S.R.M INSTITUTE OF SCIENCE AND TECHNOLOGY

(DEEMED UNIVERSITY) S.R.M. ENGINEERING COLLEGE

DEPARTMENT OF B.TECH BIOINFORMATICS BATCH 2004 - 2005

CURRICULUM I Year – 1

st Semester

SUB CODE SUBJECT NAME L T P C

TThheeoorryy

MA 111 Mathematics-I for Biotechnologists 3 1 0 4

LE 101 English-I 3 0 0 3

PH 101 Physics-I 3 0 0 3

CY 101 Chemistry-I 3 0 0 3

GE 101 Basic Engineering-I 4 0 0 4

GE 103 Basic Engineering-II 4 0 0 4

PPRRAACCTTIICCAALLSS

PH 103 Physics Laboratory 0 0 2 1

CY 103 Chemistry Laboratory 0 0 2 1

GE 105 Computer Practice 0 0 3 2

ME 101 Workshop Practice 0 0 3 2 Total 20 1 10 27

I Year – 2nd

Semester

SUB CODE SUBJECT NAME L T P C

Theory

MA 142 Mathematics-II 3 1 0 4

CY 152 Chemistry-II 3 1 0 4

CS 156 Computer Programming (C&C++) 3 0 2 4

BT 102 Biochemistry 3 0 0 3

BT 104 Microbiology 3 0 0 3

GE 108 Biology (Common for all branches) 2 0 0 2

GE 106 Value Education 1 0 0 1 PRACTICALS

GE 104 Engineering Drawing 1 0 4 3

CY 156 Chemistry Laboratory 0 0 3 2 Total 19 2 9 26

II Year – 3rd

Semester

SUB CODE SUBJECT NAME L T P C

TThheeoorryy BI 201 Molecular Biology & Genetics 3 1 0 4

BI 203 Biophysics 3 0 0 3 BI 205 Bioinformatics 3 1 0 4

BI 207 Introduction to Data Structures 3 1 0 4

BI 209 Java Programming 3 1 0 4

LE201/203 Language(Phase-I) 2 0 0 2

PPRRAACCTTIICCAALLSS

BI211 Java Programming Laboratory 0 0 3 2

BI213 Basic Biotechnology Laboratory 0 0 4 2 Total 17 4 7 25

II Year – 4th

Semester SUB CODE SUBJECT NAME L T P C

TThheeoorryy

MA 262 Biostatistics For Bioinformatics 3 1 0 4

BI 202 Biological Databases and Gene Sequencing 3 1 0 4

BI 204 Genomics 3 0 0 3

BI 206 Bioinformatics Algorithms 3 0 2 4

BI 208 Introduction to Database Management Systems 3 1 0 4

BI 210 PERL Programming 3 0 0 3

LE 202/204 Language (Phase-II) 2 0 0 2

PRACTICALS

BI 212 PERL Programming Laboratory 0 0 3 2

BI 214 Biocomputing Laboratory - I 0 0 3 2 Total 20 3 8 28

3rd Year – 5th

Semester

SUB CODE SUBJECT NAME L T P C

Theory

BI301 Proteomics and Transcriptomics 3 0 0 3

BI303 Internet programming 3 1 0 4

BI305 Data mining and Data Warehousing 3 0 0 3

BI307 Molecular Phylogeny and Evolution 3 1 0 4

BI309 Medical Informatics 3 0 0 3

BI311 Structural biology 3 0 0 3

GE301 Personality Development – I 0 0 1 1 Practical

BT311 Genetic Engineering Laboratory 0 0 3 2

BI315 Internet Programming Laboratory 0 0 3 2

Total 18 2 7 25

3rd Year – 6th

Semester

SUB CODE SUBJECT NAME L T P C

Theory

BI300 Metabolomics and Metabolic Engineering 3 0 0 3

BI302 Chemoinformatics 3 1 0 4

BI304 Molecular Mechanics 3 1 0 4

BI306 Computational Neuroscience 3 1 0 4

BI308 Computer Aided Drug Designing 3 0 0 3

GE302 Personality Development – II 0 0 1 1

Elective I 3 0 0 3 Practical

BT208 Immunology laboratory 0 0 3 2

BI310 Drug designing laboratory 0 0 3 2

Total 18 3 7 26

4th Year – 7th

Semester

SUB CODE SUBJECT NAME L T P C

Theory

BI401 Genetic Algorithm 3 1 0 4

BI403 Molecular Dynamics 3 1 0 4

BI405 Pharmacogenomics and Pharmacogenetics 3 0 0 3

BI407 Immunoinformatics 3 0 0 3

Elective II 3 0 0 3

Elective III 3 0 0 3 Practical

BI409 Biocomputing Laboratory II 0 0 3 2

BI411 Mini Project 0 0 6 3

Total 18 2 9 25

8th

Semester

SUB CODE SUBJECT NAME L T P C

Theory

BI400 Total Quality Management 3 0 0 3

Elective IV 3 0 0 3

Elective V 3 0 0 3 Practical

BI402 Project 0 0 16 8

BI404 Comprehension 1 0 0 1

Total 10 0 16 18

Total credits to be earned for the award of the degree: 200

Group I Electives

SUB CODE SUBJECT NAME L T P C

BI350 Image Processing 3 0 0 3

BI352 Genetic Engineering 3 0 0 3

BI354 Artificial Intelligence 3 0 0 3

BI356 Immunology 3 0 0 3

BI358 Neural Networks 3 0 0 3

Group II Electives SUB CODE SUBJECT NAME L T P C

BI450 Microarray – Technique and applications 3 0 0 3

BI452 Protein engineering 3 0 0 3

BI454 Bioconfinement of Genetically Modified Organisms 2 0 2 3

BI456 Bioprocess Principles 3 0 0 3

BI458 Biodiversity and Management for Biotechnology 3 0 0 3

Group III Electives

SUB CODE SUBJECT NAME L T P C

BI451 Pattern Recognition Techniques 3 0 0 3

BI453 Fuzzy logic 3 0 0 3

BI455 Computer Graphics 3 0 0 3

BI457 Advanced Java Programming 3 0 0 3

BI459 3D modeling & Animation 3 0 0 3

Group IV Electives

SUB CODE SUBJECT NAME L T P C

BI460 Management for Information Technology 3 0 0 3

BI462 Nanobiotechnology 3 0 0 3

BI464 Biopython 3 0 0 3

BI466 Microbial genomics 3 0 0 3

BI468 Systems biology 3 0 0 3

Group V Electives

SUB CODE SUBJECT NAME L T P C

BI461 Simulation and Modelling 3 0 0 3

BI463 Microfluidics 3 0 0 3

BI465 Evolutionary Computing 3 0 0 3

BI467 Plant genomics 2 0 0 3

BI469 Natural Language Processing 3 0 0 3

SCHEME OF EXAMINATION

Passing Minimum Course Duration In Hours

Internal Marks

External Marks

Total

External Aggregate

All Theory And Practical Courses

3 hrs. 30 70 100 35 50

Project Work 100 100 200 50 100

Comprehension 50 50 100 25 50

Seminar 100 -- 100 -- --

I SEMESTER

LE101 ENGLISH L T P C 3 0 0 3

PURPOSE To provide an adequate mastery of technical and communicative English Language training primarily, reading and writing skills, secondarily listening and speaking skills. INSTRUCTIONAL OBJECTIVES To provide language training to the engineering students which will enable them to understand and acquire knowledge in technical subjects. UNIT I LISTENING 5

1. Listening Comprehension – Listening Practice – Hints on Listening –Practice Questions 2. Note Taking – Note Taking Strategies

UNIT II SPEAKING 7

• Expressing Opinions (agreement / disagreement) – Offering Suggestions Technical Definition - Defining – Describing Objects - Exercise

• Audio equipment : Types of Pronunciation – Word stress / social context, science and technology context-sentence stress and intonation.

UNIT III READING 7

• Skimming – Scanning -close reading – Reading Comprehension – Transferring Information - Exercise – An unseen passage should be given and questions may be asked in the form of True or False statements, MCQ, short answers.

• Transcoding : Interpreting tables, flow charts UNIT IV WRITING 12

• Grammar – Parts of Speech(advanced) – prefixes and suffixes – Preposition + relative – Tense forms – Active and Passive voice – Abbreviations – punctuation - Exercise

• Technical Report Writing – Lab Report - Exercise

• Art of Writing – Written Language – Rules for effective writing – Technical Essay Writing - Exercise

• Letter Writing – Formal Letters – Letter to a News paper – Letter Inviting Dignitaries – Letter of Application – Placing an Order – Curriculum Vitae – Invitation – Exercise

• Note Making – Strategies – Organising Notes - Exercise

• UNIT V FOCUS ON AND COMMUNICATION AND “COMPUNICATION” 9

a) Communication – Basic Concepts – Process – Kinds – Routes – Forms – Factors – Barriers – Triangles – Communication (Communicate through Computers – Power Point & Tele Conferencing).

b) Dialogue Writing – How to write a dialogue - Enact dialogues between two or three people

c) Mini Project Report Writing – Mini Project may submitted during course work – Example Topics like Internet – Role of Language – Communication – Technology – English Literature etc.

INTERNAL ASSESSMENT 5 Assignment and Mini Project Report Writing – Mini Project may be submitted during course work. Based on the test performance and project report of the students marks may be awarded. TOTAL 45 TEXT BOOKS

• Abraham Benjamin Samuel “Practical Communication (Communicative English), LSRW2000”, SRMEC - June 2002

REFERENCE BOOKS

• Herbert. A.J. The structures of Technical English Orient Longman 1995.

• Pickett and Laster, ‘echnical English, Writing, Reading and Speaking’, New York Harper and Row Publications, 1997.

• Swan, Michael, ‘Basic English Usage’, Oxford University Press, 1984.

• Interactive course in phonetics and spoken English published by Acoustics Engineers(ACEN) 2002.

• Warner, Tony, “Communication Skills for Information Systems”, Pitman Publishing, London, 1996.

• Munter, Mary, “Business Communication Strategy and Skill”, Prentice Hall Inc., New Jersey, 1987.

• Day Robert.A. 1983, “How to Write and Publish a Scientific Paper” Vikas Publishing House Pvt Ltd, New Delhi,1979.

• Staff of the Department of Humanities and Social Sciences, Anna University, “English for Engineers and Technologist Vol. – I”. Orient Longman, 1990.

MA111 MATHEMATICS – I L T P C (Common for BT, BI & GN Branches) 3 1 0 4 UNIT I – MATRICES 9 *Review of determinants, its properties and applications. Rank of a Matrix – Consistency and Inconsistency of a system of m linear equations in ‘n’ unknowns – Eigen values and Eigen vectors – Cayley-Hamilton theorem – Diagonalisation – Orthogonal Reduction of Quadratic forms to Canonical forms. UNIT II - TRIGONOMETRY 9 *Review of complex numbers – De Moivre’s theorem and its applications

Expansion of sin nθ, cos nθ in terms of sin θ and cos θ. Expansion of tan nθ in terms of tan θ.

Expansions of sinnθ and cos

nθ in terms of sines and cosines of multiples of θ. Hyperbolic

functions and inverse hyperbolic functions. Separation into real and imaginary parts of complex functions. UNIT III - GEOMETRICAL APPLICATIONS OF DIFFERENTIAL CALCULUS 9 *Review of Limits, Continuity, Differentiation and Derivatives of simple functions Curvature – Cartesian and polar coordinates – Circle of Curvature - Involutes and Evolutes – Envelopes. UNIT IV - INTEGRAL CALCULUS 9 *Review of types of integration Properties of definite integrals – Reduction formulae: e

axx

n, sin

nx, cos

nx, sin

nx cos

mx (without

proof) – Double integrals - Double integrals in polar coordinates – Change of order – Area as a Double integral – Triple integrals. UNIT V - BETA AND GAMMA FUNCTIONS 9 Definition of Beta, Gamma integrals – Relation between them – Properties – Evaluation of Definite integrals in terms of Beta and Gamma functions-Simple applications. TUTORIAL 15 TOTAL 60 * No questions should be asked in the Review part TEXT BOOKS

• Grewal B.S., Higher Engineering Mathematics, 36th edition, Khanna Publishers, 2002.

(Unit I – Chapter 2 Section 2.9.1., 2.11,2.13 – 2.18, Unit II – Chapter 19 section 19.5,19.7,19.9,19.11-19.15,Unit III – Chapter 4 Section 4.13 – 4.16(1,2), Unit IV – Chapter 6 Section 6.1- 6.3, 6.5(a),6.7 Chapter 7- Section 7.1 – 7.5, Unit V – Chapter 7 Section 7.14 – 7.16)

REFERENCE BOOKS

• Kreyszig.E, Advanced Engineering Mathematics, 8th edition, John Wiley & Sons,

Singapore, 2001.

• Veerarajan T., Engineering Mathematics, Tata McGraw Hill Publishing Co., New Delhi, 2000.

• Kandasamy P etal. Engineering Mathematics, Vol. I (4th revised edition), S.Chand &

Co., New Delhi, 2000.

• Narayanan S., Manicavachagom Pillay T.K., Ramanaiah G., Advanced Mathematics for Engineering students, Volume I (2

nd edition), S.Viswanathan Printers and Publishers,

1992.

• Venkataraman M.K., Engineering Mathematics – First Year (2nd

edition), National Publishing Co., Chennai, 2000.

• Ramamurthy V. etal. Engineering Mathematics – Vol. I & II, Anuradha Publications.

PH101 PHYSICS L T P C (Common for all Branches) 3 0 0 3

PURPOSE The purpose of this course is to develop scientific temper and analytical capability in the engineering graduates through learning of physical concepts and their applications in engineering and technology. Comprehension of some basic physical concepts will enable graduates to logically solve engineering problems they would come across in the fast developing new technologies in their engineering career. INSTRUCTIONAL OBJECTIVES At the end of the course, student should be able to:

1. Understand scientific concepts 2. Logically explain the concepts 3. Apply the concepts in solving engineering problems 4. Explain scientifically the new developments in engineering and technology 5. Relate industrial developments to developments in the physical phenomena

UNIT I ACOUSTICS 9 Vibrating systems - longitudinal and transverse waves – expression for velocity in solids and fluids - Ultrasonic - production – magnetostriction and piezo-electric methods – properties – applications in industry and medicine – acoustics of buildings (elementary ideas)

UNIT II ELECTROSTATICS AND ELECTRODYNAMICS 9 Electric field and potential - Gauss Theorem – proof (coulomb’s law) – applications – line charge, hollow cylinder, hollow spherical conductor, solid spherical conductor - Divergence and curl of a vector, introduction to Maxwell's equation – derivation - wave equation for electromagnetic waves - propagation in free space. UNIT III LASERS AND FIBER OPTICS 9 Lasers – Absorption and emission - Coherence and monochromatism - Three and four level laser systems - mode locking and Q-switching lasers - He-Ne, CO2, Nd: YAG and Ga As lasers - Introduction to Holography -applications of laser in industry, medicine and communication – Fiber optics - Optical fiber - physical structure, basic theory, mode types - optical fiber characteristics - application of optical fibers in information technology, communication and sensors (briefly). UNIT IV CRYSTAL PHYSICS 9 Crystalline and non-crystalline materials – Bravais lattice – crystal systems –simple crystal structures (NaCl, CsCl and diamond) – packing factor for SC, BCC, FCC and HCP structures – Miller indices- inter planar separation – imperfection in crystals(point and line) – Bragg’s law – X-ray diffraction methods to study crystal structures(Laue's method, Bragg's spectrometer and powder photograph method). UNIT V NON-DESTRUCTIVE TESTING OF MATERIALS 9 Liquid penetrant –magnetic particle – eddy current methods – x-ray radiography – fluoroscopy – Gamma ray radiography – ultrasonic scanning methods – ultrasonic flaw detector (pulse echo technique)- thermography TOTAL 45 TEXT BOOKS

• Arumugam .M., “Engineering Physics”, Anuradha publishers 1998. • Gaur & Gupta, “Engineering Physics”, Dhanpatrai & sons, V edition 1986. • John Thiruvadigal.D, Ponnusamy.S, Vasuhi.P.S and Kumar.C, " Physics for

Technologies", Vibrant Publications 2004.

REFERNCE BOOKS • Jordan.C.and Balmain.K.G. “Electromagnetic Waves and Radiating System,” (2nd ed.). • Prentice Hall of India 1994 • Feynman R.P, Leighton R.B, Sands.M, “The Feynman Lectures on Physics Vol,I, II, III”,

Narosa publishing House, New Delhi 1995 • Thyagarajan.K.and Ghatak A.K.”Laser Theory and Applications”, Mac Millan India Ltd.

New Delhi 1992

• C.K.Kao “Optical Fiber System Technology, Design and Applications,” McGraw Hill, 1982

CY101 CHEMISTRY L T P C

(Common for all branches) 3 0 0 3 PURPOSE To develop analytical capability to characterize, transform and use materials in engineering and to have in depth knowledge of chemistry of matter. INSTRUCTIONAL OBJECTIVES At the end of the course:

• Student should be able to understand and explain the concepts logically.

• Apply knowledge gained in solving related engineering problems.

• Understand the role of applied chemistry in the field of engineering.

UNIT I ELECTROCHEMISTRY and CORROSION AND ITS CONTROL 9 Electrodics: Measurement of conductance – Different types of electrodes, Electrochemical cell – reversible and irreversible cell – concentration cells - Nernst equation, – Application of EMF measurements Corrosion – Dry and wet corrosion, Differential aeration corrosion - mechanism, factors affecting corrosion – Corrosion control, different methods – Importance of selection of materials and design in reducing corrosion. UNIT II HIGH POLYMERS 9 Classification of polymers,- functionality,- polymerization reactions, Different types of polymerization catalyst – Anionic, cationic and free radical. Effect of polymer structure on properties – strength, plastic deformation, crystallinity, chemical resistance, Plastics- Classifications with examples - compounding of plastics, moulding techniques – Compression, injection, transfer, laminations, blowing. Elastomers- vulcanisation – synthetic rubber – styrene, butyl, nitrile, neoprine, sillicone rubbers. UNIT III WATER TREATMENT 9 Quality parameters, estimation of hardness by EDTA method. softening of water – zeolite process, demineralization by ion-exchanger – Treatment of water for domestic purpose – disinfection . Desalination – reverse osmosis. Waste water Treatment: Importance of dissolved oxygen in water – Determination of COD, BOD. Treatment of domestic waste water- primary, secondary, tertiary treatment. UNIT IV PHASE EQULLIBRIA 9 Clausius-Clapeyron equation – Phase transitions, Phase rule and its terms. One component system – water. Thermal analysis - Two component system:- one system from each class - Simple Eutectic and compound formation.,solid solution formation . Applications of eutectics. UNIT V INSTRUMENTAL ANALYTICAL TECHNIQUES 9 Basic principles and applications of electroanalytical methods: Potentiometery, Voltammetry, Amperometry and polarography. TOTAL 45

TEXT BOOKS

• Jain P.C & Monika jain, “Engineering Chemistry”, Danpat Rai,12th Ed.1998.

• Sadasivam V., “Modern Engineering Chemistry- A simplified approach”, Kamakya publications 2001

• Willard H.A., Merit L.L and Dean J.A., “Instrumental methods of analysis” 6th Edition

Van Nostrand, 1986.

• Kamaraj P. & Arthanareeswari M., “Applied Chemistry”, Sudhandhira Publications, 2nd

Edition, 2003.

REFERENCE BOOKS

• Uppal M.M, “A text books of Engineering Chemistry”, Khanna Publishers.1986.

• Dara S.S, Chand S. & Co., “A text books of Engineering Chemistry”, 10th revised Ed,

2003.

• Glasstone .S & Lewis, “Elements of Physical Chemistry” MacMillan Education 2nd

Ed, 1987.

• Kuriacose J.C. and Rajaram J. “Chemistry in Engineering and Technology”, Volume II, Tata McGraw Hill p.b. Co., 1988.

GE101 BASIC ENGINEERING – I L T P C

(Common for all Branches) 4 0 0 4 PART - A CIVIL ENGINEERING L T P C

2 0 0 2 PURPOSE To get exposed to the glimpses of Civil Engineering topics that are essential for an Engineer.

IINNSSTTRRUUCCTTIIOONNAALL OOBBJJEECCTTIIVVEESS

• To know about different materials and their properties.

