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Post Graduate Diploma In Bioinformatics Assam University :: Silchar Detailed Course Structure and Syllabus The Programme The Post Graduate Diploma in Bioinformatics is of one year duration. The Programme has been organized in two semesters, First semester and second semester.
COURSE STRUCTURE Sl. No. Name of the modules Semester -I
Total marks
Pass Marks
70
30
70
30
70 30
30 10
240
100
70
30
70
30
30 90
10 30
Sub-Total (B)
260
100
TOTAL (A+B)
500
200
a) b) c) d)
PGDBI-T1: Modern Biology and Basic Bioinformatics PGDBI-T2: Basic Computer Application and Fundamentals of Programming PGDBI-T3: Biostatistics and Basic Mathematics PGDBI-P1: Practical
Sub-Total (A) Semester-II e) f) g) h)
PGDBI-T4: Introduction to Database and Programming PGDBI-T5: Genomics, Proteomics and Structural Biology PGDBI-P2: Practical PGDBI-Project: Project/Dissertation work
PGDBI-T1: Modern Biology and Basic Bioinformatics Unit-1 1. Basics of cell biology: Structure and Functions of Cellular Organelles, Cell Cycle, Chromosome Structure, Cellular Metabolic Pathways 2. Basics of Genetics: Mendel`s works and experiments, chemical basis of heredity 3. Pathway of Carbohydrate, Lipid and Nitrogen metabolism Unit-2 1. Molecular Biology: Structure of Nucleic acids, Structure of a Gene, Central Dogma, Concepts of Genetic code and ORF`s, DNA Replication, Chromosomal Aberration 2. Mutation and its implications , Amino acid structure and properties, Different levels of protein structure, Concepts of pH and Buffer 3. Genome Sequencing Techniques, Polymerase Chain Reaction, Chromatographic Techniques, Gel Electrophoresis, Blotting Techniques Unit-3 1. Introduction to Biological Databases: NCBI, EMBL, PIR, SWISS-Prot, PubChem Compound, KEGG-Pathway, ChEMBL, BindingDB. Analysis of Three Dimensional Structure of Proteins, RCSB-PDB 2. Computation of various parameters using proteomics tools at the ExPASy server and EMBOSS 3. Repositories for high throughput genomic sequences: EST, STS GSS, etc.; Genome Databases at NCBI, EBI, TIGR, SANGER. Unit-4 1. Detection of ORF`s, Outline of Sequence assembly, Mutation Matrices, Pair wise Sequence Alignments, BLAST and FASTA 2. Multiple Sequence Alignment and Phylogenetic Analysis. 3. Restriction Enzymes and rDNA Technology
Suggested Readings: a) David W Mount, Bioinformatics: Sequence And Genome Analysis, Cold Spring Harbor Press. b) Terence A Brown, Genomes 3. Oxford: Wiley-Liss c) Benjamin Cummings, Becker's World of the Cell by Jeff Hardin d) Attwood, Introduction to Bioinformatics
PGDBI-T2: Basic Computer Application and Fundamentals of Programming Unit-1 1. Fundamentals of Computer, Basic Applications of Computer; Components of Computer System, Central Processing Unit (CPU), VDU, Keyboard and Mouse, Other input/output Devices, Computer Memory, Concepts of Hardware and Software; Concept of Computing, Data and Information 2. Basics of Operating System; Popular Operating Systems (Windows, Linux, DOS); Introduction to Internet, www, HTML and URL`s 3. Understanding Word Processing: Word Processing Basics; Text creation and Manipulation; Formatting of text; Using Spread Sheet: Basics of Spreadsheet; Manipulation of cells; Formulas and Functions; Basics of presentation package and application Unit-2 1. Communication using the Internet: Basic of Computer networks; LAN, MAN, WAN; Concept of Internet; Applications of Internet; What is ISP; Knowing the Internet; Basics of internet connectivity (MODEM, ROUTER, SWITCH, wired connection etc.) 2. WWW and Web Browsers: World Wide Web; Web Browsing software, Search Engines; Understanding URL; Domain name; IP Address; 3. Communications and collaboration: Basics of electronic mail; Getting an email account; Unit-3 1. The C Language and its Advantages; The Structure of a C Program; Writing C Programs; Building an Executable