwood and C. Woolverton; Prescott, Harley, Klein's Microbiology; McGraw-
HillHigher Education, 2008, 7th edition.
7. K. Murphy, P. Travers and M. Walport; Janeway's Immunobiology; Taylor & Francis Publishers,
2008, 7th edition.

Reference books:
1. K. Todar, Todar's Online Textbook of Bacteriology (available free of cost at
http://textbookofbacteriology.net/).
2. R.A. Goldsby, T.J. Kindt and B.A. Osborne; Kuby Immunology; W. H. Freeman & Co, 2000,
6th edition.

Unit 1: Algorithms (7 hours)

Algorithms; asymptotic analysis of algorithms; NP complete problems; algorithm types; brute
force; divide and conquer; sorting algorithms – string matching – naïve, KMP and approximate
string matching algorithms.

Unit 2: Advanced sequence analysis (6 hours)

Dynamic programming algorithm: Introduction to PAM and BLOSUM matrices; differences
between distance and similarity matrices. Global and local pairwise alignment methods –
SmithWaterman and Needleman-Wunsch algorithms. Concepts behind multiple sequence
alignment; ClustalW, TCoffee. BLAST, sequence search, difference versions of BLAST, gapped
BLAST and BLAT.

Unit 3: Motifs and phylogeny (14 hours)

Basic concept and definition of sequence patterns, motifs and profiles, various types of pattern
representations viz. consensus, regular expression (prosite-type) and profiles. Use of Hidden
Markov model (HMM) in assigning homology. Phylogeny: sequence evolution, distance matrices,
phylogeny construction by UPGMA, neighbour joining and parsimony methods. Derivation of PAM
and BLOSUM matrices, evolution model for nucleic acids.

Unit 4: Protein structure analysis (5 hours)

Protein secondary structure calculation – DSSP, membrane topology prediction, ligand-receptor
interactions, composition of active sites in functional proteins, conformational change and activity,
allostery, effects of point mutations on proteins structure and function.
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Textbooks:
1. N. C Jones and Pavel & Pevzner; Introduction to Bioinformatics Algorithms; The MIT Press,
2004
2. P. G. Higgs and T. K Attwood; Bioinformatics and Molecular Evolution; Blackwell Publishing,
2005

Reference books:
1. A. M. Lesk; Introduction to Bioinformatics; Oxford University Press, 2002.
2. N. Gautham; Bioinformatics: Databases and Algorithms; Alpha Science, 2006.
3. D. W. Mount; Bioinformatics Sequence and Genome Analysis; Cold Spring Laboratory Press,
2001.
4. J. Bedell; I. Korf, M. Yandell; BLAST; O’Reilly Press, 2003.
5. F. J. Burkowski; Structural Bioinformatics An Algorithmic Approach; CRC Press, 2009. 6. J. M.
Keith; Bioinformatics Vol. 1, Data, sequence analysis & evolution; Humana Press, 2008.
7. R. Durbin; Biological sequence analysis; Cambridge University Press, 1998.
8. R. M. Holmes; A cell biologists’ guide to modeling and bioinformatics; Wiley Interscience,
2007.

Unit 1: Statistics – fundamental concepts (7 hours)

Data representation: Qualitative and quantitative data types, tabulation and visual display of data,
Plotting line plot, scatter plot, frequency histograms, pie-chart, heat map and 3D plots.
Statistical parameters: Mean, median, variance, standard deviation, percentile points and their
meaning. Skewness and curtosis, correlation coefficients, moments.
Probability theory: Concept of probability, probability theorems, permutations and combinations,
conditional probability, Bayes theorem, applications to bioinformatics.
Frequency distribution, discrete and continuous data types, Bernoulli trial, binomial, Poisson and
Gaussian distributions, uniform, exponential and gamma distributions.
Essentials of R statistical package, applications of bioconductor packages.

Unit 2: Hypothesis testing and error analysis (10 hours)

Random sampling, central limit theorem, confidence intervals and p-value. Testing of hypothesis,
chi-square test, t-tests, Z-tests, Welch's test, Wilcoxon-Mann-Whitney test, tests for comparing
proportions and the one way and two way Analysis of the Variance (ANOVA).
Error analysis and error estimates for formulas, Type-I and Type-II errors, power of statistical test.
Error bars on plots.
Hypothesis testing of data from biological experiments with examples.

Unit 3: Regression analysis (7 hours)

Linear regression, least square fit to a linear, polynomial and exponential curves, regression
analysis of few data sets from biological experiments.

Unit 4: Data reduction methods (8 hours)

Fundamentals of Markov chains and Hidden Markov Models, clustering algorithms. Demonstration
of these methods with bioinformatics data.
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Reference books:
1. W. W. Daniel, Biostatistics - Basic concepts and methodology for the health sciences; Wiley
Student edition, 2013.
2. R. B. D. Agostini Sr., L. M Sullivan and A. S Beiser; Introductory Applied Biostatistics,
Thomson Brooch, 2006.
3. M. R. Spiegel, J. J Schiller and R. A. Srinivasan, Probability and Statistics; Schaum's outline
Series, McGraw-Hill Companies Inc., 3rd Indian edition.
4. R. V. Hogg and E. Tanis, Probability and Statistical Inference; Pearson Education Inc, Asia,
2001.

5. Advanced C, C++ and Introduction to Java Programming S2

Advanced C (11 hours) Unit

1:
Dynamic memory allocation; function pointers; advanced data structures – list, stack, queue.

Textbooks and Reference books:

1. B. W. Kernighan and D. Ritchie; The C Programming Language; Pearson Education India, 2nd
edition, 2015.
2. E. Balagurusamy; Programming in ANSI C; McGraw Hill Education India Private Ltd, 7 th edition,
2017.
3. H. Schildt; C – The Complete Reference; McGraw Hill Education, 4th edition, 2017.

C++ Programming (11 hours) Unit 2:

Introduction to object orientation; challenges of moving onto OOP from other paradigms; OOAD
vs OOP ; How C++ supports OOP; other paradigms C++ supports; approach towards problem
solving under OOAD and OOP.

Unit 3:
Headers; directives; moving towards a class; structure of C vs class of C++; access specifiers; effect
of access specifiers at class level; creation of objects from classes; effect of access specifiers at
object level; memory space of an object; data types and data structures under C++; arrays,
vectors, string manipulation; control statements/looping; functions – different types like recursive
function, parameter passing.

Unit 4:
Objects and methods; base class vs derived class; effect of access specifiers on base class and
derived classes; method overriding; method overloading; private, public and protected
derivations; abstract class; abstract method; virtual derivations;
classic diamond derivation.

Unit 5:
Polymorphism; what is run time polymorphism
Files and file handling in C++; exception handling in C++; writing exception handlers.

Textbooks and Reference books:

1. B. J. Stroustrup; The C++ Programming Language; Addison Wesley, 4th edition, 2013.
2. H. Schildt; The Complete Reference C++; Tata McGraw Hill, 1998.
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3. B Stroustrup; Programming – Principles and Practice Using C++; Addison Wesley, 2nd edition,
2014.

