B.Tech. (Full Time) – Bioinformatics Curriculum & Syllabus ......B.Tech. (Full Time) – Bioinformatics Curriculum & Syllabus 2007-08 Faculty of Engineering & Technology SRM University

B.Tech. (Full Time) – Bioinformatics

Curriculum & Syllabus

2007-08

Faculty of Engineering & Technology SRM University

SRM Nagar, Kattankulathur – 603 203

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S.R.M UNIVERSITY B.Tech. BIOINFORMATICS

CURRICULUM AND SYLLABUS 2007-08

SEMESTER- I Code Category Course L T P C Theory LE0101 G English 1 0 2 2 MA0111 B Mathematics-I 3 2 0 4 PH0101 B Physics 3 0 0 3 CY0101 B Chemistry 3 0 0 3 GE0101 E Basic Engineering-I 4 0 0 4 Practical PD0101 G Personality Development-I* 0 0 2 - GE0107 G NSS /NCC/NSO/YOGA 0 0 2 1 PH0103 B Physics Laboratory 0 0 2 1 CY0103 B Chemistry Laboratory 0 0 2 1 GE0105 B Computer Literacy 0 0 2 1 AR0130 E Engineering Drawing 1 0 4 3 Total 15 2 16 23 Total Contact Hours 33

SEMESTER – II Code Category Course L T P C Theory GE0108 G Value education 1 0 0 1 MA0142 B Mathematics-LS-II 3 2 0 4 PH0102 B Material science 2 0 2 3 GE0104 B Principles of Environmental Science 2 0 0 2 GE0106 E Basic Engineering II 4 0 0 4 BT0104 P Cell Biology 3 0 0 3 BT0102 P Biochemistry 3 0 0 3 Practical PD0102 G Personality Development – II* 0 0 2 - ME0120 E Workshop practice 0 0 4 2 CS0140 E Computer Practice 1 0 2 2 Total 19 2 10 24 Total Contact Hours 31 G: General programme comprising language/communication skills, humanities and social sciences, economics and principles of management, and NSS/NCC/NSO/YOGA. B: Basic sciences comprising Computer Literacy with Numerical Analysis, Mathematics, Physics, and Chemistry. E: Engineering Sciences and Technical Arts comprising Engineering Graphics, Workshop Practice, Basic Engineering, etc. P: Professional subjects corresponding to the Branch of Studies, which will include core subjects, electives, and project work.

* Audit course

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SEMESTER – III Code Category Course L T P C Theory LE0201/0203/0205 G German/Japanese/French Language -Phase-I 2 0 0 2 BI0201 B Computer Skills 1 0 2 2 MA0201A B Numerical Methods 3 2 0 4 BI0203 P Introduction to Algorithms 3 0 0 3 BI0205 P Introduction to Bioinformatics 3 0 0 3 BI0207 P Introduction to Data Structures 3 0 0 3 BI0209 P Java Programming 3 0 0 3 BI0211 P Microbiology 3 0 0 3

Practical PD0201 G Personality Development - III 0 0 2 1 BI0217 P Basic Biotechnology Laboratory 0 0 2 1 BI0213 P Computational Biology Laboratory 0 0 2 1 BI0215 P Java Programming Laboratory 0 0 2 1 Total 21 2 10 27 Total Contact Hours 33

SEMESTER – IV Code Category Course L T P C Theory LE0202/0204/ 0206

G German/Japanese/French Language -Phase-II 2 0 0 2

MA0242 B Probability and Statistics 3 2 0 4 CY0204 P Structural Chemistry 3 0 0 3 BI0200 P Molecular Biology & Genetics 3 0 0 3 BI0202 P Bioinformatics Algorithms 3 2 0 4 BI0204 P Introduction to Database Management

Systems 3 0 0 3

BI0206 P Immunology 3 0 0 3 BI0208 P Comprehension - I 0 2 0 1

Practical PD0202 G Personality Development - IV 0 0 2 1 BI0210 P Biotechnology Laboratory 0 0 2 1 BI0212 P DBMS Laboratory 0 0 2 1 Total 20 6 6 26 Total Contact Hours 32

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SEMESTER –V Code Category Course L T P C Theory BI0301 P Recombinant DNA Technology 3 0 0 3 BI0303 P Molecular Phylogeny and Evolution 3 0 0 3 BI0305 P Biophysical Chemistry 3 0 0 3 BI0307 P Genomics and Transcriptomics 3 0 0 3 BI0309 P PERL Programming & Bioperl 3 0 0 3 E1 P Elective I 3 0 0 3 Practical PD0301 G Personality Development - V 1 0 2 2 BI0311 P Genetic Engineering Laboratory 0 0 2 1 BI0313 P Perl Programming Laboratory 0 0 2 1 BI0315 P Industrial Training – I 0 0 2 1 Total 18 0 10 23 Total Contact Hours 28 SEMESTER –VI Code Category Course L T P C Theory BI0300 P Internet programming 2 0 2 3 BI0302 P Proteomics 3 0 0 3 BI0304 P Immunoinformatics 3 0 0 3 BI0306 P Molecular Simulation of Biomolecules 3 0 0 3 BI0308 P Systems Biology 3 0 0 3 E2 P Elective II 3 0 0 3 BI0310 P Comprehension - II 0 2 0 1 Practical PD0302 G Personality Development – VI 1 0 2 2 BI0312 P Immunoinformatics Laboratory 0 0 2 1 BI0314 P Molecular Simulation of Biomolecules

Laboratory 0 0 2 1

Total 19 2 6 23 Total Contact Hours 27 SEMESTER –VII Code Category Course L T P C Theory BI0401 P Chemoinformatics 3 0 0 3 BI0403 P Systems approach to Biology 3 0 0 3 BI0405 P Pharmacogenomics and Pharmacogenetics 3 0 0 3 BI0407 P Metabolomics and Metabolic Engineering 3 0 0 3 E3 P Elective III 3 0 0 3 Practical BI0409 P Chemoinformatics Laboratory 0 0 2 1 E4 P Elective IV - Lab 0 0 2 1 BI0411 P Industrial Training – II* 0 0 2 1 Total 15 0 6 18 Total Contact Hours 21 SEMESTER –VIII

Code Category Course L T P C Theory BT0402 P Biosafety, Bioethics, IPR & Patents 2 0 0 2 BI0402 P Medical Informatics 2 0 0 2

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Practical BI0404 P Project Work 0 0 16 8 Total 4 0 16 12 Total Contact Hours 20 SUMMARY TABLE Semester I II III IV V VI VII VIII Total %

Total 23 24 27 26 23 23 18 12 176 100.00 G 3 1 3 3 2 2 0 0 14 7.95 B 13 9 6 4 0 0 0 0 32 18.18 E 7 8 0 0 0 0 0 0 15 8.52 P 0 6 18 19 21 21 18 12 115 65.34

TOTAL CREDITS TO BE EARNED FOR THE AWARD OF THE DEGREE: 176

LIST OF ELECTIVES

A student is required to choose a module during the 5th semester (for Elective 1,2,3,&4) . The student will not be permitted to move from one module to another during 6th and 7th semesters.

Module I SUB CODE SUBJECT NAME L T P C

BI0351 Microbial genomics 3 0 0 3 BI0350 Microarray – Technique and applications 3 0 0 3 BI0451 Genetic Algorithms 3 0 0 3 BI0471 Advanced Bioinformatics Laboratory 0 0 2 1 Module II SUB CODE SUBJECT NAME L T P C

BI0353 Protein engineering 3 0 0 3 BI0352 Bioconfinement of Genetically Modified Organisms 3 0 0 3 BI0453 Nanobiotechnology 3 0 0 3 BI0473 Enzyme technology Laboratory 0 0 2 1 Module III SUB CODE SUBJECT NAME L T P C

BI0355 Artificial Intelligence 3 0 0 3 BI0354 Computational Neuroscience 3 0 0 3 BI0455 Biopython 3 0 0 3 BI0475 Biopython laboratory 0 0 2 1 Module IV SUB CODE SUBJECT NAME L T P C

BI0357 Neural Networks 3 0 0 3 BI0356 Image Processing 3 0 0 3 BI0457 Advanced Java Programming 3 0 0 3 BI0477 Advanced Java laboratory 0 0 2 1 Module V SUB CODE SUBJECT NAME L T P C

BI0359 Drug and Pharmaceutical Biotechnology 3 0 0 3 BI0358 Cancer Biology 3 0 0 3 BI0459 Stem Cell in Health Care 3 0 0 3 BI0479 Medical Biotechnology Laboratory 0 0 2 1

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Module VI SUB CODE SUBJECT NAME L T P C

BI0361 Machine learning in Bioinformatics 3 0 0 3 BI0360 Data mining in Bioinformatics 3 0 0 3 BI0461 Nutrigenomics 3 0 0 3 BI0481 Advanced computational biology laboratory 0 0 2 1

SEMESTER I

L T P C LE0101 ENGLISH 1 0 2 2

Prerequisite Nil

PURPOSE To provide an adequate mastery of technical communicative English Languages training primarily, reading 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. LISTENIN Listening Practice – Hints on Listening – Practice Questions Note Taking: Note Taking Strategies. SPEAKING Definitions: Expressing Opinions (agreement / disagreement )-Offering Suggestion – Technical Definition – Defining – Describing Objects –speaking practice. Phonetics: Pronunciation – Phonetic transcription-Stress-Intonation READING Comprehension: Skimming-scanning-close reading-Comprehension – Transferring Information – Exercise – An unseen passage should be given and questions may be asking in the form of True or False statements, MCQ, short answers. Transcoding: Interpreting tables, flow charts, pie chart, bar diagram, tree diagram, graphs WRITING Art of Writing: Writing Language – Rules for effective writing – Technical Essay Writing – Exercise Report Writing: Technical Report Writing – Lab Report – Exercise. Letter Writing: Formal Letters – Letter to the Editor – Letter Inviting Dignitaries – Letter of Application – Placing an Order – Placing Curriculum Vitae – Placing an order. Dialogue Writing FOCUS ON AND COMMUNICATION AND “COMPUNICATION” Communication: Basic Concepts – Process – Kinds – Routes – Forms – Factors – Barriers – Triangles Communication (Communicate through Computers – Power Point & Tele Conference). INTERNAL ASSESSMENT Based on the submission and test performance of the students marks may be awarded.

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TEXT BOOKS 1. Abraham Benjamin Samuel, Practical Communication (Communicative English) LSRW2000, SRMEC

– June 2002 Edition. 2. Staff of the Department of Humanities and Social Science, Anna University, English for Engineers /

BEC and Technologist Vol., Orient Longman, 1990.

REFERENCE BOOKS 1. Herbert. A. J. The structure of Technical English Orient Longman 1995. 2. Pickett and Laster, Technical English, Writing, Reading and Speaking, New York Harper and Row

Publications, 1997. 3. Interactive course in phonetics and spoken English , Acoustics Engineers (ACEN) 2002. 4. Munter, Mary, Business Communication Strategy and Skill, Prentice Hall Inc., New Jersey, 1987.

L T P C

MA0111 MATHEMATICS – LS1 3 2 0 4 Prerequisite Nil

(COMMON TO BT, BI, BME, BP, GE, FPE) PURPOSE: To impart analytical ability in solving mathematical problems as applied to the respective branches of Engineering. INSTRUCTIONAL OBJECTIVES At the end of the course, the students should have been exposed Fully with the knowledge of Matrices and its applications the trigonometry, the concepts of Differential Calculus and Integral Calculus and their simple applications. MATRICES *Review types of matrices, properties. Inverse matrix Cramer’s rule for solving a system of linear equations. – Rank of Matrix – Consistency and Inconsistency of a system of m linear equations in ‘n’ unknowns –Cayley Hamilton theorem – Eigen values and eigen vectors of a real matrix. TRIGONOMETRY *Review of complex numbers-De Moiver’s theorem and its applications- Expansion of sin cosn nθ θ in terms

of sin cosandθ θ - Expansion of tan nθ in terms of tan θ - Expansion of sin cosn n

andθ θ in terms of sines and cosines of multiples of θ - Hyperbolic functions and inverse hyperbolic functions. DIFFERENTIAL CALCULUS Differentiation and Derivatives of simple functions – Successive Differentiation – Various forms of Algebraic and Trigonometric functions – Problems. INTEGRAL CALCULUS

Various types of integration –by – Reduction formula for , sin , cos , sin cosax n n n n m

e x x x x (without proof)-Problems APPLICATIONS OF DIFFERENTIAL CALCULUS & INTEGRAL CALCULUS Applications of differential calculus & integral calculus-Tangent & Normal-Radius of curvature – Velocity and acceleration -Integral calculus - Length & Area.

*No questions should be asked in the Review part TEXT BOOK

1. Grewal B.S, Higher Engg Maths, Khanna Publications, 38th Edition. 2. Veerajan, T., Engineering Mathematics, Tata McGraw Hill Publishing Co., New Delhi, 2000. 3. Dr. V. Ramamurthy & Dr. Sundarammal Kesavan Engineering Mathematics – Vol.I & II Anuradha

Publications, Revised Edition 2006.

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REFERENCE BOOKS: 1. Kreyszig. E, Advanced Engineering Mathematics, 8th edition, John Wiley & Sons. Singapore, 2001. 2. Kandasamy P et al. Engineering Mathematics, Vol.I (4th revised edition), S. Chand &Co., New Delhi,

2000. 3. Narayanan S., Manicavachagom Pillay T.K., Ramanaiah G., Advanced Mathematics for Engineering

students, Volume I (2nd edition), S. Viswanathan Printers and Publishers, 1992. 4. Venkataraman M.K., Engineering Mathematics – First Year (2nd edition), National Publishing Co.,

Chennai, 2000. L T P C PH0101 PHYSICS 3 0 0 3 Prerequisite Nil PURPOSE The purpose of this course is to develop scientific temper and analytical capability through learning physical concepts and their applications in engineering and technology. Comprehension of some basic physical concepts will enable the students to logically solve engineering problems. INSTRUCTIONAL OBJECTIVES At the end of the course, the student will be able to:

1. Understand the general scientific concepts required for technology, 2. Apply the concepts in solving engineering problems, 3. Explain scientifically the new developments in engineering and technology, and 4. Get familiarized with the concepts, theories, and models behind many technological applications.

PROPERTIES OF MATTER AND SOUND Properties of Matter: Hooke’s law – Twisting couple on a cylinder – Shafts – Torsion pendulum – Bending of beams – Bending moment – Uniform bending and non-uniform bending – I shape girder. Sound: Shock waves – Mach number (simple problems) – Ultrasonic production (magnetostriction and piezoelectric methods) and application – Acoustics of buildings – Sources and impacts of noise – Sound level meter – Control of noise pollution. ELECTROMAGNETISM AND MICROWAVES Electromagnetism: Divergence, curl and gradient – Maxwell’s equations – Wave equation for electromagnetic waves – Propagation in free space – Poynting vector – Rectangular and circular wave guides. Microwaves: Properties and applications – Generation by magnetron and reflex klystron oscillator – Travelling wave tube – Biological effects. OPTICS Photometry: Principles and Lummer-Brodhun photometer. Lasers: Principles and characteristics – Types of lasers (CO2, excimer, NdYAG, GaAs, free electron) – Holographic mass storage. Optical Fiber: Principles – Physical structure and types – Optical fiber communication. Photoelasticity: Theory and applications. CRYSTAL PHYSICS AND CRYOGENICS Crystal Physics: Crystal directions – Planes and Miller indices – Basic symmetry elements – Translational symmetry elements – Reciprocal lattice – Diamond and HCP crystal structure – Imperfections in crystals. Cryogenics: Methods of liquefaction of gases (cascade process, Linde’s process, and adiabatic demagnetization process) – Measurement of cryogenic temperatures. ENERGY PHYSICS Introduction to non-conventional energy sources – Solar cells – Thermoelectric power generators – Thermionic power generator – Magneto hydrodynamic power generator – Fuel cells (H2O2) – Solid state batteries (Lithium) – Low voltage and high voltage nuclear cells – Thermocouple based nuclear cell – Ultra capacitors. TEXT BOOKS

1. Arumugam, M., Engineering Physics, 2nd edition, Anuradha Publishers, Kumbakonam, 2003. 2. Gaur and Gupta, Engineering Physics, 7th edition, Dhandapani and Sons, New Delhi, 1997. 3. Thiruvadigal, J. D., Ponnusamy, S., Vasuhi, P. S. and Kumar, C., Physics for Technologists, 5th

edition, Vibrant Publication, Chennai, 2007.

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REFERENCE BOOKS 1. Vasudeva, A. S., Modern Engineering Physics, Revised edition, S. Chand and Company Ltd., New

Delhi, 2004. 2. Vasudevan, D. N., Fundamentals of Magnetism and Electricity, 11th edition, S. Chand and Company

Ltd., New Delhi, 1983. 3. Nair, K. P. R., Atoms, Molecules and Lasers, Narosa Publishing House, New Delhi, 2006. 4. Pillai, S. O., Solid State Physics, 5th edition, New Age International (P) Ltd., New Delhi, 2004. 5. Khan, B. H., Non-Conventional Energy Resources, Mechanical Engineering Series, Tata McGraw Hill

Publishing Company Ltd., New Delhi, 2006. L T P C CY0101 CHEMISTRY 3 0 0 3

Prerequisite Nil PURPOSE To impart a sound knowledge on the principles of chemistry involving the different application oriented topics required for all engineering branches. INSTRUCTIONAL OBJECTIVES The students should be conversant with

1. The role of applied chemistry the field of engineering. 2. The knowledge of water quality parameters and the treatment of water. 3. The principles involves in corrosion and its inhibitions. 4. Important analytical techniques, instrumentation and the applications. 5. Knowledge with respect to the phase equlibria of different systems.

TECHNOLOGY OF WATER Water quality parameters: Physical, Chemical & Biological - Hardness of water – estimation of hardness (EDTA method & O. Hehner”s method), Alkalinity – determination – disadvantages of using hard water in boilers: Scale, sludge formation – disadvantages – prevention – treatment: Internal conditioning – phosphate, calgon and carbonate conditioning methods – External: Zeolite, ion exchange methods - desalination – reverse osmosis and electrodialysis - domestic water treatment. CORROSION AND ITS CONTROL Corrosion: Basic concepts – principles, mechanism of chemical, electrochemical corrosion – Pilling Bedworth rule – galvanic corrosion – differential aeration corrosion - pitting corrosion - stress corrosion - factors influencing corrosion. Corrosion control: cathodic protection – sacrificial anodic method – corrosion inhibitor. Protective coatings: surface preparation for metallic coatings - electro plating and electroless Plating - chemical conversion coatings – anodizing, phosphating & chromate coating. PHASE EQUILIBRIA Phase rule: Statement – explanation of the terms involved - one component system (water system only). Condensed phase rule - thermal analysis – two component systems: simple eutectic, Pb-Ag; Br, Cd - solid solution Cu-Ni and compound formation Mg-Zn - applications of eutectics. POLYMERS AND REINFORCED PLASTICS Classification of polymers – types of polymerization reactions – mechanism of addition polymerization: free radical, ionic and Ziegler – Natta - effect of structure on the properties of polymers – strength, plastic deformation, plastics elasticity and physical nature –Preparation and properties of important resins:- Polyethylene, PVC, PMMA, Polyester, Teflon Bakelite, Epoxy resins, compounding of plastics, moulding methods - injection, extrusion, compression and calendaring - reinforced plastics – FRP – Carbon, Graphite, Glass– applications. INSTRUMENTAL METHODS OF ANALYSIS Basic principles, instrumentation of potentiometry, flame photometry – applications- Elementary theory – principle – instrumentation of UV – visible spectroscopy and atomic absorption spectroscopy and infrared spectroscopy.

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TEXT BOOKS 1. Jain P.C and Monika Jain, Engineering Chemistry, Danpat Raj publishing company (P) Ltd, New Delhi

– 2002. 2. Dara S.S, Textbook of Engineering Chemistry, S. Chand & Company Ltd, New Delhi 2003. 3. Willard H.A., Merit L.L and Dean J.A., Instrumental methods of analysis, 6th Edition Van Nostrand,

1986. REFERENCE BOOKS

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

2. Jeyalakshmi.R & Ramar. P, Engineering Chemistry, 1st Edition, Devi Publications, Chennai 2006. 3. Kamaraj P & Arthanareeswari. M, Applied Chemistry, 2nd Edition, Sudhandhira Publications, 2003. 4. Arivalagan. K, Engineering Chemistry, 1st Edition, Mass publications, 2007. 5. P. Kamatchi, Applied Chemistry-I, Ponnuswamy publications, Chennai. 6. Dr. Helen P Kavitha, Engineering Chemistry - I, ILA Publications, 2002

L T P C GE0101 BASIC ENGINEERING - I 4 0 0 4

Prerequisite Nil

PART A CIVIL ENGINEERING

PURPOSE To get exposed to the glimpses of Civil Engineering topics that is essential for an Engineer. INSTRUCTIONAL OBJECTIVES

1. To know about different materials and their properties. 2. Engineering aspects related to buildings. 3. To know about importance of Surveying. 4. To know about the transportation systems. 5. To get exposed to the rudiments of engineering related to Dams, Water Supply, Transportation system

and Sewage Disposal. BUILDING MATERIALS AND THEIR PROPERTIES Introduction - Civil Engineering – Building Materials – Brick, Stone, Cement, Steel, Concrete, timber – Properties – Uses. Units – Stress, strain and three modulii of elasticity – factor of safety - Centre of Gravity and Moment of Inertia for rectangle and circular section – simple problems. BUILDINGS AND THEIR COMPONENTS Buildings – Classification - Components of buildings and their functions Foundations - functions – classification of foundations – Bearing capacity Floorings – functions - Types - Cement Concrete flooring – Mosaic flooring - Marble flooring Roofs - Types – Requirements – Madras Terrace roof. Tall structure – types of structural systems. UTILITY AND SERVICES Surveying - Objective – Principles – Classification – Instruments used for Surveying. Dams - Purpose – Selection of site – Classification – Gravity dam (cross-section details only) Transportation system - Classification – Roadway - components – classification of roads - Railway – Cross-section of permanent way- components parts and functions- Docks and Harbour – classification – Terminology Bridges –components of a bridge - types of bridges. Water supply - Sources - Standards of drinking water (BIS) – elementary treatment methods – RO System Sewage disposal – Septic tank – function and components. TEXT BOOKS

1. Raju K.V.B., Ravichandran P.T., Basics of Civil Engineering, Ayyappa Publications, Chennai, 2000. 2. Ramesh Babu, Civil Engineering, VRB Publishers, Chennai, 2000.

