B.Tech.

BIOINFORMATICS (FULL TIME) LIST OF COURSES ATTENDED: MA0111 MATHEMATICS LS1 Prerequisite Nil Grade B Credits 4

PURPOSE: To impart analytical ability in solving mathematical problems as applied to the respective Engineering.

branches

of

INSTRUCTIONAL OBJECTIVES 9 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. Grade BCredits 3

PH0101

PHYSICS 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. Grade BCredits 3

CY0101

CHEMISTRY 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.

GE0101

BASIC ENGINEERING I Prerequisite Nil

Grade B-

Credits 4

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. 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 PH0103 PHYSICS LABORATORY Prerequisite Nil Grade B+ Credits 1

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 30 1. Determination of Youngs 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 CY0103 CHEMISTRY LABORATORY Prerequisite Nil Grade BCredits 1

PURPOSE An integrated laboratory course consists of experiments from applied chemistry and is designed to illustrate the underlying principles of measurement techniques, synthesis, dynamics and chemical transformation. INSTRUCTIONAL OBJECTIVES Students should be able to understand the basic concept and its applications. LIST OF EXPERIMENTS 30 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 Winklers 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. PH0102 MATERIALS SCIENCE Prerequisite Nil Grade A Credits 3

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 6. Get familiarized with the concepts of Nano Science and Technology.

PRACTICALS 1. 2. 3. 4. 5. 6. 7. Band gap determination using Post office box. Dielectric constant measurement. Photoconductivity measurement. Resistivity determination for a semiconductor wafer using Four probe method. Determination of Hall coefficient and carrier type for a semiconductor material. To trace the hysteresis loop for a magnetic material. Magnetic susceptibility Quinckes method.

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8.

Determination of thermal conductivity Lees Disc method

9. Visit to Nano Technology Laboratory .

GE0104 PRINCIPLES OF ENVIRONMENTAL SCIENCE Prerequisite Nil Grade C+ Credits 2

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 GE0106 BASIC ENGINEERING II Prerequisite Nil Grade C Credits 4

PART A ELECTRICAL ENGINEERING 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 B ELECTRONICS ENGINEERING PURPOSE This course provides comprehensive idea about circuit analysis, working principles of machines and common measuring instruments. It also provides all fundamentals of circuit components, electronic devices, transducers and integrated circuits. INSTRUCTIONAL OBJECTIVES 1. To understand the basic concept of magnetic, AC and DC circuits. 2. To explain the working principle, construction and applications of DC and AC machines. 3. To gain knowledge about the fundamentals of electric components, devices, transducers, measuring instruments and integrated circuits. BT0104 CELL BIOLOGY Prerequisite Nil Grade C Credits 3

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 Grade BT0102 BIOCHEMISTRY Prerequisite Nil C+ Credits 3

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 CS0140 COMPUTER PRACTICE Prerequisite Nil Grade B Credits 2

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. LE0201 GERMAN LANGUAGE PHASE I Prerequisite Nil Grade BCredits 2

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.

BI0201

COMPUTER SKILLS Prerequisite Nil

Grade B-

Credits 2

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 LIST OF EXPERIMENTS 1. Displaying a line of text in a form. 2. Control structures Entry controlled loop (for/if) 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. Grade MA0202 NUMERICAL METHODS Prerequisite Nil BCredits 4 15

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 Grade BI0203 INTRODUCTION TO ALGORITHMS Prerequisite Nil BCredits 3

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. Grade BI0205 INTRODUCTION TO BIOINFORMATICS Prerequisite Nil BCredits 3

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 5. Drug discovery and pharmacoinformatics BI0207 INTRODUCTION TO DATA STRUCTURES Prerequisite Nil Grade D Credits 3

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 Grade C+ Credits 3

BI0209

JAVA PROGRAMMING 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. Grade Credits

BI0211 (=BT0207)

MICROBIOLOGY 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. Credits BI0211 BASIC BIOTECHNOLOGY LABORATORY Prerequisite Nil 1

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 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 Lowrys method / Biuret method. 9. Estimation of cholesterol by Zaks method. 10. Separation of amino acids - Thin layer chromatography. 11. Separation of sugars - Paper chromatography 12. Biochemical estimation of DNA /RNA using Spectrophotometer Grade BI0213 COMPUTATIONAL BIOLOGY LABORATORY Prerequisite Nil B+ Credits 1 30

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 BI0215 JAVA PROGRAMMING LABORATORY Prerequisite Grade C+ C 1 30

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. LE0202 GERMAN LANGUAGE PHASE - II Prerequisite GERMAN LANGUAGE PHASE - I Grade B C 2 30

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.