Basic Java (10 hours) Unit 6:

History of Java, Features of Java, JVM, JRE and JDK.
Java Quick Start: Learning the basics of Java in comparison to C++. Object oriented programming
in Java: Classes, interfaces and packages; access modifiers; constructors; the this and super
references; inner classes and nested classes; anonymous classes. Object derivations.

Unit 7:
Garbage collection; Fundamentals of Java garbage collection, advantages, limitations.

Unit 8:
Packages and spplets; The java.lang and java.util: object class; class class and the reflection API;
dystem and tuntime classes; properties class; wrapper classes; overview of other classes. Vector,
ArrayList, LinkedList, iterator and enumeration; collections and algorithms. The javax.swing
package: GUI development using the javax.swing package: class hierarchy; working with
containers and layout managers; working with components; event handling; menu system;
drawing and painting.

Unit 9:
The java.io Package inputstream, outputstream, reader, writer, and their sub-classes; file class;
randomaccess file class, streamtokenizer. Applets: applications of applet; the applet lifecycle;
loading applets.

Textbooks and Reference books:

1. K. Arnold, J. Gosling, D. Holmes; The Java Programming Language; Addison Wesley, 4th edition,
2005.
2. H. Schildt; The complete reference Java; Tata Mcgraw Hill, 2002; 5th edition.

6. Immunology, Microbiology and Biochemistry – Laboratory P4

1. Staining of blood smears and identification of blood cell types by microscopyand flow
cytometry. 2. Studying antigen-antibody specificity by indirect and sandwich EISA,
Ouchterlony double diffusion test and immunoelectrophoresis.
3. FACS, western blotting, and immunofluorescence.
4. Demonstration of raising antibodies.
5. Purification of immunoglobulins by salt precipitation.
6. Blood grouping: Understanding multiple alleles in humans.
7. Histology experiments: sectioning, mounting and staining of different tissues from
mouse/plant/human.
8. Analysis of plant/bacterial/fungal pigments, protein and DNA using UV-Vis
spectrophotometry.9. Testing of enzymatic activity of salivary amylase using Km, Vmax, IC50,
LB plot, Dixon plot, temperature and pH.
10. Cell counting, gram staining and motility using microscopy.
11. Isolation of bacteria from environmental sources, such as soil/water/air using plate exposure
andspread plate techniques.
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12. Biochemical tests for bacterial identification: catalase, oxidase, indole, glucose fermentation,
motility and hemolysis.
13. Monitoring bacterial growth by turbidometry.
14. Screening of bacterial strains producing industrially–relevant enzymes such as amylase,
pectinase or lipase.

Textbooks and Reference books:

1. D. R. Randall, Molecular Biology Laboratory Manual, Available online
(available free of cost at https://archive.org/details/MolecularBiologyLaboratoryManual_456).
2. S. Surzycki; Human Molecular Biology Laboratory Manual; Wiley-Blackwell, 2003.
3. K. V. Chaitanya; Cell and Molecular Biology: A Lab Manual; PHI Learning Press, 2013.
4. D. Vodopich and R. Moore; Biology Laboratory Manual; McGraw-Hill Education, 2014, 10th
edition.
5. J. G. Cappuccino and C. T. Welsh; Microbiology: A Laboratory Manual; Pearson, 2016, 11th
edition.
6. Fluorescence-activated cell sorting (FACS)
https://www.youtube.com/watch?v=TDRhCWaYRsg
7. Intro to spectrophotometry https://www.youtube.com/watch?v=gzXJ5Aj52s0
8. E. Harlow and D. Lane; Antibodies, A Laboratory Manual, CSHL Press, 1988.
9. D T. Plummer; An Introduction to practical biochemistry, Tata McGraw Hill, 1988.
10. B. E Alfred, Benson's microbiological applications, 9th edition, McGraw Hill, 2004.
11. D. S. Hage and J. Cazes. Handbook of Affinity Chromatography, 2nd edition, CRC Press, 2005.

7. Advanced Bioinformatics – Laboratory P2

1. Install BLAST locally, create a database locally; use various command-line parameters to
improve search criteria, identification of false-positives and interpretation of results from
Blast, manipulating results from Blast to extract regions of sequences with significant hits.
2. Write a code to compare two sequences for similarity and homology.
3. Write a code to compute edit distances between sequences.
4. Write codes for coordinate conversion and editing.
5. Global and pairwise alignment using online and offline tools. Study the effects of different
scoring matrices and gap penalty schemes on the alignment.
6. Collate sequences of proteins based on homology, create multiple sequence alignment using
localinstallation of ClustalW.
7. Create phylogenetic tree using offline tools.
8. Extract profiles from multiple sequence alignment and compare them with conserved
structural regions in the PDB structure for a given family of proteins.
9. Locally install HMM and PFam databases. Create an HMM model using the multiple sequence
alignment, search a sequence database using the HMM model, search a gene sequence
against Pfam-A. Emit a sequence using an HMM model.
10. Protein structure analysis using open-source tools.

Textbooks:
1. I. Korf, J. Bedell and M. Yandell; BLAST: An Essential Guide to the Basic Local Alignment Search
Tool; O’Reilly Media, 2003.
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2. M. S. Rosenberg (Ed.); Sequence Alignment: Methods, Models, Concepts, and Strategies;
University of California Press, 2009.

Reference books:
1. N. C Jones and A. Pavel; Introduction to Bioinformatics Algorithms; The MIT Press, 2004.
2. P. G. Higgs and T. K Attwood; Bioinformatics and Molecular Evolution; Blackwell Publishing,
2005.
3. D. J. Russel (Ed.); Multiple Sequence Alignment Methods; Springer Science+Business Media
LLC, 2014.
4. M. Gollery (Ed.); Handbook of Hidden Markov Models in Bioinformatics; Chapman and
Hall/CRC, 2008.
Online references:
https://www.pymolwiki.org/
https://www.cgl.ucsf.edu/chimera/tutorials.html
https://www.coursera.org/learn/bioinformatics-pku#

8. Biostatistics and R Programming – Laboratory P2

1. R software installation and basic R usage

2. Mathematical operations and string manipulation
3. Basic data structures: Vectors, data frames, lists and matrices
4. Logical statements and loops: If-else statememts, for and while loops, break
5. Writing user defined functions and packages
6. Reading and writing tables and files
7. R graphics library: Line plots, histograms, pie charts, bar plots and other plots
8. Computation of statistical parameters
9. Correlation studies of data
10. Error analysis and error bars
11. Binomial, Poisson and Gaussian distrbutions and deviates
12. Demonstrations and study of Central Limit Theorem through data
13. Hypothesis testing and p-value computation
14. Parametric tests – Performing one and two parametric Z tests, family of t-tests, tests for
proportion, chi-square tests
15. Analysis of the variance – Performing one factor and two factor ANOVA
16. Non-parametric tests – Wilcoxon Mann Whitney tests, Kruskal Wallis test
17. Regression analysis: Least square linear regression with errors and non-linear regression of
data
18. Using Biostrings library for RNA and DNA sequence analysis
19. Using Excel spreadsheet for statistics calculations.
20. Using GraphPad for basic biostatistics.
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9. Advanced C, C++, JAVA – Laboratory P4

Advanced C:
1. Dynamic memory allocation (heap memory management)
2. Function pointers; (working with functions using powerful pointer techniques)
3. Advanced data structures – list, stack, queue (working with important advanced data
structures and creating efficient programs).