• Engineering aspects related to buildings.

• To know about importance of Surveying.

• To know about the transportation systems.

• To get exposed to the rudiments of engineering related to Dams, Water Supply and Sewage Disposal.

UUNNIITT II MMAATTEERRIIAALLSS AANNDD BBUUIILLDDIINNGGSS 1100 Introduction - Civil Engineering – Materials – Brick, Stone, Cement, Steel, and Concrete – Properties – Uses – factor of safety. Buildings – Classification - Components of buildings - Foundations - Functions – Classification of foundations – Bearing capacity - Floorings – Requirements - Cement Concrete flooring – Mosaic flooring - Marble flooring - Roofs - Types – Requirements – Madras Terrace roof . UUNNIITT IIII SSUURRVVEEYYIINNGG –– AAPPPPLLIICCAATTIIOONN OOFF SSUURRVVEEYYIINNGG 1100 Surveying - Objective – Principles – Classification – Instruments used for Surveying. Dams - Purpose – Selection of site – Classification – Gravity dam (cross-section details only) UUNNIITT IIIIII TTRRAANNSSPPOORRTTAATTIIOONN,,WWAATTEERR SSUUPPPPLLYY AANNDD SSEEWWAAGGEE DDIISSPPOOSSAALL 1100 Transportation system - Classification – Components of Roads - Railway – Cross-section of permanent way- requirements, Bridges – bridge site and components of a bridge site - Harbour – classification. Water supply - Sources - Standards of drinking water – Distribution system – Sewage – types – septic tank – function and components. TOTAL 30 TEXT BOOKS

• Raju K.V.B., Ravichandran P.T., Basics of Civil Engineering, Ayyappa Publications, Chennai, 2000.

• Ramesh Babu, Elements of Civil Engineering, VRB Publishers, 2000. REFERENCE BOOKS

• Rangwala,S.C., Engineering Materials, Charotar Publishing House, Anand, 1980.

• National Building Code of India, Part V, Building Materials, 1983.

• Surendra Singh, Building Materials, Vikas Publishing Company, New Delhi, 1996.

PART B MECHANICAL ENGINEERING L T P C 2 0 0 2

PURPOSE To familiarise the students with the basics of Mechanical Engineering. INSTRUCTIONAL OBJECTIVES To familiarize with

• The Source of Energy and Power Generation

• The various metal joining processes and metal working process

• The Basic theory of Lathe & Drilling Machines UNIT I SOURCES OF ENERGY AND POWER PLANTS 10 Non–renewable and renewable sources of energy–various types, characteristic, advantages/disadvantages. Thermal – steam, gas and diesel - Hydro and Nuclear power plants – its layout, element / component description, advantages, disadvantages, locations in India. UNIT II METAL JOINING AND SHEET METAL PROCESSES 10 Welding-Gas and Arc welding only– Introduction, types, equipments, tools and accessories, techniques employed, applications, advantages / disadvantages. Introduction to Brazing and soldering

Sheet Metal Work-Introduction, equipments, tools and accessories, Sheet Metal working process – various types, applications, advantages / disadvantages. UNIT III MACHINING 10 Lathe – Introduction, types, description of main components, cutting tools, work holding devices , Basic operations performed. Drilling machine- Introduction, types, and description, drilling tools. Tapping – tap tools. TOTAL 30 TEXT BOOKS

• Venugopal.K., “Basic Mechanical Engineering”, Anuradha Publishers, 1997.

• Prabhu.T.J., Jai Ganesh.V., Jebaraj.S., “Basic Mechanical Engineering”, Scitech Publications, 2000.

REFERENCE BOOKS

• Hajra Choudhary S.K. & Hajra Choudhary A.K., “Elements of Manufacturing Technology” Vol. I & II”, Media Publishers, 1986.

• Palanichamy M.S., “Basic Civil & Mechanical Engineering”, TMH, 1991.

GE103 BASIC ENGINEERING – II L T P C (Common for all Branches) 4 0 0 4 PART - A ELECTRICAL ENGINEERING L T P C

2 0 0 2 PURPOSE This course provides comprehensive idea about circuit analysis, working principles of machines and common measuring instruments. It also provides all fundamentals of circuit components electronic devices, transducers and integrated circuits. INSTRUCTIONAL OBJECTIVES At the end of the course students will be able

• To understand the basic concepts of magnetic, AC & DC circuits.

• To explain the working principle, construction & applications of DC & AC machines.

• To gain knowledge about the fundamentals of electric components, devices, Transducers, Measuring Instruments & integrated circuits.

PART A

UNIT I MAGNETIC CIRCUITS 8 Definition of mmf flux and reluctance analysis of composite magnetic circuits, leakage flux, fringing, magnetic materials and B-H relationship.

Faradays laws, induced emf’s and inductances. Energy storage in magnetic systems, Hysteresis and eddy currents. UNIT II AC AND DC CIRCUITS 12 Definition symbols and units of all circuits parameters like current of resistance etc. Ohms law, Kirchoff's law. Average and RMS values concept of phasor representation. RLC series and parallel circuits, resonance simple problems in DC & AC circuits. Introduction to Three phase systems, Generation of Three phase EMF-Waveform and phase sequence. UNIT III ELECTRICAL MACHINES AND WIRING 10 Electrical Machines : Working principle, construction and applications of DC machines and AC machines (transformer, three phase and single phase induction motors and alternators). Wiring : Types of wiring, joint box and looping systems, Wiring diagrams of staircase and corridor wiring. Working and characteristics of incandescant S.V and M.V lamps, Basic principles of earthing.

PART - B ELECTRONICS ENGINEERING L T P C 2 0 0 2 UNIT I ELECTRONIC COMPONENTS AND DEVICES 10 Passive components – Resisters, Inductors and Capacitors and their types Semiconductor : Energy band diagram – Intrinsic and Extrinsic semiconductors – PN junction diodes and Zener diodes – characteristics. Rectifiers : Half wave and full wave rectifier – capacitive filter – wave forms – ripple factor – regulation characteristics. Transistors : PNP and NPN transistors – theory of operation – Transistor configurations – characteristics – comparison. Special semiconductor devices : FET – SCR – LED – V I characteristics – applications. UNIT II TRANSDUCERS AND MEASURING INSTRUMENTS 10 Transducers : General features and classification of tranducers, Resistive Transducers – Potentiometer, Unbonded strain gauge-Bonded strain gauge-Load cell, Inductive transducers – Differential output tranducers – LVDT, Flow transducers – Variable are flow meter, Temperature Transducers – Thermistors, Thermocouple and pyrometers. Measuring Instruments : Basic principles and classification of instruments, Moving coil and moving iron instruments, CRO – Principles operation. UNIT III DIGITAL ELECTRONICS 10 Digital Fundamentals : Number system – Boolean Theorems – DeMorgan’s Theorems Logic gates – Implementation of Boolean Expression using Gates. Integrated Circuits: IC fabrication – Monolithic Technique.

TOTAL 60 TEXT BOOKS

• Muraleedharan K.A, Muthususbramanian R and Salivahanan S, "Basic Electrical, Electronics and Computer Engineering" Tata McGraw Hill 1999.

• Mehta V K, “Principles of Electronics", S.Chand & Co., 1980

• Kalsi H S, Electronic Instrumentation", ISTE publication, 1995. REFERENCE BOOKS

• Kothari D P and Nagrath I J, "Basic Electrical Engineering", Tata McGraw Hill, 1991

• Mithal G K, Electronic Devices & Circuits, Khanna Publications, 1997

• Ben .G. Streetman, "Solid State Electronics Devices, Prentice Hall of India, 1999

PH103 PHYSICS LABORATORY L T P C (Common for all Branches) 0 0 2 1

PURPOSE The purpose of this course is to develop scientific temper and analytical capability among the engineering graduates. INSTRUCTIONAL OBJECTIVES At the end of the course, student should be able to:

• Understand scientific concepts

• Develop the skill in arranging and handling different measuring instruments

• Determine the errors in various measurements and planning / suggesting how these contributions may be made of the same order so as to make the error in the final result small.

LIST OF EXPERIMENTS

1. To determine the frequency of AC, using vibrating rod/tuning fork method. 2. Determination of velocity of ultrasonic waves in liquids. 3. Particle size determination using laser 4. Calibration of voltmeter & ammeter 5. Determination of field intensity – Field along the axis of a circular coil 6. Determination of wave length-Diffraction grating. 7. Determination of dispersive power of a prism using spectrometer. 8. Determination of laser parameters - divergence and wave length for a given laser

source – Laser Grating 9. Study of attenuation and propagation characteristics of an optical fiber cable. 10. Determination of temperature co-efficient of resistance - Carey –Foster’s Bridge.

TOTAL 30 REFERENCE BOOKS

• Ouseph C.G., Practical Physics , S.Viswanathan Publishers, 1981

• Aroro C.L., Practical Physics, S. Chand & Co., 1989.

• John Thiruvadigal.D, Ponnusamy.S, Vasuhi.P.S and Kumar.C, "Hand Book of Practical Physics", Vibrant Publications 2004.

CY103 CHEMISTRY LAB L T P C

(Common for all Branches) 0 0 2 1

PURPOSE An integrated laboratory course consists of experiments from applied chemistry and is designed to illustrate the underlying principles of measurement techniques, synthesis, dynamics and chemical transformation. INSTRUCTIONAL OBJECTIVES Students should be able to understand the basic concept and its applications. LIST OF EXPERIMENTS

1. Estimation of total hardness, permanent and temporary hardness by EDTA method. 2. Determination of Chloride content in water by Volhard’s method. 3. Determination of COD in waste water. 4. Conductometeric titration – determination of strength of an acid. 5. Estimation of iron by potentiometer – titration. 6. Determination of molecular weight of polymer by viscosity average – method. 7. Determination of dissolved oxygen in a water sample by Winkler’s method 8. Determination of corrosion rate. 9. Determination of pH / Acidity of water sample. 10. Estimation of Copper in ore. 11. Estimation of nickel in steel. 12. Determination of solubility product of sparingly soluble salts.

TOTAL 30 REFERENCE BOOKS

• Practical Chemistry – I, 2004 Edited by Dr. R. Jeyalakshmi.

• Practical Chemistry by Kamaraj & Arthanareeswari, Sudhandhira Publications, 2003.

GE105 COMPUTER PRACTICE L T P C 0 0 3 2

PURPOSE To familiarize the students with the fundamentals of operating systems, office package tools and Programming basics INSTRUCTIONAL OBJECTIVES

1. Introduction to DOS, UNIX, Windows

2. Word , Excel, Powerpoint , Access 3. C Programming Basics

LIST OF EXPERIMENTS CYCLE - I Fundamentals of Computers and Introduction to Operating Systems Organization of Computers, Generation, Modern Computers , Applications Operating Systems : DOS , UNIX , WINDOWS , Introduction to GUI. CYCLE-II Office Automation Word Processing , DataBase Management , Spread sheet Package , Presentation tools. CYCLE –III C Programming Basics 1. Sum of Series , Sine, Cosine, Exponential 2. Counting number of words,vowels, lines in a text 3. Programs using Builtin math functions 4. Conversions : Hex to Decimal, Binary to Octal etc. 5. Matrix operations : Multiplication, Symmetric, Inverse 6. Student mark processing

Similar Problems covering basics of C Language TOTAL 45 TEXT BOOKS

• Sheela Kumar.T., Sridhar.S.S. , “ Computer Practice “, Anuradha Publishers,2003.

• Mullish Cooper , “The Sprit of C” , Jaico Books, 2002

• Vikas Gupta, “Computer Course Kit”, Wiley-dreamtec India Pvt Ltd, 2002. REFERENCE BOOKS

• Balaguruswamy .E. “Programming in ANSI C”, TataMcGraw Hill, 2004.

• Ed Bott, Woody Leonhard , “Using Office 2000”, PHI, 2000. ME101 WORK SHOP PRACTICE L T P C

(Common for all branches) 0 0 3 2 PURPOSE To provide the students with hands on experience on different trades of engineering like fitting, carpentary, smithy, welding and sheet metal. INSTRUCTIONAL OBJECTIVES To familiarize with

• The basics of tools and equipments used in fitting, carpentary, sheet metal, welding and smithy

• The production of simple models in the above trades LIST OF EXPERIMENTS EMPHASIS TO BE LAID ON REAL LIFE APPLICATIONS WHEN FRAMING THE EXERCISES. 1. FITTING Tools & Equipments – Practice in chipping, filing & Drilling. Making Vee Joints, Square, dovetail joints, Key making. 2. CARPENTARY Tools & Equipments- Planing practice- Making Half Lap, dovetail, Mortise & Tenon joints, a mini model of a single door window frame( Frame only) 3. SHEET METAL Tools & equipments – Fabrication of a small cabinet, Rectangular Hopper, etc., 4. WELDING Tools & equipments – Arc welding of butt joint, Lap Joint, Tee Fillet. Demonstration of Gas welding, TIG & MIG.

5. SMITHY Tools & Equipments – Making simple parts like hexagonal headed bolt, chisel. TOTAL 45 REFERENCE BOOKS

• Kannaiah.P. & Narayanan,K.C. “Manual on Workshop Practice”, Scitech Publications, Chennai, 1999.

• Venkatachalapathy, V.S. “First year Engineering Workshop Practice”, Ramalinga Publications, Madurai, 1999.

II SEMESTER

MA142 MATHEMATICS II L T P C (Bio-Technology) 3 1 0 4 UNIT I - ALGEBRA 9 Binomial, exponential and logarithmic series (without proof) – problems on summation, approximation and coefficients. UNIT II - FUNCTIONS OF SEVERAL VARIABLES 9 Functions of two variables – partial derivatives – total differentiation – Taylor’s expansion – maxima and minima of functions of two and three variables – constrained extremum – Lagrange’s method – Jacobians. UNIT III - DIFFERENTIAL EQUATIONS 9 Differential equations of first order and higher degree – higher order differential equations with constant coefficients – variable coefficients – simultaneous equations – method of variation of parameters. UNIT IV - VECTOR CALCULUS 9 * Review of Vector Algebra. Gradient, divergence and curl – solenoidal and irrotational fields – directional derivatives – line integrals – surface integrals – volume integrals. Integral theorems (without proof) and its applications. UNIT V - THREE DIMENSIONAL ANALYTICAL GEOMETRY 9 Direction cosines and direction ratios of a line – angle between two lines. Equation of a plane – equation of a straight line – shortest distance between two skew lines – coplanar lines. TUTORIAL 15 TOTAL 60 * No questions should be asked in the Review part TEXT BOOKS

• Kandasamy P etal. Engineering Mathematics, Vol. I (4th revised edition), S.Chand &

Co., New Delhi, 2001 (Unit I – Chapter 2,3,4)

• Grewal B.S., Higher Engineering Mathematics, 36th edition, Khanna Publishers, 2001

(Unit II – Chapter 5 except Section 5.6, 5.10, Unit III – Chapter 13 except Section 13.8 (II), 13.10, Unit IV – Chapter 8 Section 8.4 – 8.6, 8.8-8.18, Unit V – Chapter 3 Section 3.13 – 3.17)

REFERENCE BOOKS

• Kreyszig.E, Advanced Engineering Mathematics, 8th edition, John Wiley & Sons,

Singapore, 2001.

• Kandasamy P etal. Engineering Mathematics, Vol. I & II (4th revised edition), S.Chand &

Co., New Delhi, 2000.

• Narayanan S., Manicavachagom Pillay T.K., Ramanaiah G., Advanced Mathematics for Engineering students, Volume I, & II (2

nd edition), S.Viswanathan Printers and

Publishers, 1992.

• Venkataraman M.K., Engineering Mathematics – Vol.III – A (13th edition), National Publishing Co., Chennai, 1998.

• Ramamurthy V, etal Engineering Mathematics Vol. I and II, Anuradha Publications.

CY152 CHEMISTRY II L T P C 3 0 0 3

PURPOSE The course provides advanced topics in chemistry required for bio-technology. It covers important aspects of metal complexes, colloids, toxicology, dynamics of chemical process and solutions INSTRUCTIONAL OBJECTIVE At the end of the course:

• Student should be able to understand and explain the concepts logically.

• Apply knowledge gained in solving related engineering problems.

• Understand the role of applied chemistry in the field of engineering. UNIT I DYNAMICS OF CHEMICAL PROCESS 9 Basic concepts – Chemical kinetics Reaction rates, integrated rate laws, Half live periods, Temperature dependence of reaction rate. The formulation of rate laws, unimolecular reactions and chain reaction (structure and rate laws) – laws of photochemical reactions (eg: HBr reaction only). Fundamental concepts and definition of catalysis. – Mechanism of catalysis action enzyme catalysis Michaelis - Menten equation. UNIT II KINETIC PROPERTIES OF SOLUTION 9 Fundamental concepts – dilute solutions- osmosis, Osmotic pressure – measurements. Van't Half's theory. Raoult's law – Henry law – solution of electrolyte. Molecular weight calculation by depression of freezing point and elevation of boiling point. Determination and application, CST- steam distillation – miscibility, fraction distillation. Distribution law, basic concepts of extraction process. UNIT III COLLOIDS 9 Concepts, different methods of preparation-physical, chemical- characteristics of colloidal system. Important properties of colloids – optical – electrical – kinetic. Purification –Methods – dialysis – ultra filtration. Important applications of colloids UNIT IV CHEMISTRY OF ENVIRONMENT 9 Analysis of effluent liquid streams – BOD, COD - trace elements (AAS method only) -Analysis of gaseous effluent streams – particulate matter, Oxides of nitrogen, sulphur, carbon, hydrogen sulphide, Bio Chemical effects of lead, mercury, carbon monoxide, nitrogen oxides, oxides of sulphur, ozone and cyanide. Introduction to bio corrosion and its prevention. UNIT V METAL COMPLEXES 9 Basic concepts – Nomenclature of the complexes - IUPAC. Crystal field theory-features – splitting of d-orbitals in tetrahedral- square planner - octahedral geometry. Metal carbonyls only – structure of (Fe, Co, Cr & Ni).

TOTAL 45

TEXT BOOKS

• Puri B.H.and Sharma L.R., “Principles of Physical Chemistry”, S.Nagin Chand and Company, Delhi (1994).

• Kund and Jain, “Physical Chemistry”, S.Chand and Company, Delhi (1996)

• Kuriacose J.C., and Rajaram,J., “Chemistry in Engineering and Technology “, Volume 1 & 2, Tata McGraw Hill Publishing Co., Ltd, New Delhi, 1989.

• “Comprehensive Chemistry to Bio-Engineers”, Dr.R,Jeyalakshmi, Dr.P.Kamatchi, P.Ramar, S.Kannan, Devi publications (in print).

REFERENCE BOOKS

• Gordon M. Barrow, “Physical Chemistry”, Sixth Edition, Tata McGraw Hill (1996).

• Dr.Dhiraj sud "Engineering Chemistry" Millennium Edition S.K. Kataria and Sons, 2000.

• Dara S.S., “A text books of Engineering Chemistry”, S.Chand and company Ltd., 2003 revised edition..

• Samuel Glasstone, “Physical Chemistry”, Macmillan II edition, 1969.

• Sharma B.K. “Industrial Chemistry”, V Edition, Geol publishing House, Meerut, U.P., V edition (1997 – 1998).