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REFERENCE BOOKS 1. Rangwala, S.C., Engineering Materials, Charotar Publishing House, Anand, 1980. 2. National Building Code of India, Part V, Building Materials, 2005 3. Surendra Singh, Building Materials, Vikas Publishing Company, New Delhi, 1996

PART B MECHANICAL ENGINEERING

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

1. The basic machine elements 2. The Sources of Energy and Power Generation 3. The various manufacturing processes

MACHINE ELEMENTS Springs: Helical and leaf springs – springs in series and parallel. Cams: Types of cams and followers – Cam profile. Power Transmission: Gears (terminology, spur, helical and bevel gears, gear trains). Belt drives (types). Chain drives. Simple Problems. ENERGY Sources: Renewable and non-renewable (various types, characteristics, advantages/disadvantages). Power Generation: External and internal combustion engines - Hydro and nuclear power plants (layouts, element/component description, advantages, disadvantages, applications). Simple Problems. MANUFACTURING PROCESSES Sheet Metal Work: Introduction – Equipments – Tools and accessories – Various processes (applications, advantages / disadvantages). Welding: Types – Equipments – Tools and accessories – Techniques employed (applications, advantages / disadvantages (gas and arc welding only)) – Gas cutting – Brazing and soldering. Lathe Practice: Types - Description of main components – Cutting tools – Work holding devices – Basic operations. Simple Problems. Drilling Practice: Introduction – Types – Description – Tools. Simple Problems. TEXT BOOKS

1. Kumar, T., Leenus Jesu Martin and Murali, G., Basic Mechanical Engineering, Suma Publications, Chennai, 2007.

2. Prabhu, T. J., Jai Ganesh, V., Jebaraj, S., Basic Mechanical Engineering, Scitech Publications, Chennai, 2000.

REFERENCE BOOKS

1. Hajra Choudhary, S.K. and Hajra Choudhary, A. K., Elements of Manufacturing Technology Vols. I & II, Media Publishers, 1986.

2. Nag, P.K., Power Plant Engineering, Tata McGraw-Hill, New Delhi, 2006. 3. Palanichamy, M.S., Basic Civil & Mechanical Engineering, Tata McGraw-Hill, New Delhi 1991. 4. Nagpal G. R., Power Plant Engineering, Khanna Publisher, Delhi, 2004

L T P C PD0101 PERSONALITY DEVELOPMENT - I 0 0 2 0 Prerequisite Nil PURPOSE The purpose of this course is to build confidence and inculcate various soft skills and to help Students to identify and achieve their personal potential INSTRUCTIONAL OBJECTIVES 1. To guide thought process. 2. To groom students' attitude.

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3. To develop communication skill. 4. To build confidence. METHODOLOGY The entire program is designed in such a way that every student will participate in the class room activities. The activities are planned to bring out the skills and talents of the students which they will be employing during various occasions in their real life. 1. Group activities + individual activities. 2. Collaborative learning. 3. Interactive sessions. 4. Ensure Participation 5. Empirical Learning Self-analysis SWOT - Time management - Creative chain story telling Vocabulary games I – Attitude - Interpersonal skills Motivation I - Vocabulary games II - Article review Team building exercise - Critical Thinking - Event Management Business situation - Leadership Qualities – Review SCHEME OF INSTRUCTION Marks allocated for regular participation in all oral activities in class SCHEME OF EXAMINATION Complete internal evaluation on a regular Basis

L T P C GE0107 NSS/NCC/NSO/YOGA 0 0 2 1 Prerequisite Nil

I. YOGA SYLLABUS

PRACTICE LECTURE

I Meditation – Agnai, Asanas, Kiriyas, Bandas, Muthras Benefits of Agnai Meditation

II Meditation Santhi Physical Exercises (I & II) Benefits of santhi Meditation

III Kayakalpa Yoga Asanas, Kiriyas, Bandas, Muthras Lecture & Practice IV Meditation Santhi Physical Exercises III & IV Analysis of Thought V Meditation Thuriyam Kayakalpa Asanas, Kiriyas, Bandas, Muthras Benefits of Thuriyam VI Meditation Thuriyam Kayakalpa Asanas, Kiriyas, Bandas, Muthras Attitude VII Meditation Thuriyam Kayakalpa Asanas, Kiriyas, Bandas, Muthras Importance of Arutkappy

& Blessings VIII Meditation Santhi Kayakalpa Asanas, Kiriyas, Bandas, Muthras Benefits of Blessings

Hours = 30 TEXT BOOKS: 1. Vedatri Maharshi , “Yoga for Modern Age” 2. Vedatri Maharshi, “ Simplified Physical Exercises”

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II. NATIONAL SPORTS ORGANISATION (NSO) Each student must select two of the following games and practice for two hours per week. An attendance of 80% is compulsory to earn the credits specified in the curriculum.

LIST OF GAMES:

1. Basket Ball 2. Football 3. Volley Ball 4. Ball Badminton 5. Cricket 6. Throwball

III. NATIONAL CADET CORPS (NCC)

Any student enrolling as a member of National Cadet Core (NCC) will have to attend sixteen parades out of twenty parades each of four periods over a span of academic year.

Attending eight parades in first semester will qualify a student to earn the credits specified in the curriculum.

IV. NATIONAL SERVICE SCHEME (NSS)

A student enrolling as member of NSS will have to complete 60 hours of training / social service to be eligible to earn the credits specified in the curriculum.

L T P C

PH0103 PHYSICS LABORATORY 0 0 2 1 Prerequisite

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

1. Understand scientific concepts in measurement of different physical variables 2. Develop the skill in arranging and handling different measuring instruments and 3. Get familiarized with 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 EXPERIMENT

1. Determination of Young’s Modulus of the material – Uniform bending 2. Determination of Rigidity Modulus of the material – Torsion Pendulum 3. Determination of velocity of Ultrasonic waves in liquids 4. Determination of dispersive power of a prism using spectrometer 5. Determination of laser parameter – Divergence and wavelength for a given laser source – laser grating 6. Particle size determination using laser 7. Study of attenuation and propagation characteristics of optical fiber cable 8. Calibration of voltmeter using potentiometer. 9. Calibration of ammeter using potentiometer. 10. Construction and study of regulation properties of a given power supply using IC

REFERENCE BOOKS

1. Chattopadhyay, D., Rakshit, P. C. and Saha, B., An Advanced Course in Practical Physics, 2nd edition, Books & Allied Ltd., Calcutta, 1990.

2. Chauhan and Singh, Advanced Practical Physics, Revised edition, Pragati Prakashan, Meerut, 1985. 3. Thiruvadigal. J. D., Ponnusamy. S., Vasuhi. P. S. and Kumar. C, Hand Book of Practical Physics, 5th

edition, Vibrant Publication, Chennai, 2007.

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L T P C CY0103 CHEMISTRY LABORATORY 0 0 2 1

Prerequisite Nil 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. Preparation of standard solutions. 2. Estimation of total hardness, permanent and temporary hardness by EDTA method. 3. Conductometric titration – determination of strength of an acid. 4. Estimation of iron by potentiometer – titration. 5. Determination of molecular weight of polymer by viscosity average – method. 6. Determination of dissolved oxygen in a water sample by Winkler”s method 7. Determination of Na / K in water sample by Flame photometry. 8. Estimation of Copper in ore. 9. Estimation of nickel in steel. 10. Determination of total alkalinity and acidity of a water sample.

REFERENCE

1. Chemistry department manual, Edition, 2007.

L T P C GE0105 COMPUTER LITERACY 0 0 2 1 Prerequisite Nil

PURPOSE This Lab Course will enable the students to understand the basics of computer and to know the basics of MS-Office. INSTRUCTIONAL OBJECTIVES

1. To learn the basics of computer. 2. To work on Ms-Word, Ms-Excel, Ms-Power Point and Ms-Access

EXPERIMENTS TO IMPLEMENT

1. Study experiment on evolution of computer programming languages. 2. Suggest some of the Network Topologies that can be incorporated in your campus. Justify your choice. 3. Experiments to demonstrate directory creation and file creation. 4. Create a document with all formatting effects. 5. Create a document with tables. 6. Create labels in MS word. 7. Create a document to send mails using mail merge option. 8. Create an Excel File to analyze the student’s performance. Create a chart for the above data to depict it

diagrammatically. 9. Create Excel sheet to use built-in-function. 10. Create Excel sheet to maintain employee information and use this data to send mails using mail merge. 11. Create a Power Point presentation for your personal profile with varying animation effects with timer. 12. Consider student information system, which stores student personal data, mark information and non-

academic details. * Use MS Access to create Tables and execute SQL queries to do this following

* Display all student records. * Display student details with respect to his identity. * Delete some records from the table. * Find total marks obtained by student in each list.

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TEXT BOOK 1. Introduction to Information Technology, ITL Education Solutions Ltd., Pearson 2nd Edition, 2006.

L T P C AR0130 ENGINEERING DRAWING

(Only First Angle Projection is to be followed) 1 0 4 3

Prerequisite Nil PURPOSE

1. To draw and interpret various projections of 1D, 2D and 3D objects. 2. To prepare and interpret the drawings of buildings.

INSTRUCTIONAL OBJECTIVES To familiarize with

1. The construction of geometrical figures 2. The projection of 1D, 2D & 3D elements 3. Sectioning of solids and development of surfaces 4. Preparation and interpretation of building drawing

FUNDAMENTALS OF ENGINEERING GRAPHICS Lettering, two dimensional geometrical construction, conics, representation of three -dimensional objects – principles of projections – standard codes – projection of points. PROJECTION OF LINES AND SOLIDS Projection of straight lines- projection of solids – auxiliary projections SECTIONS AND DEVELOPMENTS Sections of solids and development of surfaces.

PICTORIAL PROJECTIONS Orthographic projection- isometric projection of regular solids & combination of solids- Conversion of orthographic to isometric. BUILDING DRAWING Building Drawing – plan, elevation and section of single storied residential (or) office building with flat RCC roof and brick masonry walls having not more than 3 rooms (planning / designing is not expected in this course). TEXT BOOKS

1. Ramachandran, S., Engineering Drawing, Private Publication, Chennai, 2002. 2. Natarajan. K.V., Engineering Drawing & Graphics, Private Publication, Chennai, 1990. 3. Narayanan K.L & Kannaiah P., Engineering Graphics, Scitech Publications, Chennai, 1999.

REFERENCE BOOKS

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

2. Venugopal. K., Engineering Drawing & Graphics, New Age international Pvt. Ltd., 2001. SEMESTER II

L T P C GE 0108 VALUE EDUCATION 1 0 0 1 Prerequisite Nil

PURPOSE To provide guiding principles and tools for the development of the whole person recognizing that the individual is comprised of Physical, Intellectual, Emotional and Spiritual dimensions.

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INSTRUCTIONAL OBJECTIVES To help individuals think about and reflect on different values. To deepen understanding, motivation and responsibility with regard to making personal and social choices

and the practical implications of expressing them in relation to themselves, others, the community and the world at large.

To inspire individuals to choose their own personal, social, moral and spiritual values and be aware of practical methods for developing and deepening

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

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. 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. Professional values – Definition – Competence – Confidence – Devotion to duty –Efficiency – Accountability – 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. 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. REFERENCE BOOKS 1. Dr. S. Ignacimuthu S. J., “Values for life”, Better yourself Books, Bandra Mumbai-600 050 (1999). 2. “Values(Collection of Essays)”., Published by : Sri Ramakrishna Math., Chennai—4.,(1996) 3. Prof. R.P.Dhokalia., “Eternal Human Values”, NCRT –Campus Sri Aurobindo Marg., New Delhi - 110

011. 4. Swami Vivekananda., “Education”, Sri Ramakrishna Math., Chennai-4(1957) 5. “Tirukural” (English Translation by Dr.G.U.Pope). 6. “The Bible” 7. “The Kuran” 8. “The Bagavath Geetha”

L T P C MA 0142 MATHEMATICS – LS2 3 2 0 4

Prerequisite MA0111

(Common to BT , GE, BI, BME, BP & FPE) PURPOSE : To impart analytical ability in solving mathematical problems as applied to the respective branches of Engineering. INSTRUCTIONAL OBJECTIVES: At the end of the Course the students 1. Should have understood maxima and minima of two and three variables 2. Should have been fully exposed to Differential equations and Multiple integrals

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3. Should have been able to apply Vector Calculus and three dimensional coordinate Geometry to their branches of Engg.

FUNCTIONS OF SEVERAL VARIABLES Functions of two variables – partial derivatives – total differentiation – Taylor’s expansion – maxima and minima of functions of two and three variables – Jacobians. DIFFERENTIAL EQUATIONS Differential equations of first order and higher degree – higher order differential equations with constant coefficients – variable coefficients – method of variation of parameters. MULTIPLE INTEGRALS Double integration in Cartesian and polar coordinates – Change of order of integration – Area as a double integral – Triple integration in Cartesian coordinates. VECTOR CALCULUS *Review of Vector Algebra. Gradient, divergence and curl – solenoidal, and irrotational fields – directional derivatives – line integrals – surface integrals – volume integrals, Integral theorem (without proof) and its applications- cubes and parallelopipeds THREE DIMENSIONAL ANALYTICAL GEOMETRY Direction cosines and direction ratios of a line – angle between two lines. Equation of a plane – equation of straight line – shortest distance between two skew lines – coplanar lines. *No questions should be asked in the Review part TEXT BOOK

1. Grewal B.S, Higher Engg Maths, Khanna Publications, 38th Edition. 2. Veerajan, T., Engineering Mathematics, Tata McGraw Hill Publishing Co., 3. New Delhi,2000. 4. Dr.V.Ramamurthy & Dr. Sundarammal Kesavan, Engineering Mathematics – Vol I & II

Anuradha Publications, Revised Edition 2006. REFERENCE BOOKS: 1. Kreyszig.E, Advanced Engineering Mathematics, 8th edition, John Wiley & Sons. Singapore,2001. 2. Kandasamy P etal. Engineering Mathematics, Vol.I & II (4th revised edition), S.Chand &Co., New

Delhi,2000. 3. Narayanan S., Manicavachagom Pillay T.K., Ramanaiah G., Advanced Mathematics for Engineering

students, Volume I & II (2nd edition), S.Viswanathan Printers and Publishers, 1992. 4. Venkataraman M.K., Engineering Mathematics – Vol. III (13th edition), National Publishing Co.,

Chennai,1998.

L T P C PH0102 MATERIALS SCIENCE 2 0 2 3 Prerequisite Nil PURPOSE The purpose of this course is to develop comprehension of the rapidly changing technological scenario and the requisite expertise for appropriate selection of materials for specific engineering applications. INSTRUCTIONAL OBJECTIVES At the end of the course, the student will be able to:

1. Understand electrical properties of materials, 2. Understand the properties and applications of semi conducting materials, 3. Understand general properties and applications of magnetic and dielectric materials, 4. Understand the behaviour of materials on exposure to light, 5. Understand general properties and application of modern engineering and bio materials, and

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6. Get familiarized with the concepts of Nano Science and Technology. ELECTRONIC AND PHOTONIC MATERIALS Electronic materials: Importance of Classical and Quantum free electron theory of metals – Fermi energy and Fermi Dirac distribution function – Variation of Fermi level with temperature in intrinsic and extrinsic semiconductors – Hall effect – Dilute Magnetic Semiconductors (DMS) and their applications – High temperature Superconductivity. Photonic materials: LED and LCD materials – Photo conducting materials – Nonlinear optical materials (elementary ideas) and their applications. MAGNETIC, DIELECTRIC AND MODERN ENGINEERING MATERIALS Magnetic materials: Ferrites and garnets – Magnetic bubbles and their applications – Giant Magneto Resistance (GMR) – Colossal Magneto Resistance (CMR). Dielectric materials: Various polarization mechanisms in dielectrics (elementary ideas) and their frequency and temperature dependence – Dielectric loss – Piezo electric and ferro electric materials and their applications. Modern engineering materials: Shape memory alloys – Metallic glasses – Advanced ceramics and composites. BIO MATERIALS Classification of biomaterials – Comparison of properties of some common biomaterials – Effects of physiological fluid on the properties of biomaterials – Biological responses (extra and intra vascular system) – Metallic, Ceramic and Polymeric implant materials – Introduction to bio sensors and tissue engineering. NANO MATERIALS AND NANOTECHNOLOGY Basic concepts of Nano science and technology – Quantum wire – Quantum well – Quantum dot – Properties and technological advantages of Nano materials – Carbon Nanotubes and applications – Material processing by Sol – Gel method, Chemical Vapour deposition and Physical Vapour deposition – Microwave Synthesis of materials – Principles of SEM, TEM and AFM. MECHANICAL PROPERTIES OF MATERIALS Stress Strain diagram for different engineering materials – Engineering and true stress strain diagram – Ductile and brittle material – Tensile strength – Hardness – Impact strength – Fatigue – Creep – Fracture (Types and Ductile to brittle transition) – Factors affecting mechanical properties. PRACTICALS

1. Band gap determination using Post office box. 2. Dielectric constant measurement. 3. Photoconductivity measurement. 4. Resistivity determination for a semiconductor wafer using Four probe method. 5. Determination of Hall coefficient and carrier type for a semiconductor material. 6. To trace the hysteresis loop for a magnetic material. 7. Magnetic susceptibility – Quincke’s method. 8. Determination of thermal conductivity – Lee’s Disc method 9. Visit to Nano Technology Laboratory (optional)

TEXT BOOKS

1. S.O. Kasap, Principles of Electronic Materials and Devices, Tata McGraw Hill Edition, New Delhi, 2002.

2. Van Vlack, L.H., Material Science for Engineers, 6th edition, .Addision Wesley, 1985. 3. Thiruvadigal, J. D., Ponnusamy, S. and Vasuhi.P. S., Materials Science, 5th edition, Vibrant

Publications, Chennai, 2007. REFERENCE BOOKS

1. Rolf E. Hummel, Electronic Properties of materials, Narosa Publishing House, New Delhi, 1994. 2. Raghavan V., Materials Science & Engineering – A First Course, 5th edition, Prentice Hall of India,

New Delhi, 2005. 3. Khanna O. P., A Text Book of Material Science & Metallurgy, Revised edition, Dhanpat Rai

Publications, New Delhi, 2006. 4. Sujata V. Bhat, Biomaterials, 2nd edition, Narosa Publishing House, New Delhi, 2006.

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5. Mick Wilson, Kamali Kannangara, Michells Simmons and Burkhard Raguse, Nano Technology – Basic Science and Emerging Technologies, 1st edition, Overseas Press, New Delhi, 2005.

L T P C GE0104 PRINCIPLES OF ENVIRONMENTAL SCIENCE 2 0 0 2

Prerequisite Nil PURPOSE The course provides the comprehensive knowledge in environmental science, environmental issues and the management. INSTRUCTIONAL OBJECTIVES

1. The importance of environmental education, ecosystem and ethics. 2. Knowledge with respect to biodiversity and its conservation. 3. To create awareness on the various environmental pollution aspects and issues. 4. To educate the ways and means to protect the environment. 5. Important environmental issues and protection

ENIVRONMENT AND ECOSYSTEMS Environmental education: definition - scope - objectives and importance. Concept of an ecosystem – types (terrestrial and aquatic ecosystems) – structure and function – ecological succession - food chains, food webs and ecological pyramids BIODIVERSITY Introduction: definition - genetic, species and ecosystem diversity - value of biodiversity: consumptive use, productive use, social, ethical, aesthetic and option values - threats to biodiversity: habitat loss, poaching of wildlife - endangered and endemic species of India, Conservation of biodiversity: in-situ and ex-situ conservations. POLLUTION AND WASTE MANAGEMENT Air and water pollution – classification of pollutants and their effects – control measures of air pollution. Waste water treatment (general) – primary, secondary & tertiary stages. Solid waste management: causes - effects of municipal waste, hazardous waste, bio medical waste - process of waste management. CURRENT ENVIRONMENTAL ISSUES Environmental ethics -issues and possible solutions- population explosion, climatic change, ozone layer depletion, global warming, acid rain and green house effect. Sustainable development: definition, objectives and environmental dimensions of sustainable development- environmental audit for sustainable development. ENVIRONMENTAL PROTECTION National and international concern for environment: Important environmental protection acts in India – water, air (prevention and control of pollution) act, wild life conservation and forest act – functions of central and state pollution control boards - international effort – key initiatives of Rio declaration, Vienna convention, Kyoto protocol and Johannesburg summit.

