THIRD SEMESTER

Lectures-3 Tutorial-1 Credits-4

HUM-201 ENGINEERING ECONOMICS & BUSINESS ORGANIZATION

Unit I : Introduction to Economics

Introduction to Economics, its importance, principles, approaches and use of study,
Engineering and economics, Economic problems, economic good and wealth, demand
and supply, competition, monopoly, theory of firm, money and its function, theory of
money and choice, the bank and iys functions, employment and income, gross national
product, net national product consumption, savings and investment.

Unit II : Features of Indian Economy-I

Broad features of Indian Economy, Natural resources and economic development,
Infrastructure in the Indian Economy, Agriculture development, green revolution,
population, population theories, unemployment , poverty and balance regional
development. Economic growth and economic development , Indian industries,
industrials policy, industrialization in India, role , plan and pattern of Industrialization,
public vs practice sectors, economic reforms in India, India’s five year plans.

Unit III : Features of Indian Economy –II

The indigenous and modern banking system in India, reserve bank of India, monetory
and fiscal policies, financial institutions and SEBI, free trade protection, India’s foreign
trade and WTO, balance of payments, Indian currency system and foreign exchange,
foreign capital investment , foreign aid and FEMA.

Unit IV : Introduction to Business Organization –I

Concept , nature and scope of business, business and its environment, profit
maximization vs social responsibility of business, business ethics, business enterprise,
entrepreneurship, promotions, types and functions, stages in company formation, concept
of business growth, rationale and types of growth , rationale and types of growth
strategies, joint venture-definition, scope, role and problems of small business, concepts
and features of public enterprise, multinationals.

Unit V : Introduction to business Organization –II

Time value formoney, simple and compound interest , annuity , depreciation, definitions,
characteristics, life and salvage value, method of proving for depreciation, relationship
between depreciation, repairs, renewals, depletion cost, replacement , amortization and
present worth.

Books :-
1.Economics of Development & Planning Agraeal & Lal, Vikas Pub.
2. Engineering Economics Tarachand
3. Economics Samualson
4. Business Organization Shukla
 BI-201 - Discrete Structures
Lectures-3 Tutorial-1 Credits-4

Propositional and predicate calculus: Logic Propositions and logical operations truth
tables and proposition generated by a set equivalence and implication. The laws of first
order predicate logic, mathematical systems. Fuzzy sets, operations on fuzzy sets, Fuzzy
Relations, properties and operations on fuzzy relations.

Relations : definitions, graphs of relations, properties of relations, matrices of relations,

equivalence relations, Posets, Lattices , Complemented Lattices, Sub lattices.
Distributive and Modular lattices. Boolean Algebra.

Graph Theory: Notions & terminology, directed and undirected graphs, incidence and
degrees, Sub-graphs, Walks paths, cycles, circuits, components, connectedness
algorithms, shorter path algorithm. Euclidian and Hamiltonian graphs, The traveling
Salesman Problem, Trees: Spanning trees, rooted trees and binary trees.

Discrete numeric functions, Generating functions, Recursion and recurrence relation,

many faces of recursion, sequences solving a recurrence relation including non-
homogeneous finite order linear relations.

Coding Theory, Binary symmetric channel, Coding Process, decoding, error detection
and correction codes.
Vector Spaces : Linear Independence, bases, Subspaces, dimensionality, Linear
mapping, linear in-equality, inner products, norms.

TEXT BOOK :
Applied Discrete Structures for Computer Science by A Doerr and K Levasser.
Reference Books :

1. Discrete Mathematical Structures for Computer Science by B Kolman & R.C.

Busby.
2. Discrete Mathematical Structures with Application to Computer Science by
J.P.Trembley & R.P.Manohar.
3. Graph Theory by F.Harary.
4. Elements of Discrete Mathematics by C.Liu.
5. Graph Theory with Application to Computer Science by N.Deo.
 BI-202 - Microbiology

Lectures-3 Tutorial-1 Credits-4

Introduction and historical perspective -Discovery of the microbial world, controversy

over spontaneous generation, role of microorganisms in transformation of organic matter
and in the causation of diseases, development of pure culture methods, enrichment
culture methods.

Methods in Microbiology -Principles of microbial nutrition, Culture media, Theory and

practice of sterilization, Pure culture techniques, Enrichment culture techniques for
isolation of chemoautotroph, chemoheterotrophs and photosynthetic microorganisms.

Prokaryotic structure and function -functional anatomy of bacteria: cell envelope, cell
wall, cytoplasmic membrane, capsule, surface appendages, cytoplasm and cytoplasmic
inclusions.

Microbial nutrition and growth -The definition of growth, mathematical expression of

growth, growth curve, measurement of growth and growth yields, synchronous growth,
continuous culture, culture collection and maintenance of cultures.

Overview of basic metabolism and microbial nutrition Metabolic diversity among

microorganisms -Photosynthesis in microorganisms; Role of chlorophylls, carotenoids
and phycobilins; Calvin cycle; Chemolithotrophy; hydrogen- ironnitrite- oxidizing
bacteria; nitrate and sulfate reduction; methanogenesis and acetogenesis; Fermentations -
diversity, nitrogen fixation.

Books & References

1. General Microbiology by R.Y. Stanier, J.L. Ingraham, M.L.Wheelis and P.R.

Painter. Publisher : Macmillian
2. Microbiology VI Edition by M.J. Pelczar, E.C.S. Chan and N.R. Kreig.
Publisher : Tata McGraw Hill
3. Principles of Microbiology by R.M. Atlas. Publisher Wm C. Brown Publisher.
4. The microbes – An Introduction to their Nature and Importance by P.V.
Vandenmark and B.L. Batzing. Publishers : Benjamin Cummings.
5. The Microbial World by Roger Y. Stanier. Publisher : Prentice Hall
6. Microbiology by Tortora, Funke and Chase. Publisher Benzamin & Cummings
7. Principles of Fermentation Technology by Salisbury, Whitaker and Hall.
Publisher : Aditya Books Pvt. Ltd.
8. Industrial Microbiology by Casida. Publisher : New Age International
9. Industrial Microbiology by Prescott and Dunn. Publisher : C.B.S. Publishers
 BI-203 - Biochemistry

Lectures-3 Tutorial-1 Credits-4

Introduction, aims and scope Chemical foundations of Biology -Properties of

water, acids, bases and buffers, covalent bonds, Non-covalent interactions in
biological systems.
Introduction to biomolecules - Carbohydrates -Sugars; Polysaccharides;
Glycoproteins -structure and function. Vitamins and Coenzymes Lipids -
classification, structure and function. Lipids and biological membranes, Transport
across cell membranes; Lipid linked proteins and lipoproteins. Proteins -Amino
acids and peptides -classification, chemical reactions and physical properties.
Introduction to protein structure and function. Enzymes - Introduction to kinetic
and catalytic mechanisms of enzymes; Regulation of enzyme activity; Effects of
physical parameters on enzyme activity. Nucleic acids -nitrogenous bases,
nucleotides, types, structure and properties of nucleic acids Separation
techniques for biomolecules.
Metabolism and bioenergetics -First and second law, free energy and chemical
equilibrium, Organic reaction mechanisms, Design of metabolism -concept of
t:1Go, ATP-ADP cycle. Cellular energy transactions -role of mitochondria and
chloroplast
Carbohydrate metabolism -glycolysis pathway and reactions, Glycogen
breakdown and synthesis, control of glycogen metabolism, glycogen storage and
its disease Citric acid cycle -Overview, Metabolic sources of Acetyl Co-A,
enzymes and regulation, The amphibolic nature of the Citric acid cycle Electron
transport chain and oxidative photophosphorylation -mitochondrion and electron
transport, phosphorylation and control of ATP production Gluconeogenesis, The
glyoxylate pathway, Biosynthesis of Oligosaccharides and glycoproteins,
Pentose phosphate pathway