CS156 COMPUTER PROGRAMMING ( C and C++) L T P C 3 0 2 4

PURPOSE This course gives a fundamental understanding of the Languages C and C++. INSTRUCTIONAL OBJECTIVES Basics of C Language and its constructs Programming in preliminary and advanced levels Detailed understanding of OOPs and C++ language Understanding and programming in inheritance, polymorphism UNIT I INTRODUCTION TO C LANGUAGE 8 History of C Language- Simple C Program – Variables – Constants - C data types – enumeration – typedef - keywords – operators – precedence – constructs – symbols – conventions – the main function - expressions , basic input/output (I/O) techniques and Program control mechanisms. Compiling and executing a C program. Simple programs for I/O functions ,usage of various datatypes. UNIT - II CONTROL STRUCTURES AND FUNCTIONS 9 Preprocessing Directives, Built in Library functions – mathematical, character, string , Control flow -Statements and blocks, If-Else, Switch statement, While and For loops, Do-While loops, Break and Continue. Functions and Program Structure - The C preprocessor, Variable initialization, Static and Register variables,External variables, Header Files, Functions, parameter passing - returning values. Programs for builtin functions, control structures, user defined functions. UNIT III ARRAYS, STRUCTURES AND POINTERS 9 Arrays -Array notation, Array initialization ,operations on Arrays - sorting , Dynamic Memory allocation. Structures - Purpose and usage of structures, Declaring a structure, Array of structures, Pointers to structures, Self-referential structures, Table lookup, Typedef and Unions Programs for Array operations- sorting, Structures usage- record processing UNIT - IV FUNDAMENTALS OF OOP AND C++ 9 Software Evolution – Procedure Oriented Programming Paradigm- Basic Concepts of Object Oriented Programming, Advantages and applications – Introduction to Objects,classes, features of OOP. Introduction to C++, A simple C++ program – Structure of a program, Class example, creating, compiling and executing the source file, Tokens, Identifiers, Datatypes, Operators in C++, Manipulators , cast operators , Precedence , Control structures in C++ Programs for declaring class, creating objects for simple problems, usage of control structures in C++. UNIT V FEATURES OF OOP 10 Constructors – Destructors – Copy constructors - Functions -parameter passing – Overriding – Operator Overloading, Strings and manipulations – access specifiers Inheritance – types of inheritance, examples – problems on the above topics Programs to illustrate Overloading , Inheritance , overriding. L: 45 P: 30 Total: 75 TEXT BOOKS

• Mullish Cooper, “The Sprit of C”, Jaico books 2002

• Stephen Prata, “C++ Primer Plus”, fourth edition, 2003

REFERENCE BOOKS

• E.Balagurusamy , “Programming in C” , Tata McGraw Hill

• Harvey Deital and Paul Deital , “ C++ How to Program”

• S. B. Lippman & J. Lajoie, “C++ Primer”, 3rd

Edition, Addison Wesley, 2000.

BT102 BIOCHEMISTRY L T P C 3 0 0 3

PURPOSE Deals with the study of structural and functional aspects of biomolecules. INSTRUCTIONAL OBJECTIVES

• To study the structure and properties of carbohydrates.

• Discuss the structure, properties and reactions of proteins and amino acids

• Discuss the structure, properties of fats and lipids

• To study the composition, structure and functions of nucleic acids

• To discuss the functions, deficiency symptoms, properties and structural aspects of vitamins.

UNIT I CARBOHYDRATES 9 Definition, classification, preparation, properties, reactions, functions and structure of mono and disaccharides. Polysaccharides – structural aspects of starch. Metabolism of carbohydrates. UNIT II PROTEINS 9 Amino acids – classification, properties and reactions. Proteins – composition, classification, general properties, reactions and functions. General structure of proteins – primary, secondary, tertiary and quaternary. Structural aspects of insulin. Metabolism of proteins UNIT III FATS AND LIPIDS 9 Definition, classification, structure, properties, reactions and functions of lipids. Metabolism of fat. UNIT IV NUCLEIC ACIDS 9 Composition, structure, properties of nucleosides, nucleotides. DNA – primary and secondary structure of A, B and Z forms – supercoils, denaturation and renaturation and other properties. RNA – classification, structure and functions of tRNA, rRNA and mRNA. Nucelic acid metabolism. UNIT V VITAMINS 9 Definition, classification, general sources, functions, deficiency symptoms, properties and structural aspects of vitamin A,D,E,K,C, Thiamine, riboflavin, niacin and biotin. TOTAL 45 TEXT BOOKS

• Lehninger A.L., Nelson D.L., Cox .M.M, “Principles of Biochemistry”, CBS Publications, 1993.

• Stryer L. “Biochemistry”, Fourth Edition, W.H. Freeman & Company, New York, 1999.

REFERNECE BOOKS

• Voet D. Voet G, “Biochemistry”, Second Edition, John Wile and Sons, 1994.

• Zubay.G, “Biochemistry”, Second Edition, Maxwell Macmillan International Editors, 1987.

• Conn, E and P.K. Stump, “Outlines of Biochemistry”, Willey Eastern Ltd., New Delhi, 1984.

• Albert, L. Lehninger et al, “Biochemistry”, 5th edition, Worth Publishing, 2000.

BT104 MICROBIOLOGY L T P C

3 0 0 3 PURPOSE Introducing the fundamentals of microbiology through the study of the characteristics of microorganisms, multiplication, growth in different media, metabolic pathways, effects of microbe and their control.

INSTUCTIONAL OBJECTIVES

1. To highlight the roles and characteristics of microorganisms 2. To impart knowledge on the basic concept of replication in microorganisms 3. To study in detail the growth of microorganisms and impact of environment on their

growth 4. To evaluate explicitly, the metabolic pathways, role of microbes in public health; insight

into the physical and chemical control of microorganisms. UNIT I HISTORY & MICROSCOPY 7 Classification of Micro Organisms - Concepts – (Haeckel’s and Whiltaker’s 3 & 5 kingdom); History of Microbiology; Characteristics of microorganisms; Taxonomical methods of studying microorganisms (Intuitive, numeric & genetic); Microscopy-light, electron and laser optic system; micrometry. UNIT II STRUCTURE AND ORGANISATION 12 Structure, Organisation & reproduction of archaebacteria, eubacteria, yeast, fungi, algae, bacteriophage, plant viruses and animal viruses. UNIT III NUTRITION AND GROWTH 8 Nutritional requirements and nutritional grouping of microrganisms; Growth of micro organisms in different media (simple, complex and defined) – Growth curve; Axenic culture,Synchronus culture,Continuous culture; Different methods of enumeration of micro organisms; Methods of preservation of microbes; Effects of physical and chemical factors on microbial growth; control of microrganisms UNIT IV METABOLISM AND BIOENERGETICS 10 Metabolic pathways – Embden – Meyerhof, Pentose phosphate and Entner – Doudoroff pathways, TCA cycle) – Bio energetics (laws of thermodynamics, Oxidation, reduction and electron carriers); Cycling of elements, nitrogen fixation; Biosynthesis of macromolecules. UNIT V ENVIRONMENTAL APPLICATION AND PUBLIC HEALTH 8 Leaching of ores by microorganisms; Biofouling; Microorganisms and their role in pollution control (Bacteria & fungi). Microbiology of air, drinking water and waste water; Microbial indicators of pollution; Role of microbes in public health and Diseases caused by microbes; Food poisoning and Food spoilage; Microbes in extreme environments.

TOTAL 45

TEXT BOOKS

• Pelczar M.J, “Microbiology”, Chan ECS and Krieg NR

• Prescott, Harley and Klen, “ Microbiology”, McGraw Hill publications Fifth edition 2003

GE 106 VALUE EDUCATION L T P C (Common for all branches) 1 0 0 1

UNIT – I 3 Value Education—Introduction – Definition of values – Why values? – Need for Inculcation of values – Object of Value Education – Sources of Values – Types Values:

• Personal values

• Social values

• Professional values

• Moral and spiritual values

• Behavioral (common) values UNIT- II 3 Personal values – Definition of person – Self confidence – Self discipline – Self Assessment – Self restraint – Self motivation – Determination – Ambition – Contentment – Humility and Simplicity - Sympathy and Compassion – Gratitude -Forgiveness – Honesty – Courtesy.

UNIT – III 3 Social values – Definition of Society – Units of Society - Individual, family, different groups – Community – Social consciousness – Equality and Brotherhood – Dialogue – Tolerance – Sharing – Responsibility – Co-operation Freedom – Repentance and Magnanimity. UNIT – IV 3 Professional values – Definition – Competence – Confidence – Devotion to duty –Efficiency – Accountablility – Respect for learning /learned – Willingness to learn-Open and balanced mind – Team spirit – Professional Ethic – Willingness for Discussion – Aims – Effort – Avoidance of Procrastination and slothfulness –Alertness. UNIT – V 3 Behavioral values – Individual values and group values – Good manners at home and outside – Equality – Purity of thought, speech and action – Understanding the role of religion – Faith – Understanding the commonness of religions – respect for other faiths – unity in diversity – Living together – Tolerance – Non-violence – Truthfulness – Common aim – Unified effort towards peace – Patriotism.

TOTAL 15 RREEFFEERREENNCCEE BBOOOOKKSS

• Dr. S. Ignacimuthu S. J., Values for life, Better yourself Books, Bandra

• Mumbai-600 050 (1999).

• Values(Collection of Essays)., Published by : Sri Ramakrishna Math., Chennai—4.,(1996)

• Prof. R.P.Dhokalia.,Eternal Human Values NCRT –Campus Sri Aurobindo Marg., New Delhi - 110 011.

• Swami Vivekananda., Education., Sri Ramakrishna Math., Chennai-4(1957)

• Tirukural (English Translation by Dr.G.U.Pope).

• The Bible

• The Kuran

• The Bagavath Geetha

GE 108 BIOLOGY L T P C (Common for all branches) 2 0 0 2

PURPOSE It makes the students knowledgeable in basic cognitive aspects of the brain and relations with modern machines INSTRUCTIONAL OBJECTIVES

• To study human systems – nervous system, circulatory system

• To understand brain functions

• To understand the cognitive aspects of the brain

• To relate man machine interaction towards product development.

UNIT I HUMAN SYSTEMS 6 Nervous system, brain, parts of brain and their functions; circulatory system, heart and its function. UNIT II BRAIN FUNCTIONS 6 Perception, behavioral sequences, reflexes, instincts, emotions, thinking and other integrative activities. UNIT III COGNITIVE CAPABILITIES 6 Attention, Thinking, Evaluating, Insight, Abstraction, Creativity, Choice, Purpose, Planning, Generalization, Judgement, Introspection, Programming, Interest, Preference, Discrimination, Learning, Habituation, Memory, recognition, retention, Knowledge UNIT IV MEMORY 6 Memory stratification, Methods of processes used by the memory manager, Genetic structure UNIT V MAN – MACHINE INTERACTION 6 Experience, learning, problem solving abilities and product development.

TOTAL 30 TEXT BOOKS

• Elementary Biology, K.N.Bhatia and M.P.Tyagi 2002, Trueman Book Company, Jalandhar

• The Human Brain : Essentials of behavioural Neuroscience, Jackson Beatty 2001, Sage Publications India Pvt. Ltd., Delhi

REFERENCE BOOKS

• Cognitive aspects of the Brain Relations with modern computers, Jose Molina 2003, Molwick.

GE104 ENGINEERING DRAWING L T P C

(Only First Angle Projection is to be followed) 1 0 4 3 PPUURRPPOOSSEE To draw and interpret various projections of ID, 2D and 3D objects. INSTRUCTIONAL OBJECTIVES To familarise with

The construction of geometrical figures The projection of 1D, 2D & 3D elements.

UNIT I FUNDAMENTALS OF ENGINEERING DRAWING 3 Lettering two dimensional geometrical construction, conics, and representation of three – dimensional objects – principles of projections – standard codes projection of points. UNIT II PROJECTION OF LINES 3 Projection of straight lines. UNIT III PROJECTION OF SOLIDS 4 Projection of solids – auxiliary projections UNIT IV PICTORIAL PROJECTIONS – I 3 Orthographic projection, isometric projection of regular solids & combination of solids. UNIT V PICTORIAL PROJECTIONS – II 2 Conversion of orthographic to isometric. Introduction of perspective projection. PRACTICALS 60 TOTAL 75 TEXT BOOKS

• Ramachandran.S, “Engineering Drawing”, Private Publications, Chennai, 2002.

• Natarajan.C.R., “Engineering Drawing & Graphics”, Private Publication, Chennai, 1990. • Narayanan K.L & Kannaiah P., “Engineering Graphics”, SciTech Publications, Chennai,

1999. REFERENCE BOOKS

• Bhatt.N.D., “Elementary Engineering Drawing”, (First Angle Projection), Charotar Publishing Co., Anand, 1999.

• Venugopal .K, “Engineering Drawing & Graphics”, New age international Pvt. Ltd., 1999.

CY 156 CHEMISTRY LABORATORY II L T P C

0 0 3 2 PPUURRPPOOSSEE To develop analytical capability to Characterize, transform and use materials in engineering and to have in depth knowledge of chemistry of matter. INSTRUCTIONAL OBJECTIVES Students should be able to understand the basic concept and its applications.

LIST OF EXPERIMENTS 1. Determination of TOTAL alkanity and acidity of a water sample. 2. Phase rule – simple eutectic ( two component system ) 3. Estimation of percentage of lime. 4. Determination of rate constant for hydrolysis of ester. 5. Preparation of colloids solution (sol) of starch and its purification. 6. Determination of partition coefficient of iodine in water and carbon tetra chloride. 7. Determination of melting point and molecular weight. 8. Estimation of barium by gravimetric method. 9. Estimation of percentage composition of Glycerol (Viscometer method) 10. Estimation of Cobalt by gravimetry.

TOTAL 45 REFERENCE BOOKS:

• Practical Chemistry – II, 2004 –edited by Dr. R. Jeyalakshmi. • Analytical Methods in Chemistry by Kamaraj & Arthanareeswari, Sudhandhira

Publications, 2004.

III SEMESTER

BI 201 MOLECULAR BIOLOGY & GENETICS L T P C 3 1 0 4

PURPOSE The course is aimed to make the student understand the fundamentals concepts and basic principles such as structure of DNA / RNA, transcription, translation gene regulation, and RNA splicing and also the Mendelian genetics. INSTRUCTIONAL OBJECTIVES To impart knowledge on

• Nucleic acids and their characteristics

• Transcription and translation

• Gene regulation and mutation

• Mendelian genetics

UNIT I STRUCTURE OF NUCLEIC ACID 9 Structure of DNA, different forms of DNA and RNA, Identification of DNA as genetic material by Griffith, , Avery, McLeod and McCarty, Frankel and Singer, Hershey and Chase, Messelson and Stahl experiment. UNIT II DNA REPLICATION AND MUTATION 10 Semi-Conservative replication, replication of DNA in eukaryotes, molecular basis of Mutation, classification of mutation UNIT III GENE EXPRESSION AND REGULATION 10 Genetic code, transcription – prokaryotes and eukaryotes, Post transcriptional modification, Translation in prokaryotes and Eukaryotes, Post translational modification, Gene Regulation – Lac operon model UNIT IV MENDELIAN GENETICS 7 Mendel’s laws – monohybrid dihybrid inheritance, multiple alleles, structure and organization of chromosome in prokaryote and eukaryote UNIT V CROSSING OVER AND LINKAGE 9 Linkage – types of linkage, crossing over and their types, Recombination mapping by two point and three point text cross mapping in bacteria

TUTORIAL15 TOTAL 60 TEXT BOOKS

• T.A.Brown, “Genetics- A molecular approach”, Chapman & Hall, Third edition, 1998 - for UNIT I, II & III.

• Benjamin Lewin, “Gene VII”, Oxford University Press, 2000- for UNIT I, II & III.

• Gardener, Simmons and Snustad, “Principles of Genetics “, John wiley & sons, 1991.-for UNIT IV and V.

REFERENCE BOOKS

• H.K.Jain, “Genetics – Principles, Concepts, and Implications”, Oxford, 1999.

• C.B Powar, “Genetics – VOL 1 & 2”, Himalaya Publishing House, 2003.

• John Ringo,”Fundamental Genetics”, Cambridge, 2004.

BI 203 BIOPHYSICS L T P C 3 0 0 3

PURPOSE To introduce the theories and concepts of biophysics of biomolecules which are considered important in biotechnology applications. INSTRUCTIONAL OBJECTIVES

• Learn the structures of biological molecules

• To understand the concepts of structural analysis

• Lear the techniques for analysis and determination of structure of biomolecules. UNIT I INTRODUCTION 6 Levels of structures in biological macromolecules – Basic strategies in biophysics conformational analysis – forces that determine protein and nucleic acid structure – basic problems – polypeptide chain geometrics – potential energy – calculations – observed values for rotation angles, hydrogen bonding, hydrophobic interactions and water. Structures – ionic interactions – disulphide bonds. UNIT II STRUCTURAL ANALYSIS 10 Structural analysis of macromolecules, Prediction of proteins structure nucleic acids – general characteristics of nucleic acid structure – geometrics, glycoside bond, notational isomers and those puckering backbone rotational isomers and ribose puckering backbone forces stabilizing ordered forms, base pairing, base stacking tertiary structure of nucleic acids. UNIT III KINETICS 12 Kinetics of ligand interactions, biochemical kinetics studies unimolecular reactions, simple biomolecular multiple intermediates, steady state kinetics, catalyst efficiency – relaxation spectrometry, ribonuclease as an example. UNIT IV TECHNIQUES FOR STUDY OF MACROMOLECULES 10 Techniques for the study of biological structure and function. Size and shape of macromolecules methods of direct visualization of macromolecules as hydrodynamic particles – macro molecular diffusion – ultra centrifugation – viscometry – X-ray crystallography. UNIT V DETERMINATION OF STRUCTURE OF BIO MOLECULES 7 Determination of molecular structures. X-ray fiber diffraction electron microscopy, neutron scattering – light scattering. TOTAL 45 TEXT BOOKS:

• Cantor, Charles R., Paul R Schimmel. “Biophysical Chemistry”, W.H.Freeman & Co.

BI205 BIOINFORMATICS L T P C 3 1 0 4 PURPOSE Aims at providing an elementary knowledge of bioinformatics and Biological Information on the web. INSTRUCTIONAL OBJECTIVES

• Scope of bioinformatics

• Types of Databases and their use

• DNA structure and Analysis

• Pairwise and Sequence alignment

• Internet resources and Data mining. UNIT–-I INTRODUCTION 9 Introduction - Definitions-Analytical approaches-Applications-Three Levels, Components and Principles of Bioinformatics –Biological databases available in public domain-Inputs for Emergence of Bioinformatics- Commercial uses of Bioinformatics-Role of Bio and Chemo Informatics in drug design- Bioinformatics in Life sciences-Biological Information to knowledge- Biocomputing -Developing Bioinformatics Computer Skills. UNIT–II INFORMATION RESOURCES 9 Information Networks: Internet Facilities used in the web browser-HTTP-HTML-URL-European Molecular Biology Network. Protein Information Resources: Biological databases-primary sequence databases-Composite sequence databases-Secondary databases-composite protein pattern databases-structure classification databases. Genome Information Resources: DNA sequence databases-specialized genomic resources. UNIT-III DNA SEQUENCE ANALYSIS 8 Introduction-DNA Analysis-Gene Structure and DNA sequences- Finding Protein coding regions-Assembling sequence fragments. UNIT- IV ALIGNMENT TECHNIQUES 10 Pairwise Alignment Technique: Database searching-algorithms and programs-comparing two sequences- identity and similarity-global and local alignment- pairwise database searching. Multiple sequence Alignment: Goal of multiple sequence alignment-Computational Complexity-Manual methods-Simultaneous methods-Progressive methods-Databases of multiple alignment-Secondary database searching-Analysis packages. UNIT-V BIOLOGICAL INFORMATION ON THE WEB 9 Introduction-BLAST Algorithm-The role of NCBI - NCBI’s Database-Genomic Resources-Tools-EBPNET-Introduction-Genes and Information Needed-Public Biological Databases-Major Biological Data and Information sources-Other Bioinformation providers-Data Mining -Data Visualisation tools and techniques 10. TUTORIAL 15 TOTAL 60 TEXT BOOKS

• T K Attwood, D J parry-Smith,”Introduction to Bioinformatics”,Pearson Education,1st

Edition, 11th Reprint 2005.Chapters:

• C S V Murthy,”Bioinformatics”,Himalaya Publishing House,1st Edition 2003.Chapters:

REFERENCE BOOKS

• Stephen A.Krawetz,David D.Womble,”Introduction To Bioinformatics A Theoretical and Practical Approach”,HumanA Press,2003

• Hooman H.Rashidi,Lukas K.Ruehler,”Bioinformatics Basics-Applications in Biological Science and Medicine”,CRC press

• Jean-Michel Claverie,Cedric Notredame,”Bioinformatics-A Beginner’s Guide”,Wiley

• S.C.Rastogi & others, “ Bioinformatics- Concepts,Skills, and Applications”,CBS Publishing,2003

• Michael R Barnes & Ian C Gray , “ Bioinformatics for Geneticists”,John Wiley,2003.