C++:
4. Headers; directives; structure of C vs class of C++; (skeletal code of C++ with multiple
paradigms)
5. Access specifiers; effect of access specifiers at class level; creation of objects from classes;
dffectof access specifiers at object level,objects and methods; base class vs derived class;
dffect of access specifiers on base class and derived classes; (building blocks (level 1) of OOP in
C++) 6. Memory space of an object; data types and data structures under C++; arrays,
vectors, string manipulation; (building blocks (level 2) of OOP in C++)
7. Control statements/looping; functions – different types like recursive function, parameter
passing (assignments involving division of work among functions, analysis from difference
paradigm perspective)
8. Method overriding; method overloading; private, public and protected derivations;
(advanced OOP - level 1)
9. Abstract class; abstract method; virtual derivations; classic diamond derivation;
polymorphism;
What is run time polymorphism (advanced OOP - level 2)
10. Files and file handling in C++; exception handling in C++; writing exception handlers (advanced
OOP - level 3).
11. Using C++ string and vector classes for DNA and RNA sequence manipulation, Read and
WriteFASTA/FASTQ file formats and tables, finding Open reading frames.
12. Creating C++ functions for 3D vector operations, computation of bond angles and simple
string search algorithms.

Basic Java:
13. JVM, JRE and JDK (getting first hands-on in JAVA)
14. Java quick start: learning the basics of Java in comparison to C++. Object oriented
programming in Java: classes, interfaces and packages; access modifiers; constructors; the this
and super references; inner classes and nested classes; anonymous classes. Object derivations
(assignments on building blocks of Java)
15. Fundamentals of Java garbage collection, advantages, limitations (assignments on java
memory management basics)
16. The java.lang and java.util: object class; class class and the reflection API; system and runtime
classes; properties class; wrapper classes; overview of other classes. vector, arraylist,
linkedlist, Iterator and enumeration; collections and algorithms. (hands-on assignments on
Java built-in packages)
17. The javax.swing package: GUI development using the javax.swing package: class hierarchy;
working with containers and layout managers; working with components; event handling;
menu system; drawing and painting (assignments on Java built-in packages for GUI
management and event handling)
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18. The java.io package inputstream, outputstream, reader, writer, and their sub-classes; file
class; randomaccessfile class, streamtokenizer (assignments on core building blocks for file
handling in Java)
19. Applets: applications of applet; the applet lifecycle; loading applets (assignments on co-
relating Java and web applications)

Textbooks and Reference books:

1. B. W. Kernighan and D. Ritchie; The C Programming Language; Pearson Education India, 2 nd
edition, 2015.
2. E. Balagurusamy; Programming in ANSI C; McGraw Hill Education India Private Ltd, 7 th edition,
2017.
3. H. Schildt; C – The Complete Reference; McGraw Hill Education, 4th edition, 2017.
4. B. J. Stroustrup; The C++ Programming Language; Addison Wesley, 4th edition, 2013.
5. H. Schildt; The Complete Reference C++; Tata McGraw Hill, 1998.
6. B Stroustrup; Programming – Principles and Practice Using C++; Addison Wesley, 2nd edition,
2014.
7. K. Arnold, J. Gosling, D. Holmes; The Java Programming Language; Addison Wesley, 4th edition,
2005.
8. H. Schildt; The complete reference Java; Tata Mcgraw Hill, 2002; 5th edition.

SEMESTER III
Course title L-T-P-C
1 Genomics, Transcriptomics and Proteomics 4-0-0-4 H 4
2 Data Analysis in Genomics and Transcriptomics 4-0-0-4 H 4
3 Structural Bioinformatics and Drug Design 2-0-0-2 H 2
4 Genetic Engineering and Synthetic Biology 2-0-0-2 S 2
5 (a) Introduction to Intellectual Property Law (b) Scientific Writing and 3-1-0-4 OE 4
Communication 3-1-0-4
6 Data Analysis in Genomics, Transcriptomics and Proteomics– Laboratory 0-0-2-2 P 2

7 Structural Bioinformatics and Drug Design – Laboratory 0-0-2-2 P 2

8 Genetic Engineering – Laboratory 0-0-4-4 P 4
9 Advanced JAVA and Web Applications 0-0-4-4 P 4
TOTAL 28
1. Genomics, Transcriptomics and Proteomics H4

Unit 1: Concepts of genomics (16 hours)

History of genomics; genome projects of model organisms; human genome structure and
comparative, genomics. Genomic elements, SNPs and genome-wide association studies.

Unit 2: Genome sequencing technology (10 hours)

Principle of and output from Sanger's dideoxy method versus NGS; shotgun sequencing method
and library preparations, comparative study of standard NGS methods.

Unit 3: Metagenomics and population genomics (6 hours)

 26/40
Overview of metagenomics principles, microbial and ecological aspects underlying metagenomic
experiments, applications and limitations of metagenomics, differences between metagenomics
and single-cell genomics. Definition and principle of population genomics, difference between
metagenomics and population genomics, applications of population genomics.

Unit 4: Epigenetics (11 hours)

Methylation of DNA and genetics; histone modifications, HATs and HDACs in the context of gene
expression regulation. ChIP-chip and ChIP-seq techniques; miRNA, siRNA and piRNAs. Alternative
splicing: basic concept and significance, prevalence across species and human tissues, types and
mechanisms.

Unit 5: Transcriptomics (11 hours)

Types of RNAs and the respective roles in cells. Transcriptome and techniques used for
transcriptomics; microarray and RNA-seq. Impact of transcriptomics on biology, volume of data
produced and important repositories. Comparing transcriptomics with genomics and proteomics.
Unit 6: Proteomics (10 hours)
Proteome profiling methods, 2-D electrophoresis image comparisons; yeast two-hybrid system,
protein arrays, mass spectrometry data processing and analysis; pathway analysis and identifying
protein-protein interactions with mass scale expression data.

Textbooks:
1. J. P. Tremblay and J. Paul; An Introduction to Data Structures with Applications; McGraw Hill,
1984, 2nd edition.
2. G. P. Quinn and M. J. Keough; Experimental Design and Data Analysis for Biologists;
Cambridge University Press, 2002.
3. S. Knudsen; Guide to Analysis of DNA Microarray data; Wiley, 2004, 2nd edition.
4. E. D. Hoffmann and V. Stroobant; Mass Spectrometry: Principles and applications; Wiley,
2007, 3rd edition.
5. A. Zhang, Advanced Analysis of Gene Expression Microarray Data; World Scientific Publishing,
2006.