MA0242

PROBABILITY AND STATISTICS

Grade B-

C 4

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 CY0204 STRUCTURAL CHEMISTRY Prerequisite Nil Grade BC 3

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. Grade BI0200 MOLECULAR BIOLOGY & GENETICS Prerequisite C+ C 3

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. BI0202 BIOINFORMATICS ALGORITHMS Prerequisite Nil Grade BC 4

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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. 5. Clustering and trees. Gusfields G, Algorithms on strings, trees and sequences- Computer Science and Computational Biology, Cambridge University Press 1997. Steffen Schulze-Kremer, Molecular Bioinformatics: Algorithms and Applications, Walter de Gruyter, 1996. Grade BC 3

1.

BI0204

INTRODUCTION TO DATABASE MANAGEMENT SYSTEMS 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. 1. Peter Rob, Carlos Coronel, Database Systems Design, Implementation, and Management, 4th Edition, Thomson Learning, 2001. BI0206 (=BT0205) IMMUNOLOGY Prerequisite Nil Grade BC 3

PURPOSE Aimed at introducing the science of immunology and detail study various types of immune systems their classification structure and mechanism of immune activation. INSTRUCTIONAL OBJECTIVES 1. The immune system, their structure and classification, genetic control of antibody production 2. Cellular immunology 3. Mechanism of activation in hypersensitive immune reaction Grade C BI0208 COMPREHENSION - I B+ 1 Prerequisite Nil

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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. UNIT 1 CELL BIOLOGY 3 Evolution of cells- cells biology tools- Structure of a cell- function of different organelles- cell regulationCell signaling- cancer. UNIT 2 BIOCHEMISTRY 3 Carbohydrate metabolism- Fat metabolism- Protein Metabolism- Photosynthesis- Nucleic acid metabolismMicrobial metabolism energy production UNIT 3 BIOINFORMATICS 3 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. UNIT 4 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. 3

UNIT 5 MICROBIOLOGY 3 Microscopic examination of microorganisms morphology and fine structure of bacteria- Microbial metabolism energy production- Fungi- Algae- Protozoa- environmental microbiology. P 2 C 1

BI0210

BIOTECHNOLOGY LABORATORY 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 30

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9. 10. 11. 12. 13. 14. 15.

Production of polyclonal antibodies preparation of antigen protocol for immunization in rabbits Methods of bleeding-purification of polyclonal antibodies Antigen-antibody reaction-Haemagglutination, precipitation-Widal and VDRL Immunodiffusion, Immunoelectrophoresis. Affinity chromatiography for antibody purification. ELISA-DOT and plate ELISA Western blotting Grade C 1

BI0212

DBMS LABORATORY Prerequisite Nil

C+

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 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 30

Grade BI0301 (=GN 0306) RECOMBINANT DNA TECHNOLOGY Prerequisite Nil C+

C 3

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 Grade BI0303 MOLECULAR PHYLOGENY AND EVOLUTION Prerequisite Nil C+ C 3

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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 BI0305 BIOPHYSICAL CHEMISTRY Prerequisite Nil Grade C+ C 3

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. Grade BI0300 GENOMICS AND TRANSCRIPTOMICS Prerequisite Nil C C 3

PURPOSE The students will be aware of the structure and functions of the genomes together with the computational approaches to analyze the genomes. INSTRUCTIONAL OBJECTIVES It gives emphasize on 1. Structure and organization of genomes 2. Computational approaches to analyze the genomes 3. Microarray 4. Functional and comparative genomics 5. Basics of Transcriptomics Grade BI0309 PERL PROGRAMMING & BIOPERL Prerequisite Nil C+ C 3

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

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Grade BI0311 GENETIC ENGINEERING LABORATORY Prerequisite Nil C

C 1

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. Grade BI0313 PERL PROGRAMMING LABORATORY Prerequisite Nil BC 1 30

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 30 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. 8. Grade C BI0315 INDUSTRIAL TRAINING-I Prerequisite A1

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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.