• Andreas D Baxevanis & B F Francis,” Bioinformatics- A practical guide to analysis of genes & proteins”,John Wiley,2002

BI 207 INTRODUCTION TO DATA STRUCTURES L T P C 3 1 0 4

PURPOSE

The purpose of this subject is to study about the basic fundamentals of data structures and their applications in ‘C’

OBJECTIVES

• Basic fundamentals and stack, queue Implementation

• Trees and their applications

• Various types of sortings

• Graphs and their applications

• Various search techniques

UNIT-I LINEAR DATA STRUCTURES 9 Algorithm Analysis-Mathematical background, Model, Running Time Calculations; Linear Data Structures: List ADT-Array and Cursor Implementations, Stack ADT, Queue ADT-Array and List Implementation and Applications.

UNIT- II NON-LINEAR DATA STRUCTURES 9 Trees: Binary Trees-Binary Tree Representations-Tree Traversals, AVL Trees-Single and Double Rotation, Splay trees, B-Trees; Priority Queue: Binary Heap, Applications and variations of Priority Queue.

UNIT-III SORTINGS 9 Sorting- Exchange sorts-Selection and Tree sorting-Insertion Sort- Heap Sort- Merge Sort- Quick Sort - Bucket Sort.

UNIT- IV GRAPH ALGORITHMS 9 Definition and Representation of graphs, Topological sort, Shortest-Path Algorithms, Network flow problems, Minimum Spanning Tree, Application of Depth-First Search.

UNIT- V SEARCHING 9 Basic Search Techniques-Tree Searching-General Search Trees-Hashing

TUTORIAL 15 TOTAL 60 TEXT BOOKS

• Mark Allen Weiss,”Data Structures and Algorithm Analysis in C”,Addison Wesley Publications,2

nd Edition,1998.Chapters:2,3,4,5,6,7,9,10.

• Aaron M.Tanenbaum,Yedidyah Langsam,Moshe J.Augensten,”Data Structures Using C”,PHI.Chapters:5,6,7.

REFERENCE BOOKS

• Jeffrev Esakov Tom Weiss,”Data Structures An Advanced Approach using C”,PHI.

• Alfred V.Aho,John E. Hopcroft,Jeffrey D.Ullman,”Data Structures and

• Algorithms”, 10th Reprint 2004, Pearaon Education.

• Jean-Paul Tremblay, Paul G.Sorenson”, An Introduction to Data Structures with Applications”,2

nd Edition,Tata Mcgraw-Hill Edition

BI 209 JAVA PROGRAMMING L T P C 3 1 0 4 PURPOSE The purpose of this subject is to study about basics of Java Programming and applying it in Bioinformatics. OBJECTIVES

• Operators of Java and its applications

• Control statements of Java.

• Threading in Java.

• Event Handling and controls in Java

• Using Java in Bioinformatics. UNIT- I INTRODUCTION 8

An Overview of Java: OOP, A Simple Program,Data Types,Variables, amd Arrays,Operators:Arithmethic Operators, The Bitwise Operators, Relational Operators and Logical Operators UNIT- II CONTROL STATEMENTS 10 Control Statements. Introducing Classes, Methods and Classes, Inheritance, Packages and Interfaces, Exception Handling. UNIT- III THREADING AND APPLETS 10 Multithreaded Programming: Java Thread Model, Creating a Thread and Multiple Threads, Synchronization and Interthread Communication, I/O Applets, the Applet class. UNIT- IV EVENT HANDLINGS AND CONTROLS 10 Event Handling, Using AWT controls, Layout Managers and Menus UNIT- V APPLICATIONS 7 Application of Java in bioinformatics. TUTORIAL 15 TOTAL 60 TEXT BOOKS

1. Herbert Schildt, “The Complete Reference JAVA 2 Fourth Edition”, Tata Mcgraw Hill.Chapters:2,3,4,5,6,7,8,9,10,11,12

BI 211 JAVA PROGRAMMING LABORATORY L T P C 0 0 3 2 PURPOSE This Lab Course will enable the students to implement the various programming techniques in JAVA. INTRUCTIONAL OBJECTIVES To implement the following java Programming Techniques and to apply it in Bioinformatics. LIST OF EXERCISES Programs to implement the following Java Programming Techniques.

1. Arrays. 2. Inheritance. 3. Polymorphism. 4. Package and Interface. 5. Exception 6. Threads. 7. AWT, Event Handling & I/O. 8. Applets.

TOTAL 45 REFERENCE:

• Departmental Lab reference manual

BI213 BASIC BIOTECHNOLOGY LABORATORY L T P C 2 0 0 3 PURPOSE Provides an opportunity to experimentally verify the theoretical concepts already studied. It also helps in understanding the theoretical principles in a more explicit and concentrated manner.

INSTRUCTIONAL OBJECTIVES The students should be able to develop their skills Develop their skills in the preparation, identification and quantification of microorganisms Isolation of plasmid DNA, genomic DNA and RNA Electrophoresis

LLIISSTT OOFF EEXXPPEERRIIMMEENNTTSS

1. Sterilization techniques 2. Media preparation 3. Microscopy and Micrometry 4. Isolation, enumeration and purification of microbes from a given sample 5. Staining Techniques (Simple, Gram staining, spore staining and Hanging drop technique) 6. Preparation of Agarose Gel 7. Isloation of Genomic DNA from blood 8. Isloation of RNA 9. Formaladyhyde gel elctrophoresis of RNA 10. UV mutation

IV SEMESTER

MA 262 BIOSTATISTICS FOR BIO-INFORMATICS L T P C 3 1 0 4 PURPOSE To provide an introduction to the study of Biostatistics, or the use of numerical techniques to extract information from data and facts.

OBJECTIVES

• To provide basic knowledge about statistics

• To provide the calculation tools to various distribution methods.

• Testing techniques for samples.

• Analysis knowledge and correlation methods UNIT-I NUMERICAL MEASURES Review of types and frequency distribution-Measures of central tendency – mean, median, Mode –Measures of Dispersion- range, interquartile range , Variance and Standard deviation, Coefficient of Variation-Chebychev’s inequality and Applications. UNIT –II PROBABILITY: Events and Probability- Conditional probability- Baye’s Theorem.Probability distribution- Binomial Distribution, Poisson Distribution-Normal distribution and Application problems. UNIT- III HYPOTHESIS TESTING: One and Two sided confidence intervals- types of error-Student’s t test - F- test - the chi-square test 2X2 tables, rXc tables - paired samples –Independent samples- equal variances- unequal variances. UNIT- IV ANALYSIS OF VARIANCE One way analysis of variance- sources of variation- Multiple comparisons procedures and applications. Comparison of two proportions. UNIT- V CORRELATION AND REGRESSION The two way scatter plot- Pearson’s correlation coefficient- spearman’s rank correlation coefficient. Regression concepts-the population regression line- the method of least squares- inference for regression coefficients – inference for predicted values. TUTORIAL 15 TOTAL 60 TEXTBOOK

• Marcello Pagano and Kimberlee Gauvreau, “Principles of Biostatistics”, Thomson Learning, 2

nd Edition.

Unit I: 2.1,3.1-3.4 Unit II 6.1-6.3,7.1-7.4. Unit III 9.1-9.4,10.4,12.1,15.1,11.1-11.2 Unit IV 12.1.1,12.1.2,12.2,14.6. Unit V 17.1-17.3,18.1,18.2

REFERENCES:

• Wayne W. Daniel, “Bio statistics: A Foundation for Analysis in the Health sciences “ , John Wiley and Sons, 7

th Edition

• Warren J. Ewens and Gregory R. Grant , “Statistical Methods in Bioinformatics an introduction”, Springer International Edition

• N.Gurumani , “ An Introduction to BIOSTATISTICS”, MJP Publishers

• Norman T.J. Bailey , “ Statistical Methods in Biology” , Cambridge, 3rd

Edition BI 202 BIOLOGICAL DATABASES AND

GENE SEQUENCING L T P C

3 1 0 4 PURPOSE This course enables the students to understand the biological databases, their importance and the gene sequencing methods. INSTRUCTIONAL OBJECTIVES This course emphasizes on the following:

• Importance of biological databases

• Different types of Biological databases

• DNA and genome sequencing methods UNIT I INTRODUCTION TO BIOLOGICAL DATABASES 8 Definition of biological database, Importance of biological databases, description of different file formats, bioinformatics resources in the NET UNIT II NUCLEIC ACID SEQUENCE DATABASES 12 DNA sequence databases, RNA databases, and EST databases, Published text, transcription factor databases. Sequence retrieval system like Entrez and SRS. UNIT III PROTEIN DATABASES 12 Primary, composite and secondary sequence databases, structural databank like PDB, structure classification database like SCOP, CATH. UNIT IV SPECIALIZED DATABASES 5 Metabolic pathway databases, boutique databases, bibliographic databases UNIT V DNA AND GENOME SEQUENCING METHODS 8 DNA sequencing methods: Sanger dideoxy method and Maxam-Gilbert method, shot gun approach for genome sequencing. TUTORIAL 15 TOTAL 60 TEXT BOOKS

• T.K.Attwood, “Introduction to bioinformatics”, Prentice hall, I edition, 2001.

• P. K. Gupta, “Cell and Molecular Biology”, Rastogi publications, II edition, 2003. REFERENCE BOOKS

• David W. Mount, “Bioinformatics: Sequence and Genome Analysis”, Cold spring harbor, II edition, 2004.

• Arthur M.Lesk, “Introduction to bioinformatics”, Oxford university press, 2002. BI204 GENOMICS L T P C 3 0 0 3 PURPOSE The students will be aware of the structure and functions of the genomes together with the computational approaches to analyze the genomes. INSTRUCTIONAL OBJECTIVES It gives emphasize on

• Structure, function and organization of genomes

• Computational approaches to analyze the genomes

• Microarray

• Functional and comparative genomics UNIT I GENOMES AND THEIR EVOLUTION 12 Prokaryotic and eukaryotic genomes, structure, organization, function. Evolution of genomes UNIT II GENOME SEQUENCING AND HGP 10 Genomics: Genome Sequencing, Fragment Assembly, Genome Assembly, Human Genome Project- Aims, goals and achievements. UNIT III GENOME ANALYSIS AND DNA DATABASES 9 Alignment methods- Dot plot method, dynamic programming methods, BLAST and FASTA. DNA databases with special reference to GenBank. UNIT IV GENE REGULATORY NETWORK AND MICROARRAY 8 Gene regulatory network and the models, DNA microarray and the analysis of data using clustering methods. UNIT V FUNCTIONAL AND COMPARATIVE GENOMICS 6 Introduction to functional and comparative genomics, Methods to perform comparative genomics TOTAL 45 TEXT BOOKS

• T.A.Brown, “Genome”, John Wiley & sons, II edition- for UNIT I & II.

• Bioinformatics: Sequence and Genome Analysis, David W. Mount, Cold Spring Harbor Laboratory Press, I edition, 2001- for UNIT III & V.

• Stekel Dov, “Microarray bioinformatics”, Cambridge University Press, 2003- for UNIT IV. REFERENCE BOOKS

• Issac S kohane, “Microarrays for an integrative genomics”, The MIT Press, 2002.

• Benjamin Lewin, “Gene VII”, Oxford University Press, 2000- for UNIT I, II & III.

BI206 BIOINFORMATICS ALGORITHMS L T P C 3 0 2 4 PURPOSE The purpose of this subject is to study various Algorithm design techniques and applying it in Bioinformatics INSTRUCTIONAL OBJECTIVES

• Notation and different types of Algorithms

• Mapping Algorithms and Greedy approaches.

• Dynamic programming for sequence alignment

• DNA analysis using graph Algorithms.

• Clustering and trees. UNIT I INTRODUCTION Algorithms and Complexity: Biological algorithms versus computer algorithms – The change problem –Correct versus Incorrect Algorithms – Recursive Algorithms – Iterative versus Recursive Algorithms – Big-O Notations – Algorithm Design Techniques. UNIT II GREEDY ALGORITHMS Molecular Biology Primer – Exhaustive Search – Mapping Algorithms – Motif-Search Trees – Finding Motifs – Finding a Median String – Greedy Algorithm – Genome Rearrangements – Sorting by Reversals – Approximation Algorithms – A Greedy Approach to Motif Finding. UNIT III DYNAMIC PROGRAMMING ALGORITHMS DNA Sequence comparison – Manhattan Tourist Problem – Edit Distance and Alignments – Longest Commons Subsequences – Global Sequence Alignment – Scoring Alignment – Local Sequence Alignment – Alignment with Gap Penalties – Multiple Alignment-Gene Predictions – Approaches to Gene Prediction - Spiced Alignment – Divide and Conquer Algorithms. UNIT IV GRAPH ALGORITHMS

Graphs – Graphs and Genetics – DNA Sequencing – Shortest Superstring Problem – DNA arrays as an alternative sequencing techniques – Sequencing by Hybridization – Path Problems – Fragment assembly in DNA Sequencing – Protein Sequencing and Identification – The Peptide Sequencing Problem – Spectrum Graphs – Spectral Convolution and Alignment – Combinatorial Patter matching. UNIT V CLUSTERING AND TREES Clustering and trees – Gene expression analysis – Hierarchical clustering-k-means clustering – Clustering and corrupted Cliques – Evolutionary Trees – Distance-based tree reconstruction – Reconstruction trees from additive matrices – Evolutionary trees and hierarchical clustering – Character-based tree reconstruction – Small and large Parsimony Problem – Hidden Markov Models- Randomized Algorithms. TEXT BOOK

• Neil.C.Jones and Pavel.A.Pevzner, “An Introduction to Bioinformatics Algorithms”, MIT Press, First Indian Reprint 2005.

REFERENCES

• Gusfields.G Algorithms on strings, trees and sequences: ComputerScience and Computational Biology, Cambridge University Press 1997.

• Gary Benson Roderic page(Eds), “Algorithms in Bioinformatics”, Springer International Edition, First Indian Reprint 2004.

IT208 DATABASE MANAGEMENT SYSTEM L T P C 3 1 0 4 UNIT I: INTRODUCTION Overview of RDBMS, Advantages of RDBMS over DBMS, Normalization, Oracle data types. Introduction to SQL, DDL, DML & TCL Commands. Data Definition Language, Data Manipulation Language, Transaction Control & Data, Control Language Grant & Revoke Privilage Command. UNIT II SET OPERATORS AND FUNCTIONS Operators in SQL plus,Set operators, Joins-Kinds of Joins, Table aliases, Sub queries, Multiple & correlated Sub queries. Functions-Single Row, Date Character,Numeric,Conversion, Group functions. UNIT III VIEW AND PARTITIONS Constraints, Locks & Table Partitions. Constraints-Domain, Referential Integrity Constraints. Locks, Table Partitions, Synonym, Sequences, View, Partition View, Index-Unique, Composite. UNIT IV MYSQL AND DATABASES IN MOLECULAR BIOLOGY MYSQL-Introduction,MYSQL as an RDBMS Tool, Datatypes and Commands. Databases in Molecular Biology – Bibliographic, Pub Med- Primary Derived Databases, Sequencing and Structure Databases-Value Addition to the Data base; Compilation, Maintenance and Distribution UNIT V SEQUENCING DATABASES Sequencing Databases-DNA and proteins Sequencing, GenBank and Swiss Prot, Derived Databases-Pfam, BLOCKS, etc. Structure Databases-Collection, validation of Structure Data, PDB and NDB, Derived Databases, SCOP, PALI, etc. REFERENCE BOOKS

• George Koch and Kevin Loney; ORACLE 8-The COMPLETE REFERENCE, Tata MCGraw –Hill Edition, 1998.

• Michael Abbey and Michael J. Correy; ORACLE 8- ABEGINNERS GUIDE,1997

BI 210 PERL PROGRAMMING L T P C 3 0 0 3 UNIT – I UNIX OS AND EDITORS Unix OS:Working Environment- Navigating in Unix-creating and manipulating sequence files-emacs editor-Vi editor-FTP UNIT – II UNIX COMMANDS Advanced Unix commands-Introduction-ls-cat-more-,Advanced Unix commands-mv-rm-rmdir-uniq-sort-,Advanced Unix commands-grep. UNIT – III PERL Introduction to Perl:scalars,Arrays-Using standard Perl modules-Perl regular expressions I. UNIT –IV PERL ARRAY OPERATIONS Perl debugger-Advanced array operation-Perl regular expression II. UNIT –V PERL CONTROL STATEMENT AND FUNCTIONS. Perl control statements-FILE I/O- Perl subroutines and Functions. TEXT BOOKS

• Harshawardhan P Bal,”Perl Programming for Bioinformatics”, Tata McGraw Hill,2003. REFERENCE BOOKS

• D.Curtis Jamison, Perl Programming for Bioinformatics & Biologists, John Wiley & Sons, INC., 2004

• Michael Moorhouse Paul Barry,” Bioinformatics Biocomputing and Perl”,Wiley

BI 212 PERL PROGRAMMING LAB L T P C 0 0 3 2 PRACTICAL

1. Computer Programming Lab I– Unix and Perl 2. Unix Commands 3. Working with vi, emacs editors. 4. Simple programs using Operators, Control Strucures, Subroutines, Hash Traversal

Functions, Launching External Programs Special Variables. 5. Simple programs using File Functions, Special Conditionals Command Line Args; Basic

I/O. 6. Setuid / setgid Perl Scripts Random Number Generation 7. Creating a static HTML file by a Perl Program

REFERENCE BOOKS

• Lab Manual

• D.Curtis Jamison, Perl Programming for Bioinformatics & Biologists, John Wiley & Sons, INC., 2004

BI214 BIOCOMPUTING LABORATORY L T P C 0 0 3 2

1. Knowledge of different biological database 2. Sequence retrieval from biological database 3. Identification of gene sequence 4. Identification of protein sequence 5. Sequence similarity searching of nucleotide sequences 6. Sequence similarity searching of protein sequences 7. Multiple sequence alignment 8. Dynamic programming method- local alignment 9. Dynamic programming method- global alignment

10. Pattern finding in proteins REFERENCE BOOKS

• Lab Manual V SEMESTER

BI301 PROTEOMICS AND TRANSCRIPTOMICS L T P C

3 0 0 3

PURPOSE This course helps the students to understand the proteomics and transcriptomics from the scratch INSTRUCTIONAL OBJECTIVES

• Various Protein identification and Quantitation methods

• Protein chips

• Basics of Transcriptomics UNIT I: INTRODUCTION 7 An Overview of Proteomics, Need, scope and challenges of proteomics, strategies for Protein Separation: 2D gel electrophoresis- principle and applications, Liquid chromatography- principle and applications, multidimensional liquid chromatography UNIT II: PROTEIN IDENTIFICATION AND QUANTITATION 9 Strategies for Protein Identification: Protein Identification with antibodies, protein sequence determination by chemical degradation, MS- principles, instrumentation and applications in proteomics, Strategies for Protein Quantitation: Quantitative proteomics with standard 2D gels, multiplexed proteomics, quantitative with mass spectrometry UNIT III: STRUCTURAL PROTEOMICS 10 Protein structures, techniques for solving protein structures, Protein- protein interactions- principles and methods to study them, Protein Modification in Proteomics. UNIT IV PROTEIN CHIPS 9 Protein Chips and Functional Proteomics, Applications of Proteomics in disease diagnosis, drug development and plant biotechnology. UNIT V: TRANSCRIPTOMICS 10 Features of RNA secondary structure, Basics of RNA structure prediction, Limitations of prediction, Development of RNA prediction methods, Methods –Self- complementary regions in RNA, minimum free energy method, MFOLD, Sequence covariation method TOTAL 45 TEXT BOOK

• R. M. Twyman, "Principles of Proteomics (Advanced Text Series)", Bios Scientific, 2004.