Reference books:
1. T. A. Brown; Genomes; Bios Scientific Publishers Limited, 2002.
2. B. R. Korf and M. B. Irons; Human Genetics and Genomics; Wiley, 2013, 4th edition.
3. A. M. Lesk; Introduction to Genomics; Oxford University Press, 2012, 2nd edition.

2. Data Analysis in Genomics and Transcriptomics H4

Unit 1: Transcriptome analysis (9 hours)

Concepts in microarray data analysis: gene expression analysis using RNA-seq data, statistical
methods; relative merits of various platforms. Primers design for downstream validation; mapping
algorithms such as Burrow-Wheeler. Measuring gene, lncRNA, siRNA from RNA-seq data.

Unit 2: Genome analysis (10 hours)

Sequence assembly concepts and challenges in assembling short reads; algorithms for assembling
short reads using graph theory such as Hamiltonian cycle and de Bruijn; writing code for
assembling reads. Gene prediction and annotation; gene ontology (GO); Identification somatic and
 27/40
germline variations from genome resequence: SNPs, SNVs, translocation, copy number variation.
Concepts behind genome-wide association studies. Introduction to various applications.

Unit 3: Computational epigenomics (9 hours)

Concepts and algorithms to measure transcriptional regulation; methylation and alternative
splicing; CHiP-seq and bisulfite-seq; small RNA analysis, validation of whole-genome datasets.

Unit 4: Metagenome and metatranscriptome analysis (11 hours)

16SrRNA data analysis, clustering/phylogenetic tree based of alignment, clustering based on
composition. Concepts behind self-organizing maps, principal component and other clustering
tools. Annotation of metagenome by various properties including phage, plasmid, crispr-spacer,
anti-microbial genes.
Unit 5: Comparative genomics (9 hours)
Genome-wide annotation methods; identification of synteny between various genomes and
challenges. UCSC browser-based collation of annotation for given variants. Comparative
metagenome/metatranscriptome.

Unit 6: Proteomics analysis (8 hours)

2D gel analysis, spectrum to assembling peptide sequence, comparison with reference databases
and annotation, differential protein expression, mass-spec protein sequencing, proteome
annotation and analysis.

Unit 7: Cloud computing (8 hours)

On-demand computing, AWS, Google cloud, EC2, scalable distributed computing, hadoop,
mapreduce, docker, setting up secured accounts, pipeline creation and automation for large-scale
analysis.

Textbooks and Reference books:

1. G.P. Quinn and M. J. Keough; Experimental design and data analysis for biologists;
Cambridge University Press, 2002.
2. S. Knudsen; Guide to analysis of DNA microarray data; Wiley, 2nd edition, 2004.
3. E. D. Hoffmann and V. Stroobant; Mass spectrometry: Principles and applications; Wiley, 3 rd
edition, 2007.
4. A. Zhang; Advanced analysis of gene expression microarray data; World Scientific
Publishing, 2006.
5. N. Rodriguez-Ezpeleta; Bioinformatics for High Throughput Sequencing; Springer; 2012.
6. Y. M. Kwon and S. C. Ricke; High-Throughput Next Generation Sequencing: Methods and
Applications; Humana Press; 2011.
7. J. R. Chapman; Protein and Peptide Analysis by Mass Spectrometry, Springer, 2 nd edition,
1996.

3. Structural Bioinformatics and Drug Design H2

Unit 1: Molecules on computers (4 hours)

Brief outline on storing and retrieving molecules as images and graphs. Detailed description with
exercises on SMILES system for small molecules. Introduction to coordinate systems – fractional,
orthogonal coordinate systems, internal and cartesian coordinates representations. Applied
examples of Interconversion of different coordinate formats. PDB and NDB database overview.
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Detailed description PDB format for molecular structures. Overview of graphical representation of
molecules – ribbons, cartoons and molecular surfaces – definitions of CPK, molecular and solvent
accessible surfaces.

Unit 2: Comparing molecules (5 hours)

Introduction to Rotation matrices. Deriving 2D and 3D rotation matrices. Properties of rotation
matrices. Rotations about standard coordinate axes, internal axes of objects and any arbitrary
axis. Comparing two objects using Euler angles. Algorithms to superpose molecular structures,
detailed discussion of choice of equivalent pairs in the structures compared, root mean square
displacement (RMSD). Kabsch algorithm, contact maps and distance alignment – DALI, structure
based sequence alignment.

Unit 3: Molecular simulations and force field (11 hours)

Definitions of ab initio, semi-empirical and force field methods. Components of a force field
equation – bond stretching – Hooke’s law, Morse potential, angle bending, torsional terms,
Improper torsion and out of plane bending terms. Non-bonded interactions – deriving partial
charges, Lennard-Jones potential and parameterization. Cross terms in a force field equation.
Introduction to water models (SPC, TIP3P, TIP4P, BF and ST2) and united atom force fields.
Concepts of energy minimization and conformational sampling – conformational space and finding
minimum energy conformation, derivative and non-derivative methods. Detailed description of
simplex, steepest descent and conjugate gradient methods of energy minimization. Introduction
to Newton-Raphson methods, quasi Newton methods. Merits and demerits of various
minimization methods.

Unit 4: Homology modelling and conformational sampling (7 hours)

Concepts and algorithms related to homology modelling. Secondary structure prediction,
ChouFassman, GOR and Neural Network methods. Protein threading, twilight zone, structure
prediction, loop modelling. Principles of molecular dynamics simulations, time integration
algorithms, time steps, cut-offs and long range electrostatic interactions. Periodic boundary
conditions and particle mesh Ewald methods. Monte-Carlo simulations. Conformational sampling
– NVE and NVT ensembles.

Unit 5: Docking and drug design (5 hours)

Overview of drug discovery: Properties of a drug like molecule, structure based and ligand based
drug design. Predicting potential binding sites on a protein structure, high-throughput virtual
screening to identify lead molecules, docking algorithms. Protein-protein docking methods. Ligand
based drug design – pharmacophore mapping and QSAR studies. Lead optimization and additional
in silico validations.

Textbooks:
1. P. E. Bourne and J. Gu; Structural bioinformatics; 2nd edition. John Wiley and Sons. 2009.
2. F. J. Burkowski; Structural bioinformatics: An algorithmic approach; CRC Press. 2008.
3. A. Leach; Molecular modelling – principles and applications; Pearson Education Ltd, 2001.

Reference books:
1. P. Clote and R. Backofen; Computational molecular biology: an introduction; Wiley & Sons,
2000.
2. J. M. Keith; Bioinformatics; Vol 2: Structure, function and applications; Humana Press.
2008.
 29/40
3. A. K. Konopka and M. J. C. Crabb; Compact handbook of computational biology; Marcel
Dekker, New York, 2004.