TEXT BOOKS

1. Sharma.B.K. and Kaur, “Environmental Chemistry” Goel Publishing House, Meerut, 1994. 2. De. A.K., “Environmental Chemistry”, New Age International (p) lt., New Delhi, 1996. 3. Kurian Joseph & R. Nagendran, “Essential of Environmental Studies” Pearson Education, 2004.

REFERENCE BOOKS

1. Dara S.S., A Text Book of Environmental Chemistry and pollution control, S.Chand & Company Ltd., New Delhi, 2004.

2. Jeyalakshmi. R, Principles of Environmental Science, 1st Edition, Devi Publications, Chennai 2006. 3. Kamaraj. P & Arthanareeswari. M, Environmental Science – Challenges and Changes, 1st Edition,

Sudhandhira Publications, 2007. 4. Arivalagan. K, Ramar. P & Kamatchi. P, Principles of Environmental Science, 1st Edition, Suji

Publications, 2007.

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L T P C GE0106 BASIC ENGINEERING – II 4 0 0 4 Prerequisite Nil

PURPOSE This course provides comprehensive idea about circuit analysis, working principles of machines and common measuring instruments. It also provides fundamentals of electronic devices, transducers and integrated circuits. INSTRUCTIONAL OBJECTIVES

1. At the end of the course students will be able 2. To understand the basic concepts of magnetic, AC & DC circuits. 3. To explain the working principle, construction, applications of DC & AC machines & measuring

instruments. 4. To gain knowledge about the fundamentals of electric components, devices, transducers & integrated

circuits.

PART A ELECTRICAL ENGINEERING

ELECTRICAL MACHINES Definition of mmf- flux and reluctance-leakage flux, fringing, magnetic materials and B-H relationship- Problems involving simple magnetic circuits- Faraday’s laws- induced emfs and inductances, brief idea on Hysteresis and eddy currents- Working principle, construction and applications of DC machines and AC machines (1-phase transformers, 3-phase induction motors, single phase induction motors – split phase, capacitor start and capacitor start & run motors). AC & DC CIRCUITS Circuit parameters, Ohms law, Kirchhoff’s law. Average and RMS values, concept of phasor representation- RLC series circuits and series resonance, RLC parallel circuits (includes simple problems in DC & AC circuits)-Introduction to three phase systems – types of connections, relationship between line and phase values. (Qualitative treatment only) WIRING & LIGHTING Types of wiring- wiring accessories- staircase & corridor wiring- Working and characteristics of incandescent, fluorescent, SV & MV lamps- Basic principles of earthing, simple layout of generation, transmission & distribution of power. TEXT BOOKS

1. Muthusubramanian. R, Salivahanan. S, Muraleedharan. K.A, Basic Electrical, Electronics and Computer Engineering, Tata McGraw - Hill, 1999

2. Mehta V K, Principles of Electronics, S Chand & Co, 1980

REFERENCE BOOKS 1. Mithal G K, Electronic Devices and Circuits, Khanna Publications, 1997. 2. Kothari D P and Nagrath I J, Basic Electrical Engineering, Tata McGraw Hill, 1991

PART B ELECTRONICS ENGINEERING

ELECTRONIC COMPONENTS AND DEVICES Passive components – Resistors, Inductors and Capacitors and their types. Semiconductor: Energy band diagram, Intrinsic and Extrinsic semiconductors, PN junction diodes and Zener diodes – characteristics. Transistors: PNP and NPN transistors – theory of operation – Transistor configurations – characteristics – comparison. Special semiconductor devices: FET – SCR – LED – V I characteristics – applications. Rectifiers: Half wave and full wave rectifier – capacitive filter – wave forms – ripple factor – regulation characteristics.

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TRANSDUCERS AND MEASURING INSTRUMENTS Transducers: General features and classification of transducers, Resistive Transducers – Potentiometer, Unbonded strain gauge-Bonded strain gauge-Load cell, Inductive transducers – Differential output transducers – LVDT, Flow transducers, Temperature Transducers – Thermistors, Thermocouple and pyrometers. Measuring Instruments: Basic principles and classification of instruments, Moving coil and moving iron instruments, CRO – Principle of operation. DIGITAL ELECTRONICS & LINEAR ICs Digital Fundamentals: Number systems – Boolean Theorems – DeMorgan’s Theorem - Logic gates – Implementation of Boolean Expression using Gates. Integrated Circuits: IC fabrication – Monolithic Technique, Function of Operational Amplifier. TEXT BOOKS

1. Muthusubramanian. R, Salivahanan. S, Muraleedharan. K.A, Basic Electrical, Electronics and Computer Engineering, Tata McGraw - Hill, 1999.

2. Metha V.K, Principles of Electronics, S. Chand & Co., 1980. 3. Kalsi H S, Electronics Instrumentation, ISTE publication, 1995

REFERENCE BOOKS

1. Kothari D. P and Nagrath IJ, Basic Electrical Engineering, Tata McGraw- Hill, 1991. 2. Thomas L.Floyd , Electronic devices, Addison Wesley Longman (Singapore) Pvt . Ltd., 5th Edition, 2001.

L T P C

BT0104 CELL BIOLOGY 3 0 0 3 Prerequisite Nil PURPOSE The course is aimed to make the student understand the basic concept of cell structure, membrane, cellular functions of different types of cell, modes of cellular signaling and signal amplification INSTRUCTIONAL OBJECTIVES

1. To study cell structure and functions of organelle functions 2. Exposure on transportations through cell membrane 3. To focus on different receptors and model of signaling 4. To introduce the concept of cell signaling

AN OVERVIEW OF CELLS AND CELL RESEARCH Origin and evolution of cells, cells as experimental models, tools of cell biology – chemistry of cells – molecular composition of cells, central role of enzymes, metabolic energy, biosynthesis of cell constituents, cell membrane. CELL STRUCTURE AND FUNCTION – I Nucleus- Endoplasmic reticulum- Gorge apparatus and Lissome- Bioenergetics and Metabolism – Mitochondria- chloroplasts- Paroxysms. CELL STRUCTURE AND FUNCTION – II The cytoskeleton and cell movement, cell surface – transport of small molecules, Endocytosis, cell –cell interactions-Adhesion junctions-Tight junctions-Gap junctions- Plasmodesmata CELL SIGNALING – CELL REGULATION Signaling molecules and their receptors, functions, pathways of intracellular signal transduction – the Cell Cycle –Mitosis and Meiosis –Cell death and cell renewal-Programmed cell death-Stem cells- Embryonic stem cells and therapeutic cloning. CANCER The Development and causes of cancer- tumour viruses, oncogenes, prevention and treatment.

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TEXT BOOK 1. Geoffrey M. Cooper, The Cell: A molecular approach, ASM Press, 2007. 2. Roberts, Keith Alberts, Bruce Johnson, Alexander Raff, Martin Walter, Peter Lewis, Julian, Garland

Molecular Biology of the Cell Edition 4

REFERENCE BOOK 1. Lodish, Harvey Krieger, Monty Kaiser, Chris A. Berk, Arnold, Molecular Cell Biology, W H Freeman

& Co. 2. S. C. Rastogi, Cell Biology , 3rd Edition, New Age International Pub. Ltd., India, 2001

L T P C BT0102 BIOCHEMISTRY 3 0 0 3 Prerequisite Nil PURPOSE Deals with the study of structural and functional aspects of biomolecules. INSTRUCTIONAL OBJECTIVES

1. To study the structure and properties of carbohydrates. 2. Discuss the structure, properties and reactions of proteins and amino acids 3. Discuss the structure, properties of fats and lipids 4. To study the composition, structure and functions of nucleic acids

CARBOHYDRATES, LIPIDS AND PROTEINS Monosaccharides- complex carbohydrates- glycoproteins- lectins- Lipids and cell membranes – types of membrane lipids- phospholipids and glycolipids from bimolecular sheets- Protein structure and function – Primary- Secondary- Tertiary- Quarternary Structures. METABOLISM OF CARBOHYDRATES Glycolysis- Glucogenesis- Citric acid cycle and Glycogen metabolism. PROTEIN METABOLISM Protein turnover and Amino acid catabolism- Biosynthesis of amino acids. FATTY ACID METABOLISM AND NUCLEIC ACID METABOLISM Overview of Fatty Acid Metabolism- synthesis and degradation of fatty acids- Denovo synthesis of Nucleotides. OXIDATIVE PHOSPHORYLATION Oxidative Phosphorylation – regulation – light reactions of Photosynthesis TEXT BOOK

1. Jeremy M. Berg, John L. Tymozko, Lubert Styer, Biochemistry, Fifth edition, W.H. Freeman and Company.

2. Albert L. Lehninger, David L. Nelson, Michael M. Cox, Karen Ocorr, Principles of Biochemistry, W H Freeman & Co, 2005.

REFERENCE BOOK

1. Student Companion to Accompany Biochemistry, Richard I. Gumport, Jeremy M. Berg, Nancy Counts Gerber, Frank H. Deis, Jeremy Berg, W H Freeman & Co.

2. Fundamentals of Biochemistry, Donald Voet and Judith G. Voet, John Wiley, 2005

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L T P C PD0102 PERSONALITY DEVELOPMENT – II 0 0 2 0 Prerequisite Nil PURPOSE The purpose of this course is to build confidence and inculcate various soft skills and to help Students to identify and achieve their personal potential INSTRUCTIONAL OBJECTIVES

1. To guide thought process. 2. To groom students' attitude. 3. To develop communication skill. 4. To build confidence.

METHODOLOGY The entire program is designed in such a way that every student will participate in the class room activities. The activities are planned to bring out the skills and talents of the students, which they will be employing during various occasions in their real life. 1. Group activities + individual activities. 2. Collaborative learning. 3. Interactive sessions. 4. Ensure Participation. 5. Empirical Learning Puzzles I - Poster design/Caption/Slogan writing (Social issues) - Bone of contention I – debate Bone of contention II - Puzzle II - Survey and Reporting (favorite channel, music, food) Interpretation of Visuals of I & II - Vocabulary games III Book Review - Quiz I - Presentation Skills I Presentation Skills II - Analytical Thinking - Review

EVALUATION 1. Activities assessed by both group and individual participation 2. Continuous assessment based on daily participation SCHEME OF INSTRUCTION Marks allocated for regular participation in all oral activities in class SCHEME OF EXAMINATION Complete internal evaluation on a regular Basis

L T P C ME0120 WORKSHOP PRACTICE 0 0 4 2 Prerequisite Nil

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

1. The basics of tools and equipments used in fitting, carpentry, sheet metal, welding and smithy. 2. The production of simple models in the above trades.

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LIST OF EXPERIMENTS EMPHASIS TO BE LAID ON REAL LIFE APPLICATIONS WHEN FRAMING THE EXERCISES. FITTING Tools & Equipments – Practice in Filing and Drilling. Making Vee Joints, Square, dovetail joints, Key Making. CARPENTARY Tools and Equipments- Planning practice. Making Half Lap, dovetail, Mortise & Tenon joints, a mini model of a single door window frame. SHEET METAL Tools and equipments - Fabrication of a small cabinet, Rectangular Hopper, etc. WELDING Tools and equipments - Arc welding of butt joint, Lap Joint, Tee Fillet- Demonstration of Gas welding, TIG & MIG. SMITHY Tools and Equipments –Making simple parts like hexagonal headed bolt, chisel. TEXT BOOKS

1. Gopal, T.V., Kumar, T., and Murali, G., A first course on workshop practice – Theory, practice and work book, Suma Publications, 2005.

REFERENCE BOOKS

1. Kannaiah, P. & Narayanan, K.C. Manual on Workshop Practice, Scitech Publications, Chennai, 1999. 2. Venkatachalapathy, V.S. First year Engineering Workshop Practice, Ramalinga Publications, Madurai,

1999.

L T P C CS0140 COMPUTER PRACTICE 1 0 2 2 Prerequisite Nil

Common for All Branches except ME, AU, MH, AS, CS and IT

PURPOSE To introduce programming languages C and C++ as tools to solve problems and to provide hands on training. INSTRUCTIONAL OBJECTIVES: After completing the course, the students should be able to

1. Understand the program development life cycle 2. Design algorithms to solve simple problems using computers 3. Convert algorithms into C and C++ programs and execute

PROGRAMMING FUNDAMENTALS Computer Basics; Program Development Life Cycle: Flow Chart, Algorithm, Compilation and Execution; Introduction to C Language: program structure, variables, keywords, data types; Input / Output functions: scanf, printf; simple programs. DECISION AND LOOP CONTROL STRUCTURE Logical operators; Decision statements: if/else, switch/case statements; Loop control statements – for, while, do/while. ARRAYS AND FUNCTIONS Arrays: Introduction to arrays; one-dimensional arrays: declaration, reading and printing array elements, sorting and searching. Functions: Definition; declaration of functions; return statement; recursion.

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INTRODUCTION TO OOP CONCEPTS OOP concepts: data hiding, encapsulation, inheritance, overloading, polymorphism; classes and objects; constructor and destructor; simple program in C++. INHERITANCE AND OVERLOADING Inheritance: single, multiple, multilevel- overloading: Function overloading, Operator overloading. LIST OF EXERCISES: Note to the Instructors: Design exercise problems to demonstrate the use of C and C++ in the area of specialization.

1. Programs to demonstrate the use of scanf ( ) and printf( ) functions 2. Programs to evaluate arithmetic expressions 3. Programs using conditional statements 4. Programs using for, while, do…while 5. Programs on arrays 6. Programs to perform matrix addition and multiplication 7. Programs to implement functions 8. Programs to illustrate recursion 9. Program to create classes and objects using C++ 10. Program to implement Constructor and Destructor in C++ 11. Program to implement single inheritance in C++ 12. Program to implement Function overloading in C++ 13. Program to implement Operator overloading in C++

REFERENCE BOOKS

1. Computer Practice Laboratory Manual, SRM University 2. Kanetkar P.Yashwant,,Let us C, BPB publications, 2002. 3. Ashok N. Kamthane, Programming with ANSI and Turbo C, Pearson Education, 2006. 4. Herbert Schildt, The Complete Reference C++, Tata McGraw Hill, 2001, 3rd Edition. 5. Robert Lafore, Object Oriented Programming in Microsoft C++, The Waite Group, Galgotia

Publications Pvt. Ltd., 2002.

III SEMESTER

L T P C LE0201 GERMAN LANGUAGE PHASE I 2 0 0 2

Prerequisite Nil

PURPOSE This course is designed to teach the students the basics of the German language.

INSTRUCTIONAL OBJECTIVE For beginners with no knowledge of German acquiring basic verbal and communication skills. INTRODUCTION German Language, Alphabets and Pronunciation. THEMEN Name, Land, Leute, Beruf, Familie geschwister, Einkaufen, Reisen, Zahlen, Haus, Freunden, Essen and Stadium, Fest, Zeit. LISTENING Listening to the cassette and pay special attention to the meaning and sounds. Listening Comprehension – Announcements / Airport / Station / General. READING Listening to the cassette and reading it allowed. READING COMPRENSION BASICS / STATION / NEWS / NOTICE BOARDS.

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GLOSSARY Technical Words Lesson (1-5) TEXT BOOK WITH CASSETTES

1. Grundkurs Deutsch 2. Momentmal (Max Mueller Bhavan – Goethe Institute, Germany).

SCHEME OF EVALUATION Internal 50 = Listening – 10 Marks, Speaking – 20 Marks, Reading – 10 Marks and Writing = 10 Marks L T P C LE0203 JAPANESE LANGUAGE PHASE I 2 0 0 2

Prerequisite Nil

PURPOSE This course is designed to teach the students the basics of the Japanese language.

INSTRUCTIONAL OBJECTIVE For beginners with no knowledge of Japanese to acquire basic communication Skills. Alphabets (Hiragana ), Self Introduction, Greetings, Classroom expressions, Numbers, Conversation. Alphabets Hiragana (continued),Vocabularies. Counters .Time expression. Conversation Katakana and related vocabulary. Kanjis –introduction- conversation. Lesson-1 Watashiwa Nihonjin desu. Grammar-Marume &Sentence pattern.Marume. Conversation. TEXT BOOKS

1. Nihongo Shoho I main Text sold in India by the Japanese Language Teachers Association Pune. 2. Hiragana and Katakana Work Book published by AOTS Japan 3. Grammar and Kotoba ( Work Book ) 4. Japanese for Dummies.(Conversation) CD.

SCHEME OF EVALUATION Internal 50 = Listening – 10 Marks, Speaking – 20 Marks, Reading – 10 Marks and Writing = 10 Marks L T P C LE0205 FRENCH LANGUAGE PHASE I 2 0 0 2

Prerequisite Nil

PURPOSE This course is designed to teach the students the basics of the French language.

INSTRUCTIONAL OBJECTIVE For beginners with no knowledge of French to acquire basic communication Skills. INTRODUCTION AND PRONUNCIATION Introduction of the French Language, Alphabets and Pronunciation, Greetings (Wishing, Thanking and Bidding good bye), Introducing oneself & someone Presenter quelqu’un et se presenter - conversational French sentences based on the topics discussed above.

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VOCABULARY Numbers and Dates, Days, Months and Seasons, Time, Nouns, Professions and Nationalities. C;onversational sentences on weather, time, and professions. GRAMMAR Basic Verbs (Avoir, Etre, Aller, Faire) – Conjugation – Present tense, Affirmative, Negative, Interrogative, Adjectives (Qualitative), Subject Pronouns and Disjunctive Pronouns. CONVERSATION AND LISTENING Conversational sentences on physical description and expressions with verbs like avoir, etre and faire GRAMMAR Prepositions ( a, de,dans, en, sur,sous, pour….),Contracted Articles, Question Tag

(Qui, Quel, Ou, ……etc) TEXT BOOKS:

1. Panorama – Goyal Publishers 2. Apprenons le Francais I, Sarawathy publication.

SCHEME OF EVALUATION Internal 50 = Listening – 10 Marks, Speaking – 20 Marks, Reading – 10 Marks and Writing = 10 Marks

L T P C BI0201 COMPUTER SKILLS 1 0 2 2

Prerequisite Nil

PURPOSE This course allows the student to acquire knowledge in the field of Visual Basic. INSTRUCTIONAL OBJECTIVES This subject emphasizes on

1. Visual basic Programming 2. Practical MDR Application creation

INTRODUCTION Introduction-History of VB- What is VB- Integrated development environment: Introduction, project window, form layout- Toolbox- Properties window- menu bar and toolbar- operators VB PROGRAMMING Introduction to Visual programming and event driven programming-control structures- data types – arrays- Strings, dates and times: String datatype , conversion function ,date and time processing and formatting. PROCEDURES Form modules- sub procedures- function procedures- call by value vs call by reference-storage classes- recursion-Graphics: Drawing methods, properties, line control, shape control, colors. GUI CONCEPTS Controls: textbox, mask edit, combo box, list box, scroll bars, slider, menus – MDI- Multiple forms- template forms-RTB control-Check box- buttons. ERROR HANDLING AND DEBUGGING Error handling – divide by zero- on error- err object-resume statement-rethrowing errors-Break mode-Immediate window- Debugging strategies. LIST OF EXPERIMENTS

1. Displaying a line of text in a form. 2. Control structures

• Entry controlled loop (for/if)

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• Exit control loop (do while) • Switch case

3. Call by value and Call by reference. 4. Recursion 5. Sorting 6. Design an employee registration form 7. Design an MDR application 8. Graphics

TEXTBOOKS

1. Deital &Deital, T. R. Nieto, Visual basic 6- How to Program, Pearson Education, 2004. 2. E. Smith, V. Whisler, H. Marquis, Visual Basic 6 Programming Bible, Wiley- Dreamtech, 2003.

REFERENCE BOOKS 1. Wallace Wang, Visual Basic Programming for Dummies, IDG books, 1994. 2. Evangelos Petrousos, Mastering VB 6, BPB Publications, 2005.