• David W Mount, "Bioinformatics- Sequence and genome analysis ", Cold Spring Harbor Laboratory Press, second edition

REFERENCE BOOKS

• S. R. Pennington, M. J. Dunn, “Proteomics: From Protein Sequence to Function”, Springer publications, first edition

BI303 INTERNET PROGRAMMING L T P C

3 1 0 4

PURPOSE

To learn the Internet Technologies INSTRUCTIONAL OBJECTIVES

• To learn about Java, HTML, DHTML concepts

• To know about server side programming

• Knowledge of XML and its applications

UNIT I BASIC INTERNET CONCEPTS 8 History of internet-Internet addressing-TCP/IP-DNS and directory services-Internet Applications-Electronic mail, New groups UUCP, FTP, Telnet, Finger. UNIT II WORLDWIDE WEB 9 Overview – Hyper Text Markup Language- Uniform Resource Locators-Protocols-M Browsers-Plug-Ins-Net meeting and Chat-Search engines. UNIT III SCRIPTING LANGUAGE 9 Java Script Programming-Dynamic HTML-Cascading style sheets-Object model and Event model- Filters and Transitions-Active X Controls-Multimedia-Client side script UNIT IV SERVER SIDE PROGRAMMING 10 Introduction to Java Servelets – overview and architecture – Handling HTTP get & post request – session tracking – Multi-tier application - Implicit objects – Scripting – Standard actions – Directives – Custom Tag libraries UNIT V CASE STUDY – AMOEBA 9 Connecting to Databases – JDBC principles – Database access – XML – Introduction – Structuring Data – XML Namespaces – XML vocabularies – Web server

TUTORIAL 15 TOTAL 60

TEXT BOOKS

• Deital and Deital, Goldberg, “Internet & World Wide Web, How To Program”, third edition, Pearson Education, 2004

REFERENCE BOOKS

• Jame Jaworski, “Java unleased”, SAMS Techmedia Publications, 1999

• Naughton, Herbert Schildt, “Java2, Complete Reference”, 4th edition, TMH, 2000

• Deital & Deital, “Java How to program”, Prentice hall 2000

• Gary Cornell, Cay S.Horstmann, Core Java Vol.1 and Vol.2, Sun Microsystems

• Ted coombs, Jason coombs, Brewer, “ Active X source book”, John Wiley

BI305 DATA MINING AND WAREHOUSING L T P C

3 0 0 3

PURPOSE This course enables to understand the concepts of Data Warehousing and Data Mining and its applications in Bioinformatics INSTRUCTIONAL OBJECTIVES

9. OLTP and Developing a Data Warehouse. 10. Data mining techniques and algorithms. 11. Data Mining environments and applications in Bioinformatics

UNIT I DATA WAREHOUSING & OLAP 9

An Introduction to data ware housing and characteristics of a data warehouse, various aspects of data marts, Online Analytical Processing: OLTP and OLAP systems, Data Modeling, OLAP Tools, web OLAP, Decision support system. UNIT II DEVELOPING A DATA WARE HOUSE 9 Architectural strategies and Organization Issues, Design Considerations, Tools for Data Warehousing, crucial decisions in designing a Data Ware house using ORACLE 8i / SQL server UNIT III DATAMINING 9 From Data ware housing to Data Mining, Objectives of Data Mining, the Business context for Data mining, Process improvement, marketing and Customer Relationship Management (CRM), the Technical context for Data Mining, machine learning, decision support and computer technology. UNIT IV DATA MINING TECHNIQUES AND ALGORITHMS 9 Process of data mining, Algorithms, Data base segmentation or clustering, predictive Modeling, Link Analysis, Data Mining Techniques, Automatic Cluster Detection, Decision trees and Neural Networks UNIT V DATA MINING APPLICATIONS IN BIOINFORMATICS 9 Biological Sequence Data Mining, Mining Positive and Negative Knowledge in Clinical Databases Based on Rough Set Model

TOTAL 45 TEXT BOOK

1. Berry and Linoff, “Mastering Data Mining: The Art and Science of Customer Relationship Management”, John Wiley and Sons, 2001.

2. C.S.R. Prabhu, “Data Ware housing: Concepts, Techniques, Products and Applications”, Prentice Hall of India, 2001.

3. L. De Raedt, A. Siebes, “Principles of Data Mining and Knowledge Discovery”, Springer publications, 2001

REFERENCE BOOKS

• J.Han, M.Kamber, “Data Mining: Concepts and Techniques”, Academic Press, Morgan Kanf man Publishers, 2001.

• Pieter Adrians, Dolf Zantinge, “Data Mining”, Addison Wesley, 2000.

• W.H.Inmon, “ Building the DataWarehouse”, 3rd

Edition, Wiley Dreamtech 2002.

• Sam Anabory & Dennis Murray, “Data Warehousing in the real world”, Addisson Wesley, 1997.

• Amitesh Sinha, “Data Ware Housing “, Thomson Asia, 2002.

BI307 MOLECULAR PHYLOGENY AND EVOLUTION L T P C

3 1 0 4

PURPOSE This course provides the basic concept of Phylogenetics and evolution at molecular level. INSTRUCTIONAL OBJECTIVES

11. To understand the various methods of phylogenetic tree construction 12. Accuracies and statistical methods of optimization 13. Molecular evolution

UNIT I: PHYLOGENETIC TREES 9 Types, topological differences, tree building methods, Distance methods: UPGMA, LS methods, minimum evaluation methods, NJ methods, phylogenetic reconstruction. UNIT II METHODS 9 Maximum parsimony methods: Strategies of searching for MP trees, consensus trees, branch length estimation, weighted parsimony, MP methods for protein data, Maximum likelihood methods

UNIT III STATISTICAL APPROACH 9 Optimization principle and topological errors, interior branch tests, bootstrap tests, Tests of topological differences, advantages and disadvantages, molecular clocks and linearized trees UNIT IV ANCESTRAL SEQUENCES 9 Inferences of ancestral sequences- parsimony and Bayesian approaches, synonymous and non-synonymous substitutions, convergent and parallel evolution UNIT V: EVOLUTION 9 Molecular basis of evolution, synonymous and non- synonymous mutations, genetic polymorphism and evolution, Population trees from genetic markers

TUTORIAL 15

TOTAL 60 TEXT BOOK

• Masatoshi Nei, “Molecular Evolution and Phylogenetics”, Oxford University Press, 2000. REFERENCE BOOKS

• David W Mount, "Bioinformatics- Sequence and genome analysis ", Cold Spring Harbor Laboratory Press, second edition

BI309 MEDICAL INFORMATICS L T P C 3 0 0 3 PURPOSE: This subject gives the students an idea on the applications of information technology in medical field. INSTRUCTIONAL OBJECTIVES:

1. Hospital management and information system 2. Computer assisted instructions 3. Computer assisted surgical techniques 4. Telecommunications based systems

UNIT I: INTRODUCTION 9 Introduction, Hospital management and information system: functional area, pre-requisites, integrated hospital information systems, health information system, and disaster management plan UNIT II: KNOWLEDGE – BASED AND EXPERT SYSTEMS 9 Artificial intelligence, expert systems, materials and methods, computer based patient Records, computer assisted medical education UNIT III: MODULES 9 Hospital Management and Information systems- structure and functions, computer assisted patient education, computer assisted patient surgery UNIT IV: COMPUTER ASSISTED SURGICAL TECHNIQUES 9 Three-dimensional imaging: limitations of endoscopy and imaging, benefits of virtual endoscopy, materials and methods, limitations, applications, merits and demerits, surgical simulation, virtual environment UNIT V: TELECOMMUNICATIONS BASED SYSTEMS 9 Tele-medicine- needs, materials and methods, Internet tele-medicine, controversial issues, reliability, cost-analysis, applications, tele-surgery, the Internet TOTAL 45 TEXT BOOKS

• Mohan Bansal, “Medical Informatics- a primer”, Tata McGraw-Hill, 2003. REFERENCE BOOKS Charles P. Friedman, Jeremy C. (EDT) Wyatt, “Evaluation Methods in Medical Informatics”, Springer verlag, 1997 BI311 STRUCTURAL BIOLOGY L T P C

3 0 0 3

PURPOSE This subject enables the students to learn about the protein and DNA structures, which are very

important in Bioinformatics INSTRUCTIONAL OBJECTIVES

• Hierarchy of protein structure

• Super secondary structures of proteins

• Structure of DNA UNIT I BASICS 9

Basics of protein structures, alpha helix, β sheets, loop regions, topological diagrams, and β motifs: hairpin, Greek key, beta-alpha-beta, domains, and classes of proteins UNIT II ALPHA STRUCTURES 9 Alpha domain structures: coiled coil, globin fold, alpha helix packing, and hydrophobic interior.

Alpha/beta structures: parallel β strands, α/ β strands, double barrels, active sites, α/ β- horse

shoe fold, α/ β twisted open sheet structures, all α/ β structures UNIT III BETA STRUCTURES 9

β Structures: domains, motifs, barrels, active sites involving β structures, haemagglutinin, parallel

β- helix domains, Folding and flexibility UNIT IV DNA STRUCTURES 9 DNA- A, B, Z: DNA recognition in prokaryotes by Helix- Turn- Helix motifs

UNITV MEMBRANE PROTEINS 9

Information regarding membrane proteins and fibrous proteins and their importance TOTAL 45 TEXT BOOK

• Carl Branden and John Tooze, “Introduction to protein structures”, Garland publishing Inc., second edition.

• Cantor and Schimmel, ”Biophysical Chemistry”, W.H.Freeman & Co.

REFERENCE BOOKS

• Voet D. Voet G, “Biochemistry”, Second Edition, John Wile and Sons, 1994

GE301 PERSONALITY DEVELOPMENT – I L T P C

0 0 1 1 PURPOSE To train the students to better in their overall competence OBJECTIVES The students will be able to improve the skills and learn new practices, emulate good manners and get Good placement. UNIT I DEFINITION AND MEANING 5 What makes up a personality, theories on Personality, Different Personality Types

UNIT II INFLUENCES ON PERSONALITY – I 5 Personal Factors – Human Traits, Ego, Perception, Self – esteem, Conscience. UNIT III INFLUENCES ON PERSONALITY – II 5 Anxiety, Stress, Leadership, Motivation, Attitude TOTAL 15 TEXT BOOK:

• S.P.Sharma “Personality Development”.

• Gearge Weinberg , “Practical Ways To A Powerful Personality”, 1999

• Dale Carnegie,”How To Win Friends And Influence People”, 2001

• Dale Carnegie, “Public Speaking”, 2000

BT311 GENETIC ENGINEERING LABORATORY L T P C

0 0 3 2 PURPOSE Provides an opportunity to experimentally verify the theoretical concepts of genetic engineering already studied. it also helps in understanding the theoretical principles in a more explicit and concentrated manner. INSTRUCTIONAL OBJECTIVES

• The student will be able to understand and develop the concept of recombinant DNA technique

• Partial digestion of bacterial genomic DNA using Sau3A

• Restriction enzyme digestion of pUC 18/19 using BamH1 and Alkaline Phosphatase treatment.

• Purification of digested DNA

• Ligation of DNA fragment with plasmid DNA

• Preparation of competent cells

• Transformation in E.Coli

• Isolation of recombinants plasmid and confirmation of insert DNA in plasmid.

• Preparation of DNA probe

• Southern Hybridisation

• Colony Hybridisation REFERENCE BOOKS

• Sambrook et al “ Molecular Cloning” A Laboratory manual

BI315 INTERNET PROGRAMMING LABORATORY L T P C

0 0 3 2 PURPOSE This laboratory course gives a complete understanding of the Internet programming concepts using Java application, applets, HTML, XML and MS-FrontPage. INSTRUCTIONAL OBJECTIVES

• Implementing HTML

• Practicing RMI, JDBC, JSP

• Animation concepts LIST OF EXPERIMENTS 1. Exercises on creating HTML pages 2. Implementation of Package Bio-Data 3. Shapes Class Hierarchy 4. Animation using Java Applets 5. MS-FrontPage

6. Implementation of simple TCP/IP Client and server 7. Operations on Employee table using JDBC 8. Constructing a simple database using XML 9. An interactive Web application in JSP 10. Using cookies to track users in browsers from the web servers 11. Constructing a secured FTP client – server application REFERENCE BOOKS

• Laboratory Manual

VI SEMESTER BI300 METABOLOMICS AND METABOLIC ENGINEERING L T P C 3 0 0 3 PURPOSE This course provides the fundamental knowledge on upcoming field of metabolomics and the metabolic engineering in post genomics era. INSTRUCTIONAL OBJECTIVES

• Metabolic engineering

• Comprehensive models cellular reactions

• Regulation of metabolic pathways

• Metabolic flux analysis and its applications UNIT I: INTRODUCTION 9 Importance of metabolic engineering, Comprehensive models for cellular reactions, material balances and data consistency UNIT II: REGULATION OF METABOLIC PATHWAYS 10 Regulation of enzymatic activity, Regulation of enzyme concentration, regulations at whole cell level, regulation of metabolic networks, Examples of pathway manipulation: extension of product spectrum and novel products. UNIT III: SYNTHESIS 10 Metabolic pathways synthesis algorithm, Case study, metabolic flux analysis, determination of metabolic fluxes by isotope labeling, UNIT IV: APPLICATIONS 9 Metabolic fluxes in mammalian cell cultures, metabolic control analysis- fundamentals, determination of metabolic controls coefficients, MCA of linear and branched pathways, theory of large deviations, metabolic network analysis- grouping of reactions UNIT V: FLUX ANALYSIS OF METABOLIC NETWORKS 7 Bottom- up and Top- down approaches, case study, optimization of flux amplification, consistency tests and experiment validation

TOTAL 45

TEXT BOOK:

• Gregory N. Stephanopoulos, “Metabolic Engineering: Principles and Methodologies”, Academic press, First Edition.

REFERENCE BOOKS:

• S. Cortassa, “An Introduction to Metabolic and Cellular Engineering”, World scientific public company Ltd. 2002

BI302 CHEMOINFORMATICS L T P C 3 1 0 4

PURPOSE This course provides knowledge on upcoming field of chemoinformatics. INSTRUCTIONAL OBJECTIVES

• Molecular descriptors

• High throughput screening

• Virtual screening

• Combinatorial chemistry and library design UNIT I: REPRESENTATION OF STRUCTURES 9 Representation and Manipulation of 2D Molecular Structures, Representation and Manipulation of 3D Molecular Structures UNIT II: MOLECULAR DESCRIPTORS AND MODELS 10 Molecular Descriptors: Introduction, Descriptors Calculated from the 2D Structure, Descriptors Based on 3D Representations, Data Verification and Manipulation, Computational Models: Introduction, deriving a QSAR Equation: Simple and Multiple Linear Regression, Designing a QSAR "Experiment", Principal Components Regression, Partial Least Squares, Molecular Field Analysis and Partial Least Squares UNIT III: SIMILARITY METHODS 10 Similarity Methods: Similarity Based on 2D Fingerprints, Similarity Coefficients, 2D Descriptor Methods, 3D Similarity, Selecting Diverse Sets Of Compounds: Cluster Analysis, Dissimilarity-Based selection methods, Cell-Based Methods, Optimization Methods, Comparison and Evaluation of Selection Methods UNIT IV: HIGH THROUGHPUT AND VIRTUAL SCREENING 9 Analysis of High-Throughput Screening Data: Data Visualisation, Data Mining Methods, Virtual Screening: Drug-Likeness and Compound Filters, Structure-Based Virtual Screening, The Prediction of ADMET Properties UNIT V: COMBINATORIAL CHEMISTRY AND LIBRARY DESIGN 7 Diverse and Focussed Libraries, Library Enumeration, Combinatorial Library Design Strategies, Approaches to Product-Based Library Design, Multiobjective Library Design, Practical Examples of Library Design

TUTORIAL 15 TOTAL 60

TEXT BOOK:

• Andrew R Leach, Valerie J Gillet, “An Introduction to Chemoinformatics”, Kluwer academic publishers, 2003.

REFERENCE BOOKS:

• Johann Gasteiger, Thomas Engel, “ Chemoinformatics: A Textbook”, Wiley-VCH, 2003

BI304 MOLECULAR MECHANICS L T P C 3 1 0 4 PURPOSE This course provides the fundamental knowledge of Molecular Modeling INSTRUCTIONAL OBJECTIVES

• Basics in molecular mechanics

• Force fields

• Simulation methods UNIT I INTRODUCTION 9 Useful concepts in Molecular Modeling- one electron and poly electron atoms and molecules- molecular orbital calculations- Hartree-Fock equations

UNIT II ABINITIO METHODS 10 Approximate molecular orbital theories- semi-empirical methods- huckel theory- performance of semi-empirical methods- Advanced ab initio methods, density functional theory and solid- state quantum mechanics. UNIT III EMPIRICAL FORCE FIELD MODELS 10 Molecular mechanics force fields- bond stretching, angle bending, torsional terms; improper torsions and out- of -plane bending motions- non- bonded interactions- hydrogen bonding in molecular mechanics- simulation of liquid water- united atom force fields- energy function

derivatives- treatment of delocalised Π system- force fields of inorganic and solid state systems UNIT IV ENERGY MINIMIZATION 8 Non-derivative minimization methods- derivative minimization methods- I order minimization methods- second derivative methods- Quasi Newton methods-applications- determination of transition structures and reaction pathways- solid-state systems UNIT V COMPUTER SIMULATION METHODS 8 Calculation- phase space-practical aspects- boundaries- monitoring the equlibration- truncating the potential and minimum image convention- long-range forces- analysis

TUTORIAL 15

TOTAL 60

TEXT BOOK

• Andrew R. Leach, “ Molecular Modelling- Principles and applications”, Prentice hall, II edition

BI306 COMPUTATIONAL NEUROSCIENCE L T P C 3 1 0 4 PURPOSE This course enables the students to understand the computational neuroscience from the basics. INSTRUCTIONAL OBJECTIVES

• Neurons, Population dynamics

• Perceptions, models of neuroscience

• Supervised Learning and Rewards Systems

UNIT I: INTRODUCTION 9 Definition, Domains in Computational Neuroscience, Emergence and from exploration to a theory of the brain, Modeling biological neurons, Basic synaptic mechanisms and the generation of action potentials: Hodgkin-Huxley equations, dendritic trees, the propagation of action potentials, and compartmental models, Hodgkin-Huxley neuron UNIT II SPIKING NEURONS AND RESPONSE VARIABILITY 9 Integrate-and-fire neurons, the spike-response model, Spike time variability, and Noise models for IF neurons, Neurons in a Network, Population Dynamics, and Networks with non-classical synapses: the sigma-pi node. Representations and the neural node: Information in spike trains, Population coding and decoding, distributed representation UNIT III FEED-FORWARD MAPPING NETWORKS 9 Perception, function representation, and look-up tables, The sigma node as perception, Multi-layer mapping networks, Learning, generalization and biological interpretations, Self-organizing network architectures and genetic algorithms, Mapping networks with context units, Probabilistic mapping networks, Associators and synaptic plasticity: Associative memory and Hebbian learning, Hebian plasticity, features of associators and Hebbian learning UNIT IV AUTO-ASSOCIATIVE MEMORY AND NETWORK DYNAMICS 9 Short-term memory and reverberating network activity, Long-term memory and auto-associators, Point attractor networks: The Grossberg-Hopfield model, sparse attractor neural networks,

Chaotic networks, biologically more realistic variations of attractor networks, Continuous attractor and competitive networks. UNIT V SUPERVISED LEARNING AND REWARDS SYSTEMS 9 Motor learning and control, the delta rule, generalized delta rules, Reward learning, System level organization and coupled networks: System level anatomy of the brain, Modular mapping networks, Coupled attractor networks, working memory, Attentive vision, an interconnecting workspace hypothesis TOTAL 45 TEXT BOOK

• Thomas Trappenberg, “Fundamentals of Computational Neuroscience”, oxford University Press, June 2002.

REFERENCE BOOKS

• Lytton, William W, “From Computer to Brain - Foundations of Computational Neuroscience, Springer publications, 2002.

BI308 COMPUTER AIDED DRUG DESIGNING L T P C

3 0 0 3 PURPOSE: This subject portraits the fundamentals and applications of computer aided drug designing INSTRUCTIONAL OBJECTIVES:

• Fundamentals of Computer Aided Drug Designing (CADD)

• Drug development

• Methods and applications UNIT I: APPLICATION OF MOLECULAR MODELING IN DRUG DESIGN 8 Molecular modeling in drug discovery, three dimensional pharmacophores, molecular docking, De-novo ligand designing, and structure-based methods, molecular similarity UNIT II: DRUG DISCOVERY 9 Drug discovery: targets and receptors, target identification and validation, drug interactions, small molecule drugs UNIT III: DRUG DEVELOPMENT 11 Pharmacodynamics, Pharmacokinetics, toxicology, animal tests, formulations and delivery systems, future perspectives UNIT IV: SUCCESS STORIES OF CADD 9 Recent successes and limitations of CADD, recent techniques and applications in pharmacophores mapping UNIT V: QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP (QSAR) 9 Analysis of QSAR, computational approaches to chemical libraries

TEXT BOOK

• Andrew R. Leach, “ Molecular Modelling- Principles and applications”, Prentice hall, II edition (unit I)

• Rick Ng, “Drugs: From Discovery to Approval”, John Wiley & sons, 2004. (Units II, III).