Grade BI0307 INTERNET PROGRAMMING Prerequisite Nil B

C 3

PURPOSE To learn the Internet Technologies INSTRUCTIONAL OBJECTIVES 1. To learn about Java, HTML, DHTML concepts 2. To know about scripting languages. Grade BI0302 PROTEOMICS Prerequisite Nil BC 3

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 BI0304 IMMUNOINFORMATICS Prerequisite Nil Grade BC 3

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 Grade BI0306 MOLECULAR SIMULATION OF BIOMOLECULES Prerequisite Nil BC 3

PURPOSE

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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

BI0308

SYSTEMS BIOLOGY Prerequisite Nil

Grade C+

C 3

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 BI0310 COMPREHENSION - II Prerequisite Nil Grade BC 1

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. UNIT 1 MOLECULAR BIOLOGY AND rDNA TECHNOLOGY 3 Structure of DNA- Replication- Mendelian Genetics Transcripton -translation - gene regulationRestriction enzymes-DNA And RNA Polymerases- cloning vectors-Cloning Techniques- cDNA libraryconstruction of genomic DNA library - codon usage database. UNIT 2 IMMUNOLOGY AND PHYLOGENY 3 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. UNIT 3 BIOPHYSICAL AND STRUCTURAL CHEMISTRY 3 Basic strategies in biophysics conformational analysis- hydrogen bonding; hydrophobic interactions -Kinetics of ligand interactions- Determination Of Structure Of BioMolecules-Theory of bondingcarbohydrates- proteins- stereoisomerism- Conformation and Configuration UNIT 4 IP, PERL AND DBMS 3

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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. UNIT 5 BIOINFORATICS ALGORITHMS 3 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.

Grade BI0312 IMMUNOINFORMATICS LABORATORY Prerequisite Nil C

C 1

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 BI0314 MOLECULAR SIMULATION OF BIOMOLECULES LABORATORY Prerequisite Nil P 2 C 1 30

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. 30

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5. 6. 7.

Model validation using What Check and Pro Check Docking using DOCK or AUTODOCK or HEX. Target Ligand from PDB Sum. Grade BC 3

BI0401

CHEMOINFORMATICS 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 4. Combinatorial chemistry and library design Grade C+ C 3

BI0403

SYSTEMS APPROACH TO BIOLOGY 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 Grade B+ C 3

BI0405

PHARMACOGENOMICS AND PHARMACOGENETICS Prerequisite Nil

PURPOSE This course gives the in-depth knowledge on Pharmacogenomics and Pharmacogenetics INSTRUCTIONAL OBJECTIVES 1. Promise of personalized medicines 2. Drug response. 3. Pharmacogenetics 4. Serial Analysis of Gene Expression (SAGE) - functional biology- mapping of disease loci BI0407 METABOLOMICS AND METABOLIC ENGINEERING Prerequisite Nil Grade C C 3

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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 Grade B+ C 1

BI0409

CHEMOINFORMATICS LABORATORY 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. BI0400 (=BT0402) BIOSAFETY, BIOETHICS, IPR & PATENTS Prerequisite Nil Grade C C 2 30

PURPOSE This course creates awareness on the Biosafety, bioethics, Intellectual property rights and patenting of biotechnological 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 Grade C+ C 2

BI0402

MEDICAL INFORMATICS Prerequisite Nil

PURPOSE: This subject gives the students an idea on the applications of information technology in medical field.

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

ELECTIVES Grade BI0353 PROTEIN ENGINEERING Prerequisite Nil C C 3

PURPOSE The course imparts advanced knowledge on proteins through a detailed study of protein Structure, its characteristics property and significance in biological systems INSTRUCTIONAL OBJECTIVES 1. To focus and advanced knowledge on primary secondary structure of and their determined 2. Protein design principles and database analysis Grade BI0352 (=GN451) BIOCONFINEMENT OF GENETICALLY MODIFIED ORGANISMS Prerequisite Nil A C 3

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 BI0453 NANOBIOTECHNOLOGY Prerequisite Nil Grade B C 3

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

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Grade BI0473 (=BT0423) ENZYME TECHNOLOGY LABORATORY Prerequisite Nil B

C 1

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 30 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. DEGREE THESIS PROJECT: BI0404 PROJECT WORK Prerequisite Nil Grade A C 8

Insilico characterization of uncharacterized proteins in MUS MUSCULUS (strain C57BL/6).

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