Version of a C Program, Data Types, Operands, Operators, and Arithmetic Expressions 2. Input/Output Management, The getchar() and putchar() Functions and Single-character I/O, Formatted Input and the scanf() Function, The Control-flow Program Statements, Looping Statements, The Data-checking Process 3. Arrays, Command-line arguments, File Input and Output, Combining Command-line Arguments and File I/O Unit-4 1. Introduction to PERL; variables; Array; Initialization and manipulation 2. Arithmetic and logical operators; Conditional statement and Loops; Regular expressions; Function and subroutines 3. Application of PERL in Bioinformatics; concatenating DNA fragments; DNA to RNA; Reading protein Files; Finding motifs; ORFs; DNA to protein; Reading sequence form file; Converting PERL to executable file. Suggested Readings: a) P.K. Sinha, Fundamentals of computer b) Greg Johnson, Introduction to PERL c) Yashwant Kanetkar, Let us C
PGDBI-T3: Biostatistics and Basic Mathematics Unit-1 1. Measure of central tendency and dispersion. 2. Introduction: Nature of Statistics, Uses of Statistics, Statistics in relation to other disciplines, Abuses of Statistics. 3. Types of Data: Concepts of population and sample, quantitative and qualitative data, cross-sectional and time-series data, discrete and continuous data, different types of scales. Unit-2 1. Bivariate data – scatter diagram, correlation coefficient and its properties, Correlation ratio, Correlation Index, Concept of Regression, Principles of least squares, Fitting of polynomial and exponential curves. 2. Rank correlation – Spearman’s and Kendall’s measures. 3. Sampling Distributions: Introduction: Concepts of Random Sampling, Statistics and Sampling Unit-3 1. Elements of Hypothesis Testing : Null and Alternative hypotheses, Simple and Composite hypotheses, Critical Region, Type I and Type II Errors, Level of Significance and Size, p-value, Power 2. Distributions of Statistics: Illustrations using different distributions, reproductive properties of the distributions. 3. Sampling Distributions : χ2 distribution, distributions of the mean and variance of a random sample from a normal population; t and F distributions; distributions of means, variances and correlation coefficient Unit-4 1. Matrix; Determinants and their application; 2. Complex numbers; Binomial theorem; Coefficient 3. Bayes’ theorem and probability Suggested Readings: a) Zar, Biostatistics. b) Chakraborty, A class book of Mathematics, S Chand & Comp.
PGDBI-T4: Introduction to Database and Programming Unit-1 1. Introduction; Characteristics of Database approach; Advantages of using DBMS
approach; A brief history of database applications; Data models, schemas and instances; Three-schema architecture and data independence; 2. Database languages (DDL and DML) and interfaces; Database system environment; Centralized and client-server architectures; Classification of Database Management systems. 3. ENTITY-RELATIONSHIP MODEL: Entity Types, Entity Sets, Attributes and Keys; Relationship types, Relationship Sets, Refining the ER Design; ER Diagrams, Unit-2 1. SQL Data Definition and Data Types; Specifying basic constraints in SQL; Schema
change statements in SQL; Basic queries in SQL; Insert, Delete and Update statements in SQL; Database programming issues and techniques; 2. Informal Design Guidelines for Relation Schemas; Functional Dependencies; Normal Forms Based on Primary Keys; General Definitions of Second and Third Normal Forms; Boyce-Codd Normal Form. 3. Update Operations, Transactions and dealing with constraint violations; Unary Relational Operations: SELECT and PROJECT; Relational Algebra Operations from Set Theory; Binary Relational Operations : JOIN and DIVISION; Additional Relational Operations; Unit-3 1. Introduction to Php; How php better than other language; How php works with the web server; Php tags. Web architecture: MVC model, API, URL 2. Basic Development concepts: Php Syntex; Datatype; Operator; Variable; If else statement. Switch case. 3. Array: Array Structure; Type of array; Single and multi-dimensional array; Creating and deleting file; Reading and writing file; Creating and deleting folder. Unit-4 1. OOPs Concept; Class and object; Properties of object; Encapsulation and abstraction; Inheritance; Polymorphism; Abstract class. 