• Paul S Charifson, “Practical Application of Computer-Aided Drug Design”,

GE302 PERSONALITY DEVELOPMENT – II L T P C

0 0 1 1

PURPOSE To train the students to better in their overall competence OBJECTIVES The students will be able to improve the skills and learn new practices, emulate good manners and get good placement. UNIT I SKILLS FOR BETTER PERSONALITY – MANAGING ONESELF 5 Time Management, Negotiation Skills, Communication Skills (Public Speaking, Presentation Skills and Writing Skills.), G.P. and Personal Interviews. UNIT II SKILLS FOR BETTER PERSONALITY – MANAGING INTERPERSONAL RELATIONS 5 Conflict Management, Problem Solving Skills, Building and Managing Teams, Non – verbal Communication Skills. UNIT – III OTHER DIMENSIONS TO PERSONALITY DEVELOPMEN 5 Mind Reading, Philanthropy, Emulating Role – models. Self – actualization, Information Technology and its Impact on Personality. TOTAL 15 TEXT BOOK

• S.P.Sharma, “Personality Development”.

• George Weinberg , “Practical Ways To A Powerful Personality”, 1999

• Dale Carnegie,” How To Win Friends And Influence People”, 2001

• Dale Carnegie, “Public Speaking”, 2000

BT208 IMMUNOLOGY LABORATORY L T P C 0 0 4 2

PURPOSE Provides an opportunity to experimentally verify the theoretical concepts already studied. it also helps in understanding the theoretical principles in a more explicit and concentrated manner INSTRUCTIONAL OBJECTIVES The students should be able to develop their skills

• Isolation of antibodies

• Purification of antibodies

• Immunoelectrophoresis

• Blood grouping

• Leucocyte count

• PBMC preparation and their enumeration

• Production of polyclonal antibodies – preparation of antigen – protocol for immunization in rabbits

• methods of bleeding-purification of polyclonal antibodies

• Antigen-antibody reaction-Haemagglutination, precipitation-Widal and VDRL

• Immunodiffusion, Immunoelectrophoresis.

• Affinity chromatiography for antibody purification.

• ELISA-DOT and plate ELISA

• Western blotting REFERENCE BOOKS

• A hand book of Practical and Clinical Immunology by Talwar GP and Gupta SK Vol.12 CBS Publication

BI310 DRUG DESIGNING LABORATORY L T P C 0 0 3 2

PURPOSE This Lab Course will enable the students to familiarize themselves with drug designing aspects. INSTRUCTIONAL OBJECTIVES

• To identify the targets

• To find the possible drug targets LIST OF EXERCISE Homology modelling of proteins Threading methods Characterization of proteins Analysis of 2D and 3D structures of proteins Finding the active sites in a receptor Docking methodologies

REFERENCE

• LAB MANUAL

VII SEMESTER BI401 GENETIC ALGORITHM L T P C 3 1 0 4 PURPOSE This course gives a complete understanding of the concepts of Genetic algorithm. INSTRUCTIONAL OBJECTIVES Mathematical foundations for Genetic algorithm, operators Applications of Genetic Algorithms. Genetic based machine learning and its applications.

UNIT I INTRODUCTION TO GENETIC ALGORITHM 9 Introduction to Genetic Algorithm – Robustness of Traditional Optimization and Search methods – Goals of optimization-GA versus Traditional methods – Simple GA – GA at work –Similarity templates (Schemata) – Learning the lingo - Mathematical foundations: The fundamental theorem - Schema processing at work. – The 2-armed & k-armed Bandit problem. –The building Block Hypothesis. – Minimal deceptive problem. UNIT II GA OPERATORS 11 Data structures – Reproduction- Roulette-wheel Selection – Boltzman Selection – Tournament Selection-Rank Selection – Steady –state selection –Crossover mutation – A time to reproduce, a time to cross. – Get with the Main program. – How well does it work. – Mapping objective functions to fitness forum. – Fitness scaling. Coding – A Multi parameter, Mapped, Fixed – point coding – Discretization – constraints. UNIT III APPLICATIONS OF GA 11 The rise of GA – GA application of Historical Interaction. – Dejung & Function optimization – Current applications of GA - Advanced operators & techniques in genetic search: Dominance, Diploidy & abeyance – Inversion & other reordering operators. – Other mine-operators – Niche & Speciation – Multi objective optimization – Knowledge-Based Techniques. – GA & parallel processes – Real life problem. UNIT IV INTRODUCTION TO GENETICS-BASED MACHINE LEARNING 7 Genetics – Based Machine learning – Classifier system – Rule & Message system – Apportionment of credit: The bucket brigade – Genetic Algorithm – A simple classifier system in Pascal. – Results using the simple classifier system. UNIT V APPLICATIONS OF GENETICS-BASED MACHINE LEARNING 7 The Rise of GBMC – Development of CS-1, the first classifier system. – Smitch’s Poker player. – Other Early GBMC efforts. –Current Applications.

TUTORIAL 15

TOTAL 60

TEXT BOOK

• David E. Gold Berg, “Genetic Algorithms in Search, Optimization & Machine Learning”, Pearson Education, 2001.

• S.Rajasekaran, G.A.Vijayalakshmi Pai, “Neural Networks, Fuzzy Logic and Genetic Algorithms“, PHI, 2003 (Chapters 8 and 9).

REFERENCE BOOKS

• Kalyanmoy Deb, “Optimization for Engineering Design, algorithms and examples”, PHI 1995.

BI403 MOLECULAR DYNAMICS L T P C 3 1 0 4 PURPOSE This course provides the knowledge on advanced Molecular Modeling INSTRUCTIONAL OBJECTIVES Molecular dynamics simulation methods Monte carlo simulation methods Conformational analysis Protein structure prediction methods UNIT I: MOLECULAR DYNAMICS SIMULATION METHODS 9 Introduction- using simple models and continuous potentials- setting up and running molecular dynamics simulations- constraint dynamics- time dependant properties- conformational changes- chain amphiphiles UNIT II: MONTE CARLO SIMULATION METHODS 9 Calculating properties by integration- metropolis methods- metropolis Monte Carlo methods- simulations of molecules- models- biased methods- different ensembles- calculating chemical potentials- Gibbs ensemble methods UNIT III: CONFORMATIONAL ANALYSIS 9 Systematic methods- model building approaches- random search methods- distance geometry- conformational space- variations- global energy minimization- structural databases- molecular fitting- clustering algorithms- dimension reduction- poling UNIT IV: IN PROTEOMICS 7 First principle methods- comparative modeling- sequence alignment- comparative models- threading- CASP- protein folding and unfolding UNIT V: CHALLENGES IN MOLECUALR MODELING 11 Free energy calculations- calculation of free energy differences- applications- calculation of enthalpy and entropy differences- partitioning free energies- free energy methods- continuum representations of solvents- the Born and Onsager models-solvation models- modeling chemical reactions and solid state defects

TUTORIAL 15

TOTAL 60

TEXT BOOK

• Andrew R. Leach, “ Molecular Modelling- Principles and applications”, Prentice hall, II edition

BI405 PHARMACOGENOMICS AND PHARMACOGENETICS L T P C 3 0 0 3

PURPOSE This course gives the in-depth knowledge on Pharmacogenomics and Pharmacogenetics INSTRUCTIONAL OBJECTIVES Promise of personalized medicines Pharmacogenetics

UNIT I: INTRODUCTION 8 Historical aspects of Pharmacogenetics, Pharmacogenomics, Biomarkers, and the promise of personalized medicine UNIT II: PHARMACOGENETICS 10 Pharmacogenetics and drug metabolism, receptors, of drug transporters UNIT III: DRUG RESPONSE 11 Inter ethnic drug response, clinical viewpoints, technologies and challenges UNIT IV: SINGLE NUCLEOTIDE POLYMORPHISM 9 Introduction, technologies for the analysis of SNPs, molecular diagnostics UNIV V: SAGE 7 Serial Analysis of Gene Expression (SAGE)- functional biology, mapping of disease loci TOTAL 45

TEXT BOOK

• Werner Kalow, Rachel F Tyndale, Urs A Meyer, “Pharmacogenomics”, Marcel Dekker Inc., 2001

REFERENCE BOOKS

• Adam Hedgecoe, “The Politics of Personalized Medicine: Pharmacogenetics in the Clinic”, Cambridge University Press, first edition.

BI407 IMMUNOINFORMATICS L T P C 3 0 0 3

PURPOSE This course gives the fundamental knowledge on Immunoinformatics INSTRUCTIONAL OBJECTIVES Methods Applied in Immunological Bioinformatics Prediction methods Application of microarray in Immunology UNIT I: SEQUENCE ANALYSIS 9 Alignments, DNA alignments, Molecular evolution and phylogeny, viral evolution and escape, prediction of functions UNIT II: METHODS 9 Methods applied in Immunological Bioinformatics- starting from sequence weighing methods to cluster analysis, applications of microarray UNIT III: APPLICATIONS 10 Prediction of Cytotoxic T Cell (MHC Class I) Epitopes, Antigen Processing in the MHC Class I Pathway UNIT IV: PREDICTION METHODS T CELL 9 Prediction of Helper T Cell (MHC Class II) Epitopes, Processing of MHC Class II Epitopes

UNIT V: B CELL EPITOPES 8 Recognition of Antigen by B Cells, vaccine design, Web-Based Tools for Vaccine Design TOTAL 45 TEXT BOOKS

• Ole Lund, “Immunological Bioinformatics”, MIT press, September 2005 REFERENCE BOOKS

• Rammensee, “Immunoinformatics: Bioinformatics Strategies for Better Understanding of Immune Function”, No. 254 [E-Book], Novartis Foundation

BI409 BIOCOMPUTING LABORATORY II L T P C

0 0 3 2 PURPOSE This laboratory course gives a complete understanding of immuno informatics, INSTRUCTIONAL OBJECTIVES Immunoinformatics LIST OF EXPERIMENTS

1. Immuno informatics 2. Epitope prediction 3. Conformational epitope prediction 4. Sequential epitope prediction 5. Promiscuous regions predictions 6. MHC-I binding sites predictions 7. MHC –II binding sites predictions

REFERENCE BOOKS

• Laboratory Manual

BI411 MINI PROJECT L T P C

0 0 6 3 PURPOSE: This is the first phase of the project work that is to be completed during the eighth semester. The students are expected to form groups and finalize project title. Requirement specification and design phases should be completed during the semester. The students are also expected to show the profound percentage of their actual work. Internal Assessment will be based on the reviews (minimum 2) conducted.

VIII SEMESTER BI400 TOTAL QUALITY MANAGEMENT L T P C 3 0 0 3 PURPOSE Total Quality Technology includes a number of methodologies, tools and techniques used at either or both strategic and operational levels INSTRUCTIONAL OBJECTIVES

To deal with interface of total quality with wide spectrum of activities ranging from design, purchasing, manufacturing, process control, technology, systems, maintenance, service and customer satisfaction

. UNIT I INTRODUCTION TO TOTAL QUALITY MANAGEMENT 6 Evolution to Total Quality Management – Classical approaches to TQM – Developed models of TQM – Japanese versus American Approach towards TQM – Humanistic approaches of TQM – contributors towards TQM –Authors: Edwards Deming, Joseph M.Juran, Philip B.Crosby, and Genichi Taguchi UNIT II TQM&PRODUCTION RELATED FUNCTIONS 6 TQM and Design – TQM and purchasing and Supply chain management – TQM and Manufacturing Technology & Systems – TQM and the Customer UNIT III QUALITY MANAGEMENT TOOLS 7 Problem Solving – Step in Problem Solving – Seven Basic Quality Control Tools – Kaizen -Quality function deployment – concept – QFD process matrix – Taguchi loss function – Pokayoke, Japanese 5 – S House keeping model, statistical process control (mean, range, fraction defective and number of defects charts) - Total preventive maintenance & TQM - JIT - Kanban System - Business process reengineering UNIT IV QUALITY ASSURANCE 8 Bench Marking – Types of Bench Marking - TQM & Employee Empowerment - Quality Circles - Self managed teams - Developing quality culture - Total Quality Culture - 3-MUs checklist - Five Ws - One H-chekclist - 4Ms checklist for quality improvement - Corporate Culture & Organizational change UNIT V QUALITY MANAGEMENT SYSTEMS 8 Difference between ISO 9000 & TQM-Quality management Systems – ISO 9000 General & Revised ISO 9000 (2000) standards – ISO 14000 Environmental Management System (EMS) standards – QS 9000 System – Quality Audits TOTAL 45 TEXT BOOK

• Sunil Sharma , “Total Quality Engineering Management”, –– Macmillan India

• Dr.D.D.Sharma – Sultan Chand, “Total Quality Management” –TQM – K.Sridhara Bhat – Himalayan Pub.

• Dale H. Besterfield, “Total Quality Management” – Pearson Education, First edition.

REFERENCE BOOKS

• Sundarajan S.M., “Total Quality Management”, –, TAT Mc Graw Hill

• Bureau of IS, Guidelines for ISO 9000 implementation. Group I Electives

BI350 IMAGE PROCESSING (same as IT451)

L T P C

3 0 0 3 PURPOSE This course provides a fundamental knowledge of Digital Image Processing Techniques INSTRUCTIONAL OBJECTIVES Digital Image fundamentals, Image Transform Image enhancement and restoration techniques Image segmentation and Compression

UNIT I DIGITAL IMAGE FUNDAMENTALS 9

Digital image – applications of digital image processing – elements of digital image processing systems – vidicon camera – line scan CCD sensor – area sensor – flash A/D converter – display – elements of visual perception – structure of the human eye – luminance – brightness – contrast – mach band effect – image fidelity criteria – colour models – RGB, CMY, HIS mathematical preliminaries of 2D systems – convolution – Fourier transform – ZS transform – toeplitz and circulant matrices – orthogonal and unitary matrices. UNIT II IMAGE TRANSFORM 9 Properties of unitary transform – 2D DFT- DCT- DST- Discrete wavelet transform – Discrete Hadamard – Walsh – Hotelling transform – SVD transform – Slant, Haar transforms. UNIT III IMAGE ENHANCEMENT AND RESTORATION 9 Contrast stretching – intensity level slicing – Histogram equalization – spatial averaging – directional smoothing – Median filtering – non linear filters – maximum, minimum, geometric mean, Harmonic mean contra-harmonic mean, Lp mean filters – edge detection – Roberts, Sobel, Isotropic, Kinsch, Campass gradient, Laplacian operators- Degradation model – unconstrained and constrained restoration – inverse filtering – removal of blur caused by uniform linear motion – Wiener filtering – geometric transformations for image restoration. UNIT IV IMAGE COMPRESSION 9 Huffman coding – truncated Huffman coding – B2, binary codes, arithmetic coding – bit plane coding – contrast area coding – Run length encoding – transform coding JPEG and MPEG coding schemes.

UNIT V IMAGE SEGMENTATION 9 Pixel based approach – feature threshold – choice of feature - optimum threshold - threshold selection methods – region based approach – region growing – region splitting –region merging, split and merge.

TOTAL 45

TEXT BOOK

• Gonzalez, R.C and Woods, R.E, “Digital Image Processing “, Addition – Wesley, 2000.

• Anil.K.Jain “Fundamentals of digital image processing”, PHI, 1997. REFERENCE BOOKS

• Umbaugh,S.E , “Computer vision and image processing”, Prentice Hall International, Inc,1998

• William. K. Pratt, “Digital image processing”. Wiley Interscience, 2000.

BI352 GENETIC ENGINEERING (same as BT303)

L T P C

3 0 0 3 PURPOSE Provides an opportunity to understand the theoretical concepts of genetic engineering principles in a more explicit and concentrated manner. INSTRUCTIONAL OBJECTIVE

• Learn the basic tools in recombinant technology

• Understand the various concepts of cloning vectors

• Learn the cloning strategies

• Acquire knowledge on the applications of genetic engineering

UNIT I BASIC TOOLS IN GENETIC ENGINEERING 8 Restriction enzymes-Classification-nomenclature; Ligases-Modifying enzymes; Probe preparation-Radioactive labels-nonradioactive labels-Different labeling methods; Southern hybridization-Northern hybridization; Autoradiography; PCR-different kinds-Application; DNA sequencing; DNA finger printing-RFLP Analysis-chromosome walking. UNIT II CLONING VECTORS-PROKARYOTES 10 Plasmid biology-Plasmids as vectors- PBR322- Derivatives of pBR 322- pUC vectors-Other artificial plasmids-Phage-Lifecycle-M13-Lambda phages-Invitro packaging-Cosmids-Phasmids-Cloning vectors in Gram positive bacteria- Cloning vectors in streptomycetes UNIT III CLONING STRATEGY 10 Construction of recombinant DNA: Preparation of competent cell-Transformation, transfection-Recombinant selection and screening; Genomic DNA library; cDNA synthesis strategies -Linkers-Adapters-Homopolymer tailing; cDNA library UNIT IV EXPRESSION VECTORS 10 Eukaryotic cloning vectors-Prokaryotic expression system-Eukaryotic expression vectors- Yeast expression system-Retroviral vectors-Bacullovirus, Mammalian cells-SV40; Gene transfer techniques UNIT V GENE MODIFICATION & APPLICATIONS 7 Mutagenesis-Deletion mutagenesis, Oligonucletoide derived mutagenesis, Site directed mutagensis-Its applications; Applications of rDNA technology in Diagnistics; Pathogensis; Genetic diversity; Therapeutic proteins-Vaccines TOTAL 45 TEXT BOOK:

• T.A. Brown, “Gene Cloning and DNA Analysis: An Introduction”, Blackwell Science (UK), 5th Edition, 2001

• Old R.W.Primrose SB, “Principles of Gene Manipulation, An Introduction to Genetic Engineering”, Blackwell Scientific Publications

REFERENCES:

• Winnacker, “From Genes to Clones: Introduction to gene technology”, VCH publishers, 1987.

BI354 ARTIFICIAL INTELLIGENCE

(Same as IT459) L T P C

3 0 0 3 PURPOSE The purpose of this course is to give students an in-depth understanding of Artificial Intelligence methodologies, techniques, tools and results. Interactions between Artificial Intelligence and other disciplines will be explored. OBJECTIVES To enable the student to understand Various searching techniques used in problem solving, deal with ignorance and vagueness Planning agents and the algorithm used.

UNIT I INTRODUCTION 6 What Is AI - The Foundations of Artificial Intelligence -The History of Artificial Intelligence, Intelligent Agents-How Agents Should Act - Structure of Intelligent Agents -Environments UNIT II SEARCH METHODS 10 Solving Problems by Searching: Problem-Solving Agents -Formulating Problems -Search Strategies -Avoiding Repeated States -Constraint Satisfaction Search. Informed Search Methods: Best-First Search -Heuristic Functions -Memory Bounded Search - Iterative Improvement Algorithms. Game Playing: Introduction: Games As Search Problems -Perfect Decisions In Two-Person Games-Imperfect Decisions - Alpha-Beta Pruning -Games That Include An Element Of Chance. UNIT III LOGICAL REASONING SYSTEMS 9 First-Order Logic: Syntax and Semantics-Extensions and Notational variations-Using First Order Logic. Introduction to Logical Reasoning system Indexing, Retrieval and Unification-Logical Programming Systems-Theorem Provers-Forward-Chaining Production Systems-Frame Systems and Semantic Networks. UNIT IV REASONING UNDER UNCERTAINTY 10 Uncertainty: Acting under Uncertainty -Basic Probability Notation - The Axioms of Probability - Bayes' Rule and its Use. Probabilistic Reasoning Systems: Representing Knowledge in an Uncertain Domain-The Semantics of Belief Networks -Inference in Belief Networks -Inference in Multiply Connected Belief Networks – Non monotonic reasoning. Dealing with ignorance: Dempster Shafer theory. Dealing with vagueness: Fuzzy logic and fuzzy sets. UNIT V PLANNING AND LEARNING 10 Planning A Simple Planning Agent -From Problem Solving to Planning -Planning in Situation Calculus -Basic Representations for planning -A Partial-Order Planning Example -A Partial-Order Planning Algorithm, Learning: A General Model of Learning Agents - Inductive Learning- Learning Decision Trees -Neural Networks - Bayesian Methods for Learning Belief Networks - Genetic Algorithms and Evolutionary Programming. Knowledge in Learning: Explanation-Based Learning. TOTAL 45 TEXT BOOK

• Stuart Russel and Peter Norvig, “Artificial Intelligence: A Modern Approach”, Prentice Hall, 1995.