Books & References

1. Cellular Biophysics I & II by Thomas F. Weiss 1995, Publisher : MIT Press

2. Biochemical calculations by I.H. Segal. Publisher : John Wiley and Sons
3. Biochemistry by C.K. Mathews, K.E. Van Holde and K.G. Ahern. Publisher:
Benjamin / Cummings.
4. Devlin’s Textbook of Biochemistry with Clinical correlations. Publisher : John
Wiley and Sons Inc.
5. Principles of Biochemistry by A.L. Lehninger, D.L. Nelson, M.M. Cox.
Publisher : Worth Publishing
6. Harper’s Biochemistry by K. Robert, M.D. Murray, D.K. Granner, P.A. Mayes
and V.I. Rodwell. Publisher : McGraw-Hill/Appleton and Lange.
7. Biochemistry by L. Stryer. Publishers : W.H. Freeman and Company
8. Tools of Biochemistry by T.G. Cooper. Publisher : John Wiley and Sons
Inc.
 BI-204- Data Structure & Algorithm using ‘C’

Lecture – 3 Tutorial – 1 Credits-4

Introduction to data structure, Primitive data structure, Static and Dynamic storage,
Sub-algorithm function, procedure, parameters, parameter passing call by value, call
by ref. Introduction to Algorithm analysis for time and space requirement, Rate of
growth and Order of notation Basic time and space analysis of an algorithm, String
Manipulation and Pattern matching Markov Algorithm Primitive and composite
function, string manipulation Application - Text handling only, Abstract Data Types.

Non-linear data structures - Concept and Technology of Storage structure of arrays

row major column major Stacks Definition, concepts, operation and application of
Stacks, Recursion and Polish notations. Queue, Priority Queue definition concepts
operation and application of Queue, Dqueue.

Linear data structures - Pointers and linked allocation concepts and operations on
singly linked list, circular linked list, doubly linked lists Associative list Application
of linked linear list, Polynomial Manipulation, Multiple precision arithmetic.

Trees - Definition and concepts storage representation and Manipulation of Binary

tree conversion of general tree to Binary trees, Threaded Binary tree, Multi-linked
structure, sparse matrices, Height balance tree, Multi weight tree, B tree, B+ tree,
graph and their representation Matrix representation of graph Breadth first and depth
first search, shortest path algorithm.

Internal Sorting External sorting - Selection sort, Bubble sort Merge sort quick sort,
radix sort, Tape sorting; Shell sort, Poly phase and Oscillating sorting, (taking best
case/worst case examples) sorting on Disk, Searching-Sequential search, Binary
search, Search trees, Hash table methods.

BOOKS :

1. Data Structure - Tremble & Sorenson

2. Data Structure in `C’ Language : by Tanenbaum
3. Data Structure by Bhagat Singh
4. Data Structure by Horowitz & Sohani
 BI-205 - Introduction to Bioinformatics

Lecture – 3 Tutorial – 1 Credits-4

Introduction, chronological history of Bioinformatics, evolution of Bioinformatics,

Objectives of Bioinformatics, Importance of bioinformatics, Bioinformatics in business,
future scope of Bioinformatics.

Bioinformatician and bioinformaticist, role, need and importance of Biology, Computer

Science, mathematics and information technology in bioinformatics, biological
classification and nomenclature, life in space and time.

Introduction, information networks, protein and genome information resources, DNA

sequence analysis, pairwise alignment techniques, multiple alignment techniques,
secondary databases, analysis packages.

The dawn of sequencing, the biological sequence or structure deficit, human genome
project and its status, homology and analogy, web browsers, European molecular biology
network, national centre for biotechnological information, specialized genomic resources.

Building a sequence search protocol, practical approach for structural and functional
interpretation, introduction to analysis package, commercial databases, softwares and
comprehensive packages, internet packages specializing in DNA and protein analysis.

BOOKS:

1. Introduction to Bioinformatics – T.K. Attwood and Parry Smith

2. Introduction to Bioinformatics – Arthur M. Lesk
3. Fundamental Concepts in Bioinformatics – Krane and Raymer
 FOURTH SEMESTER
MTH-251 - Numerical Techniques

Lecture – 3 Tutorial – 1 Credits-4

Newton forward and backward formulae, Everett and Bessel Interpolation formulae,
Lagrange’s, Hermite and spline interpolation. Implementation of these method in C.

Integration: Weddle, Gauss-Legendre, Monte Carlo methods of integration, Differential

Equations: Modified Euler, Runge-Kutta methods, Predictor-Corrector methods- Milne
Adams-Bashforth methods, Accuracy of Runge-Kutta and Milen’s methods.

Solution of algebraic and transcendental equation: Newton-Raphsan

method, Newton’s method for multiple roots, Lin-Barstow’s and Graffe’s method for
complex roots, Solution of Non-linear equations.

Non-linear Equations: Solving simple non-linear equations. Programs of simultaneous

and non-linear equations, Simultaneous Equations: Gauss elimination and Pivot, Gauss-
Siedel and Gauss-Jacobi iteration techniques. Invertion of Matrix by Cholesky’s method.

BOOKS:

1. B.S. Grewal : Numerical Algorithms, Khanna Publications.

2. Krishnamutrhy & Sen : Numerical Algorithms EWP.

3. M.K. Jain & Iyengar: Numerical Methods for Scientists & Engineers
 BI-251 - DATA BASE MANAGEMENT SYSTEM
Lecture – 3 Tutorial – 1 Credits-4

Introduction to database: Data Abstraction, Data `Models, Basic concepts of database:

Data Independence DML, DCL, DDL and structure of Data Base Management System.
Entity relationship diagram : Basic and Advance concepts Application of ER
diagram in designing database system. Relational Algebra, Tuple Relational Calculus

SQL, QUEL, Domain relational calculus, Integrity, Referential, Domain constraints,

functional dependency, Assertions, Triggers, Query processing and Query optimization
and Embedded and Dynamic SQL

Database design issues, Normalization 1NF, 2NF, 3NF, 4NF, BCNF and 5NF, live
database design problem. Security and Integrity: Security and Integrity: Use of SQL
for specifying Security and integrity. Authorization, view, Encryption. Storage structure
indexing and hashing. Different type of file organization.

Transaction & concurrency control, Schedules, testing, serializability, Lock based

Protocol, Time stamp protocol, validation technique, Multiple granularity, Multi-version
scheme Insert and delete operation, Crash recovery, Log based recovery, buffer
management checkpoints, shadow paging. Object oriented databases

Distributed database structure, Design transparency and Autonomy, Distributed Query

processing Recovery, commit protocol Deadlock handling, Multidatabase system,
Parallel database concept and related issues, Web interface to database, Database System
Architecture.

TEXT BOOK:

Database System Concept By Henry F. Korth

ABRAHAM SILBER SCHATZ
REFERENCE BOOK:

(i) Database System Concept By C.J. Date.

(ii) Database System By Aho. Ullman.
(iii) Database Systems By Rob, Coronel.
 BI-252 – Biological Sequence Analysis

Modeling Molecular Evolution; Background of DNA, An Introduction to Probability,

Conditional Probabilities, Matrix Models of Base Substitution, Phylogenetic distances.

Pairwise Alignment ; Introduction, The Scoring Model, Alignment algorithm, Dynamic

Programming with more Complex Models, Heuristic Alignment Algorithms, Linear
Space Alignment.