4. Genetic Engineering and Synthetic Biology S 2

Unit 1: Tools and methods for genetic engineering (12 hours)

Restriction endonucleases, DNA and RNA modifying enzymes – types and properties Introduction
to cloning vectors pUC,BACs, YACs, shuttle vectors Overview of molecular cloning – primer design
and PCR, gene cloning strategies and construction of cDNA and genomic libraries.

Introducing DNA into yeast, mammalian and plant cells: Preparation of competent cells,
transformation and transfection techniques (chemical and physical methods). Selection, screening
and analysis of recombinants using restriction mapping, blotting and sequencing methods.
Radioactive and non-radioactive labeling of DNA, RNA and proteins, autoradiography and
autofluorography.

Unit 2: Genome editing technologies (11 hours)

Transposable genetic elements, types and significance of transposable elements in prokaryotes
and eukartyotes, mechanism and regulation of transposition and its applications in genomics.
Recombinases, Cre and FLP recombinases and their mode of action, recombination-mediated
cassette exchange (RMCE), use of site-specific recombinases in genome manipulation. Zinc Finger
Nuclease (ZFN) technology, its uses and limitations. Transcription activator-like effector nuclease
(TALENs) design and applications. Clustered Regularly Interspaced Short Palindromic Repeat
(CRISPR) and CRISPR-associated (Cas) systems in prokaryotes, application and types of
CRISPR/Cas9 technology, uses in genome manipulation and biotechnology. Successful examples of
using gene editing in gene therapy and crop improvement. Ethical issues in genome editing.

Unit 3: Synthetic networks with biological parts and devices (4 hours)

Design and engineering of Ribosome Binding Sites (RBS), promoters, repressors, activators and
transcription terminator sequences, combinatorial and synthetic promoters. Concept of biological
logic gates, circuits and devices. Design principles for transcriptional networks with targeted
behavior. Debugging and directed evolution of biological devices and systems.

Unit 4: Metabolic engineering (5 hours)

Introduction to cell metabolism, methods of flux analysis including FBA, computational tools for
whole genome metabolic model reconstruction and integrated frameworks for design of
metabolic pathways such as retrosynthesis.

Textbooks and Reference books:

1. T. A. Brown; Gene Cloning and DNA Analysis: An Introduction; Wiley-Blackwell, 2016, 7th
edition.
2. R. Mann; Genetic Engineering: Concepts, Tools and Techniques; Syrawood Publishing
House, 2006.
3. S. B. Primrose; Principles of Gene Manipulation and Genomics; Blackwell, 2006, 7th edition.
4. E. L. Winnacker; From Genes to Clones; VcH, 1987.
5. C. Kessler; Nonradioactive Analysis of Biomolecules; Springer, 2000.
6. G. M. Cooper, Robert E. Hausman; The Cell: A Molecular Approach; Sinauer Associates,
2013,
7. 6th edition.
 8. K. Turksen; Genome Editing; Springer, 2016. 30/40
9. T. Yamamoto; Targeted Genome Editing Using Site-Specific Nucleases; Springer, 2015.
10. https://www.horizondiscovery.com/gene-editing
11. http://bioinformatics.ac.cn/synbiolgdb/
12. J. O. Krömer, L. K. Nielsen, L. M. Blank; Metabolic Flux Analysis; Springer, 2014.
13. P S. Freemont, R. I. Kitney; Synthetic Biology A Primer; Imperial College Press, 2012.
14. W. Weber, M. Fussenegger; Synthetic Gene Networks: Methods and Protocols;
Humana Press, 2016.
15. G. N. Stephanopoulos, A. A. Aristidou, J. Nielsen; Metabolic Engineering Principles
and Methodologies; Academic Press, 1998.
16. H.-J. Rehm, G. Reed; Biotechnology: Legal, Economic and Ethical Dimensions;
Volume 12, Wiley, 2008, 2nd edition.

5a. Introduction to Intellectual Property Rights OE 4

Unit 1: Understanding Intellectual Property (IP) Rights (3 hours)

Overview of IP rights; history of the patent system; rationale behind the patent system;
international treaties/conventions on IPR; statutes and cases.

Unit 2: Introduction to kinds of IP laws (14 hours)

The Law of Trade Marks: Law of registered trade marks, Indian system and international context:
registrable and unregistrable marks; distinctiveness and grounds of refusal of registration; case
studies on infringement of trademark; Well known Mark
Passing off: Common Law remedies for unfair competition; geographical indications
The Law of Copyright and Designs: understanding copyright: justification for copyright law;
International conventions; the nature of copyright and the types of works and other subject-
matter protected by copyright – literary works, dramatic works, musical works, artistic works,
finematographic films and sound recordings; case studies on infringement and defences industrial
designs and the methods of protecting them

Unit 3: Strategy for IP protection and practice (20 hours)

Criteria for patenting – novelty, inventive step, industrial application; IP databases and algorithms
to search patent databases; patent and claim interpretation; scope of protection for patents;
infringement (literal and indirect infringement) and defences (experiment, research or education,
Bolar defence, government use, etc); The international patent regimes (Paris Convention; TRIPS
agreement; PCT; Budapest treaty), overview of other patent systems – USA and the EU; patenting
vs trade secret.

Unit 4: IP rights in biology and biotechnology (7 hours)

Intellectual property and biotechnology; specific challenges in this area; strategies for patenting in
this area; parallel imports; exploitation (including technology transfer); ownership, assignment
and licensing of patents; patents and spinoffs. Unit 5: Patent law practice (10 hours)
Criteria for obtaining an Indian patent; strategies for patenting; TRIPS and Patent Corporation
Treaty (PCT); patentable subject matter (India, USA, Europe) and patentability requirements;
novelty and anticipation, inventive step and related criteria; case studies on patentable subject
matter and infringement; interpretation and understanding of statutes.
 31/40
Unit 6: Workshop and discussion (10 hours)
Importance on invention disclosure; assessing the criteria for Indian patent; patentability
Requirements and biotechnology inventions; patentability searches; assessment of novelty and
inventive step; overview of FTO, landscape and invalidity analyses
Drafting of patent specification – provisional specification and complete; claim drafting;
prosecution of patents.

Textbooks and Reference books:

1. J. Pila; The Subject Matter of Intellectual Property; Oxford University Press, 2017.
2. N. S. Sreenivasulu; Intellectual Property Law- Dynamic Interfaces; Aggarwal Law House, 2017.
3. K. C. Kankanala; Fundamentals of Intellectual Property (FUN IP); Published by Dr. Kalyan C.
Kankanala, 2013.
4. K. C. Kankanala; Indian Patent Law and Practice (Oxford India Paperbacks); Oxford India
Paperbacks, 2012.
5. All (updated) statutes: Trade Marks Act 1999; Indian Copyright Act 1957; Design Act of 2000;
Patents Act 1970
5b. Scientific Writing and Communication OE 4

Unit 1: Basics of good writing (20 hours)

Brushing up grammar: nouns and pronouns; adjectives; verbs; adverbs; prepositions;
conjunctions, articles; order of words; punctuation, vocabulary; idioms; figures of speech; active
vs. passive voice, etc. Writing skills: paragraph construction; common mistakes while writing,
better sentences, story writing; tools to edit your write-up. Comprehension, expansion of
passages, precis, paraphrasing.