2. Java: tokens and keywords; Data type; Declaring objects; garbage collection; Function overriding; Recursion; Try & Catch; Package & Interface 3. Java Thread Model; Thread priorities; JDBC, its type and application; basics of HTML. Suggested Readings: a) Korth, DBMS b) Balaguruswamy, Java Programming c) Gilmore, Beginning PHP and MySQL 5: From Novice to Professional
PGDBI-T5: Genomics, Proteomics and Structural Biology Unit-1 1. Whole Genome Analysis, Comparative Genomics, Concepts of Pharmacogenomics 2. Human Genetic Disorders; Gene Expression study using Microarray, Customized Microarray design, Public Microarray data sources 3. Gene/Protein function prediction using Machine learning tools: supervised/unsupervised learning, Neural networks etc. Unit-2 1. Basics of Protein Structure, Introduction to basic Proteomics Technology, Bioinformatics in Proteomics, Protein arrays, 2. Protein Structure and Ramachandran Plots, Protein Structure to Function Relationships. 3. Comparative Genome Analysis using Proteomics, Differential Expression on 2D-gel Unit-3 1. Basic Principles of Amino Acid Sequencing, Protein Synthesis, Isolation, Purification, Characterization and Estimation 2. Classification and comparison of protein 3D structures: Purpose of 3-D structure comparison and concepts, RMSD, Z-score for structural comparision ;Proteomics tools at the ExPASy server and EMBOSS, 3. Prediction of secondary structure: PHD and PSI-PRED methods, Protein Structure Prediction and Homology Modeling; Protein as Drug target: Some Case Studies, Unit-4 1. Molecular Interaction Fields and Docking, Concept of Active Site of Enzymes, ProteinProtein and Protein-Ligand Docking 2. Introduction to QSAR and Combinatorial Chemistry, In silico prediction ADMET properties for Drug Molecules 3. Chemo informatics and its application in Computer Aided Drug Designing
Suggested Readings: a) A. Malcolm Campbell, Laurie J. Heyer. Discovering Genomics, Proteomics and Bioinformatics. b) Branden and Tooze, Introduction to protein structure. c) Dunn & Pennington, Proteomics d) Palzkill, Proteomics
PGDBI-P1: Practical Retrieval of DNA/RNA/protein sequences; Biological sequence editing and analysis; PCR primer designing; Plasmid vector designing; Retrieving, visualization and analysis of macromolecular structure. Sequence alignment: database searches (BLAST, FASTA etc.), PSA and MSA; Draw and analysis of chemical structures; Submission of nucleotide sequence using BankIT; Gene finding and analyses of Genomes; Basic C programming (use of operator and loops); Use of Array and structures. PGDBI-P2: Practical Webpage design using HTML; Database preparation in SQL; SQL commands; operating PHP, WAMP, LAMP etc; Basic Java Programming; Creating and operating objects and classes Basic PERL programming; Designing PERL program for analysis of nucleotide and protein sequences; PGDBI-Project: Project/Dissertation The students will be assigned with a practical project at the end of the first semester which they will have to complete by the end of second semester under the supervision of a teacher concerned to the following themes. 1. 2. 3. 4. 5.
Computer Aided Drug Designing Phylogenetic Analyses Protein Structure prediction Construction of databases Developing Bioinformatics tools
The project report should be submitted to the centre and should comply with the guidelines given in the student corner of the webpage.