Marcov Chains and Hidden Marcov Models; Marcov Chains, Hidden Marcov Models,
Parameter Estimation for HMMs, HMM Model Structure, More Complex Marcov
Chains, numerical Stability of HMM Algorithms.

Multiple Sequence Alignment Methods ; What a Multiple Alignment Means, Scoring a

Multiple Alignment, Multidimensional Dynamic Programming, Progressive alignment
Methods, multiple Alignment by Profile HMM Training.

References:
Fundamental Concepts in Bioinformatics – Krane and Raymer.
Introduction to Bioinformatics – T.K. Attwood and Parry Smith.
Biological Sequence Analysis. By R. Durbin, S, Eddy, A, Krogh, G.
Mitchison.
Mathematical Models in Biology; An Introduction. By Elizabeth S. Allman
and John A. Rhodes.
 BI-253 - Modelling and Simulation

Lecture – 3 Tutorial – 1 Credits-4

System Models : Concept, environment, stochastic activities, continuous and discrete

simulation, Model Type- static, dynamic and probabilistic models. Growth and Decay
model examples. Principles of Mathematical modeling, static physical model, system
modelling.

Continuous systems models, differential equations, analog computers, analog methods,

hybrid computer, analog simulations, continuous system simulation, languases, CSMP III
hybrid simulation, feedback system, simulation of an interactive system, real time
simulation.

Discrete system simulation, probability concepts in simulation, random number

generations and their testing, stochastic variable generation, fixed time stop versus event
to event model.

Simulation of queuing systems, arrival pattern, Poisson arrival pattern, exponential

distributions, hyper-exponential distribution, service times, simulation of a single-server
queue, normal distribution, measures of queues.

Simulation languages, continuous and discrete simulation languages, block-structured

continuous simulation languages, GPSS, SIMSCRIPT, SIMULA, factor in selection of a
discrete simulation language.

BOOKS:

1. Gordan – Simulation and Modeling - PHI.

2. System simulation and modelling - Narsingh Dev - PHI
 BI-254 - Languages, Algorithms & Tools for Bioinformatics

Lecture – 3 Tutorial – 1 Credits-4

Sequence comparison, Sequence similarity search, computational models for sequence

analysis, sequence alignment, longest common subsequence problem, alignment with gap
penalties, space efficient sequence alignment, Scoring matrices for similarity search
PAM, BLOSUM etc.

Comparing a sequence against a database, method of sequence database similarity search,

BLAST, FASTA, and other methods for comparing databases of sequence and patterns-
PSI-BLAST, PHI-BLAST & PROBE etc.

Methods of optimal alignment, distance and similarity, motifs & patterns, evolutionary
basis for sequence alignment, Smith Waterman, Needleman and Wunsch dynamic
programming algorithms, progressive alignment methods, alignments presentation
methods, multiple sequence alignment (MSA), practical aspects of MSA, tools and
applications of MSA.

Programming languages – Java, Biojava, HTML, BioXML etc.,

Bioinformatic Tools – Genscan, Rasmol, Cn3D, Phylip, Oligo, Clustal W, ALSCRIPT,

MOLSCRIPT etc.

BOOKS:
1. Biojawa – Tisdall and James.
2. The comlete reference –Java2, Patrick Naughton et al.
 BI-255 - Biomathematics

Lecture – 3 Tutorial – 1 Credits-4

Growth and Decay Models in Biological; Population in Natural and Laboratory

Environments. Intoxicants and Nutrients. Stability Analysis Interacting Population with
Predation; Basic Models and Their solutions.
Epidemic Models; Deterministic models with and without Removal, General

Deterministic Models with removal and Immigration. Control of an Epidemic,

Stochastic Epidemic Model without removal.

Models in Genetics; Basic models for Inheritance, Further Discussion of Basic Model

for Inheritance of Genetic Characteristics, Models for Genetic Improvement:

Selection and Mutation, Models for Genetic Inbreeding

Pharmaco-Kinetics, Compartmental Models in terms of System of Differential

Equations. Bio-Diffusion. Diffusion of Drugs. Trans-Capillary Exchange. Oxygenation
and Deoxygenating of Blood. Cardio Vascular Flow Patterns. Temperature regulation in
Human Subjects.
Curve Fitting and Biological Modeling; Fitting curves to Data, The Method of
Least Squares, Polynomial curve Fitting.

Text Books:

1. Mathematical Biology- J. D. Murray

2. Mathematical Models in Biology and Medicine. By J. N. Kapur
3. Mathematical Models in Biology; An Introduction. By Elizabeth S.
Allman and John A. Rhodes
4. Linear Models in Biology (Pharmacy): By Cullen
5. Bio-Physics
6. Bio-FluidDynamics : By F. C. Fung
7. Bio-Fluid Mechanics: By F. C. Fung
8. Introduction to Mathematical Biology: By Rubinov.
 FIFTH SEMESTER
BI-301 - Optimization Techniques and Graph theory

Lecture – 3 Tutorial – 1 Credits-4

Linear Programming, Mathematical Model, Assumptions of Linear

Programming, simplex Method, Degeneracy, Applications, Duality, Dual Simplex
Method, & Algorithm Assignment Problem. Hungarian Method & its Algorithm.

Transportation Problem, Integer Programming :- Gomorra’s method, Branch and Bound

techniques. Integer Programming Algorithm, Dynamic Programming:- Bellman’s
Principle of optimality, Dynamic Programming Approach, optimal subdivision problem,
Decomposition, Applications in linear programming.DPP Algorithms.

Queuing Theory : Queuing problem and system, Transient and steady state
distributions in queuing system, Poisson process, Exponential process, classification of
queuing models, Model I (M/M/1) : (∝/FCFS), Model -II General Erlang Queuing model,
Model - III (M/M/1) : (N/FCFS), Model - IV (M/M/S) : (∝/FCFS), Algorithms.

Graph Theory : Finite and Infinite Graphs : Basic concepts Incidence , Degree , Isolated
Vertex , Pendent Vertex , Null Graphs .
Path and Circuits : Isomorphism , SubGraph , Walk’s Path and Circuits , Connected
Graph , Disconnected Graphs and Components. Euler’s Graphs , Hamiltonian Paths and
Circuits,Directed Graph , Undirected Graph,Adjacency Matrix, Incidence Matrix,Shortest
path algorithms , Colouring , Chromatic numbers

Games Theory : solution of games with saddle points, Minimax-Maxmin principle for
Mixed strategy games, Dominance, to reduce size of game, Graphical method, solution of
(mxn) game by simplex method & Algorithms, Job sequencing : Processing n jobs
through 2 machines, Processing n jobs through 3 machines & Algorithms, PERT – CPM:
introduction, applications, network diagram representation, Determination of the critical
path, updating.

TEXT BOOKS :
(i) S.D. Sharma Operations Research, Kedarnath Ramnath & Co. Meerut
(ii) P.K.Gupta & D.S.Hira Operations Research, S.Chand & Co.
(iii) Kantiswaroop Operations Research, S.Chand & Sons.
(iv) Gillet, B.E. Introduction to operations Research - A Computer Algorithm
Approach, McGraw Hill.
(v) Introduction to operations Research, 7/e by Hillier. TMH.
 BI-302 - Software Engineering

Lecture – 3 Tutorial – 1 Credits-4

Software characteristics, components, S/W process models, prototyping, RAD,

evolutionary models, formal methods, models, management spectrum. Software Project
Planning – objectives, scope, resources, project estimation, decomposition techniques,
empirical estimation models, make buy decision. Risk Management – S/W risks, risk
identification, risk projection, monitoring and management

Project Scheduling and Tracking – Basic concepts, task set for s/w project, selecting
tasks, refinement, scheduling, project plan. Quality assurance – meaning, movement,
reviews, measures of reliability, SQA plan, System engineering : Hierarchy, strategy
planning, area analysis, product engineering, three feasibilities. Analysis Concepts –
requirement analysis, principles, prototyping, specification, review

Design Concepts and Principles- Software design and engineering, design process,
principles, concepts. Effective modular design. Design Methods- Data design,
architectural design & process, transform mapping. Design steps, transaction mapping,
interface design and guide lines. Analysis Modeling – elements of analysis model, data
modeling, functional modeling, behavioral modeling, data dictionary.