L T P C

MA0201A NUMERICAL METHODS 3 2 0 4 Prerequisite Nil PURPOSE This subject enables the students to understand the basic numerical methods having application in Bioinformatics INSTRUCTIONAL OBJECTIVES This subject emphasizes on

1. Curve fitting 2. Numerical Differentiation and Integration 3. Ordinary & Partial Differential Equations

CURVE FITTING AND NUMERICAL SOLUTION OF EQUATIONS Method of Least squares-Fitting a straight line-Fitting a parabola-Fitting an exponential curve-Fitting a curve of the form y=ax b -Calculation of the squares of the residuals-Newton –Raphson method-Gauss Elimination method-Gauss Jacobi method-Gauss seidel method. FINITE DIFFERENCES AND INTERPOLATION First and higher order differences-Forward differences and backward differences and central Differences-Differences of polynomial-Properties of operations-Factorial polynomials-Shifting operator E-Relations between the operators -Interpolation –Newton-Gregory Forward and Backward Interpolation formulae-Divided differences-Newton’s divided difference formula-Lagrange’s Interpolation formula-Inverse interpretation NUMERICAL DIFFERENTIATION AND INTEGRATION Newton’s forward and backward differences –formulae to compute first and higher order derivatives-The Trapezoidal rule-Simpson’s one third rule and three eighth rule. NUMERICAL SOLUTIONS FOR ORDINARY DIFFERENTIAL EQUATIONS Solution by Taylor’s series-Euler’s Methods-Improved and modified Euler’s method- Runge-kutta methods of fourth order-Milne’s method-Adam’s Bashforth method NUMERICAL SOLUTIONS FOR PARTIAL DIFFERENTIAL EQUATIONS Classification of Partial differential equations of the second order-Difference quotients-Laplace’s equation and its solution by Liebmann’s process-Solution of Poisson’s equation-Solutions of Parabolic and Hyperbolic equations TEXTBOOKS

1. B.S. Grewal, Numerical Methods, Khanna Publishers, 6th edition, 1987. REFERENCE BOOKS

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3. M.K. Venkataraman, Numerical Methods in Science and Engineering, National Publishing Co., 1999 4. S.S. Sastry, Introductory Methods of Numerical Analysis, 2001. 5. E. Balagurusamy, Computer oriented statistical numerical methods, Tata McGraw Hill, 2000 6. M.K. Jain, SRK Iyengar and R.L. Jain, Numerical Methods for scientific and engineering computation,

Wiley Eastern Ltd., 1987. 7. M.K. Jain, Numerical Solution of Differential Equations, 1979. 8. Dr. P. Kandasamy et al, Numerical Methods, S. Chand & Co., New Delhi, 2003.

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BI0203 INTRODUCTION TO ALGORITHMS 3 0 0 3 Prerequisite Nil PURPOSE This subject gives the introduction to algorithm and its applications INSTRUCTIONAL OBJECTIVES

1. Role of algorithm in computing 2. Advanced techniques 3. Different algorithmic methods

INTRODUCTION Role of algorithm in computing- analyzing and designing algorithms- growth of functions. METHODS Recurrences- probabilistic analysis and randomized algorithms. DYNAMIC PROGRAMMING Assembly line scheduling- matrix chain multiplication- elements of Dynamic programming- LCS-Optimal binary search trees. GREEDY ALGORITHMS Problem- Elements of Greedy algorithms-Huffman codes - Theoretical foundations- task scheduling problem. STRING MATCHING ALGORITHMS String matching algorithm-NP completeness. TEXT BOOKS

1. Thomas H. Cormen, Introduction to algorithms, MIT Press, 2001. 2. Robert Sedgewick, Algorithms in C, Addison-Wesley, 1990.

REFERENCE BOOKS 1. Mark Allen Weiss, Data Structures and Algorithm Analysis in C, Pearson Education, Second Edition,

1995. 2. Udi Manber, Introduction to Algorithms: A Creative Approach, Addison-Wesley, 1989.

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BI0205 INTRODUCTION TO BIOINFORMATICS 3 0 0 3 Prerequisite Nil PURPOSE Aims at providing an elementary knowledge of Bioinformatics and Biological Information on the web. INSTRUCTIONAL OBJECTIVES

1. Scope of Bioinformatics 2. Types of Databases and their use 3. Pairwise and Sequence alignment 4. Predictive methods

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5. Drug discovery and pharmacoinformatics HISTORY, SCOPE AND IMPORTANCE Important contributions - sequencing development - aims and tasks of Bioinformatics - applications of Bioinformatics - challenges and opportunities - Computers and programs – internet - world wide web – browsers - EMB net – NCBI. DATABASES - TOOLS AND THEIR USES Importance of databases - nucleic acid sequence databases - protein sequence data bases - structure databases - bibliographic databases and virtual library - specialized analysis packages SEQUENCE ALIGNMENT METHODS Sequence analysis of biological data- models for sequence analysis and their biological motivation- methods of alignment - methods for optimal alignments; using gap penalties and scoring matrices- multiple sequence alignment – introduction - tools for msa - application of multiple sequence alignment. PREDICTIVE METHODS USING DNA AND PROTEIN SEQUENCES Gene predictions strategies - protein prediction strategies - molecular visualization-Homology - phylogeny and evolutionary trees - Homology and similarity - phylogeny and relationships. DRUG DISCOVERY AND PHARMAINFORMATICS Discovering a drug - target identification and validation - identifying the lead compound - optimization of lead compound - chemical libraries. TEXTBOOKS

1. S.C. Rastogi & others, Bioinformatics- Concepts, Skills, and Applications, CBS Publishing, 2003. 2. S. Ignacimuthu, S.J., Basic Bioinformatics, Narosa Publishing House, 1995.

REFERENCES BOOKS

1. T K Attwood, D J parry-Smith, Introduction to Bioinformatics, Pearson Education, 1st Edition, 11th Reprint 2005.

2. C S V Murthy, Bioinformatics, Himalaya Publishing House, 1st Edition 2003. 3. Stephen A. Krawetz, David D. Womble, Introduction To Bioinformatics A Theoretical and

Practical Approach, Humana Press, 2003. 4. Hooman H. Rashidi, Lukas K. Buehler, Bioinformatics Basics-Applications in Biological Science

and Medicine, CRC press, 2005.

L T P C BI0207 INTRODUCTION TO DATA STRUCTURES 3 0 0 3 Prerequisite Nil PURPOSE The purpose of this subject is to study about the basic fundamentals of data structures and their applications in ‘C’ INSTRUCTIONAL OBJECTIVES

1. Basic fundamentals and stack, queue Implementation 2. Trees and their applications 3. Various types of sortings 4. Graphs and their applications 5. Various search techniques

LINEAR DATA STRUCTURES Algorithm Analysis - Mathematical background, Model - Running Time Calculations - Linear Data Structure - List ADT Array and Cursor Implementations - Stack ADT - Queue ADT Array and List Implementation and Applications. NON-LINEAR DATA STRUCTURES

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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. SORTINGS Sorting- Exchange sorts- Selection and Tree sorting- Insertion Sort- Heap Sort- Merge Sort- Quick Sort- Bucket Sort. GRAPH ALGORITHMS Definition and Representation of graphs- Topological sort- Shortest-Path Algorithms- Network flow problems- Minimum Spanning Tree- Application of Depth-First Search. SEARCHING Basic Search Techniques- Tree Searching- General Search Trees- Hashing. TEXTBOOKS

1. Mark Allen Weiss, Data Structures and Algorithm Analysis in C, Addison Wesley Publications, 2nd Edition, 1998.Chapters-2, 3, 4, 5, 6, 7, 9, 10.

2. Aaron M. Tanenbaum, Yedidyah Langsam, Moshe J. Augensten, Data Structures Using C, PHI, 1990.Chapters-5, 6, 7.

REFERENCE BOOKS

1. Jeffrey Esakov, Tom Weiss, Data Structures An Advanced Approach using C, PHI, 1989. 2. Alfred V. Aho, John E. Hopcroft, Jeffrey D. Ullman, Data Structures and Algorithms, Pearson

Education, 10th Reprint 2004. 3. Jean-Paul Tremblay, Paul G. Sorenson, An Introduction to Data Structures with Applications, 2nd

Edition, Tata McGraw-Hill Edition, 1976.

L T P C BI0209 JAVA PROGRAMMING 3 0 0 3 Prerequisite Nil PURPOSE The purpose of this subject is to study about basics of Java Programming and applying it in Bioinformatics. INSTRUCTIONAL OBJECTIVES

1. Operators of Java and its applications 2. Control statements of Java. 3. Threading in Java. 4. Event Handling and controls in Java 5. Using Java in Bioinformatics.

INTRODUCTION An Overview of Java- OOP, A Simple Program-Data Types- Variables, and Arrays, Operators-Arithmetic Operators, The Bit wise Operators, Relational Operators and Logical Operators CONTROL STATEMENTS Control Statements - Introducing Classes - Methods and Classes – Inheritance - Packages and Interfaces- Exception Handling. THREADING AND APPLETS Multithreaded Programming- Java Thread Model, Creating a Thread and Multiple Threads, Thread Priorities- String handling- I/O Applets- the Applet class. EVENT HANDLINGS AND CONTROLS Event Handling-Key event class-Mouse event class- Text event Class- Event listener interfaces-Programs for handling mouse and keyboard events- Using AWT controls-Labels- Text field-Buttons-Check boxes- Choice controls and Scroll bars- Layout Managers and Menus

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APPLICATIONS Applications of Java in Bioinformatics: BioJAVA-Java based software used for Bioinformatics analysis (Pattern Hunter)-Java code examples TEXTBOOK

1. Herbert Schildt, The Complete Reference JAVA 2 Fifth Edition, Tata McGraw Hill, 2005.Chapters-2, 3,4,5,6,7,8,9,10,11,12,13,19,20,21,23.

2. Joseph P. Russell, Java Programming for the Absolute Beginner, Thomson Course Technology, 2001.

REFERENCE BOOKS

1. Harvey M. Deitel, Paul J. Deitel, Java: How to Program: with an Introduction to Visual J++, Prentice Hall, 1997.

2. Kim B. Bruce, Thomas P. Murtagh, Andrea Pohoreckyj Danyluk, Java: An Eventful Approach, Prentice Hall College, 2006.

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BI0211 MICROBIOLOGY 3 0 0 3 Prerequisite Nil 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. INTRODUCTION TO MICROBIOLOGY Characterization, Classification and Identification of microorganisms - Microscopic examination of Micro organisms morphology and fine structure of bacteria- cultivation of bacteria - reproduction & growth, pure cultures and cultural characteristics. MICROBIAL PHYSIOLOGY AND GENETICS Enzymes and their regulation- Microbial metabolism energy production- utilization of energy & biosynthesis - bacterial genetics. MICROBIAL PHYSIOLOGY AND GENETICS Fungi – importance, characteristics, morphology, reproduction, physiology cultivation & classification of fungi, molds & repair association with other organisms. Algae – importance of algae – characteristics of algae, classification protozoa: Ecology, importance, morphology, reproduction and classification of protozoa – control of microorganisms. VIRUSES OF BACTERIA, ANIMAL AND PLANTS Bacteriophages- General characteristics-Morphology and structure, Classification and Nomenclature- Bacteriophages of E. coli – Replication -viruses of plants and animals- Structure- Replication- Classification- isolation and identification-fatal diseases associated with viruses in animals-viroids ENVIRONMENTAL AND INDUSTRIAL MICROBIOLOGY Microbiology of soil – aquatic microbiology-Microbiology of domestic water and waste water- Microbiology of fuel and Industrial microbiology TEXTBOOKS

1. Pelczar, JR E.C.S Chan and Noel R. Krieg, Microbiology, Fifth edition Tata McGraw Hill, 2006.

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2. Prescott, Harley and Klen, Microbiology, McGraw Hill publications Fifth edition, 2003. REFERENCE BOOKS

1. Kathleen Park Talaro, Foundations in Microbiology:Basic Principles ,McGraw-Hill, 2006. L T P C PD0201 PERSONALITY DEVELOPMENT -III 0 0 2 1 Prerequisite Nil PURPOSE The purpose of this course is to build confidence and inculcate various soft skills and to help Students to identify and achieve their personal potential INSTRUCTIONAL OBJECTIVES 1. To guide thought process. 2. To groom students' attitude. 3. To develop communication skill. 4. To build confidence.

METHODOLOGY The entire program is designed in such a way that every student will participate in the class room activities. The activities are planned to bring out the skills and talents of the students which they will be employing during various occasions in their real life.

1. Group activities + individual activities. 2. Collaborative learning. 3. Interactive sessions. 4. Ensure Participation. 5. Empirical Learning Goal Setting - Problem Solving - Emotional Quotient Assertiveness - Stress Management - Quiz II Lateral Thinking (Situational) - Team Work (Role Plays) Impromptu - Text Analysis Business plan presentation I - Business plan presentation II - Chinese Whisper Picture Perfect - Case Studies - Review

SCHEME OF INSTRUCTION Marks allocated for regular participation in all oral activities in class SCHEME OF EXAMINATION Complete Internal evaluation on a regular Basis

L T P C BI0217 BASIC BIOTECHNOLOGY LABORATORY 0 0 2 1 Prerequisite Nil 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. INSTRUCTONAL OBJECTIVES The students should be able to

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1. Develop their skills in the preparation, identification and quantification of microorganisms 2. Learn methods to quantify biological compounds

LIST OF EXPERIMENTS 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. pH measurements and preparation of buffers. 7. Estimation of sugars. 8. Estimation of proteins by Lowry’s method / Biuret method. 9. Estimation of cholesterol by Zak’s method. 10. Separation of amino acids - Thin layer chromatography. 11. Separation of sugars - Paper chromatography 12. Biochemical estimation of DNA /RNA using Spectrophotometer REFERENCE BOOK

1. Departmental Lab reference manual

L T P C BI0213 COMPUTATIONAL BIOLOGY LABORATORY 0 0 2 1 Prerequisite Nil PURPOSE Provides an opportunity to practically verify the theoretical concepts already studied. It also helps the student to be familiar with the various Bioinformatics tools INSTRUCTONAL OBJECTIVES The students should be able to

1. Know about the different databases available online. 2. Learn about sequence alignment and similarity

LIST OF EXPERIMENTS

1. Knowledge of different biological database • Protein and gene sequence data bases

(NCBI, DDBJ, EMBL, SWISS PROT, PIR) • Structure databases

(MMDB, PDB, FSSP, CATH, SCOP) • Pathway Databases

(KEGG, BRENDA, METACYC, ECOCYC • Bibliographic database

(PUBMED, MEDLINE) 2. Sequence retrieval from biological database 3. Gene prediction methods 4. Analysis of protein sequence using Expasy. 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

REFERENCE BOOK 1. Departmental Lab Manual

L T P C

BI0215 JAVA PROGRAMMING LABORATORY 0 0 2 1

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Prerequisite Nil PURPOSE Provides an opportunity to practically learn the various concepts of Java INSTRUCTONAL OBJECTIVES The students should be able to

1. Write example codes for each concept in Java. 2. Learn the applications of Java 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.

REFERENCE BOOK

1. Departmental Lab reference manual

IV SEMESTER L T P C

LE0202 GERMAN LANGUAGE PHASE - II 2 0 0 2 Prerequisite GERMAN LANGUAGE PHASE - I

PURPOSE This course is designed to improve the skills in German language.

INSTRUCTIONAL OBJECTIVE To familiarize the students with the basic grammatical, verbal and communication skills. UNIT 1 SPEAKING Dialogue – Questioning / Basic queries / Conversational with practical exposure. UNIT 2 GRAMMATIK (WRITING) Verben, Wortstellung, Nomen, Pronomen, Artikel, Nominitativ, Akkusativ, Dativ, Adjective, Prasens, Perfect and Neben Satze.

GLOSSARY Technical words. Lesson (6-10) TEXT BOOKS WITH CASSETTES

A. Grundkurs Deutsch B. Momentmal (Prescribed by Max Mueller Bhavan – Goethe Institute, Germany).

SCHEME OF EVALUATION Internal 50 = Listening – 10 Marks, Speaking – 20 Marks, Reading – 10 Marks and Writing = 10 Marks

L T P C LE0204 JAPANESE LANGUAGE PHASE II 2 0 0 2

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Prerequisite JAPANESE LANGUAGE PHASE I

PURPOSE This course is designed to improve the skills in Japanese language.

INSTRUCTIONAL OBJECTIVE To familiarize the students with the basic grammatical, verbal and communication skills. Lesson 2-{Korewa Tsukue desu } – Grammar, Sentence pattern, Marume . Conversation Lesson 3 – [Kokoni denwa ga arimasu] - Grammar, Sentence pattern, Marume .Conversation Lesson 4– {Asokoni hito ga imasu} - Grammar, Sentence pattern, Marume. Lesson 5– {Akairingo wa ikutsu arimasu ka}-Grammar, Sentence pattern, Marume, Conversation. Lesson 6– {Barano hana wa ippon ikura desu ka}- Grammar, Sentence pattern.Marume.Conversation TEXT BOOKS

1. Nihongo Shoho Imain Text sold in India by the Japanese Language Teachers Association Pune. 2. Hiragana and Katakana Work Book published by AOTS Japan 3. Grammar and Kotoba ( Work Book ) 4. Japanese for Dummies. (Conversation) CD.

SCHEME OF EVALUATION Internal 50 = Listening – 10 Marks, Speaking – 20 Marks, Reading – 10 Marks and Writing = 10 Marks L T P C LE0206 FRENCH LANGUAGE PHASE II 2 0 0 2

Prerequisite FRENCH LANGUAGE PHASE I

PURPOSE This course is designed to improve the skills in French language. INSTRUCTIONAL OBJECTIVE To familiarize the students with the basic grammatical, verbal and communication skills. Sports (Ski, natation, tennis, Tour de France), Cuisine (French dishes),Cinema (Review of a film) – Articles on these topics and group discussion will be followed. GRAMMAR Possessive Adjectives, Demonstrative Adjectives, Past tense – Passé Compose (Verbe Auxiliare:.Etre et Avoir) Culture and Civilization French Monuments (Tres celebres), French History (Jeanne d’ Arc, Louis XIV, Prise de la Bastille), Culture and Civilisation (vin, fromage, mode, parfums) Transport system, government and media in France – articles on these topics. Comprehension and Grammar Comprehension passages and conversational sentences in different situations (at the restaurant, at the super market) TEXT BOOKS:

1. Panorama – Goyal Publishers 2. Apprenons le Francais II, Sarawathy Publications

SCHEME OF EVALUATION Internal 50 = Listening – 10 Marks, Speaking – 20 Marks, Reading – 10 Marks and Writing = 10 Marks

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L T P C

MA0242 PROBABILITY AND STATISTICS 3 2 0 4 Prerequisite Nil PURPOSE To provide an introduction to the study of Biostatistics, or the use of numerical techniques to extract information from data and facts. INSTRUCTIONAL OBJECTIVES

1. To provide basic knowledge about statistics 2. To provide the calculation tools to various distribution methods. 3. Testing techniques for samples. 4. Analysis knowledge and correlation methods

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. PROBABILITY Events and Probability- Conditional probability- Baye’s Theorem. Probability distribution- Binomial Distribution, Poisson Distribution-Normal distribution and Application problems. 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. ANALYSIS OF VARIANCE One-way analysis of variance- sources of variation- Multiple comparisons procedures and applications. Comparison of two proportions. 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. TEXTBOOK

1. Marcello Pagano and Kimberlee Gauvreau, Principles of Biostatistics, Thomson Learning, 2nd Edition,2000. 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

REFERENCE BOOKS

1. Wayne W. Daniel, Bio statistics- A Foundation for Analysis in the Health sciences, John Wiley and Sons, 7th Edition, 1995.

2. Warren J. Ewens and Gregory R. Grant, Statistical Methods in Bioinformatics an introduction, Springer International Edition, 2005.

3. N. Gurumani, An Introduction to Biostatistics, MJP Publishers 4. Norman T.J. Bailey, Statistical Methods in Biology, Cambridge, 3rd Edition, 1995

L T P C CY0204 STRUCTURAL CHEMISTRY 3 0 0 3

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Prerequisite Nil PURPOSE Introduce the theories and concepts of structure of chemical compounds that are considered important in chemo informatics. INSTRUCTIONAL OBJECTIVES Students are expected to have acquired a thorough and comprehensive understanding of various types of chemical bonding, a good exposure to stereochemistry and conformational analysis and principles of spectroscopy for structural elucidation. CHEMICAL BONDING Introduction- chemical bonding: ionic bond, covalent bond, coordination bond and hydrogen bond - their characteristics- Factors affecting covalent bond – Inductive effect – applications – strength of acids, bases – electromeric effect – applications. Conjugation – mesomerism and resonance: applications, hyper conjugation – intra molecular interaction - hydrogen bond – application. THEORY OF CHEMICAL BONDING The valence bond approach – Sigma and pi bonds - Hybridization – Bond length – Bond angle – Bond energy – Dipole moment interaction – Modification of VB Theory – VSEPR theory – Shapes of simple molecules – concepts of Molecular orbital theory- applications to simple molecule H2, H2+, N2, O2, & CO. CHEMISTRY OF CARBOHYDRATE, PROTEINS Carbohydrates – Classification – D and L – Sugars- relative configuration of sugars: Glucose, Lactose, Maltose, fructose, starch – Structures and chemical properties an elementary account (Elucidation of Structure not necessary)- Amino acids: classification, stereochemistry, chemical properties peptides- Proteins – classification, structure and chemical properties. STEREOCHEMISTRY Isomerism- Types – structural – stereoisomerism – optical isomerism – elements of symmetry & chirality – Resolution – Racemisation – Asymmetric synthesis – Walden inversion – Stereo specific and stereo selective synthesis – Tautomerism – Difference between Tautomerism and resonance. CONFORMATIONAL ANALYSIS Conformation and Configuration – conformational isomers – various notations- New Mann, sawhorse, Fisher – representations, inter conversion – stereoisomerism. Conformations of cyclohexane – Geometrical isomerism – Nomenclature of E and Z system – Optical activity – Symmetry elements and chirality - Optical isomerism – Optical isomers of lactic acid, Malic acid and tartaric acid – Specification of configuration – D & L notation, R & S notation – Sequence rules - specification of configuration of compounds with more than one chiral carbons.