Unit 2: Software for handling commonly used document types (6 hours)

Introduction to proprietary and free document software. Preparing and modifying doc/docx/odt
files and ppt/odp files. Effective use of the many features of xls/xlsx/ods files. Creating, editing,
merging and splitting pdf files. Zipping files.

Unit 3: Scientific writing (14 hours)

Structure of a paper: abstract, title, introduction, methods, results and conclusions; general rules
of formatting scientific documents; writing a paper in a particular journal's style; how to cite a
publication; identifying and avoiding plagiarism.

Unit 4: Professional writing (5 hours)

Composing a variety of professional emails and letters; preparing an effective resume.
Unit 5: Effective oral presentations (5 hours)
Essential principles of a good talk; preparing to make presentations; preparing effective
powerpoint presentations; talks for different kinds of audiences.

Unit 6: Other modes of communication (14 hours)

Short accounts of scientific discoveries for the layman; social media and science communication;
using social media to transmit a scientific discovery that has influenced you.

Textbooks and Reference books:

1. N. D. V. Prasada Rao (revised); Wren & Martin's High School English Grammar and
Composition Book; S. Chand & Co. Ltd; Revised edition, 1995.
 32/40
2. T. L. H. Smith-Pearse; English Errors of Indian Students; Oxford, 5 revised edition; 1997.
th

3. J. Butcher and C Drake; Butcher's Copy-editing: The Cambridge Handbook for Editors, Copy-
editors and Proofreaders; Cambridge University Press; 4th edition, 2006.
4. P. Sebranek, V. Meyer and D. Kemper; Writers Inc: A Student Handbook for Writing &
Learning; Great Source Education Group Inc,1995.
5. R. A. Day; Scientific English: A Guide for Scientists and other Professionals. Greenwood Press;
3rd Revised edition, 2011.
6. M. Raman and S. Sharma; Technical Communication; Principles and Practice; Oxford
UniversityPress, New Delhi; 2nd Edition, 2012.
7. D. Carnegie; The Quick and Easy Way to Effective Speaking; Simon & Schuster; Reissue edition,
1990.
8. J. V. Vilanilam; More effective communication; A manual for professionals, Response Books
(SAGE Publications); 1st edition, 2000.
9. Y.N. Bui; How to Write a Master's Thesis Paperback; 2nd edition, 2013.

6. Data Analysis in Genomics, Transcriptomics and Proteomics – Laboratory P2

1. Assembling short reads from a organism using VELVET; computing N50/L50, coverage and
length of longest contig.
2. Annotate a given assembled genome using gene prediction tools including GenScan and
Augustus; BLAST the predicted genes against databases for functional annotation.
3. Mapping of short reads tfrom exome-seq data on to the respective reference genome;
identification of SNPs; annotating the SNPs using UCSC browser; subtracting and intersecting
vcf files from various samples using bedtools.
4. Mapping RNA-seq dataset onto the reference genome; extract read counts per gene using a
gtf file; compute RPKM; find out genes differentially expressed between two samples; identify
biomarker using DESeq (R package).
5. Map RNA-seq reads to the reference genome using Tophat to identify differential splice
events and fusion transcripts.
6. Assemble two transcriptomes using Trinity and compare the gene expression using cufflink,
cuffdiff family of tools.
7. Map reads from CHiP-seq experiment to the respective reference genome and identify peaks
using MACS; compare differential peaks between two biological states; compare the peaks
with respectivf gene expression profile.
8. Map reads from bisulfite-seq and identify hyper/hypo methylated sites on the genome using
methyKit; identify differential methylation between two conditions; compare methylation
profile to the respective transcriptome profile.
9. Classify the phylum using a dataset of 16SrRNA sequencing of a microbiome using QIIME;
identify differential microbial population between two samples both at the OUT level and
abundance.
10. Assemble short reads from metagenome sequencing using metaVELVET; classify the
community using 16SrRNA analysis.
11. Annotate contigs from metagenome assembly by identifying CRISPR-SPACER, phage, plasmid,
antimicrobial resistant genes.
12. Identify ICE element within a given infectious microbe.
13. Create synteny between the genomes of two related species using CoGe and other tools.
 33/40
14. 2-D electrophoretic profiling of protein samples.

Textbooks and Reference books:

1. G. P. Quinn and M. J. Keough; Experimental design and data analysis for biologists; Cambridge
University Press, 2002.
2. E. D. Hoffmann and V. Stroobant; Mass spectrometry: Principles and applications; Wiley, 3rd
edition, 2007.
3. A. Zhang; Advanced analysis of gene expression microarray data; World Scientific Publishing,
2006.
4. N. Rodriguez-Ezpeleta; Bioinformatics for High Throughput Sequencing; Springer; 2012.
5. Y. M. Kwon and S. C. Ricke; High-Throughput Next Generation Sequencing: Methods and
Applications; Humana Press; 2011.
6. Big Data Analysis for Bioinformatics and Biomedical Discoveries; CRC Press (2015); Available
at: https://www.crcpress.com/Big-Data-Analysis-for-Bioinformatics-and-Biomedical-
Discoveries/Ye/p/book/9781498724524.
7. RNA-seq Data Analysis: A Practical Approach; CRC Press, 2014; Available at:
https://www.crcpress.com/RNA-seq-Data-Analysis-A-Practical-Approach/Korpelainen-
Tuimala- Somervuo-Huss-Wong/p/book/9781466595002.
8. Wang, X. Next-Generation Sequencing Data Analysis; CRC Press, 2016.
9. A J. Link and J LaBaer; Proteomics: A Cold Spring Harbor Laboratory Course Manual; Cold
Spring Harbor Laboratory Press; 2009.

7. Structural Bioinformatics and Drug Design – Laboratory P2

Viewing, editing and analysing molecules

1. Molecular modelling using physical kits and software tools. Graphical representations of
molecules using open source software.
2. Coordinate format conversion using shell scripts or software tools. Building 3D structures of
ligands and drug like molecules. Geometrical calculations in molecules, distances, angels,
torsions, electrostatic surface, hydrophilicity, B-factor distribution etc.
3. Introduction to PDB files – editing- fixing non-standard residues and alternate conformers.
Extracting sequence from coordinates. Editing PDB files – chain ids, residue numbers etc.
4. Inducing point mutations and analyzing molecular interactions, intra and inter molecular
interactions, salt bridges and crystal contacts. First and second order hydration shell analysis.
Protein – ligand and protein-protein interactions.

Comparing protein molecules

5. Calculation of RMSD between two protein structures using C-alpha, main chain atoms, all
common atoms as equivalent pairs.
6. Domain movement analysis using DYNDOM.