Software Testing Methods- Fundamentals, Test case design, white box testing, basic path
testing, control testing, black-box testing. Testing strategies-strategic approach, criteria for
completion testing, unit testing, validation testing, system testing. Software quality-
McCall’s quality factor, FURPS, Framework for software matrices.

Object-Oriented software engineering- Management of Object-oriented software

projects. Object-oriented analysis, domain analysis, object-oriented design- issues,
landscape, system design process, task data and resource management. Object-oriented
testing- Testing OOA and OOD models, unit and integration testing. Software Reuse
management issues, reuse process, domain engineering building reusable components,
economics of reuse.

TEXT BOOKS:
1. R. Pressman- Software Engineering- A Practitioner’s Approach Mc GrawHill.
2. Soummerville- Software Engineering, PHI
3. P. Jalote- Software Engineering, Narosa.
4. A Leon & M Leon- Fundamentals of s/w engineering, Vikas.
 BI-303 - Biological Databases and their Management

Lecture – 3 Tutorial – 1 Credits-4

Introduction to database: Data Abstraction, Data `Models, Basic concepts of

database: Data Independence DML, DCL, DDL and structure of Data Base
Management System, Entity relationship diagram: Basic and Advance
concepts Application of ER diagram in designing database system. Relational
Algebra, Tuple Relational Calculus

Database design issues, Normalization 1NF, 2NF, 3NF, 4NF, BCNF and
5NF, database design problem. Security and Integrity: Use of SQL for
specifying Security and integrity. Authorization, view, Encryption. Storage
structure indexing and hashing. Different type of file organization.

Transaction & concurrency control, Schedules, testing, serializability, Lock

based Protocol, Time stamp protocol, validation technique, Multiple
granularity, Multi-version scheme Insert and delete operation, Crash recovery,
Log based recovery, buffer management checkpoints, shadow paging. Object
oriented databases.

Distributed database structure, Design transparency and Autonomy,

Distributed Query processing Recovery, commit protocol Deadlock handling,
Multidatabase system, Parallel database concept and related issues, Web
interface to database, Database System Architecture

Introduction to biological databases, Nucleic acid sequence data banks:

Genbank, EMBL, DDBJ, TrEMBL, GenPept, nucleotide sequence databank,
cDNA databanks, AIDS Virus sequence data bank, rRNA data bank, Protein
sequence data banks: NBRF-PIR, SWISSPROT, Signal peptide data bank etc.

REFERENCE BOOKS:

(i) Database System Concept By C.J. Date.

(ii) Database System By Aho. Ullman.
(iii) Database Systems By Rob, Coronel.
 BI-304 - Computational Phylogenetics

Lecture – 3 Tutorial – 1 Credits-4

Introduction to trees, concept of evolutionary trees, phylogenetic trees, relationship of

Phylogenetic analysis to sequence alignment, genome complexity and Phylogenetic
analysis, sequence alignment based on evolutionary model.

Methods of phylogenetic analysis like distance matrix, Fitch and Margoliash method,
maximum parsimony method, maximum likely hood method, unweighted pair group
method with arithmetic mean (UPGMA), neighbour-joining method and character based
methods, evaluation of phylogenetic methods.

Converting sequence similarity to distance scores, choosing an outgroup, correcting of

distances between nucleic acid sequences for multiple changes and reversions,
comparison of protein sequences and protein encoding genes, comparison of open
reading frames by distance methods.

Reliability of Phylogenetic predictions, problems and complications from Phylogenetic

analysis, automated tools for Phylogenetic analysis, bootstrapping and jack knife
replicates, jumbling sequences.

Books:
1. Bioinformatics – Sequence and Genome analysis By David W. Mount
2. Molecular Evolution and Phylogenetics – Nei and Kumar.
 BI-305 – Computational Genomics & Proteomics

Lecture – 3 Tutorial – 1 Credits-4

Genes, genomes, proteins , proteomes, eavesdropping on the transmission of genetic

information, picking out genes in the genomes, genomes of Prokaryotes, genomes of
Eukaryotes, the genome of Homo sapiens (human genome), genome analysis.

Genome information resources, specialized genomic resources, the genome of the

bacterium Escherichia coli, the genome of the archaeon Methanococcus jannaschii, the
genome of the simplest organism Mycoplasma genitalium, mapping between the maps,
high-resolution maps.

Single nucleotide polymorphisms (SNPs), protein coding genes, repeat sequences,

genetic diversity in anthropology, genetic diversity and personal identification, genetic
analysis of cattle domestication, Evolution of genomes, horizontal gene transfer,
comparative genomics of Eukaryotes, genomes of Saccharomyces cervisiae (baker's
yeast), Caenorhabditis elegans, Drossophila melanogaster (Fruit fly), Arabidopsis
thaliana etc.

Genome rearrangements, the breakpoint graph, expected reversal distance, signed

permutations, interleaving graphs and hurdles, algorithm for sorting by reversals,
transforming men in to mice, duality theorem and genomic distance.

Different types of structures of proteins, protein classification, tools for proteome

analysis, different structural proteins, methods of structure prediction (known folds and
unknown folds), prediction of protein functions, Proteome analysis, computational
proteomics, peptide sequencing, peptide identification problem, spectral alignment of
peptides, spectral convolution.

BOOKS:
1. Bioinformatics – A practical guide to the analysis of Genes and Proteins –
Baxevanis and Fancis Ouellette, Wiley Interscience, New York.
2. Computational Molecular Biology – An algorithmic approach – Pavel A. Pevzner
3. Modern Genetic Analysis :Integrating Genes and Genomes - AnthonyJ.F.
Griffiths,William M. Gelbart,Jeffery H. Miller
 BI-306 - Data Mining and Data Warehousing

Lecture – 3 Tutorial – 1 Credits-4

Need for data warehouse, definition, goals of data warehouse, Data Mart, Data warehouse
architecture, extract and load process, clean and transform data, star, snowflake and
galaxy schemas for multidimensional databases, fact and dimension data, Designing fact
tables. partitioning, partitioning strategy – horizontal partitioning, vertical partitioning,

Data warehouse and OLAP technology, multidimensional data models and different
OLAP operations, OLAP Server: ROLAP, MOLAP and HOLAP. Data warehouse
implementation, efficient computation of data cubes, processing of OLAP queries,
indexing OLAP data.

Data preprocessing, data integration and transformation, data reduction, Discretization

and concept Hierarchy Generation, Data mining primitives, Types of Data Mining, Data
Mining query language, Architectures of data mining. data generation & Summarization
based characterization, Analytical characterization, Mining class comparisons, Mining
descriptive statistical measures in large data bases.

Mining Association Rules in large databases: Association rule mining, single dimensional
Bookan association rules from Transactional DBS, Multi level association rules from
transaction DBS, multidimensional association rules from relational DBS and DWS,
Correlation analysis, Constraint based association mining.

Classification and Prediction : Classification by decision tree induction, Back

propagation, Bayesian classification, classification based in association rules, Prediction,
classifier accuracy, Cluster analysis, partitioning and hierarchical methods, Denrity based
methods Grid based methods, web mining, Temporal and spatial data mining.