TEXTBOOKS

1. Soni. P.L, Text book of Organic Chemistry, 20th Edition, Sultan Chand and Sons, New Delhi. 2. K.S. Tewari, N.K. Vishonoi, A Text book of organic chemistry, Vikhyas publishing house, 1998. 3. E.L. Eliel & S.H Wilen, Stereo Chemistry, John Wiley & Sons, 1994

REFERENCE BOOKS 1. D. Nasipur, Stereo Chemistry of Organic Chemistry, 2nd Edition, Wiley Easkera Ltd, 1991. 2. I.L. Finar, Organic Chemistry, Vol. I, Vol. II, Addisan – Wesly Longman, 1973. 3. R.T. Morrison, R.W. Boyd, Organic chemistry, Prentice Hall, 2002.

L T P C BI0200 MOLECULAR BIOLOGY & GENETICS 3 0 0 3

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Prerequisite Nil 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

1. Nucleic acids and their characteristics 2. Transcription and translation 3. Gene regulation and mutation 4. Mendelian genetics

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

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

2. Benjamin Lewin, Gene VII, Oxford University Press, 2000- for UNIT I, II & III. 3. Gardener, Simmons and Snustad, Principles of Genetics, John Wiley & sons, 1991.-for UNIT IV

and V. REFERENCE BOOKS

1. H.K. Jain, Genetics – Principles, Concepts, and Implications, Oxford, 1999. 2. C.B Powar, Genetics – VOL 1 & 2, Himalaya Publishing House, 2003. 3. John Ringo, Fundamental Genetics, Cambridge, 2004.

L T P C

BI0202 BIOINFORMATICS ALGORITHMS 3 2 0 4 Prerequisite Nil PURPOSE The purpose of this subject is to study various Algorithm design techniques and applying it in Bioinformatics INSTRUCTIONAL OBJECTIVES

1. Notation and different types of Algorithms 2. Mapping Algorithms and Greedy approaches. 3. Dynamic programming for sequence alignment 4. DNA analysis using graph Algorithms.

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5. Clustering and trees. 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. 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. 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. 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. 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. TEXTBOOKS

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

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

REFERENCE BOOKS

1. Gusfields G, Algorithms on strings, trees and sequences- Computer Science and Computational Biology, Cambridge University Press 1997.

2. Steffen Schulze-Kremer, Molecular Bioinformatics: Algorithms and Applications, Walter de Gruyter, 1996.

L T P C

BI0204 INTRODUCTION TO DATABASE MANAGEMENT SYSTEMS 3 0 0 3 Prerequisite Nil PURPOSE Designing database for different applications is an important area of program development. This course provides the students to understand the problems with file processing system and how it can be handled effectively in Database System through various design tools, design techniques and algorithms. INSTRUCTIONAL OBJECTIVES The course provides the following essential skills in database technology:

1. Design of database for any given problem 2. Provide the proof for good database design after carefully eliminating certain problems inherent in

Initial Database Design. 3. Design Logical Database Schema and Mapping it to implementation level schema through Database

Language Features.

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INTRODUCTION File Processing System- Advantages of DBMS over File Processing System- Data- Database- DBMS- Data model- Data Independence- Data Catalog- DBMS Architecture & Data Abstraction- DBMS Languages- DBMS System Structure- ER Model: Objects, Attributes and its Type, Entity and Entity Set, Relationship & Relationship Set- DATABASE DESIGN Design Issues in choosing attributes or entity set or relationship set- Constraints- Super Key- Candidate Keys- Primary Key- ER Diagram Notations- Goals of ER Diagram- Weak Entity Set- ER Diagram Construction- Tabular Representation of Various ER Schema- Views STRUCTURED QUERY LANGUAGE SQL: Overview, The Form of Basic SQL Query, UNION, INTERSECT, and EXCEPT- Nested Queries- Aggregate Functions- Null Values. RELATIONAL MODEL DESIGN TECHNIQUE Pitfalls in relational database- Decomposing bad schema- Need for Decomposition- Desirable Properties of Decomposition- 1NF- Super Key & Functional dependency: Closure of Functional Dependency Set- Closure of Attribute Set- Minimal Functional Dependency Set- 2NF- BCNF- 3 NF. 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. TEXTBOOKS

1. Abraham Silberschatz, Henry F. Korth, S. Sudarshan, Database System Concepts, McGraw-Hill, 4th Edition, 2002.

2. Raghu Ramakrishnan, Johannes Gehrke, Database Management System, McGraw Hill, 3rd Edition 2003.

REFERENCE BOOKS

1. Elmashri & Navathe, Fundamentals of Database System, Addison-Wesley Publishing, 3rd Edition, 2000.

2. Date C.J, An Introduction to Database, Addison-Wesley Pub Co, 7th Edition, 2001. 3. Jeffrey D. Ullman, Jennifer Widom, A First Course in Database System, Prentice Hall, AWL 1st

Edition, 2001. 4. Peter Rob, Carlos Coronel, Database Systems – Design, Implementation, and Management, 4th

Edition, Thomson Learning, 2001.

L T P C BI0206 IMMUNOLOGY 3 0 0 3 Prerequisite Nil 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

1. The immune system, their structure and classification, genetic control of antibody production 2. Cellular immunology 3. Mechanism of activation in hypersensitive immune reaction

OVERVIEW OF THE IMMUNE SYSTEM Innate Immunity- adaptive immunity- comparative immunity cells and organs the immune system – Antigens. IMMUNOGLOBULIN STRUCTURE AND FUNCTIONS Basic structures of Immunoglobulins – I g classes and biological activities, Antigenic determinants on Ig- B Cell receptor, Monoclonal antibodies – cytokines – complement system

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ANTIGEN – ANTIBODY INTERACTIONS Antibody Affinity and activity – Precipitation reactions- agglutination reactions- Radio immunoassay-ELISA-Western blotting, Immunoprecipitation, Immunofluroscence, immunoelectron microscopes, flow cytometers-MHC Antigen processing & presentations. T CELL & B CELL MATURATION, ACTIVATION & DIFFERENTIATION T Cell receptor- T Cell maturation, activation and differentiation B Cell generation- activation and differentiation cell mediated effectors responses. IMMUNE SYSTEM IN HEALTH & DISEASE Leukocyte migration and inflammation - hypersensitive reactions - immune response to infection diseases - vaccines. TEXT BOOK

1. Richard A. Golds, Tharmas J. Kindt, Kuby Immunology, Barbara Osborne. W.H. Freeman and company, fourth edition 2000.

2. A. K. Chakravarty, Immunology and Immunotechnology, Oxford University Press, 2006. REFERENCE BOOKS

1. Charles Janeway, Immunobiology: The Immune System in Health and Disease, Garland Science, 2005. 2. Richard Coico, Geoffrey Sunshine, Immunology: A Short Course, John Wiley & Sons, 2007.

L T P C BI0208 COMPREHENSION - I 0 2 0 1

Prerequisite Nil

PURPOSE In this course, the students will be made to review the subjects taught in the earlier semesters.

INSTRUCTIONAL OBJECTIVES

1. To emphasize the importance of basic core subjects taught in the previous semesters. 2. To improve the technical knowledge, problem-based learning, and principles of techniques. 3. To counsel students to improve their basic knowledge so that they will be better prepared for the

campus interview.

CELL BIOLOGY Evolution of cells- cells biology tools- Structure of a cell- function of different organelles- cell regulation- Cell signaling- cancer. BIOCHEMISTRY Carbohydrate metabolism- Fat metabolism- Protein Metabolism- Photosynthesis- Nucleic acid metabolism- Microbial metabolism energy production BIOINFORMATICS Databases: DNA, Protein, Structure, Bibliographic - Sequence alignment: Global & local- Scoring matrices- multiple sequence alignment-gene prediction methods- protein prediction methods- homology modeling- evolutionary relationships- molecular visualization tools. JAVA AND DATA STRUCTURES Greedy Algorithms – String Matching Algorithms- Dynamic programming- data structures: linear, non linear- graph algorithms- hashing- Oops concept-classes- inheritance- applets- event handling. MICROBIOLOGY Microscopic examination of microorganism’s morphology and fine structure of bacteria- Microbial metabolism energy production- Fungi- Algae- Protozoa- environmental microbiology. Scheme of Assessment Answers to objective questions will be evaluated TEXT BOOK

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1. Herbert Schildt, The Complete Reference JAVA 2 Fifth Edition, Tata McGraw Hill, 2005 2. Pelczar, JR E.C.S Chan and Noel R. Krieg, Microbiology, Fifth edition Tata McGraw Hill, 2006. 3. Mark Allen Weiss, Data Structures and Algorithm Analysis in C, Addison Wesley Publications, 2nd

Edition, 1998 4. S.C. Rastogi & others, Bioinformatics- Concepts, Skills, and Applications, CBS Publishing, 2003 5. Thomas H. Cormen, Introduction to algorithms, MIT Press, 2001. 6. Jeremy M. Berg, John L. Tymozko, Lubert Styer, Biochemistry, Fifth edition, W.H. Freeman and

Company 7. Geoffrey M. Cooper, The Cell: A molecular approach, ASM Press, 2007.

REFERENCE BOOKS 1. Lodish, Harvey Krieger, Monty Kaiser, Chris A. Berk, Arnold, Molecular Cell Biology, W H Freeman

& Co. 2. Albert L. Lehninger, David L. Nelson, Michael M. Cox, Karen Ocorr, Principles of Biochemistry, W H

Freeman & Co, 2005 3. Hooman H. Rashidi, Lukas K. Buehler, Bioinformatics Basics-Applications in Biological Science and

Medicine, CRC press, 2005. 4. Jean-Paul Tremblay, Paul G. Sorenson, An Introduction to Data Structures with Applications, 2nd

Edition, Tata McGraw-Hill Edition, 1976.

L T P C PD0202 PERSONALITY DEVELOPMENT - IV 0 0 2 1 Prerequisite Nil PURPOSE The purpose of this course is to build confidence and inculcate various soft skills and to help Students to identify and achieve their personal potential INSTRUCTIONAL OBJECTIVES

1. To guide thought process. 2. To groom students' attitude. 3. To develop communication skill. 4. To build confidence.

METHODOLOGY The entire program is designed in such a way that every student will participate in the class room activities. The activities are planned to bring out the skills and talents of the students which they will be employing during various occasions in their real life. 1. Group activities + individual activities. 2. Collaborative learning. 3. Interactive sessions. 4. Ensure Participation. 5. Empirical Learning Motivation II - Interpretation of Visuals of I & II Humor in real life - Body language - Collage and poster designing and slogan writing Brain Teasers – JAM - Current News Update I Current News Update II - Enactment (SKIT –I) - Enactment (SKIT – II) Survey and Reporting (heroes, sports persons etc.) - Quiz III - Review EVALUATION

1. Activities assessed by both group and individual participation 2. Continuous assessment based on daily participation

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SCHEME OF INSTRUCTION Marks allocated for regular participation in all oral activities in class SCHEME OF EXAMINATION Complete internal evaluation on a regular Basis

L T P C BI0210 BIOTECHNOLOGY LABORATORY 0 0 2 1 Prerequisite Nil 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

1. Isolation of genomic DNA and RNA 2. Electrophoresis 3. Immunological methods like antigen antibody reactions

LIST OF EXPERIMENTS

1. Isloation of Genomic DNA from blood 2. Formaladyhyde gel elctrophoresis of RNA 3. Isolation of antibodies 4. Purification of antibodies 5. Immunoelectrophoresis 6. Blood grouping 7. Leucocyte count 8. PBMC preparation and their enumeration 9. Production of polyclonal antibodies – preparation of antigen – protocol for immunization in

rabbits 10. Methods of bleeding-purification of polyclonal antibodies 11. Antigen-antibody reaction-Haemagglutination, precipitation-Widal and VDRL 12. Immunodiffusion, Immunoelectrophoresis. 13. Affinity chromatiography for antibody purification. 14. ELISA-DOT and plate ELISA 15. Western blotting

REFERENCE BOOK

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

L T P C BI0212 DBMS LABORATORY 0 0 2 1 Prerequisite Nil 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

1. To create simple databases 2. Write queries to extract the data in the databases

LIST OF EXPERIMENTS

1. Simple Queries

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2. Built-in-functions 3. Group Functions 4. Multiple sub-queries 5. SQL Views & Triggers 6. Simple PL/SQL Procedures 7. PL/SQL Procedures accessing Databases 8. Mini Project

REFERENCE BOOK

1. Departmental Lab reference manual

V SEMESTER

L T P C BI0301 RECOMBINANT DNA TECHNOLOGY 3 0 0 3 Prerequisite Nil PURPOSE The subject deals with different strategies of gene cloning and construction of genomic and cDNA library and applications of recombinant DNA technology INSTRUCTIONAL OBJECTIVES

1. To strengthen the knowledge on various strategies of gene cloning 2. To impart the knowledge on gene expression

MOLECULAR TOOLS FOR GENE CLONING Restriction enzymes-host controlled modifications-restriction modification systems-Types-nomenclature- 4, 6 and 8 cutters-frequency of occurrence of restriction sites- palindromic and non-palindromic recognition sequences - isoschizomers- enzymes producing cohesive ends and blunt ends- enzymes producing 5’ and 3’ overhangs- recleavable filled-in 5’ overhangs-enzymes producing compatible cohesive ends-Dam, Dcm and CpG methylation sensitivity of restriction enzymes-star activity of restriction enzymes. DNA and RNA polymerases – thermostability-fidelity-strand displacement- nick translation-template specificity (DNA/RNA polymerase)- product specificity-E coli DNA polymerase, T4 DNA polymerase, Klenow fragment, Klenow fragment (3’ to 5’ exo deleted), Taq DNA polymerase, Pfu DNA polymerase, reverse transcriptase, terminal transferase, T7 RNA polymerase. DNA/RNA modifying enzymes-methylases-CpG methylase (M.Sss I), dam methylase, M.EcoR I.. Ligases – Ecoli DNA ligase, T4 DNA ligase, T4 RNA ligase. RNases-RNaseI, RNaseA, RNaseH - Nucleases – RNase free DNAse-Exonuclease I, Exonucelase III, Mung Bean Nuclease. Kinases - T4 polynucleotide kinase. Phosphatases- Topoisomerase. VECTORS FOR GENE CLONING Introduction to cloning vectors, plasmid vectors (high copy and low copy), phage vectors, cosmid vectors, phasmid vectors, BAC vectors and YAC vectors CLONING TECHNIQUES Cloning after restriction digestion - blunt and cohesive end ligation – creation of restriction sites by PCR- cloning using linkers and adapters - cloning after homopolymer tailing. Strategies for cloning PCR products – TA cloning -TOPO-TA cloning-TOPO-Blunt cloning-cloning blunt end PCR product using SfrI restriction enzyme and T4 DNA ligase (PCR-Script Amp Cloning Kit from Stratagene). CONSTRUCTION OF GENE LIBRARIES Construction of cDNA library- construction subtractive cDNA library – construction of genomic DNA library – BAC library – YAC library EXPRESSION OF RECOMBINANT PROTEIN IN E.COLI Plasmid expression vectors-general features, promoters used in expression vectors -cloning of genes in correct reading frame in expression vector- purification of recombinant protein using Histidine tag, GST tag, chitin

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binding domain and intein. Codon use in different organisms-codon usage database-codon optimization to increase the expression of recombinant protein.

TEXT BOOKS

1. Sandy B. Primrose, Richard M. Twyman, Principles of gene manipulation, Blackwell Publishing, 2001. 2. Sambrook and Russell, Molecular Cloning – A Laboratory Manual, CSHL Press, 2002.

REFERENCE BOOK

1. Jerney D. Wale and Malcolm Von Schants, From Genes to Genomes: Concepts and Applications of DNA Technology, John Wiley & Sons, 2002.

2. T.A. Brown, Gene cloning –An Introduction, Nelson Thornes Limited, 1998.

L T P C BI0303 MOLECULAR PHYLOGENY AND EVOLUTION 3 0 0 3 Prerequisite Nil PURPOSE This course provides the basic concept of Phylogenetics and evolution at molecular level. INSTRUCTIONAL OBJECTIVES

1. To understand the various methods of phylogenetic tree construction 2. Accuracies and statistical methods of optimization 3. Molecular evolution

PHYLOGENETIC TREES Types- topological differences- tree building methods- Distance methods- UPGMA- LS methods- minimum evaluation methods- NJ methods- phylogenetic reconstruction. METHODS Maximum parsimony methods- Strategies of searching for MP trees- consensus trees- branch length estimation- weighted parsimony- MP methods for protein data- Maximum likelihood methods STATISTICAL APPROACH Optimization principle and topological errors- interior branch tests- bootstrap tests- Tests of topological differences- advantages and disadvantages- molecular clocks and linearized trees ANCESTRAL SEQUENCES Inferences of ancestral sequences- parsimony and Bayesian approaches- synonymous and non-synonymous substitutions- convergent and parallel evolution EVOLUTION Molecular basis of evolution- synonymous and non- synonymous mutations- genetic polymorphism and evolution- Population trees from genetic markers

TEXTBOOKS

1. Masatoshi Nei, Molecular Evolution and Phylogenetics, Oxford University Press, 2000. 2. Roderick D.M. Page, Dr Edward C. Holmes, Molecular Evolution: A Phylogenetic Approach,

Blackwell Publishing, 1998. REFERENCE BOOKS

1. David W Mount, Bioinformatics- Sequence and genome analysis , Cold Spring Harbor Laboratory Press, second edition, 2004.

2. Jin Xiong, Essential Bioinformatics, Cambridge University Press, 2006.

L T P C BI0305 BIOPHYSICAL CHEMISTRY 3 0 0 3 Prerequisite

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

1. To understand the structures of biological molecules 2. To understand the concepts of structural analysis 3. To learn the techniques for analysis and determination of structure of biomolecules.

INTRODUCTION 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. STRUCTURAL ANALYSIS Structural analysis of macromolecules - alpha helix- β sheets- loop regions 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. KINETICS Kinetics of ligand interactions - biochemical kinetics studies unimolecular reactions - simple bimolecular multiple intermediates - steady state kinetics - catalyst efficiency - relaxation spectrometry - ribonuclease as an example. TECHNIQUES FOR STUDY OF MACROMOLECULES 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. DETERMINATION OF STRUCTURE OF BIO MOLECULES Determination of molecular structures - X-ray fiber diffraction electron microscopy - neutron scattering- light scattering.

TEXTBOOK

1. Cantor, Charles R., Paul R Schimmel, Biophysical Chemistry, W.H. Freeman & Co, 2007. 2. Alan Cooper, Biophysical Chemistry, Royal Society of Chemistry, 2004.

REFERENCE BOOK

1. Alan G. Marshall, Biophysical Chemistry: Principles, Techniques, and Applications, Wiley, 1978. 2. Richard H. Templer, Robin Leatherbarrow, Biophysical Chemistry: Membranes and Proteins, Royal

Society of Chemistry, 2002.

L T P C BI0307 GENOMICS AND TRANSCRIPTOMICS 3 0 0 3 Prerequisite Nil 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

1. Structure and organization of genomes 2. Computational approaches to analyze the genomes

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3. Microarray 4. Functional and comparative genomics 5. Basics of Transcriptomics

GENOMES AND THEIR ORGANIZATION Prokaryotic and eukaryotic genomes- structure- organization-Genomics: Genome Sequencing- Fragment Assembly- Genome Assembly- Human Genome Project- Aims- goals and achievements. GENOME ANALYSIS AND DNA DATABASES Alignment methods- Dot plot method- dynamic programming methods: BLAST and FASTA- DNA databases with special reference to GenBank. GENE REGULATORY NETWORK AND MICROARRAY Gene regulatory network and the models- DNA microarray and the analysis of data using clustering methods. FUNCTIONAL AND COMPARATIVE GENOMICS Introduction to functional and comparative genomics- Methods to perform comparative genomics TRANSCRIPTOMICS 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 TEXT BOOKS

1. T.A. Brown, Genome, John Wiley & sons, II edition. 2. David W. Mount, Bioinformatics: Sequence and Genome Analysis, Cold Spring Harbor Laboratory

Press, I edition, 2001 3. Stekel Dov, Microarray Bioinformatics, Cambridge University Press, 2003

REFERENCE BOOKS

1. Issac S Kohane, Microarrays for an integrative genomics, The MIT Press, 2002. 2. Benjamin Lewin, Gene VII, Oxford University Press, 2000

L T P C BI0309 PERL PROGRAMMING & BIOPERL 3 0 0 3 Prerequisite Nil PURPOSE PERL is one of the important programming languages for Bioinformatics INSTRUCTIONAL OBJECTIVES This subject enables the students

1. To understand the basic commands in Unix 2. Control statements in PERL

UNIX OS AND EDITORS Unix OS-Working Environment- Navigating in Unix-creating and manipulating sequence files-emacs editor-Vi editor-FTP UNIX COMMANDS Advanced Unix commands-Introduction-ls-cat-more-, Advanced Unix commands-mv-rm-rmdir-uniq-sort-,Advanced Unix commands-grep. PERL Introduction to Perl-scalars, Arrays-Using standard Perl modules-Perl regular expressions I. PERL ARRAY OPERATIONS AND CONTROL STATEMENTS

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Perl debugger-Advanced array operation-Perl regular expression II- Perl control statements-FILE I/O- Perl subroutines and Functions. BIOPERL Installation and usage of bioperl modules

TEXTBOOKS

1. Harshawardhan P Bal, Perl Programming for Bioinformatics, Tata McGraw Hill, 2003. 2. James Tisdall, Mastering Perl for Bioinformatics, O’Reilly, 2003.