REFERENCE BOOKS

• George F Luger, “Artificial Intelligence”, Pearson Education, 4th Edition, 2001.

• Engene Charniak and Drew Mc Dermott, “Introduction to Artificial Intelligence”, Addison Wesley, 2000.

• Nils J. Nilsson, “Principles of Artificial Intelligence”, Narosa Publishing House, 2000.

• Dan W. Patterson, “Introduction to Artificial Intelligence and Expert systems”, Prentice Hall of India, 1992.

• Robert J Schalkoff, “Artificial Intelligence: An Engineering Approach”, McGraw Hill, 1990.

BI356 IMMUNOLOGY (Same as BT207)

L T P C

3 0 0 3 PURPOSE Aimed at introducing the science of immunology and detail study various types of immune systems their classification structure and mechanism of immune activation. INSTRUCTIONAL OBJECTIVES The immune system, their structure and classification, genetic control of antibody production Cellular immunology Mechanism of activation in hypersensitive immune reaction UNIT I IMMUNE SYSTEM 6 Lymphocytes-their origin and differentiation- antigen-their structure and classification-complement and their biological functions-Types of immune responses-anatomy of immune response UNIT II HUMORAL IMMUNITY 12 B Lymphocytes-their activation-structure and function of immunoglbulin-immunoglobulin classes and subclasses-genetic control of antibody production-monoclonal antibodies-diagnosis-idiotypes-idiotypic antibodies-Major Histo Compatability complex-HLA UNIT III CELL MEDIATED IMMUNITY10 Thymus derived lymphocytes (T cells), their classification-antigen presenting cells-macrophages-langerhans cells-their origin and functions-mechanism of phagocytosis-immunosuppression-immunolotolerance. UNIT IV TRANSPLANTATION ANDAUTOIMMUNITY 10 Graft rejection-evidence and mechanism of graft rejection-prevention of graft rejection-immuno suppressive drugs-Role of HLA mechanism of immunity to tumor antigens-Auto antiboides in human-autoimmune disorders UNIT V MOLECULARIMMUNOLOGY 7 Preparation of vaccines-application of DNA technologies catalytic antibodies-Immunotherapy with genetically engineered antibodies-techniques-Immunodiffusion, RIA, ELISA western blot-Epitope mapping

TOTAL 45 TEXT BOOK

• Janus Kuby “Immunology” W.H.Freeman&Co.

• Roitt, I.M., Brastoff.J., and Male D.K., “Immunology” Mosby Publication

BI358 NEURAL NETWORKS L T P C

3 0 0 3 PURPOSE This course provides a way to study the Artificial Neural Networks and its applications. INSTRUCTIONAL OBJECTIVES To learn the basics of ANN in comparison with Human brain To learn the various architectures of building an ANN and its applications Advanced methods of representing information in ANN like self-organizing networks and competitive learning

UNIT I INTRODUCTION 9 Artificial Neural Networks - Architectures, Definition and Fundamental Concepts - A Brief Overview - Engineering Approaches to Neural Computing - The Mappings View point - The Structure Viewpoint - Learning Approaches - Mathematical Foundations for ANN Study: Vector and Matrix Fundamentals - Geometry for State - Space Visualization- Optimization.

UNIT II PERCEPTRONS 9 Elementary ANN Building Blocks: Biological Neural Units - Artificial Unit Structures - Unit Net Activation to Output Characteristics - Artificial Unit Model Extensions - Single Unit Mappings and Perceptron : Introduction - Linear Separability - Techniques to Directly Obtain Linear Unit Parameters - Perceptrons and Adaline / Madaline Units and Networks - Multilayer Perceptrons - Gradient Descent Training using Sigmoidal Activation Functions. UNIT III PATTERN ASSOCIATORS & FEEDFORWARD NETWORKS 9 Introduction to Neural Mappings and Pattern Associator Applications: Neural Network based pattern associators - The Influence of Psychology on PA Design and Evaluation Linear Associative Mappings - Training and Examples - Hebbian or Correction based learning - Feed Forward Networks and Training : Multilayer Feedforward Network Structure - The Delta Rule - Architecture – Hidden Layer--Mapping Capability. UNIT IV EXTENSIONS AND ADVANCED TOPICS 9 Feedforward Pattern Associator Design - Weight Space - Error Surfaces and Search - Generalization - Output Error Norms - Higher Order Derivative Based Training - Stochastic Optimization for Weight Determination - Network Architecture Determination Problem - Genetic Algorithms for Network Training – Network Cascade Correlation - Minimization – Inversion. UNIT V COMPETITIVE AND SELF-ORGANISING NETWORKS 9 Introduction - Formal Characterization and General Clustering Procedures - Competitive Learning Architectures and Algorithms - Self - Organising Feature Maps - Adaptive Resonance Architectures - RBF Networks and Time Delay Networks - ANN Hardware and Implementation.

TOTAL 45 TEXT BOOK Robert.J.Schalkoff, “Artificial Neural Networks”, McGraw Hill International Ed..1997. REFERENCE BOOKS James. A.Freeman and David. M.Skapura, “Neural Networks Algorithms, Applications and programming Techniques”, Pearson Education, 2002. Simon Haykin,"Neural Networks - A Comprehensive Foundation”, Pearson Education Asia. 2002. B.Yegnanarayana,"Artificial Neural Networks", Prentice -Hal of India, 2001. Group II Electives

BI450 MICROARRAY- TECHNIQUES AND APPLICATIONS L T P C 3 0 0 3 PURPOSE This course provides core knowledge on techniques and applications of Microarray. INSTRUCTIONAL OBJECTIVES Microarray designing Image processing and normalization Analysis of Microarray data UNIT I: INTRODUCTION 9 Microarray- making and using microarrays, types of Microarray, sequence databases for microarrays UNIT II: COMPUTER DESIGN OF OLIGONUCLEOTIDE PROBES 9 Introduction- filtering- cross-hybridization prediction- Image processing UNIT III: NORMALIZATION 9 Introduction- data cleaning and transformation-within array normalization- between array normalization- measuring and qualifying microarray variability

UNIT IV: ANALYSIS 12 Analysis of differentially expressed genes- fundamental concepts and hypothesis rules-analysis of relationships between genes, tissues or treatments- classification of tissues and samples UNIT V: EXPERIMENTAL DESIGN 6 Blocking, randomization and blinding- choice of technology-data standards, storage and sharing TOTAL 45 TEXT BOOK Dov Stekel,” Microarray Bioinformatics”, Cambridge University Press, 2003. REFERENCE BOOKS David W Mount, "Bioinformatics- Sequence and genome analysis ", Cold Spring Harbor Laboratory Press, second edition

BI452 PROTEIN ENGINEERING L T P C 3 0 0 3 PURPOSE The course imparts advanced knowledge on proteins through a detailed study of protein Structure, its characteristics property and significance in biological systems INSTRUCTIONAL OBJECTIVE To focus and advanced knowledge on primary secondary structure of and their determined Protein design principles and database analysis UNIT I PRIMARY AND SECONDARY STRUCTURE 9 Primary structure and its determination secondary structure prediction and determination of super secondary structures, proteins folding pathways. UNIT II RECEPTORS 9 Membrane proteins and receptors, bacteriohodopsin, photosynthetic centres, epidermal growth factor. Insulin and PDGF receptors and their interaction with effectors, protein phosphorylation, immunoglobulins, Nucleotide and binding proteins, enzymes serine proteases, ribonuclease, lysozyme UNIT III ENGINEERING OF MACROMOLECULES 9 Basic outline, Rational and steps involved in protein engineering. Protein design principles and examples UNIT IV DATA ANALYSIS METHODS 9 Protein database analysis methods, to alter primary structure of proteins, Theory, Interactive graphics programme, perturbation UNIT V METHODS OF PROTEIN ENGINEERING 9 Methods of Proteins engineering, Immunotoxins, Drug Designing.

TOTAL 45 TEXT BOOK

• Moody PCE, and Wilkinson AJ – “ Protein Engineering ”, IRL press oxford 1990

• Branden C, Tooze R “Introduction of Protein structure”, Garland 1993. REFERENCE BOOKS

• Creighton, TE, “ Proteins “, Freeman WH Second Ed 1993

BI454 BIOCONFINEMENT OF GENETICALLY MODIFIED

ORGANISMS (same as GN451)

L T P C

3 0 0 3 PURPOSE This course deals with the importance of bioconfinement of genetically modified organisms. INSTRUCTIONAL OBJECTIVES

• To make the students to understand the need of bioconfinement of genetically engineered organisms

• To impart knowledge on methods of bioconfinement UNIT I INTRODUCTION TO BIOCONFINEMENT 9 Genetically Engineered Organisms --Bioconfinement -- Methods of Bioconfinement, International Aspects -- History of Confinement -- Social Acceptability of Bioconfinement Methods, UNIT II NEED FOR BIOCONFINEMENT 9 Risk factors -- Effects on Nontarget Species -- Delaying the Evolution of Resistance -- Food Safeth and Other Issues -- Need for Bioconfinement UNIT III BIOCONFINEMENT OF PLANTS AND ANIMALS 9 Genetically Engineered Trees -- Transgenic Grasses -- Transgenic Algae Effectiveness at Different Spatial and Temporal Scales -- Monitoring and Managing Confinement Failure -bioconfinement of fish, and insects UNIT IV BIOCONFINEMENT OF VIRUSES, BACTERIA, AND OTHER MICROBES 9 Introduction -- Potential Effects or Concerns, and Need for Bioconfinement in Viruses, Fungi, and Bacteria UNIT V BIOLOGICAL AND OPERATIONAL CONSIDERATIONS FOR BIOCONFINEMENT 9 Execution of Confinement -- International Aspects -- Bioconfinement – Bioconfinement Research TOTAL 45 TEXT BOOK

• Biological confinement of genetically engineered organisms by national research council : National Academics press

BI456 BIO PROCESS PRINCIPLES L T P C

3 0 0 3 PURPOSE This subject puts emphasis on the basic engineering principles of bioprocess. It also highlights the modern application of biotechnological process and the role of bio process engineer in biotechnological industry INSTRUCTIONAL OBJECTIVE To study the historical development of bio process technology To evaluate the kinetics and thermodynamics of enzymatic process To teach the principle of sterilization design To study the stoichiometry and energetics of cell growth and product formation To evaluate the kinetics and mechanism of microbial growth

UNIT I INTRODUCTION TO BIOPROCESS 6

Historical development of bioprocess technologies, an overview of traditional and modern applications of biotechnological processes, role of bioprocess engineer in the biotechnology industry, concept of Bioprocess outline of an integrated bioprocess and the various (upstream and downstream) unit operations involved in bioprocesses, generalized process flow sheets UNIT II FERMENTATION PROCESS 8 General requirements of fermentation processes, Different types of fermentations, Basic design and construction of fermentor and ancillaries, main parameters to be monitored and controlled in fermentation processes, an overview of aerobic and anaerobic fermentation processes and their application in the biotechnology industry solid-substrate fermentation and its applications. UNIT III METABOLIC STOICHIOMETRY AND ENERGETICS 10 Stoichiometry of cell growth and product formation, elemental balances, degrees of reduction of substrate and biomass available, electron balances, yield coefficient of biomass and product formation maintenance coefficients, energetics analysis of microbial growth and product formation, oxygen consumption and heat evolution in aerobic cultures, thermodynamic efficiency of growth. Kinetics and thermodynamics of enzyme-catalyzed reactions UNIT IV MEDIA DESIGN AND STERILIZATION FOR FERMENTATION PROCESS 12 Designing of media for fermentation processes, examples of simple and complex media, design and usage of various commercial media for industrial fermentations, thermal death kinetics of micro organisms, batch and continuous heat sterilization of liquid media, filter sterilization of liquid media, air, design of sterilization equipment. UNIT V KINETICS OF MICROBIAL GROWTH AND PRODUCT FORMATION 9 Phases of cell growth in batch cultures, simple unstructured kinetic models for microbial growth, Monod model, growth of filamentous organisms. Growth associated (primary) and non-growth associated (secondary) product formation kinetics, Laedeking – Piret models, substrate and product inhibition on cell growth and product formation. Introduction to structured models for growth and product formation TOTAL 45 REFERENCE BOOKS Bailey and Ollis, “Biochemical Engineering Fundamentals”, McGraw Hill (2nd Ed.). 1986. Shule and Kargi, “Bioprocess Engineering”, Prentice Hall, 1992. Alba S., Humphrey E and Milli N.R., “Bio Chemical Engineering”, Academic Press, 1973. BI458 BIODIVERSITY AND MANAGEMENT FOR

BIOTECHNOLOGY L T P C

3 0 0 3 PURPOSE This course creates awareness on the management, and diversification of bio-technological processes INSTRUCTIONAL OBJECTIVE To introduce the characterizations and distributions of biodiversity To familiarize the students, with the principles, monitoring, analysis of biodiversity and ecosystem To emphasize on communication biotechnology To highlight upon the economic values and human influences on biodiversity To create awareness on measures for conservation of biodiversity

UNIT I INTRODUCTION 9 Introduction – characterization of biodiversity magnitude and distribution of biodiversity Generation and maintenance and loss of biodiversity UNIT II BIODIVERSITY ASSESSMENT AND MONITORING 9 Biodiversity and ecosystem functioning basic principles ecosystem analysis inventorying and monitoring pf biodiversity the resources base of biodiversity assessments

UNIT III COMMUNICATION BIOTECHNOLOGY 9 Data and information management and communication biotechnology UNIT IV ECONOMICS OF BIODIVERSITY 9 Human influences on biodiversity economics values of biodiversity UNIT V BIODIVERSITY CONSERVATION 9 Measures for conservation of Biodiversity and sustainable use of its components TOTAL 45 TEXT BOOKS Heywood V.H and Watscen R.T, “ Global Biodiversity Assessments ” Cambridge Univ Press 1995 Group III Electives BI451 PATTERN RECOGNITION TECHNIQUES L T P C 3 0 0 3 PURPOSE This course provides a way to learn the various pattern recognition techniques and their applications. INSTRUCTIONAL OBJECTIVES Pattern features and Statistical techniques. Cluster analysis and synthetic pattern recognition. Feature extraction techniques and advances in the field.

UNIT I INTRODUCTION 7 Pattern and features – Training and learning in pattern recognition systems – Pattern recognition approaches – Statistical pattern recognition – Syntactic pattern recognition – Neural pattern recognition – Reasoning driven pattern recognition – Discriminant functions – Linear and Fisher’s discriminant functions. UNIT II STATISTICAL PATTERN RECOGNITION 10 Gaussian model – Supervised learning – Parametric estimation – Maximum likelihood estimation – Bayesian parameter estimation – Perceptron algorithm – LMSE algorithm – Problems with Bayes approach – Pattern classification by distance functions – Maximum distance pattern classifier. UNIT III CLUSTER ANALYSIS 8 Unsupervised learning – Clustering for unsupervised learning and classification – C-means algorithm – Hierarchical clustering procedures – Graph theoretic approach to pattern clustering – Validity of clustering solutions. UNIT IV SYNTACTIC PATTERN RECOGNITION 8 Elements of formal grammar – String generation as pattern description – Recognition of syntactic description – Parsing – Stochastic grammar and applications – Graph based structural representation. UNIT V FEATURES EXTRACTION AND RECENT ADVANCES 12 Entropy minimization – Karhunen –Loeve transformation – Neural network structures for pattern recognition – Unsupervised learning – Self organizing networks – Fuzzy pattern classifiers – Genetic algorithms – Application to pattern recognition. TOTAL 45 TEXT BOOK Earl Gose, Richard Johnsonbaugh, Steve Jost, “Pattern Recognition and Image Analysis”, Prentice Hall of India Private Ltd., New Delhi – 110 001, 1999. Duda R.O. and Hart P.E., “Pattern Classification and Scene Analysis”, Wiley, New York, 1973.

REFERENCE BOOKS Morton Nadler and Eric Smith P., “Pattern Recognition Engineering”, John Wiley and Sons, New York, 1993. Touand, Gonzalez R. “Patten Recognition Principles” Addison Wesley, 1974. Robert J, Schalkoff, “Pattern Recognition: Statistical, Structural and Neural Approaches”, John Wiley & Sons Inc., New York, 1992. BI453 FUZZY LOGIC L T P C 3 0 0 3 PURPOSE This course presents a detailed knowledge of Fuzzy logic principles, systems and its applications. INSTRUCTIONAL OBJECTIVES Fuzzy sets and representations. Fuzzy relations and Logic. Fuzzy systems and applications. UNIT I INTRODUCTION 9 Crisp sets: an overview-Basic types of fuzzy sets - Basic Concepts of fuzzy sets-Characteristics and Significance - Fuzzy sets Vs Crisp sets – Additional properties of Alpha Cuts – Representation of Fuzzy sets – Extension principle for Fuzzy sets - Operations on Fuzzy Sets – types of operations- Fuzzy compliments, Union, Intersection – Combination of Operations – Aggregation Operations- Fuzzy Arithmetic – Fuzzy numbers – Linguistic variables – Arithmetic Operation on Intervals And Fuzzy numbers – Lattice of Fuzzy numbers - Fuzzy Equation. UNIT II FUZZY RELATION 9 Fuzzy Relation - Crisp & Fuzzy Relations - Projections & Cylindric Extensions – Binary Fuzzy Relations – Binary Relations on a Single Set – Fuzzy Equivalence Relations – Fuzzy Compatibility Relations – Fuzzy Ordering Relations – Fuzzy Morphisms – Compositions of Fuzzy Relation – Fuzzy Relation Equations – General Discussion – Problem Partitioning – Solution Method – Fuzzy Relation Equation– Approximate Solutions – The use of Neural Networks-Possibility Theory – Fuzzy Measures – Evidence Theory – Possibility Theory – Fuzzy Sets & Possibility Theory - Possibility Theory Vs Probability Theory. UNIT III FUZZY LOGIC 9 Fuzzy Logic – Classical logic – Multi valued Logic – Fuzzy Propositions & Quantifiers – Linguistic Hedges – Inference from Conditional Fuzzy Propositions - Inference from Conditional & Qualified Propositions - Inference from Quantified Propositions - Uncertainty Based Information – Information & Uncertainty – Non specificity of Crisp Sets & Fuzzy sets- Fuzziness of Fuzzy sets – Uncertainty in Evidence Theory – Uncertainty Measures – Principles of Uncertainty-Approximate Reasoning – Fuzzy Expert Systems – Fuzzy Implication & Its selections – Multi conditional Approximate Reasoning – The Role of Fuzzy Relation Equations – Interval Valued Approximate Reasoning UNIT IV FUZZY SYSTEMS 9 Fuzzy Systems – General Discussion – Overview of Fuzzy Controllers and Example – Fuzzy systems & Neural Networks – Fuzzy Neural Networks – Fuzzy Automata – Fuzzy Dynamic Systems-Pattern Recognition – Introduction – Fuzzy clustering – Fuzzy Pattern Recognition – fuzzy Image Processing-Fuzzy Databases & Information Retrieval Systems – General Discussion – Fuzzy Databases –Fuzzy Information Retrieval. UNIT V APPLICATIONS 9 Engineering & Other applications – Introduction – Civil Engineering – Mechanical Engineering – Industrial Engineering – Computer Science Engineering – Reliability Theory – Robotics – Medicine – Economics – Decision Making-Fuzzy Systems & Genetic Algorithms – Fuzzy Regression – Interpersonal Communication. TOTAL 45 TEXT BOOK

George J. Klir & Bo Yuan, “Fuzzy Sets And Fuzzy Logic Theory And Applications REFERENCE BOOKS George J. Klir & Tina A. Folger,”Fuzzy Sets Uncertainty & Information”, PHI, 2001. J.S.R.Jang, C.T.Sun, E.Mizutani, “ Neuro-Fuzzy and Soft Computing “, PHI, 2003 BI455 COMPUTER GRAPHICS L T P C 3 0 0 3 PURPOSE This course on Computer Graphics will provide an in-depth knowledge of Graphics principles and its applications. INSTRUCTIONAL OBJECTIVES Graphics Primitives and Hardware requirements. 2D and 3D representations and Algorithms. User interfaces and Coloring and illumination techniques for surfaces.