Text Books:

1. Building Data Ware House by W.H.Inmon, John Wiley & Sons

2. Data warehousing by S . Anahory and D.Murray, Pearson Education, ASIA
3. Data Mining Concepts & Techniques by Jiawei Han & Micheline Kamber;
Harcourt India PVT Ltd.
4. TMH Oracle 8i Building Data Ware Housing by Michall Corey, M.Abbey, I
Azramson & Ben Taub.
5. Data Mining, Practical Machine Cearing tools & techniques with Java by I.H.
Whiffen (Morgan Kanffmen)
6. Data Ware Housing with oracle by Sima Yazdanri & Shirky S. Wong
7. Data Mining Techniques by A.K. Pujari , University Press.
 SIXTH SEMESTER
BI-351 - Machine Learning

Lecture – 3 Tutorial – 1 Credits-4

Foundation of pattern recognition, Biological data in digital symbol sequences, genomes

diversity, size and structure, information content recognition of biological sequences,
probabilistic modelling and inferences, statistical mechanics.

Machine learning foundation, Bayesian modelling, Bayesian inference and induction,

machine learning algorithms, dynamic programming, gradient descent, Markov chain,
evolutionary and genetic algorithms.

Introduction to neural networks, backpropagation, sequence encoding and output

interpretations, sequence correlations, prediction performance evaluation, Hidden
Markov models, likelihood and basic algorithms, applications of HMMs.

Probabilistic graphical models in bioinformatics, probabilistic models of evolution,

substitution probabilities and evolutionary rates, optimal trees and learning, stochastic
grammars and linguistics, applications of grammars to biological sequences.

BOOKS:
1. Bioinformatics – Machine learning approach by Baldi & Brunak
2. Statistical methods in Bioinformatics: an introduction – Ewens and Grant.
 BI_352 - COMPUTER NETWORKS
Lecture – 3 Tutorial – 1 Credits-4

Use of computer networks; Type of networks; Network software: protocol hierarchies.

Design; issues for the layers, interface and services, types of services, services
primitives; Reference models: The OSI reference model, TCP/IP reference model,
Example networks: The Internet, Novel Netware, Window NT.

Physical layer: Transmission media: magnetic media, Twisted pair, Base band /
broadband coaxial cable, fiber optics; Analog, digital, wireless transmission;
Transmission and switching; ISDN system architecture, Satellite versus fiber;
Terminal handling. The Data link layer Design issues: services provided, framing, Error
control, flow control; Error detection and correction; Error correcting codes, Error
detecting codes; Elementary data link protocols: Unrestricted simplex, simplex stop and
wait, simplex protocol for noisy channels; sliding window protocols: one bit, go back n,
selective repeat; DLL in the Internet.

Medium access sub layer :

Static/dynamic channel allocation in LANs and MANs; multiple access protocols:
ALOHA, carrier sense, collision free, limited contention, wireless LAN; IEEE standard
802 for LANs and MANs: Ethernet; token bus, token ring, comparison of 802.3, 802.4,
802.5; Bridges: bridges from 802.x and 802.y, Transparent bridges, High speed LANs.
Network Layer :
Design issues, Internet organization of network layer; Rating algorithms: optimality
principle, shortest path, flooding, Flow - bared, hierarchical, multicast, broadcast;
congestion control algorithms: General principle, prevention, Traffic shaping, choke
packets, load shading etc.; Internetworking: How network differ, connectionless
internetworking, Tunneling, internetworking, fragmentation, firewalls; Network layer
in the Internet: IP protocol, IP address, subnets, OSPF, BGP, FTP, telnet, email. etc.
Network Programming :
Basically Sockets : Overview, Unix Domain Protocols, Overview, Unix Domain
Protocols, socket-address, socket-system calls, reserved ports, passing file descriptions,
I/O asynchronous & multiplexing, socket implementations.

TEXT BOOK:
1. Computer Networks by Leon & Garcia
2. Local Area Networks by KeiserWindows Network Programming by
R. Davis, Add Wesley
3. Unix Network Programming by S. Davis, PHI
4. Computer Networks by A.S. Tanenbaum
 BI-353 - Genetic Engineering:

Lecture – 3 Tutorial – 1 Credits-4

Introduction to genetic engineering, enzymes involved in manipulation of genetic

material, restriction endonucleases, DNA polymerase, DNA ligases, Kinases, vectors
used in genetic engineering, plasmids and cosmids, phages, transposons, yeast artificial
chromosome.

Detection of target DNA, labeling of nucleic acids, labeling techniques, nick translation,
end labeling, primer extension, random priming methods, concept and use of linkers and
adapters, radioactive and non-radioactive phosphatases, reverse transcriptase.

Chemical synthesis of oligonucleotides, exonucleases, ribonucleases and proteases,

genomic and cDNA library, DNA foot printing, polymerase chain reaction (PCR) and its
applications, site directed mutagenesis, cell fusion techniques, southern and northern
blotting, in vivo expression techniques.

Applications of genetic engineering, gene transfer in animal and plant cells, generations
of novel plants and animals, diagnostics of genetic expressions, protein and metabolic
engineering, ethical issues and patenting of genetically modified objects.

BOOKS:
1. Biological sequence analysis: Probabilistic models of proteins and nucleic
acids – Durbin R., et al.
2. Genomics: the science and technology behind human genome project, Cantor
and Smith
 BI-354 - AI and Soft Computing techniques

Lecture – 3 Tutorial – 1 Credits-4

Introduction to AI various types of production system. Analysis of problem for

developing an AI system. Problem characteristics, Production system and its
characteristics. BFS, DFS, and Different heuristic search techniques- Hill climbing,
Ascent Hill climbing, Constraint satisfaction. A* algorithm AO* Algorithm,

Knowledge Representation: Representation and mappings, Approaches to knowledge

representation, Issue in knowledge representation, Knowledge representation using
predicate logic resolution, and unification algorithm. Knowledge representation using
rules procedural versus declarative knowledge logic programming, Forward and back
ward reasoning .Symbolic reasoning under uncertainty monotonic and non monotonic
reasoning. Semantic nets, Frames Conceptual dependency.

Natural language processing and study of its different phases, Game planning Minimax
Search procedure, Adding Alpha Beta cut-offs, Iterative deepening Planning components
of planning system Goal stack planning Nonlinear and Hierarchical planning.

Statistical reasoning Probability and Bayes Theorem Certaininty factor and rule base
system Baysiean Networks Dempster Shafer Theory Fuzzy Logic. Understanding Parallel
and distributed AI Psychological Modeling, Parallelism in reasoning system.

Introduction to learning, various learning techniques Introduction to Expert System .

Connectionist Model Hopfield networks leraning in Neural Networks Application
Common Sense Common Sense ontologies and Memory organizations

TEXT BOOKS :

1. AI by Rich & Knight.

2. AI by Norwing.
 BI-355 - Advanced algorithms for Bioinformatics

Lecture – 3 Tutorial – 1 Credits-4

Introduction: Analyzing algorithm, growth of functions, asymptotic notation, standard

notation and common functions. Divide and Conquer approach: Performance analysis
of binary search, quick sort, merge sort, heap sort.

Recurrences: Substitution method, iteration method, master method, proof of master

theorem. Red-Black Trees: Properties of red-black trees, Rotations, insertion, deletion.
Augmenting Data Structures: Dynamic order statistics, How to augment a data
structure.

Dynamic Programming: Elements of Dynamic Programming, Matrix –chain

multiplication, optimal binary search tree. Greedy Algorithm: Elements of the greedy
strategy, Huffman codes, A task scheduling problem, Amortized Analysis: Aggregate
method, accounting method, potential method.