REFERENCE BOOKS

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

2. Michael Moorhouse, Paul Barry, Bioinformatics Biocomputing and Perl, Wiley, 2004.

L T P C E1 ELECTIVE I 3 0 0 3 Prerequisite Nil L T P C PD0301 PERSONALITY DEVELOPMENT - V 1 0 2 2 Prerequisite Nil PURPOSE The purpose of this course is to build confidence and inculcate various soft skills and to help Students to identify and achieve their personal potential INSTRUCTIONAL OBJECTIVES At the end of the course the students will be able to

1. Acquire the important soft skills for employment 2. Take part in group discussions and job interviews confidently 3. Appear for placement aptitude tests confidently 4. Gain self-confidence to face the placement process

METHODOLOGY The entire program is designed in such a way that every student will participate in the class room activities. The activities are planned to bring out the skills and talents of the students, which they will be employing during various occasions in their real life.

1. Group activities + individual activities. 2. Collaborative learning. 3. Interactive sessions. 4. Ensure Participation. 5. Empirical Learning

Syllogism - Binary Logic [cause & effect] - Assertive & Counter Argument - Simple Interest - Time & Work - Time & Distance Upstream &Downstream Reasoning - Verbal Comprehension I - Verbal Comprehension II- Compound Interest Logarithms - Surds & Indices Verbal Reasoning I - Verbal Reasoning II - Verbal Reasoning III – Percentage – Test – Averages Deductive Reasoning I - Deductive Reasoning II - Language Usage I - Decimal Fractions - Profit & Loss – Probability Language Usage II - Logic Games I - Logic Games II – Area - Pipes & Cisterns – Test

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SCHEME OF INSTRUCTION Marks allocated for regular participation in all oral activities in class SCHEME OF EXAMINATION Complete internal evaluation on a regular Basis

L T P C BI0311 GENETIC ENGINEERING LABORATORY 0 0 2 1 Prerequisite Nil PURPOSE The practical deals with advanced techniques that is essential for genetic engineering and recombinant DNA technology INSTRUCTIONAL OBJECTIVES To give hands-on training in advanced molecular biology techniques LIST OF EXPERIMENTS

1. Partial digestion of bacterial genomic DNA 2. Restriction enzyme digestion of pUC 18/19 and Alkaline Phosphatase treatment. 3. Purification of digested DNA 4. Ligation of DNA fragment with plasmid DNA 5. Preparation of competent cells 6. Transformation in E. coli 7. Isolation of recombinants plasmid and confirmation of insert DNA in plasmid. 8. PCR and RT-PCR 9. Colony Hybridisation 10. Southern Hybridisation 11. Northern hybridization

REFERENCE BOOK

1. Laboratory Manual 2. Sambrook and Russell, Molecular Cloning – A Laboratory Manual, CSHL Press, 2002

L T P C

BI0313 PERL PROGRAMMING LABORATORY 0 0 2 1 Prerequisite Nil 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 student will be able to understand and develop the concept of analyzing scientific data using perl LIST OF EXPERIMENTS

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

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

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REFERENCE BOOK 1. Lab Manual D. Curtis Jamison, Perl Programming for Bioinformatics & Biologists, John Wiley &

Sons, INC., 2004.

L T P C BI0315 INDUSTRIAL TRAINING-I 0 0 2 1 Prerequisite Nil The student has to undergo industrial training for a minimum period of two weeks in the winter/summer vacation of the IV semester. After undergoing the training in an industry, the student will be asked to submit a report that will be evaluated.

VI SEMESTER

L T P C BI0300 INTERNET PROGRAMMING 2 0 2 3 Prerequisite Nil PURPOSE To learn the Internet Technologies INSTRUCTIONAL OBJECTIVES

1. To learn about Java, HTML, DHTML concepts 2. To know about scripting languages. 3. Knowledge of XML and its applications

INTERNET BASICS AND APPLICATIONS Basic web concepts- web server- IIS- Apache server- Introduction to HTML & CSS-Internet applications- E-mail- chat- search engines- news groups. SCRIPTING LANGUAGES Java Scripting- VB scripting- object model and event model- DOM- CGI & data base connectivity- introduction to PHP and perl. XML XML DTD- XML schema- ESS- XML Database creation- XHTML. SERVER SIDE PROGRAMMING Multi tier application- Introduction to java servlets- HTTP GET & POST request- JDBC principles- cookies- session tracking; ASP.NET Introduction to ASP.NET- using objects- data types- data access objects- connection object- command object. CASE STUDY- Developing a web based tool for sequence analysis. 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

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TEXTBOOK

1. Deital and Deital, Goldberg, Internet & World Wide Web, How To Program, third edition, Pearson Education, 2004.

2. Cerami Ethan, Xml for Bioinformatics, Springer, 2005. 3. Macdonald Mathew, Asp.Net - The Complete Reference, McGraw-Hill/Osborne, 2002. 4. Naughton, Herbert Schildt, Java2, Complete Reference, 4th edition, TMH, 2000.

REFERENCE BOOKS 1. Moss Karl, Java Servlets Ed 2, NetLibrary, 1998. 2. Pfaffenberger Bryan, HTML, XHTML, and CSS Bible, Wiley pub., 2004.

L T P C

BI0302 PROTEOMICS 3 0 0 3 Prerequisite Nil PURPOSE This course helps the students to understand the proteomics from the scratch INSTRUCTIONAL OBJECTIVES

1. Principles of electrophoretic and chromatographic techniques 2. Various Protein identification and Quantitation methods 3. Protein chips

INTRODUCTION 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 PROTEIN IDENTIFICATION AND QUANTITATION Strategies for Protein Identification: Protein Identification with antibodies, protein sequence determination by chemical degradation, MASS SPECTROMETRY AND ITS APPLICATIONS MS- principles, instrumentation and applications in proteomics, Strategies for Protein Quantitation: Quantitative proteomics with standard 2D gels, multiplexed proteomics, quantitative with mass spectrometry STRUCTURAL PROTEOMICS Protein structures, techniques for solving protein structures, Protein- protein interactions- principles and methods to study them, Protein Modification in Proteomics. PROTEIN CHIPS Protein Chips and Functional Proteomics, Applications of Proteomics in disease diagnosis, drug development and plant biotechnology.

TEXT BOOKS 1. R. M. Twyman, Principles of Proteomics (Advanced Text Series), Bios Scientific, 2004. 2. David W Mount, Bioinformatics- Sequence and genome analysis, Cold Spring Harbor Laboratory

Press, second edition, 2004. REFERENCE BOOKS

1. S. R. Pennington, M. J. Dunn, Proteomics: from Protein Sequence to Function, Springer publications, first edition, 2001.

2. Timothy Palzkill, Proteomics, Springer, 2002.

L T P C BI0304 IMMUNOINFORMATICS 3 0 0 3

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Prerequisite Nil

PURPOSE This course gives the fundamental knowledge on Immunoinformatics INSTRUCTIONAL OBJECTIVES

1. Methods Applied in Immunological Bioinformatics 2. Prediction methods 3. Application of microarray in Immunology

SEQUENCE ANALYSIS Alignments- DNA alignments- Molecular evolution and phylogeny- viral evolution and escape- prediction of functions METHODS Methods applied in Immunological Bioinformatics- starting from sequence weighing methods to cluster analysis- applications of microarray APPLICATIONS Prediction of Cytotoxic T Cell (MHC Class I) Epitopes- Antigen Processing in the MHC Class I Pathway PREDICTION METHODS T CELL Prediction of Helper T Cell (MHC Class II) Epitopes- Processing of MHC Class II Epitopes B CELL EPITOPES Recognition of Antigen by B Cells- vaccine design- Web-Based Tools for Vaccine Design

TEXTBOOKS

1. Ole Lund, Immunological Bioinformatics, MIT press, September 2005. 2. Darren R Flower, Immunoinformatics: Predicting Immunogenicity in Silico, Humana Press, 2007.

REFERENCE BOOKS

1. Rammensee, Immunoinformatics- Bioinformatics Strategies for Better Understanding of Immune Function, Wiley, 2003.

2. Darren Flower, In Silico Immunology, Springer, 2006.

L T P C BI0306 MOLECULAR SIMULATION OF BIOMOLECULES 3 0 0 3 Prerequisite Nil PURPOSE This subject portraits the fundamentals and applications of computer aided drug designing INSTRUCTIONAL OBJECTIVES

1. Fundamentals of Computer Aided Drug Designing (CADD) 2. Drug development 3. Methods and applications

APPLICATION OF MOLECULAR MODELING IN DRUG DESIGN Molecular modeling in drug discovery- three dimensional pharmacophores- molecular docking- De-novo ligand designing- and structure-based methods- molecular similarity DRUG DISCOVERY Drug discovery: targets and receptors- target identification and validation- drug interactions- small molecule drugs DRUG DEVELOPMENT Pharmacodynamics- Pharmacokinetics- toxicology- animal tests- formulations and delivery systems- future perspectives

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APPLICATIONS OF CADD Application and methods in protein engineering- Protein design principles and examples -applications in pharmacophores mapping QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP (QSAR) Analysis of QSAR- computational approaches to chemical libraries

TEXTBOOKS

1. Andrew R. Leach, Molecular Modelling- Principles and application, Prentice hall, II edition, 1996. (Unit I, unit V)

2. Rick NG, Drugs: from Discovery to Approval, John Wiley & sons, 2004. (Units II, III,). 3. Moody PCE and Wilkinson AJ, Protein Engineering- IRL press oxford 1990(unit IV)

REFERENCE BOOK

1. Thomas J. Perun, Catherine Lamb Propst, Computer-Aided Drug Design: Methods and Applications, Informa Health Care, 1989.

2. Paul S Charifson, Practical Application of Computer-Aided Drug Design, Informa Health Care, 1997.

L T P C BI0308 SYSTEMS BIOLOGY 3 0 0 3 Prerequisite Nil PURPOSE It provides a comprehensive knowledge on the concepts and applications of systems biology. INSTRUCTIONAL OBJECTIVES

1. Standard models and approaches in systems biology 2. Modeling of gene expression 3. Evolution and self organization

INTRODUCTION Basic principles of systems biology - experimental techniques. STANDARD MODELS AND APPROACHES Metabolism- enzyme kinetics and thermodynamics- metabolic networks- metabolic control analysis. BIOLOGICAL PROCESSES Signal transduction- introduction- function and structures- interactions- structural components- signaling- selected biological processes. EVOLUTION Introduction - mathematical models- prediction of biological systems- data integration. APPLICATIONS Systems biology in various fields - databases and tools- modeling tools.

TEXT BOOK

1. Edda Klipp, Ralf Herwig, Systems Biology in Practice-Concepts, Implementation and Application, Wiley VCH, I Edition, 2005.

2. Lilia Alberghina, Hans V. Westerhoff, Systems Biology: Definitions and Perspectives, Springer, 2005. REFERENCE BOOK

1. Andrzej K. Konopka, Systems Biology: Principles, Methods, and Concepts, CRC Press, 2006. 2. Darren James Wilkinson, Stochastic Modelling for Systems Biology, CRC Press, 2006.

L T P C

E2 ELECTIVE II 3 0 0 3 Prerequisite

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Nil

L T P C BI0310 COMPREHENSION - II 0 2 0 1 Prerequisite Nil PURPOSE In this course, the students will be made to review the subjects taught in the earlier semesters.

INSTRUCTIONAL OBJECTIVES

1. To emphasize the importance of basic core subjects taught in the previous semesters. 2. To improve the technical knowledge, problem-based learning, and principles of techniques. 3. To counsel students to improve their basic knowledge so that they will be better prepared for the

campus interview.

MOLECULAR BIOLOGY AND rDNA TECHNOLOGY Structure of DNA- Replication- Mendelian Genetics –Transcripton -translation - gene regulation-Restriction enzymes-DNA And RNA Polymerases- cloning vectors-Cloning Techniques- cDNA library- construction of genomic DNA library - codon usage database. IMMUNOLOGY AND PHYLOGENY Types of Immune system- Immunoglobins- monoclonal antibodies- antigen – antibody interactions-Tcell receptors- Bcell receptors- immune response to infection diseases- Types- Distance methods- Maximum parsimony methods- Maximum likelihood methods- bootstrap tests- Molecular basis of evolution. BIOPHYSICAL AND STRUCTURAL CHEMISTRY Basic strategies in biophysics conformational analysis- hydrogen bonding; hydrophobic interactions -Kinetics of ligand interactions- Determination Of Structure Of BioMolecules-Theory of bonding- carbohydrates- proteins- stereoisomerism- Conformation and Configuration IP, PERL AND DBMS Java Scripting- XML- java servlets- ASP.NET- Introduction to Perl-scalars, Arrays- Perl subroutines and Functions- Unix commands- DBMS System Structure- ER Model- Super Key- Candidate Keys- Primary Key- SQL: Overview, basic queries-1NF, 2NF,BCNF, 3NF. BIOINFORATICS ALGORITHMS Iterative and Recursive Algorithms- Mapping Algorithms for finding motifs- Greedy Algorithm for genome rearrangements- Divide and Conquer Algorithms for alignments - Fragment assembly in DNA sequencing using graph algorithm- Hierarchical clustering-k-means clustering- Reconstruction trees from additive matrices. Scheme of Assessment Answers to objective questions will be evaluated TEXT BOOK

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

2. Abraham Silberschatz, Henry F. Korth, S. Sudarshan, Database System Concepts, McGraw-Hill, 4th Edition, 2002.

3. Richard A. Golds, Tharmas J. Kindt, Kuby Immunology, Barbara Osborne. W.H. Freeman and company, fourth edition 2000.

4. T.A. Brown, Genetics- A molecular approach, Chapman & Hall, Third edition, 1998. 5. Soni. P.L, Text book of Organic Chemistry, 20th Edition, Sultan Chand and Sons, New Delhi. 6. Harshawardhan P Bal, Perl Programming for Bioinformatics, Tata McGraw Hill, 2003. 7. Cantor, Charles R., Paul R Schimmel, Biophysical Chemistry, W.H. Freeman & Co, 2007. 8. Sandy B. Primrose, Richard M. Twyman, Principles of gene manipulation, Blackwell Publishing,

2001. 9. David W Mount, Bioinformatics- Sequence and genome analysis , Cold Spring Harbor Laboratory

Press, second edition, 2004.

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REFERENCE BOOKS

1. Deital and Deital, Goldberg, Internet & World Wide Web, How To Program, third edition, Pearson Education, 2004.

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

3. C.B Powar, Genetics – VOL 1 & 2, Himalaya Publishing House, 2003. 4. Elmashri & Navathe, Fundamentals of Database System, Addison-Wesley Publishing, 3rd Edition,

2000. L T P C PD0302 PERSONALITY DEVELOPMENT VI 1 0 2 2 Prerequisite Nil PURPOSE The purpose of this course is to build confidence and inculcate various soft skills and to help Students to identify and achieve their personal potential INSTRUCTIONAL OBJECTIVES At the end of the course the students will be able to

1. Acquire the important soft skills for employment 2. Take part in group discussions and job interviews confidently 3. Appear for placement aptitude tests confidently 4. Gain self-confidence to face the placement process

METHODOLOGY The entire program is designed in such a way that every student will participate in the class room activities. The activities are planned to bring out the skills and talents of the students which they will be employing during various occasions in their real life.

1. Group activities + individual activities. 2. Collaborative learning. 3. Interactive sessions. 4. Ensure Participation. 5. Empirical Learning

Self-Introduction - Narration - Current News Update – Numbers - Height & Distance - Square & Cube Roots Current Tech Update - Verbal Aptitude Test I - GD –I - Odd man out series - Permutation & Combination - Problems on ages GD –II - Resume Writing - Mock Interview I / reading comprehension - Problems on trains – Allegation of Mixtures - Test Mock Interview II / reading comprehension - Mock Interview III/ reading comprehension - GD – III - Ratio & Proportion - Clocks - H.C.F & L.C.M GD – IV - Verbal Aptitude Test II – Review – Partnership – Puzzles – Test SCHEME OF INSTRUCTION Marks allocated for regular participation in all oral activities in class SCHEME OF EXAMINATION Complete Internal evaluation on a regular Basis

L T P C BI0312 IMMUNOINFORMATICS LABORATORY 0 0 2 1 Prerequisite Nil

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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 student will be able to use various Bioinformatics tools to analyze Immunological data 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 BOOK

1. Lab Manual

L T P C BI0314 MOLECULAR SIMULATION OF BIOMOLECULES LABORATORY 0 0 2 1 Prerequisite Nil 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 student will be able to use various Bioinformatics tools to

1. Homology modeling 2. Docking

LIST OF EXPERIMENTS

1. Analysis of 2D and 3D structures of proteins 2. Finding the active sites in a receptor 3. Homology Modeling using SPDBV 4. Model structure refinement using SPDBV. 5. Model validation using What Check and Pro Check 6. Docking using DOCK or AUTODOCK or HEX. 7. Target – Ligand from PDB Sum.

REFERENCE BOOK

1. Lab Manual

VII SEMESTER

L T P C BI0401 CHEMOINFORMATICS 3 0 0 3 Prerequisite Nil PURPOSE This course provides knowledge on upcoming field of chemo informatics. INSTRUCTIONAL OBJECTIVES

1. Molecular descriptors 2. High throughput screening 3. Virtual screening

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4. Combinatorial chemistry and library design REPRESENTATION OF STRUCTURES Representation and Manipulation of 2D Molecular Structures- Representation and Manipulation of 3D Molecular Structures MOLECULAR DESCRIPTORS AND MODELS 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 SIMILARITY METHODS 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 HIGH THROUGHPUT AND VIRTUAL SCREENING Analysis of High-Throughput Screening Data- Data Visualization- Data Mining Methods- Virtual Screening- Drug-Likeness and Compound Filters- Structure-Based Virtual Screening- The Prediction of ADMET Properties COMBINATORIAL CHEMISTRY AND LIBRARY DESIGN Diverse and Focused Libraries- Library Enumeration- Combinatorial Library Design Strategies- Approaches to Product-Based Library Design- Multi objective Library Design- Practical Examples of Library Design

TEXTBOOKS

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

2. Tudor I Oprea, Raimund Mannhold, Hugo Kubinyi, Gerd Folkers, Chemoinformatics in Drug Discovery, Wiley-VCH, 2006.

REFERENCE BOOKS

1. Johann Gasteiger, Thomas Engel, Chemoinformatics- A Textbook, Wiley-VCH, 2003. 2. Jürgen Bajorath, Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery, Humana press,

2004.

L T P C BI0403 SYSTEMS APPROACH TO BIOLOGY 3 0 0 3 Prerequisite Nil PURPOSE This course provides the knowledge on Molecular Modeling INSTRUCTIONAL OBJECTIVES

1. Molecular dynamics simulation methods 2. Monte carlo simulation methods 3. Conformational analysis 4. Protein structure prediction methods

MOLECULAR DYNAMICS SIMULATION METHODS Useful concepts in Molecular Modeling- one electron and poly electron atoms molecules- molecular orbital calculations- Hartree-Fock equations-Introduction to dynamics- using simple models and continuous potentials- setting up and running molecular dynamics simulations- constraint dynamics- time dependant properties- conformational changes- chain amphiphiles MONTE CARLO SIMULATION METHODS Calculating properties by integration- metropolis methods- metropolis Monte Carlo methods- simulations of molecules- models- biased methods- different ensembles- calculating chemical potentials- Gibbs ensemble methods

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CONFORMATIONAL ANALYSIS Systematic methods- model building approaches- random search methods- distance geometry- conformational space- variations- global energy minimization- Non-derivative minimization methods- derivative minimization methods- I order minimization methods, second derivative methods- Quasi Newton methods- structural databases- molecular fitting- clustering algorithms- dimension reduction- poling PROTEOMICS First principle methods- comparative modeling- sequence alignment- comparative models- threading- CASP- protein folding and unfolding CHALLENGES IN MOLECUALAR MODELING 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

TEXTBOOKS

1. Andrew R. Leach, Molecular Modelling- Principles and applications, Prentice hall, II edition, 1996. 2. Alan Hinchliffe, Modelling Molecular Structures, John Wiley, 2000.

REFERENCE BOOKS

1. Alan Hinchliffe, Molecular Modelling for Beginners, John Wiley and Sons, 2003. 2. Elaine A. Moore, Molecular Modelling and Bonding, Royal Society of Chemistry, 2002.

L T P C

BI0405 PHARMACOGENOMICS AND PHARMACOGENETICS 3 0 0 3 Prerequisite Nil PURPOSE This course gives the in-depth knowledge on Pharmacogenomics and Pharmacogenetics INSTRUCTIONAL OBJECTIVES

1. Promise of personalized medicines 2. Pharmacogenetics

INTRODUCTION Historical aspects of Pharmacogenetics- Pharmacogenomics- Biomarkers- and the promise of personalized medicine PHARMACOGENETICS Pharmacogenetics of drug metabolism- receptors- drug transporters DRUG RESPONSE Inter ethnic drug response- clinical viewpoints- technologies and challenges SINGLE NUCLEOTIDE POLYMORPHISM Introduction- technologies for the analysis of SNPs- molecular diagnostics SAGE Serial Analysis of Gene Expression (SAGE) - functional biology- mapping of disease loci

TEXTBOOKS

1. Werner Kalow, Rachel F Tyndale, Urs A Meyer, Pharmacogenomics, Marcel Dekker Inc., 2001. 2. J. Licinio, Ma-LiWong, Pharmacogenomics: The Search for Individualized Therapies, Wiley-VCH,

2002. REFERENCE BOOK

1. Adam Hedgecoe, The Politics of Personalized Medicine- Pharmacogenetics in the Clinic, Cambridge University Press, first edition, 2004.