Molecular simulations
7. First order and second order energy minimization, analysing short contacts before and after
minimization.
8. Homology modelling using MODELLER.
9. Molecular simulation studies in vacuo, implicit solvent as well as explicit solvent methods
using GROMACS. Analysing a molecular dynamics trajectory.
 34/40
Docking and drug design
10. Build ligand structures, creating a library of small molecules for drug screening.
Identification potential ligand binding sites on protein structures.
11. Virtual screening and docking studies using Autodock and Vina.

Textbooks:
1. P. E. Bourne and J. Gu; Structural bioinformatics 2nd edition.; John Wiley and Sons. 2009.
2. F. J.Burkowski; Structural bioinformatics: An algorithmic approach; CRC Press. 2008.
3. A. Leach; Molecular modelling – principles and applications; Pearson Education Ltd, 2001.

Reference books:
1. P. Clote and R. Backofen; Computational molecular biology: an introduction; Wiley & Sons,
2000.
2. J. M. Keith; Bioinformatics vol 2: Structure, function and applications; Humana Press, 2008. 3.
A. K. Konopka and M. J. C. Crabb; Compact handbook of computational biology; Marcel
Dekker, New York, 2004.

8. Genetic Engineering – Laboratory P4

1. Protein extraction from plant leaves and bacteria.

2. Isolation and separation of chromosomal and plasmid DNA.
3. In vitro amplification of DNA by PCR and T/A cloning in pTZ57R/T vector.
4. Transformation of bacteria and selection of recombinants by antibiotic selection and blue-
white screening.
5. Traditional cloning: restriction digestion and ligation of DNA fragments.
6. Induction of recombinant protein in E coli (via IPTG/arabinose) and validation of expression.
7. Separation of His-tagged proteins by affinity chromatography.
8. Separation of proteins by techniques such as ion-exchange and size-exclusion
chromatography.
9. Conjugation using donor and recipient E. coli strains to demonstrate horizontal gene transfer.
10. Gene sequence retrieval, analysis of regional conservation by MSA, primer designing and
restriction site analysis.
11. RNA extraction, reverse transcription PCR, and cloning cDNA.
12. Quantitative analysis of gene expression by real time PCR.

Textbooks:
1. D. R. Randall; Molecular Biology Laboratory Manual, Available online. 2009.
(available free of cost at https://archive.org/details/MolecularBiologyLaboratoryManual_456).
2. S. Surzycki; Human Molecular Biology Laboratory Manual; Wiley-Blackwell, 2003.
3. K. V. Chaitanya; Cell and Molecular Biology: A Lab Manual; PHI Learning Press, 2013.
4. D. Vodopich and R. Moore; Biology Laboratory Manual; McGraw-Hill Education, 2014, 10th
edition.
5. J. G. Cappuccino and C. T. Welsh; Microbiology: A Laboratory Manual; Pearson, 2016, 11 th
edition.
6. Bacterial Transformation Definition, Process and Genetic Engineering of E coli
https://www.youtube.com/watch?v=vdY8uCQ84_4
 35/40
7. BigDye Direct Cycle Sequencing https://www.youtube.com/watch?v=cqFTGQ_JO1c
8. Horizontal Gene Transfer in Bacteria https://www.youtube.com/watch?v=Gn3HwMkzsEk
9. https://hymanlab.mpi-cbg.de/hyman_lab/general/
10. www.bioprotocol.org

Reference books:
1. M. R. Green and J. Sambrook; Molecular Cloning: A Laboratory Manual; Cold Spring Harbor
Laboratory Press, 2012, 4th edition (Volumes 1–3).

9. Advanced Java and Web Applications P4

Advanced JAVA
Unit 1: Collections and multithreading
Collection interfaces, concrete collections, the collections framework
Creating thread and running it, multiple thread acting on single object, synchronization, thread
communication, thread group, thread priorities, daemon thread, life cycle of thread.

Unit 2: Enterprise Java Bean and Java Database Connectivity (JDBC)

Preparing a class to be a JavaBean, creating a JavaBean, JavaBean properties, types of beans,
stateful session bean, stateless session bean, entity bean.
Merging data from multiple tables: joining, manipulating databases with JDBC, prepared
statements, transaction processing.

Unit 3: Servlets
Basic Networking, URL, URI, HTTP,
Servlet overview and architecture, interface servlet and he servlet life cycle, handling
HTTP get requests, handling HTTP post requests, redirecting requests to other resources, session
tracking, cookies, session tracking with httpsession.

Unit 4: JavaServer Pages (JSP), remote method invocation and exception handling Introduction,
javaserver pages overview, a first javaserver page example, implicit objects, scripting, standard
actions, directives, custom tag libraries.
Defining the remote interface, implementing the remote interface, compiling and executing the
server and the client.
Whats an exception, writing exception handlers.

Unit 5: Bio Java An insight.

Textbooks and Reference books:

1. Anonymous; Core and Advanced Java Black Book; Dreamtech Press, 2016.
2. U. K. Roy; Advanced Java Programming; Oxford University Press, 2015.
3. Dr. Kaladhar; Bio Java – A Programming Guide; LAP LAMBERT Academic Publishing, 2012.

Web applications
Unit 6: SQL
Introduction to DBMS, RDBMS, SQL. Creating a database; altering a database; creating tables;
altering tables; dropping tables. Entity-relationship diagrams; normalization; primary keys and
foreign keys. SQL Queries, datatypes and expressions: INSERT, UPDATE, DELETE, SELECT;
 36/40
conditions using WHERE, AND and OR, sorting using ORDER BY, grouping using GROUP BY,
selecting unique records using DISTINCT. Integers, character strings, Ppoints, date; boolean
expressions, date expressions, numerical expressions. SQL operators and functions: mathematical
operators, logical operators, max(), min(), sum(), mid(), len(), round(), first(), count(), average().
Joins, views, and other miscellaneous SQL concepts.
Unit 7: Database design principles and data architecture
Introduction to normalization theory query paradigms, query languages (SQL, pSQL and mySQL)
similarity searches, approx.retrieval integrated data analysis and applications VIEWs across
databases, pathway modeling, network queries. Developing data architecture using MySQL and
oracle. Principles and developing modules on biological databases using relational system,
developing genome annotation datasets, parsing, developing tables and relational systems.

Unit 8: Overview of internet, HTML and Basic HTML Tags

Overview of the internet: Internet; web server; web browser; HTTP and HTML; domains and IP
addresses. HTML tags; pairing tags; attributes. Basic HTML Tags: html; head; body; title; headings;
paragraphs; bold, italics and underline, horizontal rule. Colour models and representations;
coloured text and background. Working with frames, images and tables: using frames; embedding
images; creating tables; formatting tables. Creating hyperlinks to other pages; creating local
hyperlinks; images as hyperlinks. Abbreviations, pre-formatted text; lists – ordered and
unordered.Forms: need, form elements.

Unit 9: XML and DTD

Need for XML; differences between XML and HTML; application of XML; XML examples. XML
basics: elements; attributes; validation. DTD: DTD declarations-internal and external; use of DTD;
DTD-XML building blocks; DTD basics: elements, attributes, entity – internal and external;
validation; examples.