Introduction: Graph and Minimum Spanning Trees, Kruskal’s and prim’s algorithm.
Single-Source Shortest Paths: The Bellman-Ford algorithm, Single-Source Shortest
Paths in directed acyclic graphs, Dijkstra’s algorithm.
All-Pairs Shortest Paths: Shortest paths and matrix representation, The Floyd-Warshall
algorithm.

Sorting Networks: A bitonic sorting network, merging network, sorting network.

Matrix Operations: Properties of matrices, Strassen’s algorithm for matrix
multiplication. Linear Programming: Stander and slack forms, Formulating problems as
linear programs, The Simplex algorithm. Introduction to NP-Completeness.

TEXT BOOKS :

(i) Fundamentals of Computer Algorithms Ellis Horowitz, Sartaj sehni galgotia

publications.
(ii) Introduction to Algorithms Cormen, Leiserson, Rivets, PHI.
 SEVENTH SEMESTER
BI-401 - THEORY OF COMPUTATION

Strings Alphabets and language, Finite state systems, Determinstic finite

automata with ∈ moves, Two way finite automata, finite automata with
output, Mealy & Moore machines

Conversion of NDFA to DFA. Removal of ∈ transition from ∈ – NDFA.

Pumping lemma for regular set, Closure properties of regular set,
Decision algorithm for Regular set, Myhill Ners de theorem and
initialization of finite automata Regular Expression and Language.

Properties of Regular languages, Context free grammar, Chomsky Normal

form, Greibach Normal form, Pumping lemma for CFL, Application for
CFL of Pumping lemma. Closure properties of CFL ,CYK algorithm,
YACC, Introduction to LR grammar.

Pushdown automata: Informal description Definition Equivalence of

PDA’s and CFL’s Prop Turning machine construction. Modification of
turning machine.

Undecidability Universal turning machine and an undecidable problem

Rice theorem Greibach theorem. Recursion finite theory. Chomsky
hierarchy, Unrestricted Grammar. Context sensitive Language
Computational Complexity theory, Intractable problem.

TEXT BOOK:

1. Introduction to Automata Theory Language and Computation,

By John
2. E. Hopcraft & Jeffary D. Ullman
3. Introduction to Automata Theory Language and Computation,
By John E. Hopcraft Jeffary D. Ullman & Rajeev Motwani.
4. Theory of Computer Science K.L.P. Mishra, N.
ChandraShekaran
 BI-402 - Computer Graphics

Lecture – 3 Tutorial – 1 Credits-4

Graphic Systems : Refresh CRT, raster-scan displays, DVST, plasma displays, LCD,
Input devices : functions provided by input devices, basic working of these input
devices, image scanners, touch panels, Input modes, request mode, event mode.

Output Primitives : Points, lines, DDA, Bresenham live & circle drawing algorithm,
ellipse generation. Filled area Primitives : scan line polygon fill algorithm, inside outside
tests, boundary fill algorithm. Line width, color, color and gray levels, character
attributes.

Two-dimensional Geometric Transformation: Basic transformation, translation, rotation,

scaling, fixed point scaling, general scaling direction. The viewing pipeline, window
viewpoint transformation. Line clipping algorithms.

Three Dimensional concepts : Polygon surfaces, plane equation, curved lines and
surfaces, quadric surfaces, spline representation, spline specification. Bezier curves and
surfaces, B-splines and surfaces, Displaying spline curves and surfaces, Horner’s rule.

Three Dimensional transformation and viewing methods : 3 D transformations, viewing

co-ordinates, transformation from world to viewing co-ordinates, parallel and perspective
projections, Back face detection, depth-buffer and A-buffer methods.

TEXT BOOK :

1. Computer Graphics by D.Hearn and M.P. Baker

2 Computer Graphics - A programming approach by Harriyton.
3. Procedural Elements of Computer Graphics by Roger.
4. Three Dimensional Computer Graphics by Folley and Dam
 BI-403 - Chemoinformatics & Drug Design

Lecture – 3 Tutorial – 1 Credits-4

Basics of biochemistry, biochemical structure of protein molecules, Introduction to

cheminformatics, history of cheminformatics, use of cheminformatics, evolution of
cheminformatics, future scope of cheminformatics, chemical information source.

Introduction to drug discovery, areas influencing drug discovery, important parameters in

drug discovery, technologies and strategies in drug discovery, cell cycle – key to drug
discovery, introduction to pharmacogenetics and pharmacogenomics, applications of
pharmacogenetics and pharmacogenomics.

Drug life cycle, drug development time lines, definition of drug discovery, stages of drug
discovery, strategic issues in drug discovery, emerging approaches to drug design and
discovery, strategy to identify possible drug target molecules.

Computer aided drug design, methods of computer aided drug design, ligand design
methods, docking algorithms and programs, drug design approaches, absorption,
distribution, metabolism, and excretion (ADME) property prediction, computer based
tools for drug design.

BOOK:
1. Introduction to Chemoinformatics by Andrew R. Leach, Valerie J. Gillet
2. Introduction to Computational Chemistry by Frank Jensen
3. Targeted and Controlled Drug Discovery - S.P.VYAS and R.K.Khar
4. Bioinformatics – Genomics, proteomics, and drug discovery, Rastogi et al.
 Elective-I
BI-411. Biomolecular Structure Interaction and Dynamics

Lecture – 3 Tutorial – 1 Credits-4

Prokaryotic gene expression, operons – positive & negative regulation, sigma

Factors, Initiation, elongation and termination of transcription – template & enzyme
Properties, Eukaryotic RNA pdymerase I, II & III transcribed genes, promoter &
regulatory sequences, transcription factors, Techniques – foot printing, Reporter genes.

Organisation of globin, immunoglobulin, HLA, rRNA and 5 sRNA genes, processing of

RNA and Proteins - Transport and Stability, stress & hormones regulated gene expression
Organization of human genome. RFLP, Fingerprinting, RAPDs, Microarrays, ESTs.

Computational methods for pathways and systems biology, databases of metabolic

pathways, Kyoto Encyclopedia of Genes and Genomes (KEGG), analysis of pathways,
Glycolysis, signaling pathways, genetic pathways.

Metabolic network properties, metabolic control analysis, simulation of cellular activities,

modelling and simulation environment for biochemical and genetic processes, E-cell,
general framework for spatial modelling and simulation of cellular physiology, V-cell.

BOOKS:
1. Biological sequence analysis: Probabilistic models of proteins and nucleic
acids – Durbin R., et al.
2. Genetic Data Analysis – Weir B.S.
3. Molecular Modelling by Andrew R. Leach
 BI-412 - Modelling Gene Mapping & Sequencing

Lecture – 3 Tutorial – 1 Credits-4

Computational gene mapping and gene hunting, genetic mapping, physical mapping,
sequencing similarity search, gene prediction, mutational analysis, comparative
genomics, introduction to restriction mapping and map assembly, gene prediction
methods, gene prediction tools, gene expression.

DNA double digest problem, multiple solutions to double digest problem, alternating
cycles in colored graphs, physical maps and alternating Eulerian cycles, transformations
in Eulerian cycles, partial digest problem, probed partial digest problem, homometric
sets.

Gene mapping, mapping with unique and non-unique probes, optical mapping, interval
graphs, mapping with restriction fragment fingerprints, Lander-Waterman statistics,
screening clone libraries, radiation hybrid mapping.

Introduction to sequencing, overlap, layout and consensus sequencing concepts, double-

barreled shotgun sequencing, shortest superstring problem, some other problems and
approaches, finishing phase of DNA sequencing.