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2. Mark A. Rothstein, Pharmacogenomics: Social, Ethical, and Clinical Dimensions, Wiley-Liss, 2003.

L T P C BI0407 METABOLOMICS AND METABOLIC ENGINEERING 3 0 0 3 Prerequisite Nil PURPOSE This course provides the fundamental knowledge on upcoming field of metabolomics and the metabolic engineering in post genomic era. INSTRUCTIONAL OBJECTIVES

1. Metabolic engineering 2. Comprehensive models cellular reactions 3. Metabolic flux analysis and its applications 4. Metabolome and its study 5. Applications of metabolomics

INTRODUCTION TO METABOLOMICS Overview of metabolomics- Metabolomics in Arabidopsis thaliana- Lipidomics. METABOLOME INFORMATICS Introduction to the ARM Database- The Genome-Based E-CELL Modeling (GEM) System- Large-Scale Simulation of Metabolism-Metabolomics and Medical Sciences INTRODUCTION TO METABOLIC ENGINEERING Importance of metabolic engineering-comprehensive models for cellular reactions-material balances & data consistency- metabolic pathway synthesis. METABOLIC FLUX ANALYSIS AND ITS APPLICATION Theory-determination of flux by isotope labeling-Metabolic control analysis- (control coefficients and summation theorems, FCC determination)-Grouping of reactions (gFCC, identification of independent pathways). FLUX ANALYSIS OF METABOLIC NETWORKS Bottom up and Top down approaches- case study-optimization of flux amplification- consistency tests and experiment validation

TEXTBOOKS

1. M. Tomita, T. Nishioka, Metabolomics- The Frontier of Systems Biology, Springer Publications, 2003. 2. Gregory N. Stephanopoulos, Metabolic Engineering- Principles and Methodologies, Academic press,

First Edition, 1998. REFERENCE BOOK

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

2. Wolfram Weckwerth, Metabolomics: Methods And Protocols, Humana Press, 2007.

L T P C E3 ELECTIVE III 3 0 0 3 Prerequisite Nil

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L T P C BI0409 CHEMOINFORMATICS LABORATORY 0 0 2 1 Prerequisite Nil 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 student will be able to use various Bioinformatics tools to visualize and build small molecules LIST OF EXPERIMENTS

1. Knowledge about different chemical data bases 2. Different chemical file formats 3. Molecule Visualization Using Rasmol

• Commands • Domain identification

3. Small molecule building, using ISIS Draw and CHEM SKETCH. 4. Creating chemical library using different chemical sketching tools.

REFERENCES

1. Laboratory Manual

L T P C

E4 ELECTIVE IV-LAB 0 0 2 1 Prerequisite Nil

L T P C BI0411 INDUSTRIAL TRAINING-II 0 0 2 1 Prerequisite Nil The student has to undergo industrial training for a minimum period of two weeks in the winter/summer vacation of the VI semester. After undergoing the training in an industry, the student will be asked to submit a report that will be evaluated

VIII SEMESTER

L T P C

BI0400 BIOSAFETY, BIOETHICS, IPR & PATENTS 2 0 0 2 Prerequisite Nil PURPOSE This course creates awareness on the Biosafety, bioethics, Intellectual property rights and patenting of bio-technological processes. INSTRUCTIONAL OBJECTIVES

1. To introduce the biosafety regulations and ethical concepts in biotechnology 2. To emphasize on IPR issues and need for knowledge in patents in biotechnology

BIOSAFETY-REGULATORY FRAMEWORK FOR GMOS IN INDIA

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Regulatory framework in India governing GMOs-Recombinant DNA Advisory Committee (RDAC), Institutional Biosafety Committee (IBC), Review Committee on Genetic Manipulation, Genetic Engineering Approval Committee (GEAC), State Biosafety Coordination Committee (SBCC), District Level Committee (DLC). Recombinant DNA Guidelines (1990), Revised Guidelines for Research in Transgenic Plants (1998), Seed Policy (2002), Prevention Food Adulteration Act (1955), The Food Safety and Standards Bill (2005), Plant Quarantine Order (2003), Regulation for Import of GM Products Under Foreign Trade Policy (2006-2007), National Environment Policy (2006). Rules for the manufacture, use/import/export and storage of hazardous microorganisms/genetically engineered organisms or cells (Ministry of Environment and Forests Notification, 1989). BIOSAFETY-REGULATORY FRAMEWORK FOR GMOS AT INTERNATIONAL LEVEL Convention of Biological Diversity (1992) – Cartagena Protocol on Biosafety – Objectives and salient features of Cartagena Protocol – Advanced Information Agreement (AIA) procedure – procedures for GMOs intended for direct use-risk assessment-risk management-handling, transport, packaging and identification of GMOs-Biosafety Clearing House-unintentional transboundary movement of GMOs-Benefits of becoming a party to the Cartagena Protocol- status of implementation in India. BIOETHICS What is bioethics- The legal and socioeconomic impacts of biotechnology-Public education of the process of biotechnology involved in generating new forms of life for informed decision-making – ethical concerns of biotechnology research and innovation. INTELLECTUAL PROPERTY RIGHTS Intellectual property rights-TRIP- GATT-International conventions patents and methods of application of patents-Legal implications-Biodiversity and farmer rights PATENTS AND PATENT LAWS Objectives of the patent system - Basic principles and general requirements of patent law-biotechnological inventions and patent law-Legal development-Patentable subjects and protection in biotechnology-The patenting living organisms. REFERENCE BOOKS

1. Beier, F.K., Crespi, R.S. and Straus, T. Biotechnology and Patent protection-Oxford and IBH Publishing Co. New Delhi.

2. Sasson A, Biotechnologies and Development, UNESCO Publications, 1988. 3. Singh K, Intellectual Property rights on Biotechnology, BCIL, New Delhi 4. Regulatory Framework for GMOs in India (2006) Ministry of Environment and Forest, Government of

India, New Delhi 5. Cartagena Protocol on Biosafety (2006) Ministry of Environment and Forest, Government of India,

New Delhi

L T P C BI0402 MEDICAL INFORMATICS 2 0 0 2 Prerequisite Nil 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

INTRODUCTION Introduction- Hospital management and information system: functional area- pre-requisites- integrated hospital information systems- health information system- and disaster management plan KNOWLEDGE – BASED AND EXPERT SYSTEMS

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Artificial intelligence- expert systems- materials and methods- computer based patient Records- computer assisted medical education MODULES Hospital Management and Information systems- structure and functions- computer assisted patient education- computer assisted patient surgery COMPUTER ASSISTED SURGICAL TECHNIQUES Three-dimensional imaging: limitations of endoscopy and imaging- benefits of virtual endoscopy- materials and methods- limitations- applications- merits and demerits- surgical simulation- virtual environment TELECOMMUNICATIONS BASED SYSTEMS Tele-medicine- needs- materials and methods- Internet tele-medicine- controversial issues- reliability- cost-analysis- applications- tele-surgery- the Internet TEXT BOOK

1. Mohan Bansal, Medical Informatics- a primer, Tata McGraw-Hill, 2003. 2. Charles P. Friedman, Jeremy C. (EDT) Wyatt, Evaluation Methods in Medical Informatics- Springer

Verlag, 1997. REFERENCE BOOKS

1. Hsinnchun Chen, Medical Informatics: Knowledge Management And Data Mining in Biomedicine, Springer, 2005.

2. F. T. De Dombal, Medical Informatics: The Essentials, Butterworth-Heinemann, 1996.

L T P C BI0404 PROJECT WORK 0 0 16 8 Prerequisite Nil At the end of the 7th semester, students will be assigned to projects based on the submitted abstracts. During the 8th semester, 3 review meetings will be conducted during which their progress will be monitored and evaluated by their oral presentations. The students are expected to submit a written thesis of their project at the end of the semester followed by viva voce examination MODULE I ELECTIVES

L T P C BI0351 MICROBIAL GENOMICS 3 0 0 3 Prerequisite Nil PURPOSE It provides a comprehensive overview of Genomics study related to microbes. INSTRUCTIONAL OBJECTIVES

1. Microbial Bioinformatics 2. Microbial metabolism 3. Genomics-Based Analysis of the Bacterial Cell Cycle 4. Plant pathogens

INRODUCTION History- Bioinformatics and microbial pathogenesis- Bacteriophage Bioinformatics- New methods of gene sequencing. GENOME ANALYSIS Comparative Microbial Metabolism- Genomic Analysis of Membrane Transport- Analysis of the Bacterial Cell Cycle.

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BACTERIAL BIODIVERSITY Concepts of Bacterial Biodiversity for the age of Genomics- Coevolution of symbionts and pathogens with their hosts. PATHOGENIC GENOMES Plant pathogen genomes - parasite genomics- genomes of pathogenic enterobacteria and thermophiles. APPLICATION Application of Genomics to Biocatalysis and Biodegradation - microbial proteomics.

TEXT BOOK

1. Fraser, Claire M, Read, Timothy, Nelson, Karen E., Microbial Genomes, Humana Press 2004. 2. Kenneth W. Adolph, Microbial Genome Methods, CRC Press, 1996.

REFERENCE BOOKS 1. Jizhong Zhou, Microbial Functional Genomics, Wiley-IEEE, 2004. 2. Thomas John Dougherty, Steven J. Projan, Microbial Genomics and Drug Discovery, CRC Press,

2003.

L T P C BI0350 MICROARRAY- TECHNIQUES AND APPLICATIONS 3 0 0 3 Prerequisite Nil PURPOSE This course provides core knowledge on techniques and applications of Microarray. INSTRUCTIONAL OBJECTIVES

1. Microarray designing 2. Image processing and normalization 3. Analysis of Microarray data

INTRODUCTION Microarray- making and using microarrays- types of Microarray- sequence databases for microarrays COMPUTER DESIGN OF OLIGONUCLEOTIDE PROBES Introduction- filtering- cross-hybridization prediction- Image processing NORMALIZATION Introduction- data cleaning and transformation-within array normalization- between array normalization- measuring and qualifying microarray variability ANALYSIS Analysis of differentially expressed genes- fundamental concepts and hypothesis rules-analysis of relationships between genes- tissues or treatments- classification of tissues and samples EXPERIMENTAL DESIGN Blocking- randomization and blinding- choice of technology-data standards- storage and sharing TEXT BOOKS

1. Dov Stekel, Microarray Bioinformatics, Cambridge University Press, 2003. 2. Helen C. Causton, John. Quackenbush, Alvis. Brazma, Microarray Gene Expression Data Analysis: A

Beginner's Guide, Blackwell Publishing, 2003.

REFERENCE BOOKS 1. David W Mount, Bioinformatics- Sequence and genome analysis, Cold Spring Harbor Laboratory

Press, second edition, 2004. 2. Uwe. R Müller, Dan V. Nicolau, Microarray Technology and Its Applications, Springer, 2005.

BI – 07-08 – SRM – E&T 64

L T P C

BI0451 GENETIC ALGORITHM 3 0 0 3 Prerequisite Nil PURPOSE This course gives a complete understanding of the concepts of Genetic algorithm. INSTRUCTIONAL OBJECTIVES

1. Mathematical foundations for Genetic algorithm, operators 2. Applications of Genetic Algorithms. 3. Genetic based machine learning and its applications.

INTRODUCTION TO GENETIC ALGORITHM 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. GA OPERATORS 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. APPLICATIONS OF GA 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. INTRODUCTION TO GENETICS-BASED MACHINE LEARNING 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. APPLICATIONS OF GENETICS-BASED MACHINE LEARNING The Rise of GBMC – Development of CS-1, the first classifier system. – Smitch’s Poker player. – Other Early GBMC efforts. –Current Applications. TEXT BOOKS

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

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

REFERENCE BOOKS

1. Kalyanmoy Deb, Optimization for Engineering Design, algorithms and examples, PHI 1995. 2. Melanie Mitchell, An Introduction to Genetic Algorithms, The MIT Press, 1996.

L T P C BI0471 ADVANCED BIOINFORMATICS LABORATORY 0 0 2 1 Prerequisite Nil

PURPOSE

BI – 07-08 – SRM – E&T 65

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 student will be able to apply Bioinformatics to various fields. LIST OF EXPERIMENTS

1. Metabolomics 2. Functional genomics 3. Comparative genomics 4. Molecular modeling & Docking 5. Micro array data analysis 6. Complete genome analysis 7. Developing software tools 8. Database creation 9. Primer design 10. Mini Project

REFERENCE

1. Laboratory Manual

MODULE II ELECTIVES

L T P C BI0353 PROTEIN ENGINEERING 3 0 0 3 Prerequisite Nil PURPOSE The course imparts advanced knowledge on proteins through a detailed study of protein Structure, its characteristics property and significance in biological systems INSTRUCTIONAL OBJECTIVES

1. To focus and advanced knowledge on primary secondary structure of and their determined 2. Protein design principles and database analysis

PRIMARY AND SECONDARY STRUCTURE Primary structure and its determination secondary structure prediction and determination of super secondary structures- proteins folding pathways. RECEPTORS 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 ENGINEERING OF MACROMOLECULES Basic outline- Rational and steps involved in protein engineering. Protein design principles and examples DATA ANALYSIS METHODS Protein database analysis methods- to alter primary structure of proteins- Theory- Interactive graphics programme- perturbation METHODS OF PROTEIN ENGINEERING Methods of Proteins engineering- Immunotoxins- Drug Designing.

TEXT BOOKS

1. Moody PCE and Wilkinson AJ , Protein Engineering,IRL press oxford 1990.

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2. Branden C, Tooze R, Introduction of Protein structure, Garland 1993. REFERENCE BOOKS

1. Creighton, TE, Proteins, Freeman WH Second Ed 1993. 2. Jeffrey L. Cleland, Charles S. Craik, Protein Engineering: Principles and Practice, Wiley-Liss, 1996.

L T P C BI0352

BIOCONFINEMENT OF GENETICALLY MODIFIED ORGANISMS

3 0 0 3

Prerequisite Nil PURPOSE This course deals with the importance of Bioconfinement of genetically modified organisms. INSTRUCTIONAL OBJECTIVES

1. To make the students to understand the need of bioconfinement of genetically engineered organisms 2. To impart knowledge on methods of bioconfinement

INTRODUCTION TO BIOCONFINEMENT Genetically Engineered Organisms -Bioconfinement - Methods of Bioconfinement, International Aspects - History of Confinement - Social Acceptability of Bioconfinement Methods. NEED FOR BIOCONFINEMENT Risk factors - Effects on Nontarget Species - Delaying the Evolution of Resistance - Food Safety and Other Issues - Need for Bioconfinement. BIOCONFINEMENT OF PLANTS AND ANIMALS Genetically Engineered Trees - Transgenic Grasses - Transgenic Algae Effectiveness at Different Spatial and Temporal Scales - Monitoring and Managing Confinement Failure -Bioconfinement of fish, and insects. BIOCONFINEMENT OF VIRUSES, BACTERIA, AND OTHER MICROBES Introduction - Potential Effects or Concerns- Need for Bioconfinement in Viruses, Fungi, and Bacteria BIOLOGICAL AND OPERATIONAL CONSIDERATIONS FOR BIOCONFINEMENT Execution of Confinement - International Aspects - Bioconfinement – Bioconfinement Research TEXT BOOK Biological confinement of genetically engineered organisms, national research council - National Academics press.

L T P C BI0453 NANOBIOTECHNOLOGY 3 0 0 3 Prerequisite Nil PURPOSE The subject focuses on the latest techniques and outcomes in Nanobiotechnology. INSTRUCTIONAL OBJECTIVES

1. Bionanomachines 2. Biomolecular design 3. Structural and functional principles 4. Present and future of Nanobiotechnology

INTRODUCTION Quest for Nanotechnology-from biotechnology to Bionanotechnology- unfamiliar world of Bionanomachines- modern biomaterials- legacy of evolution.

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STRUCTURAL PRINCIPLES Natural bionanomachinery- construction- raw materials- protein folding- self-assembly- self- organization- molecular recognition- flexibility.

FUNCTIONAL PRINCIPLES Nanoassembly- energetics- chemical transformation- regulation.

BIOMOLECULAR MOTORS Biomaterials- Biomolecular motors- traffic across membranes- Biomolecular sensing- self-replication.

PRESENT AND FUTURE Nanomedicine- DNA computers- Biosensors- Case study- nanotube synthase- ethical issues. TEXT BOOK

1. David S. Goodsell, Bionanotechnology- Lessons from Nature, Wiley-Liss, 2004. 2. Christof M. Niemeyer, Nanobiotechnology- Concepts, Applications and Perspectives, John Wiley &

Sons, 2004. REFERENCE BOOK

1. Mark A. Ratner, Daniel Ratner, Nanotechnology: A Gentle Introduction to the Next Big Idea, Prentice Hall PTR, 2003.

2. Massimiliano DiVentra, Stephane Evoy, James R. Heflin, Introduction to Nanoscale Science and Technology, Springer, 2004.

L T P C

BI0473 ENZYME TECHNOLOGY LABORATORY 0 0 2 1 Prerequisite Nil PURPOSE This course aims at educating students about the practical aspects of enzyme engineering. INSTRUCTIONAL OBJECTIVES Students completing this course should understand the extraction of enzymes, enzyme kinetics, and enzyme reactions LIST OF EXPERIMENTS

1. Isolation of high yielding microbial strains for the production of commercially important enzymes. 2. Production of commercially important enzymes from microbial sources. 3. Standardization of medium composition for the optimum production of enzymes. 4. Determination of enzyme activity and specific activity. 5. Partial purification of isolated enzymes. 6. Characterization of enzymes-Effect of pH, temperature and inhibitors on enzyme activity etc. 7. Molecular weight determination of enzyme by Gel filtration method. 8. Method of checking the purity of the enzyme -SDS-PAGE 9. Immobilization of enzymes –Different Techniques such as adsorption, entrapment, encapsulation and

cross- linking. 10. Strain improvement techniques- physical, chemical and genetic manipulation methods. 11. Development of enzyme assay methods. 12. Formulation of enzyme stability.

REFERENCE BOOKS

1. Laboratory Manual 2. R. Eisenthal and M.J. Dansen, Enzyme Assays –A Practical Approach, IRL Press, Oxford University

Press, Oxford, 1993 MODULE III ELECTIVES

L T P C

BI0355 ARTIFICIAL INTELLIGENCE 3 0 0 3

BI – 07-08 – SRM – E&T 68

Prerequisite Nil 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. INSTRUCTIONAL OBJECTIVES To enable the student to understand

1. Various searching techniques used in problem solving, deal with ignorance and vagueness 2. Planning agents and the algorithm used.

INTRODUCTION What Is AI- the Foundations of Artificial Intelligence- The History of Artificial Intelligence- Intelligent Agents- How Agents Should Act, Structure of Intelligent Agents, Environments SEARCH METHODS 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. LOGICAL REASONING SYSTEMS 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. REASONING UNDER UNCERTAINTY 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. PLANNING AND LEARNING 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. TEXT BOOKS

1. Stuart Russel and Peter Norvig, Artificial Intelligence- A Modern Approach, Prentice Hall, 1995. 2. George F Luger, Artificial Intelligence, Pearson Education, 4th Edition, 2001.

REFERENCE BOOKS

1. Engene Charniak and Drew Mc Dermott, Introduction to Artificial Intelligence, Addison Wesley, 2000. 2. Nils J. Nilsson, Principles of Artificial Intelligence, Narosa Publishing House, 2000. 3. Dan W. Patterson, Introduction to Artificial Intelligence and Expert systems, Prentice Hall of India, 1992. 4. Robert J Schalkoff, Artificial Intelligence- An Engineering Approach, McGraw Hill, 1990.

L T P C

BI0354 COMPUTATIONAL NEUROSCIENCE 3 0 0 3 Prerequisite Nil PURPOSE This course enables the students to understand the computational neuroscience from the basics.

BI – 07-08 – SRM – E&T 69

INSTRUCTIONAL OBJECTIVES

1. Neurons, Population dynamics 2. Perceptions, models of neuroscience 3. Supervised Learning and Rewards Systems

INTRODUCTION Definition- Domains in Computational Neuroscience- Brain metaphors-computer and brain- basic neuroscience- Basic synaptic mechanisms and the generation of action potentials- Nernst Potential, Hodgkin-Huxley equations, the propagation of action potentials. SPIKING NEURONS AND RESPONSE VARIABILITY Spiking neurons- concept neurons- the neural code- spike trains- cable theory- Spike time variability- post synaptic potential(PSP)- firing threshold and action potential- Neurons in a Network- Population Dynamics- rate code- Information in spike trains- Population coding and decoding- single neuron models, Hodgkin-Huxley Model, spiking neuron models, integrate and firing model, noise in spiking neuron models- compartmental modeling. FEED-FORWARD MAPPING NETWORKS From artificial neural network to realistic neural networks-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. AUTO-ASSOCIATIVE MEMORY AND NETWORK DYNAMICS Associative memory networks- 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. SUPERVISED LEARNING AND REWARDS SYSTEMS Motor learning and control, supervised learning-the delta rule and back propagation, generalized delta rules, plasticity and coding, 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 CASE STUDY- Introduction to the MATLAB programming environment, A MATLAB guide to computational neuroscience, Spiking neurons and numerical integration in MATLAB

TEXTBOOKS

1. Thomas Trappenberg, Fundamentals of Computational Neuroscience, oxford University Press, June 2002.

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

REFERENCE BOOKS

1. Gerstner and Kistler, Spiking Neuron Models. Single Neurons, Populations, Plasticity -Cambridge University Press, 2002.