UNIT I INTRODUCTION & TRANSFORMATIONS 9 Graphics Hardware: Video Display devices – Raster Scan – Random Scan – CRT – LCD – 3D Devices – Virtual Reality Systems – Touch Screens – Geometric Transformation: Co-ordinate systems – 2D, 3D Translation – Rotation – Scaling – Matrix Representation – Composite Transformation – Reflection – Shear – Between Co-Ordinate Systems – 3D Viewing: Parallel, Perspective Projection – Depth Cueing. UNIT II 2D RASTER ALGORITHMS 9 Line Algorithms – Ellipse, Circle Algorithms – Curve Algorithms – Polygons – Filling Algorithms – Clipping Algorithms – Mathematical Background: Vector, Affine spaces, Dot products & Distance – Matrices – Linear & Affine transformation – Eigen Values & Vectors – Complex numbers – Quaternions – Parametric & Non Parametric Representations. UNIT III USER INTERFACES 9 Interaction hardware – Tasks – User-Computer dialogues – Styles – Design Considerations – Modes & Syntax – Visual Design – Interaction Models – Window Management Systems – Input/Output Handling – Input Functions – Interaction Techniques – Toolkits – User Interface Management UNIT IV 3D REPRESENTATION 9 Polygon Surfaces – Curved lines & Surfaces – Quadric Surfaces – Superquadrics – Spline – Cubic Spline – Bezier Curves & Surfaces – B-Spline Curves & Surfaces – Beta Splines – Rational Splines – Fractal Geometry Methods – Shape Grammar – Visualization of Data Set. UNIT V COLOR, SURFACES AND ILLUMINATION 9 Color: Achromatic, Chromatic Color – Color Models – Reproducing Color – Applications – Visible Surface: Two variable Function – Visible Surface Algorithms – Z-buffer – Scanline – List-priority – Area-subdivision – Back-face – A-buffer – Ray-casting – Curved surface representation – Wireframes – Illumination: Models – Surface details – Shadows – Transparency – Algorithms – Rendering – Patterns – Dithering. TOTAL 45 TEXT BOOK Foley, Vandam , Feiner, Hughes , “ Computer Graphics: Principles & Practice”, Pearson Education , 2000. Hearn.D , Baker.M.P , “Computer Graphics”, 2

nd edition PHI , 2001.

REFERENCE BOOKS Harrington – “Computer Graphics”, McGraw Hill, 87. Newman W.M, Sproull R.F., “Principles of Interactive Computer Graphics” 2

nd edition, Tata

McGraw Hill, 1997.

BI457 ADVANCED JAVA PROGRAMMING L T P C 3 0 0 3 PURPOSE This course provides an in-depth knowledge of Advanced Java language and programming. INSTRUCTIONAL OBJECTIVES Java Data structure. Java Networking and Beans. Java Data Base and Graphics.

UNIT I JAVA BASICS-REVIEW 8 Java Streaming – Components and events handling – Threading concepts – Networking features – Byte code interpretation – Media Techniques. UNIT II JAVA DATA STRUCTURES 9 Lists – Linear Structures – Ordered Structures – Sorting – Trees. UNIT III ADVANCED NETWORKING AND BEANS 10 Client-Sever computing – Sockets – Content and Protocols handlers – Developing distributed applications – RMI – Remote objects – Object serialization – Bean Concepts – Events in Bean Box – Bean customization and persistence. UNIT IV JAVA DATABASE PROGRAMMING 9 Connecting to Databases – JDBC principles – Databases access – Interacting – Database search – Accessing Multimedia databases – Database support in Web applications. UNIT V RELATED JAVA TECHNIQUES 9 3D graphics – JAR file format and creation – Internationalization – Swing Programming – Advanced Java Scripting Techniques. TOTAL 45 TEXT BOOK Jame Jaworski, “Java Unleashed”, SAMS Techmedia Publications, 1999. REFERENCE BOOKS Campione, Walrath and Huml, “The Java Tutorial”, Addison Wesley, 1999. Duane A.Bailey, “Java Structures”, McGraw-Hill Publications, 1999. Jeff Frentzen and Sobotka, ‘Java Script”, Tata McGraw-Hill, 1999. BI459 3D MODELING AND ANIMATION L T P C

PURPOSE The 3D Modeling & Animation course is designed to teach the students the fundamentals of producing professional quality animation products for a variety of multimedia environments. INSTRUCTIONAL OBJECTIVES To learn the Principles and techniques of computer generated modeling To familiarize with the Principles and techniques of animation To understand the Principles and techniques of 3D modeling and 3D animation.

UNIT I DESCRIPTIVE GEOMETRICS 9 Points, Lines & Planes Combines with 3D Geometric Primitives – direct View Method – Revolution Method – Fold Line Method – Intersection of 3D Primitives. UNIT II MODELING PRIMITIVES 9

Generation of Curves & Surfaces – Bezier Curves – B Splines – Beta Splines – Nurbs – Interpolation & Approximations UNIT III FUNDAMENTALS OF ANIMATION 9 Squash & Sketch – Secondary Action – Anticipation – Exaggeration – Timing – Staging – Arc Motion – Perspective UNIT IV 3D MODELING 9 Various Views – Primitive Placements – Modeling – Light rendered 3D Image. UNIT V 3D ANIMATION 9 Lights – Camera – Object Animation – Object Metamorphosis – Hierarchical Motion Description – Editing Motion Path – Rendering Animation – Exporting to other Environments. TOTAL 45 TEXT BOOK Michael O’Rourke, “Principles of 3D Computer Animation: Modeling, Rendering & Animation with 3D Computer Graphics”, Norton, 1998.

REFERNCE BOOKS Brain A. Borsky, “Geometric Modelling Using Beta Splines”, Springer, 1989. Hearn & Baker, “Computer Graphics”, Prentice Hall of India, 1996. Group IV Electives BI460 MANAGEMENT FOR INFORMATION TECHNOLOGY L T P C

PURPOSE Most professionals are deeply involved with information technology throughout their careers. Many professionals elect to lead, or are asked to lead, an IT unit. This cross-disciplinary course introduces students to the skills needed to manage modern IT organization. OBJECTIVES To understand dynamics of IT management, strategic planning and execution. To know portfolio management and managing portfolio resources. To learn to manage application development. To understand and control information resources. To understand and describe the role of various information specialists in the provision of systems and services. Learn to manage people. To describe the global information environment and its impact on information systems and services in organizations.

UNIT I NATURE OF IT MANAGEMENT 9 IT organisation and information-IT Management-A model for the study of IT Management, Strategic importance of IT: Developing an IT strategy-IT planning. UNIT II IT TRENDS 9 Software and hardware trends-Advances in telecomm-Application portfolio resources: Introduction-Application and data resource-process for portfolio management. Managing application development: Traditional life cycle approach-Application project management –Resource allocation and control-Alternatives to traditional development-Successful end user computing. UNIT III TACTICAL AND OPERATIONAL CONSIDERATIONS 9 Developing and managing customer expectations, Problem-Change and recovery management-Managing production operations-Network management UNIT IV CONTROLLING THE INFORMATION RESOURCES 9

Accounting for IT resources-IT controls and asset protection. UNIT V PREPARING FOR ADVANCES IN IT 9 People-Orgin-Management systems. People Management-Management processes-Role of CIO. TOTAL 45 TEXT BOOK Carrol W.Frenzel, “Management of Information Technology”, Boyd and Frosee Publishing Company, 1992

REFERENCE BOOKS Dickson, Gary N, James Wetherbe, “Management Information System”, McGraw Hill, 1985. BI462 NANOBIOTECHNOLOGY L T P C PURPOSE The subject focuses on the latest techniques and outcomes in Nanobiotechnology. INSTRUCTIONAL OBJECTIVES Bionanomachines Biomolecular design Structural and functional principles Present and future of Nanobiotechnology

UNIT I: INTRODUCTION 8 Quest for Nanotechnology, from biotechnology to Bionanotechnology, unfamiliar world of Bionanomachines, modern biomaterials, legacy of evolution

UNIT II: STRUCTURAL PRINCIPLES 9 Natural bionanomachinery, construction, raw materials, protein folding, self-assembly, self- organization, molecular recognition, flexibility

UNIT III: FUNCTIONAL PRINCIPLES 10 Nanoassembly, energetics, chemical transformation, regulation

UNIT IV: BIOMOLECULAR MOTORS 10 Biomaterials, Biomolecular motors, traffic across membranes, Biomolecular sensing, self-replication

UNIT V: PRESENT AND FUTURE 8 Nanomedicine, DNA computers, Biosensors, Case study: nanotube synthase, ethical issues TOTAL 45 TEXT BOOK David S. Goodsell, “Bionanotechnology: Lessons from Nature”, Wiley-Liss, 2004. REFERENCE Christof M. Niemeyer, “Nanobiotechnology: Concepts, Applications and Perspectives”, John Wiley & Sons, 2004.

BI464 BIOPYTHON L T P C PURPOSE The subject focuses on the basic concepts and applications of Biopython.

INSTRUCTIONAL OBJECTIVES Types and operators Basic statements and functions Modules and classes Applications

UNIT I : PROGRAM STRUCTURE 7 Python program structure, builtin types, basic statements UNIT II : FUNCTIONS 8 Functions basics, scope rules, argument passing, Odds and Ends, Function Gotchas UNIT III : MODULES 9 Basics, Module files, import model, reloading, modules Gotchas, classes, Exceptions UNIT IV :TOOLS 10 Built-in Tools, Common Tasks in Python UNIT V : APPLICATIONS 11 An Automated Complaint System, Interfacing with COM: Cheap Public Relations, A Tkinter-Based GUI Editor for Managing Form Data, Design Considerations, And JPython: The Felicitous Union of Python and Java TOTAL 45 TEXT BOOK Patrick O'Brien, “Beginning Python for Bioinformatics”, O'Reilly, 2002 REFERENCE Cynthia Gibas, Per Jambeck, “Developing Bioinformatics Computer Skills”, O'Reilly, 2001 BI466 MICROBIAL GENOMICS L T P C PURPOSE It provides a comprehensive overview of Genomics study related to microbes. INSTRUCTIONAL OBJECTIVES Microbial Bioinformatics Microbial metabolism Genomics-Based Analysis of the Bacterial Cell Cycle Plant pathogens

UNIT I: INRODUCTION 9 History, Bioinformatics and microbial pathogenesis, bacteriophage Bioinformatics UNIT II: GENOME ANALYSIS 9 Comparative Microbial Metabolism, Genomic Analysis of Membrane Transport, Analysis of the Bacterial Cell Cycle UNIT III: BACTERIAL BIODIVERSITY 9 Concepts of Bacterial Biodiversity for the age of Genomics, Coevolution of symbionts and pathogens with their hosts UNIT IV: PATHOGENIC GENOMES 9 Plant pathogen genomes, parasite genomics, genomes of pathogenic enterobacteria and thermophiles UNIT V: APPLICATION 9 Application of Genomics to Biocatalysis and Biodegradation, microbial proteomics TOTAL 45

TEXT BOOK Fraser, Claire M, Read, Timothy, Nelson, Karen E. “Microbial Genomes”, Humana Press 2004. BI468 SYSTEMS BIOLOGY L T P C PURPOSE It provides a comprehensive knowledge on the concepts and applications of systems biology. INSTRUCTIONAL OBJECTIVES Standard models and approaches in systems biology Modeling of gene expression Evolution and self organization UNIT I: INTRODUCTION 8 Basic principles of systems biology, experimental techniques UNIT II: STANDARD MODELS AND APPROACHES 10 Metabolism- enzyme kinetics and thermodynamics, metabolic networks, metabolic control analysis UNIT III: BIOLOGICAL PROCESSES 9 Signal transduction- introduction, function and structures, interactions, structural components, signaling, selected biological processes UNIT IV: EVOLUTION 9 Introduction, mathematical models, prediction of biological systems, data integration UNIT V: APPLICATIONS 9 Systems biology in various fields, databases and tools, modeling tools TOTAL 45 TEXT BOOK Edda Klipp, Ralf Herwig, ”Systems Biology in Practice-Concepts, Implementation and Application”, Wiley VCH, I Edition Group V Electives BI461 SIMULATION AND MODELLING L T P C PURPOSE It provides a comprehensive knowledge on simulation and modeling INSTRUCTIONAL OBJECTIVES Protein folding problem Mathematical models Computer simulation UNIT I: PROTEIN FOLDING PROBLEM 9 Computational aspects of protein folding problem, distributed genetic algorithms on PARAM UNIT II: IMAGE SEGMENTATION 9 Genetic coding structures and algorithms for image segmentation, Cancer- a challenge for computer modeling UNIT III: MODELING 9

A model of HIV infection and its blockers, Modeling of HIV infection kinetics UNIT IV: MATHEMATICAL MODELS 9 Models of cell cycles, modeling stochastic population growth UNIT V: BIOLOGICAL SYSTEM MODELING 9 Reconstructability analysis approach, simulation of bimodal neurons and networks TOTAL 45 TEXT BOOK S. Sitharama Iyengar, “Computer modeling and simulations of complex biological systems”, CRC-Press, second edition. BI463 MICROFLUIDICS L T P C

PURPOSE This subject facilitate the understanding of the latest concepts of Microfluidics INSTRUCTIONAL OBJECTIVES Micropumps and types Design Rules for Micropumps Modelling and Simulation UNIT I: INTRODUCTION 9 Micropumps- mechanical micropumps, non- mechanical micropumps, Design Rules for Micropumps, Preliminary Design, Compression Ratio, Criterion for Switching of Valve UNIT II: MODELING AND SIMULATION 9 Background, Governing Equation for Micro-pumps, modeling of the Actuator Unit., Inlet Valve, Outlet Valve, System Model of Proposed Micro-pump, Process Development and Fabrication, Bulk Silicon Micromachining, Process Flow UNIT III: PROCESS DEVELOPMENT AND FABRICATION 9 Bulk Silicon Micromachining, Process Flow, Verification and Testing UNIT IV: APPLICATIONS 9 Development of Integrated Microfluidic Devices for Genetic Analysis, Channel Flows of Bio-Molecular Suspension UNIT V: PARTICLE IMAGE VELOCIMETRY 9 Transport of Liquid in Rectangular Micro-Channels by Electro osmotic Pumping, Development of Slip Model and Slip-Corrected Reynolds Equation for Gas Lubrication in Magnetic Storage Device, Short Notes on Particle Image Velocimetry for Micro/Nano Fluidic Measurements TEXT BOOKS Tay, Francis E.H., “Microfluidics and BioMEMS Applications”, Springer publications, 2002 BI465 EVOLUTIONARY COMPUTING L T P C PURPOSE This subject provides the in-depth knowledge on evolutionary computing INSTRUCTIONAL OBJECTIVES Evolution strategies Evolutionary programming Memetic algorithms

UNIT I: EVOLUTIONARY ALGORITHM 8 Evolutionary algorithms, Components, Applications, evolutionary computing and global optimization UNIT II: EVOLUTION STRATEGIES 10 Examples, representation, mutation, recombination, parents and survivor election, self-adaptation, Applications, evolutionary programming UNIT III: GENETIC PROGRAMMING 10 Genetic programming, parameter control in evolutionary algorithms- Examples of Changing Parameters, Classification of Control Techniques, Examples of Varying EA Parameters UNIT IV: MULTIMODAL PROBLEMS 9 Multimodal Problems and the Need for Diversity, Implicit Measures, Explicit Diversity Maintenance, Multiobjective Evolutionary Algorithms, Memetic Algorithms UNIT V: CONSTRAINT HANDLING 8 Constrained Problems, types, Ways to Handle Constraints in Evolutionary Algorithms, Application Example, Special Forms of Evolution TOTAL 45 TEXT BOOK Eiben, A. E., Smith, J. E. “Introduction to Evolutionary Computing”, Springer publications, 2003.

REFERENCE L. Kallel, B. Naudts, A. Rogers, “Theoretical aspects of evolutionary computing”, Springer publications, 2001.

BI467 PLANT GENOMICS L T P C

PURPOSE This subject gives the overall idea on the basic concepts in plant genomics INSTRUCTIONAL OBJECTIVES Computational gene finding in plants Computational modeling of gene structure in Arabidopsis thaliana Directed plant transformation for the post-genomic era UNIT I: INTRODUCTION 8 Comparative analysis of plant chromosomal DNA, Plant genome evolution: lessons from comparative genomics at the DNA level UNIT II: TECHNIQUES 9 Computational gene finding in plants, Computational modeling of gene structure in Arabidopsis thaliana UNIT III: PROFILING 9 Survey of plant genome data resources and issues in building data management systems, Comprehensive gene expression analysis by transcript profiling UNIT IV: LARGE SCALE PROTEOMICS 9 DNA microarrays for functional plant genomics, Microarray data quality analysis, Large-scale plant proteomics UNIT V: ADVANCES 10 Metabolomics - the link between genotypes and phenotypes, Gene replacement by homologous recombination in plants, Recombinase-directed plant transformation for the post-genomic era

TOTAL 45 TEXTBOOKS Chris Town, “Functional Genomics”, Springer; 1 edition BI469 NATURAL LANGUAGE PROCESSING L T P C

PURPOSE To get people to understand as much as possible about important ideas in NLP and recent work in NLP within one quarter. INSTRUCTIONAL OBJECTIVES This course is designed to introduce students to the fundamental concepts and ideas in natural language processing (NLP), and to get them up to speed with current research in the area. It develops an in-depth understanding of both the algorithms available for the processing of linguistic information and the underlying computational properties of natural languages. UNIT I INTRODUCTION 7 Introduction; Issues and Difficulties in NLP; Study of Language; Evaluating Language Understanding System; Different Levels of Language; Representations; Organization of NLP Systems; Linguistic Issues; Types of NLP Systems. UNIT II GRAMMARS & PARSING 10 Language Hierarchies and Complexity; Grammars & Sentence Structures; A Top Down Parser; A Bottom Up Chart Parser; A Top Down Chart Parser; Finite State Models, Morphological Analysis and the Lexicon; Grammars & Logic Programming; Augmented Grammars; A simple grammar with features; Parsing with features; Augmented Transition Networks (ATN); Definite clause grammars; Efficient parser; Shift reduce parser; A deterministic parser; Lexicalised and Probabilistic Parsing. UNIT III SEMANTIC INTERPRETATION 12 Three system types of semantics and logical forms; Defining semantic structure; Model theory; Semantic interpretation and compos ability; A Simple grammar & Lexicon with semantic interpretation; Prepositional phrase and verb phrases; Lexicalized semantic interpretation and semantic roles; semantic networks; Frames and scripts – truth; Meaning and Ontology; Word Net. UNIT IV LANGUAGE AND COMMUNICATION 7 Adding language; Modeling reference; Defining local discourse context and discourse entities; the need for discourse structure; Discourse Interpretation and Pragmatics. UNIT V TYPICAL SYSTEM 9 Generation; Strategies for generation; Planning English referencing expression architecture of natural language generation system; Typical systems; ELIZA; Baseball; GUS; PARRY; LADDER; SOPHIE & POET; Current trends in NLP.

TOTAL 45 TEXT BOOK James Allen, Benjamin & Cummings, “Natural Language Understanding”, Addison-Wesley Pub Co, 2nd Edition 1995. Ronald Hausser, Spring & Verleg, “Foundations of Computational Linguistics”, Springer Verlag, 1999.

REFERENCE BOOKS Gerald Gazer and Chris Mellish, “Natural Language Processing for PROLOG Programmers”, Prentice Hall of India, 1995. Ashkar Bharathi & Vineet Chaitanya & Rajeev Sangal, “Natural Language Processing: A Paining Perspective”, Prentice Hall of India, 1995.

Ralph Grishman, “Computational Linguistics: An Introduction”, Cambridge University Press, 1986. Gross & Jones & Webber, “Readings in Natural Language Processing”, Morgan Konfmann Publishers, 1986. Werner, “Talking with Computers in Natural Language”, Springer Verlag, 1986. “Building Natural Language Generation Systems”, Cambridge University Press, 2000.

BI402 PROJECT L T P C 0 0 16 8

BI404 COMPREHENSION L T P C

1 0 0 1