Course BI 301: Operating Systems & Object Oriented Programming
Unit I- Operating System: Introduction: Windows and Unix/Linux, Definition; Concepts; Function of Operating System; Batch Processing; Multiprogrammed Batch System; Time Sharing System; Parallel System; Distributed System; Real Time System.
Unit II- Process & Memory Management: Process; Process State(New, Running, Waiting, Ready, Termination); Process Control Block; Process Scheduling (Round Robin Scheduling, Priority Scheduling, Multiple Queues, Shortest Job Scheduling); Operations on Process; Basic Management of Memory; Swapping Virtual Memory; Paging.
Unit III- Input/Output Management: I/O Devices; Device Controllers; I/O Software; Device Drivers; Deadlock; Resources; Principles of Dead Lock; Detection and Recovery; Deadlock Prevention; Deadlock Avoidance.
Unit IV- UNIX/LINUX Operating Systems: Introduction; Concepts; Layers of UNIX; Role of System Administrator and Ordinary User; Tree Structure of UNIX; Root File System; /bin Directory; /dev Directory; /bin Directory; /etc Directory; /lib Directory; /proc Directory; /mnt Directory; /root Directory; /sbin Directory; /tmp Directory; /var Directory; Relative Path; Absolute Path; Creation of Directory; Creating file; removing file; Listing Files and Directories copying file; renaming file; Changing File Permission; Changing Directory Permission; Changing Group; Changing Owner; Pipe; Filters; pwd command; date command; head command; tail command less command; more command; grep command; VI Editor (Creating a new File; Inserting Text in File; Deleting Text in File; Copy , Cut & Paste Text; Save File).
Unit V– Introduction to Object-oriented programming & concepts: Object Modeling, Object-Oriented Databases, Object Database Languages, Object Database Design, Object-oriented programming with C++ (Objects, Classes, Data Abstraction & Inheritance).
Course BI 302: Biocomputing Programming
Unit I- Hyper Text Programming Language: Structure of HTML program(<HTML>, <HEAD>, <TITLE>, <BODY>); Titles & Footer; Text Formatting(Paragraph break<P>, line break<BR>); Text Styles(Bold<B>, Italics<I>, Underline<U>); Font Style, Color & Size; Image Tag(<IMG>); Table (<TABLE>, <TR>, <TH>, <TD>) & Attributes( Border, Width, Align); Frames; Forms (Text Box, Check Box, Command Button, List Box); Anchors.
Unit II- Java Script- Data Types; Literals; Variables; Arrays; Operators (Arithmetic, Comparison, Logical, String, Assignment); Condition Check(if-then-else); looping(for, while); Functions(Built-in, user defined); scope of functions; Dialog Boxes( Alert Dialog Box, Prompt Dialog Box; Confirmed Dialog Box).
Unit III- PERL- Scalar Data; Scalar Variable; List Data & Variable; Creating List Operators (Arithmetic, Relational, Increment & Decrement, Assignment, Logical); <STDIN>; print, printf & sprintf; Arrays; Assigning values to Array elements.
Unit IV-Arrays & Hashes- Accessing Array elements; Finding the length of an Array; Hashes; Accessing Hash elements; Deleting Hash elements; Processing the values of Hashes; Conditionals (if, if…else, if…elseif); while loop( while, until & do); for loop; controlling loop (last, next & redo); Manipulating Lists and Strings (Sorting, Searching, Modifying List Elements such as: push & pop, shift & unshift, splice, reverse, index, substr).
Unit V-Pattern Matching- Simple Pattern Matching, Matching group of Characters, Extracting Matches; File Handling( Creating, renaming removing files); Using PERL for CGI Scripting.
Course BI 303- Sequence Analysis
Unit I: Sequence comparison algorithm, sequence scoring schemes (weight matrix as Identify scoring, genetic code scoring scheme chemical scoring, observed substation matrix and Gap penalties.)
Unit II: Sequence database similarity searching algorithms, local alignment, global alignment, FASTA, BLAST (BLASTP, BLASTN, BLASTX, TBLASTN, TBLASTX) and similarity searching scores and their statistical interpretation.
Unit III : Motifs and Domains, algorithm for multiple alignments (CLUSTALx and CLUSTALW) Biological motifs (consensus, regular expression, profiles, PSSMs, HMMs and application for biological sequence similarity searching(PSI- & PHI BLAST, motifs, patterns)).
Unit IV: Functional genomics Strategies for generating EST and full length insert, EST clustering and assembly, statistical analysis of EST and EST data, micro array (target selection/design, image analysis, data validation, statistical analysis.)
Unit V: Phylogenetic prediction: Relationship of phylogenetic analysis to sequence alignment, Genome complexity and phylogenetic analysis, concept of evolutionary trees. Maximum parsimony method, distance method, maximum likelihood method.
Course BI 304- Genomics, Proteomics & Systems Biology
Unit I: Objective and Overview of Genome Comparisons, Genome Alignments, BLAST2, MUMmer, PipMaker, VISTA, Comparison of Gene Order, Comparative Genomics― Viruses, Microbes, Pathogens, Eukaryotes,
Unit II: Comparative Genomics Databases- COG, VirGen, CORG, HOBACGEN, Homophila, XREFdb, Gramene, Single Nucleotide Polymorphism, dbSNP and other SNP-related databases; An overview of pharmocogenomics.
Unit III: Definition, History and Scope of Proteomics, Experimental Techniques (SDS-PAGE, 2D-PAGE, X-ray crystallography, NMR spectroscopy, isoelectric focusing, mass spectroscopy, (MALDI), differencial display, protein chips and antibody microarrays, functional protein microarrays; resolution and identification of proteins), analysis of post translational modifications of proteins; Bioinformatics Approaches, Protein-Protein Interaction Networks, databases and software, DIP (Database of Interacting Proteins).
Unit IV: PPI Server, BIND - Biomolecular Interaction Network Database, PIM –Hybrigenics PathCalling Yeast Interaction Database, MINT - a Molecular Interactions Database, GRID - The General Repository for Interaction Datasets, InterPreTS - protein interaction prediction through tertiary structure.
Unit V: Systems Biology: Biological Systems--System of Molecular Networks; Ecosystem, Elements of systems modeling, Gene regulatory network and the models; Computational modeling in biology.
Note : The examiner is expected to set the question paper based on the entire course content. In Section A, the question paper shall include 5 long question (10 marks each) out of which the candidate is required to attempt 3 questions. Section B shall be based on short answers 100-200 words and shall include 4 questions of which the candidate is required to attempt 2 questions of 5 marks each. Section C shall include 10 to 20 questions of half / one mark each and shall be based on objective type / true-false / very short answers like definitions.
Course BI 305- Practical 1 (Course BI 301 & Course BI 302)
Course BI 306-Practical 2 (Course BI 303 & Course BI 304)