2. Eric L. Schwartz, Computational Neuroscience, MIT Press, 1993.

L T P C BI0455 BIOPYTHON 3 0 0 3 Prerequisite Nil PURPOSE The subject focuses on the basic concepts and applications of Biopython.

BI – 07-08 – SRM – E&T 70

INSTRUCTIONAL OBJECTIVES 1. Types and operators 2. Basic statements and functions 3. Modules and classes 4. Applications

PROGRAM STRUCTURE Python program structure- builtin types- basic statements FUNCTIONS Functions basics- scope rules- argument passing- Odds and Ends- Function Gotchas MODULES Basics- Module files- import model- reloading- modules Gotchas- classes- Exceptions OOLS Built-in Tools- Common Tasks in Python APPLICATIONS An Automated Complaint System- Interfacing with COM- Cheap Public Relations- A Tkinter-Based GUI Editor for Managing Form Data- Design Considerations- JPython- The Felicitous Union of Python and Java TEXT BOOK

1. Patrick O'Brien, Beginning Python for Bioinformatics, O'Reilly, 2002. 2. Alex Martelli, Python in a Nutshell, O'Reilly, 2006.

. REFERENCE BOOK

1. Cynthia Gibas, Per Jambeck, Developing Bioinformatics Computer Skills, O'Reilly, 2001. 2. Harvey M. Deitel, Python: How to Program, Prentice Hall, 2002.

L T P C

BI0475 BIOPYTHON LABORATORY 0 0 2 1 Prerequisite Nil 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 student will be able to understand and develop the concept of analyzing scientific data using Python. LIST OF EXPERIMENTS Header function

1. String methods 2. Operators 3. Using a class from a module 4. Fetch a PDB entry from the RCSB Web server 5. Extracting the complete CDS from a GenBank entry 6. Import from Bio.Clustalw 7. Using a class from a module 8. Fetching enzymes referenced in a SwissProt entry and display related proteins

REFERENCES 1. Laboratory manual 2. Website: http://www.pasteur.fr/recherche/unites/sis/formation/python/index.html

MODULE IV ELECTIVES

BI – 07-08 – SRM – E&T 71

L T P C

BI0357 NEURAL NETWORKS 3 0 0 3 Prerequisite Nil PURPOSE This course provides a way to study the Artificial Neural Networks and its applications. INSTRUCTIONAL OBJECTIVES

1. To learn the basics of ANN in comparison with Human brain 2. To learn the various architectures of building an ANN and its applications 3. Advanced methods of representing information in ANN like self-organizing networks and competitive

learning INTRODUCTION 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. PERCEPTRONS 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. PATTERN ASSOCIATORS & FEEDFORWARD NETWORKS 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. EXTENSIONS AND ADVANCED TOPICS 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. COMPETITIVE AND SELF-ORGANISING NETWORKS 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.

TEXT BOOKS

1. Robert J. Schalkoff, Artificial Neural Networks, McGraw Hill International Ed, 1997. 2. James. A. Freeman and David. M. Skapura, Neural Networks Algorithms, Applications and

programming Techniques, Pearson Education, 2002. REFERENCE BOOKS

1. Simon Haykin, Neural Networks - A Comprehensive Foundation, Pearson Education Asia. 2002. 2. B. Yegnanarayana, Artificial Neural Networks, Prentice -Hall of India, 2001.

L T P C

BI0356 IMAGE PROCESSING 3 0 0 3 Prerequisite Nil

BI – 07-08 – SRM – E&T 72

PURPOSE This course provides a fundamental knowledge of Digital Image Processing Techniques INSTRUCTIONAL OBJECTIVES

1. Digital Image fundamentals, Image Transform 2. Image enhancement and restoration techniques 3. Image segmentation and Compression

DIGITAL IMAGE FUNDAMENTALS 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. IMAGE TRANSFORM Properties of unitary transform- 2D DFT, DCT, DST- Discrete wavelet transform- Discrete Hadamard Walsh, Hotelling transform, SVD Transform- Slant, Haar transforms. IMAGE ENHANCEMENT AND RESTORATION 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 gradientl- 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. IMAGE COMPRESSION 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. IMAGE SEGMENTATION 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. TEXT BOOKS

1. Gonzalez, R.C and Woods, R.E, Digital Image Processing, Addition – Wesley, 2000. 2. Anil K. Jain, Fundamentals of digital image processing, PHI, 1997.

REFERENCE BOOKS 1. Umbaugh , S.E , Computer vision and image processing, Prentice Hall International, Inc,1998 2. William. K. Pratt, Digital image processing, Wiley Interscience, 2000.

L T P C

BI0457 ADVANCED JAVA PROGRAMMING 3 0 0 3 Prerequisite JAVA PROGRAMMING PURPOSE This course provides an in-depth knowledge of Advanced Java language and programming. INSTRUCTIONAL OBJECTIVES

1. Java Data structure. 2. Java Networking and Beans. 3. Java Data Base and Graphics.

JAVA BASICS-REVIEW Java Streaming – Components and events handling – Threading concepts – Networking features – Byte code interpretation – Media Techniques.

BI – 07-08 – SRM – E&T 73

JAVA DATA STRUCTURES Lists – Linear Structures – Ordered Structures – Sorting – Trees. ADVANCED NETWORKING AND BEANS 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. JAVA DATABASE PROGRAMMING Connecting to Databases – JDBC principles – Databases access – Interacting – Database search – Accessing Multimedia databases – Database support in Web applications. RELATED JAVA TECHNIQUES 3D graphics – JAR file format and creation – Internationalization – Swing Programming – Advanced Java Scripting Techniques. TEXT BOOKS

1. Jame Jaworski, Java Unleashed, SAMS Techmedia Publications, 1999. 2. Campione, Walrath and Huml, The Java Tutorial, Addison Wesley, 1999.

REFERENCE BOOKS

1. Duane A. Bailey, Java Structures, McGraw-Hill Publications, 1999. 2. Jeff Frentzen and Sobotka, Java Script, Tata McGraw-Hill, 1999.

L T P C BI0477 ADVANCED JAVA PROGRAMMING LABORATORY 0 0 2 1

Prerequisite Nil

PURPOSE The main aim is to learn the advanced features of Java and to develop skills to cope with any kind of java programming. It provides an introduction to J2ME programming to develop simple mobile applications using Java Wireless Tool Kit. INSTRUCTIONAL OBJECTIVES The students who completed this course have the ability

1. To develop network based applications. 2. To develop distributed applications in Advanced Java. 3. To learn client server programming. 4. To create J2ME applications.

LIST OF EXPERIMENTS

1. Develop a Half duplex chat program using UDP. 2. Develop a Full duplex chat program using TCP. 3. Implement RMI program to perform arithmetic functions. 4. Develop a simple application to insert and retrieve data from database. 5. Design a color bean. 6. Design a simple J2ME application to retrieve date and time

REFERENCE BOOK

1. Laboratory Manual

MODULE V ELECTIVES

L T P C BI0359 DRUG AND PHARMACEUTICAL BIOTECHNOLOGY 3 0 0 3

Prerequisite Nil

BI – 07-08 – SRM – E&T 74

PURPOSE The goal is to emphasize the importance of pharmaceutical research and its usefulness in biotechnology. INSTRUCTIONAL OBJECTIVES To impart basic concepts of drug metabolism and pharmokinetics, manufacturing principles, and product development and its quality. INTRODUCTION Development of Drug and Pharmaceutical Industry: Therapeutic agents, their use and economics- Regulatory aspects. DRUG METABOLISM AND PHARMACOKINETICS Drug metabolism: physico chemical principles, radio activity-pharma kinetic action of drugs on human bodies. IMPORTANT UNIT PROCESSES AND THEIR APPLICATIONS Bulk drug manufacturers- Type of reactions in bulk drug manufacture and processes- Special requirement for bulk drug manufacture. MANUFACTURING PRINCIPLES Compressed table- wet granulation-dry granulation or slugging-direct compression-tablet presses- coating of tablets, capsules-sustained action dosage forms-parental solution-oral liquids-injections-ointment-topical applications- Preservation, analytical methods and test for various drug and pharmaceuticals-packing: packing techniques, quality management, GMP. PHARMACEUTICAL PRODUCT AND THEIR CONTROL Therapeutic categories such as vitamins-laxatives- analgesics- nonsteroidal contraceptives- Antibiotics, biologicals- hormones. REFERENCE BOOKS

1. Leon Lachman et al, Theory and Practice of Industrial Pharmacy, 3 Edition, Lea and Febiger, 1986. 2. Remington’s, Pharmaceutical Science, Mark Publishing and Co.

L T P C

BI0358 CANCER BIOLOGY 3 0 0 3 Prerequisite Nil PURPOSE To provide knowledge about biological aspects of cancer INSTRUCTIONAL OBJECTIVES To impart basic concepts of cancer biology, various stages in carcinogenesis, molecular cell biology of cancer, cancer metastasis, and cancer therapy. FUNDAMENTALS OF CANCER BIOLOGY Regulation of Cell cycle- Mutations that cause changes in signal molecules- effects on receptor- signal switches- tumour suppressor genes- Modulation of cell cycle-in cancer- Different forms of cancers- Diet and cancer. PRINCIPLES OF CARCINOGENESIS Chemical Carcinogenesis- Metabolism of Carcinogenesis- Natural History of Carcinogenesis- Targets of Chemical Carcinogenesis- Principles of Physical Carcinogenesis- X-Ray radiation – Mechanism of radiation Carcinogenesis. PRINCIPLES OF MOLECULAR CELL BIOLOGY OF CANCER Oncogenes- Identification of Oncogenes- Retroviruses and Oncogenes- detection of Oncogenes- Growth factor and Growth factor receptors that are Oncogenes- Oncogenes / Proto Oncogenes activity- Growth factors related to transformations. PRINCIPLES OF CANCER METASTASIS

BI – 07-08 – SRM – E&T 75

Clinical significances of invasion- heterogeneity of metastatic phenotype- Metastatic cascade- Basement membrane disruption- Three step theory of invasion- Proteinases and tumour cell invasion. NEW MOLECULUS FOR CANCER THERAPY Different forms of therapy- Chemotherapy- Radiation Therapy- Detection of Cancers- Prediction of aggressiveness of Cancer- Advances in Cancer detection.

TEXT BOOKS

1. King R.J.B., Cancer Biology, Addision Wesley Longmann Ltd, U.K., 1996. 2. Ruddon.R.W., Cancer Biology, Oxford University Press, Oxford, 1995.

REFERENCES BOOKS

1. Maly B.W.J., Virology a practical approach, IRL press, Oxford, 1987. 2. Dunmock.N.J and Primrose S.B., Introduction to modern Virology, Blackwell Scientific Publications,

Oxford, 1988. L T P C

BI0459 STEM CELLS IN HEALTH CARE 3 0 0 3 Prerequisite

Nil PURPOSE The course offers an opportunity the students to understand the basics of stem cells Embryonic stem cells, Adult stem cells and genetic engineering of stem cells and their applications INSTRUCTIONAL OBJECTIVES To make the student gain knowledge in

1. Stem cell basics 2. Growing of ES cells in lab 3. Differentiation of stem cells 4. Application of stem cells

STEM CELL BASICS Unique properties of stem cells – embryonic stem cells - adult stem cells – umbilical cord stem cells – similarities and differences between embryonic and adult stem cells. Properties of stem cells – pluripotency – totipotency EMBRYONIC STEMCELLS Invitro fertilization –culturing of embryos-isolation of human embryonic stem cells – blastocyst – innercell mass – growing ES cells in lab – laboratory tests to identify ES cells – stimulation ES cells for differentiation – properties of ES cells. ADULT STEM CELLS Somatic stem cells – test for identification of adult stem cells – adult stem cell differentiation – trans differentiation – plasticity – different types of adult stem cells. STEM CELL IN DRUG DISCOVERY AND TISSUE ENGIEERING Target identification – Manipulating differentiation pathways – stem cell therapy Vs cell protection - stem cell in cellular assays for screening – stem cell based drug discovery, drug screening and toxicology. GENETIC ENGINEERING AND THERAPEUTIC APPLICATION OF STEM CELLS Gene therapy – genetically engineered stem cells – stem cells and Animal cloning – transgenic animals and stem cells – Therapeutic applications – Parkinson disease - Neurological disorder – limb amputation – heart disease - spinal cord injuries – diabetes –burns - HLA typing- Alzheimer’s disease –tissue engineering application – production of complete organ - kidney – eyes - heart – brain. REFERENCE BOOKS

1. Kursad and Turksen, Embryonic Stem cells, Humana Press, 2002. 2. Committee on the Biological and Biomedical applications of Stem cell Research, Stem cell and future

of regenerative medicine, National Academic press, 2002.

BI – 07-08 – SRM – E&T 76

L T P C BI0479 MEDICAL BIOTECHNOLOGY LABORATORY 0 0 2 1

Prerequisite Nil

PURPOSE The laboratory is designed to train the students in practical aspects of understanding stem cells, embryonic stem cells, Adult stem cells and genetic engineering of stem cells and their applications INSTRUCTIONAL OBJECTIVES To make the student gain knowledge in

1. Stem cell basics 2. Growing of ES cells in lab 3. Differentiation of stem cells 4. Application of stem cells

LIST OF EXPERIMENTS STEM CELL LAB

1. Isolation of stem cells from bone marrow 2. Characterisation of stem cells by markers 3. In vitro differentiation stem cell to different kinds of cells 4. Identification of cell type by PCR /RT-PCR 5. SDS –PAGE analysis of protein profile of stem cells 6. MHC alleles of isolated stem cells 7. RAPD finger printing of stem cells 8. Cryopreservation of stem cells 9. Revival of stem cell from Cryopreservation and viable cell counting 10. Karyotype analysis of Stem cells

REFERENCE BOOK

1. Laboratory manual

MODULE VI ELECTIVES

L T P C BI0361 MACHINE LEARNING IN BIOINFORMATICS 3 0 0 3 Prerequisite Nil PURPOSE To provide knowledge about the development and application of computer methods for management, analysis, interpretation, and prediction, as well as for the design of experiments. INSTRUCTIONAL OBJECTIVES To impart knowledge about

1. Building good probabilistic models 2. Automate the process of data analysis.

MACHINE LEARNING FOUNDATIONS Introduction-Bayesian modeling-Cox Jaynes axioms- Bayesian inference and induction- models structures- examples. MACHINE LEARNING ALGORITHMS Dynamic programming- EM/ GEM algorithms-Markov chain Monte carlo methods-simulated annealing- genetic algorithm-Neural networks. APPLICATIONS Sequence coding- correlations- Prediction: secondary structure, signal peptides and cleavage sites-applications

BI – 07-08 – SRM – E&T 77

for DNA & RNA nucleotide sequences- Performance evaluation. HIDDEN MARKOV MODELS Introduction- likelihood & Basic algorithms- Learning algorithms- Applications: general aspects, proteins, DNA and RNA PROBABILISTIC MODELS Models for phylogeny-substitution probabilities-Data likelihood-optimal trees- modeling for array data

TEXT BOOKS

1. Søren Brunak, Pierre F Baldi, Bioinformatics: The Machine Learning approach, MIT Press, 2001. 2. Steffen Schulze-Kremer, Molecular Bioinformatics: Algorithms and Applications, Walter de Gruyter,

1996. REFERENCES BOOKS

1. Balas Kausik Natarajan, Machine Learning: A Theoretical Approach, Morgan Kaufmann, 1991. 2. Yi-Ping Phoebe. Chen, Bioinformatics Technologies, Springer, 2005.

L T P C

BI0360 DATA MINING IN BIOINFORMATICS 3 0 0 3 Prerequisite Nil

PURPOSE The purpose is to teach the student how to manage and analyze large amounts of data that are generated during a scientific study. INSTRUCTIONAL OBJECTIVES To make the student gain knowledge in

1. Cluster analysis 2. Data visualization 3. Biological data mining and management

INTRODUCTION Introduction-Data cleaning- Data Preprocessing-Data Intergration-Classification Methods-Cluster analysis methods-Data visualization and Visual data mining- computational mining of biological processes. SEQUENCE AND STRUCTURE ALIGNMENT Multiple sequence alignment using antipole clustering-AntiClustAl- Comparing Clustal with AntiClustAl- RNA structure comparison and alignment models- algorithm for RNA secondary structure comparison- Structure alignment. BIOLOGICAL DATA MINING Piecewise constant modeling of sequential data- Bayesian method- examples-gene mapping-haplotype basis of gene mapping- Predicting protein folding pathways. MINING OF CHEMICAL COMPOUNDS Introduction-Methods for locating protein intracellular locations- chemical compounds-background-classification based on frequent sub graphs- experimental evaluation. BIOLOGICAL DATA MANAGEMENT Phyloinformatics- synthesizing bigger trees-Visualizing larger trees- secondary structure querying evaluation techniques- index structure for sequences- protein structure indexing

TEXT BOOK

1. Jason T. L. Wang, Data Mining in Bioinformatics, Springer, 2005. 2. Sushmita Mitra, Tinku Acharya, Data Mining: Multimedia, Soft Computing, and Bioinformatics, John

Wiley and Sons, 2003. REFERENCE BOOK

BI – 07-08 – SRM – E&T 78

1. Hui-Huang Hsu, Advanced Data Mining Technologies in Bioinformatics, Idea Group Inc, 2006. 2. Jiawei Han, Micheline Kamber, Data Mining: Concepts and Techniques, Elsevier, 2006.

L T P C BI0461 NUTRIGENOMICS 3 0 0 3

Prerequisite Nil

PURPOSE The emerging discipline of nutritional genomics, or nutrigenomics is the study of the effects of diet on the activity of an individual’s genes and health and the study of how different genetic makeups metabolize nutrients. INSTRUCTIONAL OBJECTIVES To make the student gain knowledge in

1. Impact of nutrients on gene expression 2. Bioinformatic resourses for nutrigenomics 3. Metabolomic studies

INTRODUCTION Definition-Bioinformatics and biocomputation-Converting science into practice-Research ethics and genetic privacy- Pursuit of Optimal Diets: Considerations in defining an optimal diet, the potential impact of optimal diet and lifestyle changes. GENE - ENVIRONMENT INTERACTIONS Genetic variability- Gene-environment interactions: focus on diet- Common genetic variants and their interaction with dietary factors- Metabolomics- Tools of metabolomics- Metabolome assembly and annotation- Genetic and molecular buffering of phenotypes. GENE - GENE AND GENE - ENVIRONMENT INTERACTIONS Epistasis and gene - environment interactions in obesity and diabetes- Gene gene interaction in obesity and diabetes- Dietary fat in obesity and diabetes- SREBPs and ChREBP: transcription factors, influenced by dietary lipids and glucose- Nuclear receptors -structure and function- Phytoesterogens - nutrients mimicking estrogens. BIOINFORMATICS INFRASTRUCTURE Introduction-Next generation biobanks- GMPs, GLPs and GCPs- Funding of biobanks- Biobanking in clinical trials-Informatics infrastructure -Separation of the clinical trial/patient identity management from the genotype/phenotype repository- Database architecture/ data modeling. BIOCOMPUTATION AND THE ANALYSIS OF COMPLEX DATASETS IN NUTRITIONAL GENOMICS

Nutritional genomics is part of high - throughput biology- Gene expression arrays- Proteomics and metabolomics data-Sources of complexity in nutritional genomics- Data sets in nutritional genomics- The level of complexity in gene expression experiments- Dimensionality reduction methods- Case study (microarray experiment of a dietary - intervention)- Proactive ethics and nutritional genomics. TEXTBOOK

1. Raymond L. Rodriguez, James Kaput, Nutritional Genomics: Discovering the Path to Personalized Nutrition, Wiley and Sons, 2006.

2. Gerald H. Rimbach, Lester Packer, Jürgen Fuchs, Nutrigenomics, CRC Press, 2005. REFERENCE BOOK

1. Artemis P. Simopoulos, J. M. Ordovas, Nutrigenetics and Nutrigenomics, Karger Publishers, 2004. 2. Regina Brigelius-Flohé, Hans-GeorgJoost, Nutritional Genomics: Impact on Health and Disease,

Wiley-VCH, 2006. L T P C

BI0481 ADVANCED COMPUTATIONAL BIOLOGY LABORATORY 0 0 2 1 Prerequisite

BI – 07-08 – SRM – E&T 79

Nil 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 student will be able to understand and develop the concept of analyzing scientific data. LIST OF EXPERIMENTS

1. Genome comparison 2. Genome rearrangements 3. Phylogenetic Reconstruction 4. Metabolic Pathways Reconstruction 5. Methods for detecting trans-membrane helices 6. Predicting Gene-Gene (Protein-Protein) interactions 7. Structure comparison methods 8. Predict the solvent accessibility 9. QSAR 10. Molecular docking

REFERENCES

1. Laboratory manual