DNA arrays, sequencing by hybridization (SBH), positional sequencing by hybridization,

SBH and the shortest superstring problem, SBH and the Eulerian path problem,
probability of unique sequence rearrangements, string rearrangements, design of DNA
microarrays, fidelity probes for DNA arrays.

BOOKS:
1. Techniques in Quantification and Localization of Gene Expression - Bruce K.
Patterson.
2. DNA Sequencing by Brown T.A., IRL press Oxford.
3. Mathematics of Genome analysis – Percus, Jerome K., Cambridge Univ. Press.
 BI-413 - Proteomics and Transcriptomics

Lecture – 3 Tutorial – 1 Credits-4

Protein classification, alpha-helix, beta-sheet, loops and coils, classes of protein structure,
viewing protein structure, protein structure classification databases, alignment of protein
structures, dynamic programming, distance matrix alignment (DALI), fast structure
similarity and significance of alignments.

Evolution of protein structures, Protein structure prediction, use of sequence patterns for
structure prediction, protein stability and folding, the side chains, Ramachandran plot,
protein stability and denaturation, hydrophobicity and its applications.

Computational proteomics, the peptide sequencing problem, learning Ion types, scoring
paths in spectrum graphs, peptide sequencing and antisymmetric paths, peptide
identification problem, spectral alignment and convolution.

Approaches from proteomics to genomics, importance of transcription, large scale protein

analysis, tools and techniques in proteomics and transcriptomics, protein-protein
interaction, post-translational modifications, Ab Initio approaches for protein prediction,
protein function prediction, protein prediction from a DNA sequence.

BOOKS:
1. Introduction to computational molecular biology – Setubal and Meidanis.
2. Genes VII – Lewin B., Oxford University Press.
 Elective-II
BI-421 – Perl/ Bio Perl

Lecture – 3 Tutorial – 1 Credits-4

Introduction to perl Unix basics, Editors Data structure (scalar , Array, hash),Control
structure & File handle,Regular Expression Modules,Introduction to Bioperl Bioperl
classes

References:
1. Perl Ground up Mike Macmillan, Tata Macgrawhill Publishing.
2. Programming Perl , Larrywall, O'Reilly publisher.
3. Perl Developemnt , Kobes Randy,Wainwright Peter, Shroff Publishers
4. Perl programming for Bioinformatics, Harshwardhan P. Bal, 2003,Tata McGraw-Hill
Publishing company Ltd.
 BI-422 – Molecular modelling

Lecture – 3 Tutorial – 1 Credits-4

Basic principle behind theoretical modeling, Building small molecules, and

polymers, Force field
Energy minimization Grid search method, Quantum chemical methods basic
assumptions, postulates, on symmetrical, symmetrical and ab initio methods
Potential energy surface and systematic, grid and line search methods, Molecular
graphics and surfaces basic principles, Use of ISIS draw, Use of Rasmol, Use of
MolMol, Use of Hyperchem

References:
1. Dynamics of Proteins and Nucleic Acids by J. Andrew McCammon and Stephen C.
Harvey Cambridge University Press, 1987
2. Computer modeling of Biomolecular Interactions
V.Kothekar (kothekar@hotmail.com) available directly from the author)
3. Molecular mechanics and dynamics , Brief Guide to Molecular Mechanics and
Quantum Chemical Calculations,
W. J. Hehre, J. Yu, P. E. Klunzinger and L. Lou, 1998.
4. Molecular Mechanics across Chemistry.
Anthony Rappe and Carla Casewit,
5.Molecular Dynamic: Application in Molecular Biology
by Julia M. Goodfellow, Ed.CRC Press Inc., 1990
6. Molecular Modeling : Principles & Applications
Andrew R. Leach, Prentice Hall
 BI-423 ALGORITHM ANALYSIS AND DESIGN
Lecture – 3 Tutorial – 1 Credits-4

Introduction: Analyzing algorithm, growth of functions, asymptotic notation, standard

notation and common functions. Divide and Conquer approach: Performance analysis
of binary search, quick sort, merge sort, heap sort.

Recurrences: Substitution method, iteration method, master method, proof of master

theorem. Red-Black Trees: Properties of red-black trees, Rotations, insertion, deletion.
Augmenting Data Structures: Dynamic order statistics, How to augment a data
structure.

Dynamic Programming: Elements of Dynamic Programming, Matrix –chain

multiplication, optimal binary search tree. Greedy Algorithm: Elements of the greedy
strategy, Huffman codes, A task scheduling problem
Amortized Analysis: Aggregate method, accounting method, potential method.

Introduction: Graph and Minimum Spanning Trees, Kruskal’s and prim’s algorithm.
Single-Source Shortest Paths: The Bellman-Ford algorithm, Single-Source Shortest
Paths in directed acyclic graphs, Dijkstra’s algorithm.
All-Pairs Shortest Paths: Shortest paths and matrix representation, The Floyd-Warshall
algorithm. Maximum Flow : Flow networks, The Ford-Fulkerson method, Max-flow-
min-cut theorem. Push –relabel algorithm.

Sorting Networks: A bitonic sorting network, merging network, sorting network.

Matrix Operations: Properties of matrices, Strassen’s algorithm for matrix
multiplication. Linear Programming: Stander and slack forms, Formulating problems as
linear programs, The Simplex algorithm. Introduction to NP-Completeness.

Number-Theoretic algorithms: The Chinese remainder theorem, The

RSA public-key cryptosystem.

TEXT BOOKS :

(i) Fundamentals of Computer Algorithms Ellis Horowitz, Sartaj sehni galgotia

publications.
(ii) Introduction to Algorithms Cormen, Leiserson, Rivets, PHI.
 EIGHTH SEMESTER
BI-451 - Medical Informatics

Lecture – 3 Tutorial – 1 Credits-4

Introduction, history of medical informatics, prospects of medical informatics, hospital

information and management system, computerized physician order entry, health and
disaster management plan,

Medical expert systems, computer based patient records, polyclinic module, computer
assisted medical and patient education, three dimensional imaging, virtual endoscopy

Three dimensional navigation systems, surgical simulations, volume image data file,
computer assisted surgery (CAS), merits and demerits of CAS, virtual environment,
materials and methods for virtual environment

Telecommunication based medical systems, telemedicime and tele surgery, internet and
its relay chat, internet grateful med (IGM).

BOOK:
1. Medical Informatics – A primer By Mohan Bansal
2. Bioinformatics basics applications in biological science and medicine, Rashidi
et al.
3. Biomedical Signal Analysis - Rangaraj M. Rangayyan.
 BI-452 - Neuroinformatics

Lecture – 3 Tutorial – 1 Credits-4

Introduction: Structure and functions of Neurons, passive electrical properties of

neurons, signal spread, principles of electrical circuits, the cable equation, electrical
models of real neurons, ion permeability and membrane potential at equilibrium: the
Nernest equation, the Nernest plank equation.
Ion pumps and homeostasis: sodium and potassium, the sodium pumps, the
potassium pumps, calcium, anions, the regulation of pH, action potential, Hadgkin
Huxley experiments, Hadgkin Huxley model, the mechanism of action potential.
The structure and function of voltage gated channels: structure of sodium and
potassium channels, the channel pore, mechanism of activation and inactivation, the
diversity of voltage gated channels: sodium channel, potassium channel, calcium channel.
Pre Synaptic mechanism of synaptic transmission, gap junctions, electrical
synapses, modulation of electrical synapses, chemical synapses and the calcium
hypothesis.
Excitatory transmission, Acetyl choline and cholinergic transmission, glutamate
and glutametergic transmission, inhibitory transmissions, structure of GABA receptor
and Glycine receptor.