Schema
Introduction; use of schema; examples; simple types: elements, attributes, restrictions, examples;
complex types: elements – empty, elements only, text only, mixed, examples; indicators: order,
occurrence, group, examples; data types: string, date, misc.

Unit 10: CGI, PHP and HTML forms

History of CGI; architecture and application of CGI and PHP. HTML forms revisited: HTML form
elements and attributes; text fields; text areas; radio buttons; check boxes; submit button; reset
button drop down boxes; how to create an HTML form. CGI environment variables; simple
responses.
Sending data to the server; GET and POST method; use of CGI.pm module.

Textbooks and Reference books:

1. T. King, G. Reese, R. Yarger; MySQL and mSQL; O'Reilly Media Publishers, 1999.
2. M. Gruber; Mastering SQL; M. BPB Publications, 2000.
3. D. Zak; CGI/Perl; Thomson Learning, 1st edition, 2002.
4. A. Silberschatz; Database system concepts; McGraw-Hill, 4th edition, 2002.
5. R. Elmasari and S. B. Navathe; Fundamentals of database systems; 5th edition, 2006.
6. J. D. Ullman and J. Widom; A first course in database systems; Pearson Education, 3 rd edition,
2008.
7. T. A. Powell; Complete reference HTML; Tata Mcgraw Hill, 1999.
8. D. Hunter; Beginning XML; Shroff Publishers & Distributors, 2000.
 37/40
SEMESTER IV
Course title L-T-P-C

1 Systems Biology 3-1-0-4 H 4

2 Fermentation and Downstream Processing 0-0-4-4 P 4
3 Project Work – Dissertation 8

4 Viva-Voce 2

TOTAL 18

Unit 1: Reaction kinetics (15 hours)

Mathematical formulation of elementary biochemical reactions, Law of mass action,
Co-operativity and Hill function, Enzymatic reaction kinetics and Michaelis-Menten approximation.

Unit 2: Non-linear dynamics (12 hours)

1D ordinary differential equations, fixed points and their stability, bifurcation, 2D flows, 2D linear
systems, 2D non-linear dynamics including 2D oscillations, parameter sensitivity analysis.

Unit 3: Biological examples of non-linear dynamics (8 hours)

Biological examples of simple gene regulation, auto-repression, population dynamics, insect
breakout model, two gene repressive model, glycolytic oscillations, heart beat.

Unit 4: Network analysis (16 hours)

Mathematics of networks: Networks and their representation, adjacency matrix, weighted
networks, bipartite networks.
Measures and metrics: Clustering co-efficient, centrality measures (degree, eigenvector). Random
graphs, metabolic networks and flux balance analysis.

Unit 5: Network analysis: end-user perspectives (10 hours)

Generation of regulatory networks using WGCNA
Generation of protein interaction networks via the String database
Comparisons and interpretations of protein-networks, pathways and regulatory networks in the
context gene/protein functions – mainly transcriptional regulation
Significance of non-coding RNAs in complex multicellular systems and visualization of gene-gene
interactions via Cytoscape
Comparison of complexity of networks and the cellular system in a typical bacterial vs. mammalian
cell

Unit 6: Relevance and generation of biological big data (3 hours)

The changing pace of data generation with time, the relevance of system biology to synthetic
biology and other applications, and discussions on current trends via selected research reports as
case studies.
Textbooks:
1. U. Alon; An Introduction to Systems Biology; Chapman & Hall/CRC Mathematical and
Computational Series 2014, 2nd Indian reprint.
2. E. O. Voit; A First Course in Systems Biology; Garland Science 2013.
 38/40
3. P. Nelson; Physical Models of Living Systems; W. H. Freeman and Company 2015, 1 st edition.

Reference books:
1. J. D. Murray; Mathematical Biology I: An Introduction; Springer, 3rd edition.
2. S. H. Strogatz; Nonlinear dynamics and chaos; Levant Books 2007, 1st edition.
3. M. E. J. Murray; Networks: An Introduction; Oxford Reprinted 2015, 1st edition.
4. IOM (Institute of Medicine); The Science and Applications of Synthetic and Systems Biology;
The National Academies Press 2011.
5. M Döring, A. Brüninghaus, R. Kollek, I. Petersen; Systems-Oriented Approaches in Biology:
System Biologist’s Narratives of Present, Past, and Future; In: Contextualizing Systems Biology.
Springer 2015.

2. Fermentation and Downstream Processing – Laboratory P 4 Basic characters, operation and

Basic character, operation, trouble-shooting of fermentors

1. Demonstration of different types of fermentors and operation characteristics.
2. Demonstration of different types of fermentation surface, submerged, solid state, single,
batch, continuous, dual or multiple fermentation.
3. Preparatory steps for fermentation: culture media sterilization, inoculum preparation and
enrichment of strains.
4. Methods of isolation and characterization of industrially important microorganism soil or
fermented food.
5. Microbial biomass production (fungi/bacteria/yeast) batch and continuous culture.
6. Production of baker’s yeast using molasses and its viability checking.
7. Production of curd with respect to microbial load and lactic acid formation.
8. Production of alcohol by fermentation from molasses and scale up from flask to lab
fermentor. Or Microbial production of lactic/succinic acid and scale up from flask to lab
fermentor
9. Microbial production of amylase and enzyme activity studyOr Use of laboratory scale
fermentors to overexpress a cloned protein

Bacterial growth dynamics

10. Study the diauxic growth. Calculation of generation time and growth rate of bacterial
culture in flask culture as well as small-scale fermentor.

Downstream processing for product purification

11. Downstream processing for the production of baker’s yeast.
12. Downstream processing for the production of alcohol by fermentation/microbial
production of lactic/succinic acid.
13. Downstream processing for enzyme/protein purification.

Fermentation and product purification

14. FPLC/HPLC based purification and quantitation of proteins or small molecules after
fermentation.
15. Characterization of purified enzyme for optimal pH, temperature, thermostability.
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16. Enzyme kinetics determining the Km and Vmax values.
Textbooks and Reference books:
1. P. C. Wankat; Rate controlled separations; Elsevier, 1990.
2. P. A. Belter and E. Cussler; Bioseparations; Wiley, 1985.
3. Product recovery in bioprocess technology; BIOTOL Series, VCH, 1990.
4. J. M. Asenjo; Separation processes in biotechnology; 1993.
5. A. Cinar, S. J Parulekar, C. Undey and G. Birol; Batch fermentation – modeling, monitoring
and control; Marcel Dekker, New York, NY, 2003.
6. R. I. Freshney; Culture of animal cells; John Wiley & Sons Inc., 1998.
7. M. A. Desai; Downstream processing of proteins: methods and protocols (methods in
biotechnology); Humana Press, 2000.
P. F. Stanbury et.al; Principles of fermentation technology; Elsevier Science, 2nd edition,
2003.
8. H. C. Vogel and C. C. Haber; Fermentation and biochemical engineering handbook:
Principles, process design and equipment; Noyes Publications, 2nd edition, 2007.