Books references:

1. Molecular and cellular physiology of neurons by Gordon L. Fain.

2. Brain facts by Candle.
 Elective-III
BI-461 -STATISTICAL COMPUTING
Lecture – 3 Tutorial – 1 Credits-4

Probability Theory- Sample spaces, events and probability, some rules of

probability, conditional probability, independent events and baye’s theorem.
Non-linear regression, multiple correlation and regression.

Random Numbers: Algorithms for generation of random numbers, discrete

random variables, acceptance and rejection techniques. Random Variables
and Distributions-Random variables, continuous random variables,
probability density functions. The discrete uniform distributions, Binomial,
Poisson, Hyper geometric distributions. Continuous probability distributions,
uniform, exponential and Normal distributions.

Sampling Distributions- Distribution of mean, finite populations Chi -

square, that, the F distributions, order statistics.

Hypothesis Testing-Testing of statistical hypothesis, Null hypothesis, tests of

hypothesis and significance, one failed proportions, Chi-square, t, z and F
tests, Losses and risks.

Analysis of Variance- One way and two-way analysis Programming -

Students must be encouraged to develop programs in C for correlation and
regression, standard deviation, testing of hypothesis etc. Using standard
package like SPSS.

TEXT BOOK:

Mathematical Statistics by J.E. Freund and R.E. Walpole

REFERENCE:

1) Probability and Statistics with reliability queuing and Computer

Science Applications by K.S. Trivedi.
2) Introduction to Mathematical Statistics by F. Kreyzic
3) Statistical Analysis: Computer Oriented Approach by A.A. Affi
4) Statistics- Schaum’s Series - By M.R. Spiegel
 BI-462 - UNIX AND ITS INTERNALS
Lecture – 3 Tutorial – 1 Credits-4

Introduction to Unix operating system, system structure and operating system services,
Buffer cache: buffer headers, structure of the buffer port, scenarios for the retrieval of a
buffer, reading and writing disk blocks. Advantage and disadvantage of the buffer cache.
Internal representation of the files: I nodes, structure of a regular file, directories,
conversion of a path name to an i-node, super block, i-node assignment to a new file,
allocation of disk block.

System calls for the file system: Open, read, write, file and record locking, l-seek, close,
file creation, creation of special files, change directory and change root, change owner
and change mode, STAT AND FSTA, pipes, dup, mounting and un mounting file
systems link, unlink, file system abstractions, file system maintenance.

Structure of processes: Process states and transitions, layout of system memory, the
context of a process, saving the context of a process, manipulation of the process address
space, sleep; Process control: process creation, process termination, signals shell system
boot and init process.

Process scheduling and System call for Time, Memory management policies and I/O
subsystem and I/O related concepts in UNIX

Interposes communication available facilities in UNIX, Multiprocessor systems,

(Semaphore, messages etc.) Introduction to distributed UNIX system.

TEXT BOOK

1. Design of UNIX Operating System By Maurice J. Back

REFERENCE BOOK

1) UNIX Utilities by Tare

2) UNIX Operating System BY Subhajit Das
 BI-463 - WINDOWS PROGRAMING AND VISUAL C++

Lecture – 3 Tutorial – 1 Credits-4

Introduction to Windows Program. Message processing in Windows Programming.

Message boxes and Menu and Accelerators. Dialog Box. Creating Icons, Cursor and
Bitmaps.

Introduction to Child Window Controls. Check boxes, Static control, Radio Buttons,
Scroll bars, Advance Window Controls : Toolbars up down controls, Spin control,
Progress bar, Tree view, Tab controls. Text and Font.

Working with Graphics, Consoles, Multitasking Process and Threads. Clipboard Drag
and Drops, Advance features of Windows Programming GDI Metafiles, Sound API,
DLL.

Visual C++ Basic: Introduction, Building a Basic Application, SDI and MDI, View
Document Architecture Using Microsoft Foundation Class (MFC) Library, Visual C++
resources: Application Wizard, Accelerators and Menus, Toolbars

Visual C++ And Database Management: MFC programming without View Document
Architecture,. Data Access Objects (DAO) versus Open Database Connectivity (ODBC),
Database Building Overview, Building a Database Application using ODBC, Building a
Database Application Using

BOOKS :

(i) Windows Programming , by Charles Petzold, Microsoft process.

(ii) Windows Programming, by Herbett Schildts .
(iii) VC++, by Murray, TMH.
(iv) Introduction to VC++, by Steve Holzner.
 Elective-IV

BI-471 - Molecular Imaging

Lecture – 3 Tutorial – 1 Credits-4

Overview of Protein & DNA Structure

Protein Structure Determination by X-ray diffraction: Isolation,
purification & crystalisation of proteins, Refinement of the Structures,
Crystal symmetry methods of structure determination
NMR Techniques for protein structure determination: 1D NMR, 2D
NMR (COSY & NOSY)
Imaging of Apoptosis
Imaging cell death in vivo and advances in the imaging of programmed
cell death
Applications of Molecular Imaging in Humans
Recent literature for New application of Molecular Imaging

References:

1. Introduction to Protein Structure, Branden & Tooze, Garland Publishing, Inc,

New York
2. Biophysical Chemistry, Part- I (The Conformation of Biological
Macromolecules) By: Charles R. Cantor and Paul R. Schimmel W.H. Freeman
and Company, New York
3. Recent Research Papers
 BI-472 - NEURAL NETWORKS AND FUZZY LOGIC
Lecture – 3 Tutorial – 1 Credits-4

Introduction:- Models of Neuron, Neural Networks viewed as directed grephe of

Feebdrck, network architectures, knowledge representation, applications of neural
network.
Learning Processes:- Error correction learning, memory based learning, Hebbian
learning competitive learning, Bottzmonn learning credit assignment problem, learning
with teacher learning without a teacher, learning tasks.

Memory Adeptation, Stastical neture of learning process, stastical learning theory

probably approximately correct model of learning,.
Single Layer Perceptions:- Adaptive Fillering problem, unconstrained
optimization techniques, linear least square fillers, lern-mean-square algorithm, learning
curves, learning rate anhealing techniques.
Perceptron, perceptron convagence theorem relation between the perceptron and
bayes classifier for gaussian enviroment.

Multi-leyer Perceptorns:- Some priteminaries, back-propagation algorithm, summary of

back propogation algorithm, XOR problem, Heuristic for making the back propogetion
algorithm perform better.
Output representation and decision rule, Computer experiment, Geature detection,
back-propagation and differentation, Hessian matrix, generalization, approximation of
functions virties and limitations of back-propagetion learning, accelerated convergence of
back-propogtion learning, converction networks regularization theory.

Supervized learning on Posed Hyper-surface reconstruction problem Cover’s

theorem on seperability of patterns interpolation problem regulerization network,
generalized radial basis function networks, XOR problem. How to build a support vector
machine, for paltern recognization.

Supervised learning on Posed. Hyper-surface recon struction problem. Cover’s

theorem on seperability of patterns interpolation problem regularization network,
generalized radial basis function networks, XOR problem. How to build a support vector
machine, for pattern reorganization.

TEXT BOOK:

Neural Network, Simon Haykin, Pearson Education Association

 BI-473 - Systems Biology

Lecture – 3 Tutorial – 1 Credits-4

Introduction to Systems Biology Microarray : microarray surfaces,targets and

probes, manufacturing, microarray detection and gene expression profiling Mass/Flux
Balance Analysis Systems Approach to Metabolic Networks and Protein-Protein
Interaction Networks Modeling Complex Biological Systems Approach to Numerical
Simulation of Regulatory Pathways Pharmaco-kinetics

References:
Latest Research papers