BIO-INFORMATICS

BIOINFORMATIC Session Break Up
Session No. Topic Covered Duration Scheduled Date Remark
Per Session
1 Computer Fundamentals 25
1.1 Introduction to Computers - S/W & H/W
1.2 Introduction to operating system
1.3 DOS
1.4 WINDOWS
1.5 UNIX and LINUX
1.6 Introduction to Networking
1.7 Overview
1.8 Internet,www
1.9 IP/TCP , FTP
1.1 LINUXCommands
1.11 User Commands
1.12 Application to Bioinformatics
Programming and Scripting Languages 50
2 C 14
2.1 Introduction to C
2.2 Data Types, Statements
2.3 Loops,Array
2.4 Structure
2.5 Functions
2.6 Points, Files
2.7 Data Structure
3 C++ 18
3.1 Introduction
3.2 Class and Objective
3.3 Scope and Variables, Infinite Function
3.4 Constructors and Destructors
3.5 Overloading
3.6 Inheritance
3.7 Virtual Functions Files
3.8 Data Structures and exceptional Handling
3.9 Templates
4 Java 18
4.1 Java Fundamentals
4.2 Introduction
4.3 Class and objectives
4.4 Packages and interface
4.5 MultiThreading
4.6 IO and networking
4.7 Applets
4.8 AWT
4.9 JFC and swings
4.1 JDBC
OR
DATA BASE MANAGEMENT TRACK 50
5 VB Front End 25
5.1 Introduction to VB
5.2 Understanding the intergrated Development env
5.3 Creating the VB project
5.4 Using VB Code editor
5.5 Data Type,variables and constants in VB
5.6 Using operations
5.7 Control Structures
5.8 Working with forms
5.9 Working with standard controls
5.1 Properties and Mehtods of Objectives in VB
5.11 Building a menu in VB
5.12 Error Trapping
5.13 Working with data controls
5.14 ADO database programming with connections to oracle

5.15 Manipulating the data from VB forms
6 Oracle 9i (RDBMS) 25
6.1 Introduction to DM|BMA and RDBMA
6.2 Writing a basic SQL statement
6.3 Restructuring and sorting the data
6.4 single row functions
6.5 Displaying data from the multiple functions
6.6 Using group functions
6.7 Writing sub quiries
6.8 Manipulating Data
6.9 Creating and managing tables
6.1 Including constraints, crating views
6.11 Other databse objects
6.12 Controlling user access
6.13 SQL workshop
6.14 Using set operation
6.15 Oracle 9i date time function
6.16 Enhancement to the GROUP BY clause
6.17 Advance sub quiries
TOTAL(hrs.) 75
BIOINFORMATICS Session Break Up
Session No. Topic Covered Duration Scheduled Date Remark
Per Session
1 Introduction to Bioinformatics 5
1.1 ➢ Types of biological data 1
1.2 ➢ The problems associated with the data handling & Need for computational tools 1
1.3
1.4 ➢ Fundamental types of bioinformatics analysis 1
1.5 ➢ Major branches of bioinformatics 1
1.6 ➢ Emerging trends, scope and future challenges 1
2 Biological sequence databases & sequencing methodologies: 35
2.1 ➢ Introduction & requirement for Biological databases 1
2.2 ➢ Basic classification – Primary, Secondary & Aggregated databases 2
2.3 ➢ DNA sequencing – Principles & methodologies 2
2.4 ➢ Automated sequencing machines 1
2.5 ➢ Nucleotide Sequence databases 2
2.6 ➢ Protein sequencing – Principles & methodologies 2
2.7 ➢ Protein sequence databases 2
2.8 ➢ Concept of secondary databases – PROSITE & other secondary databases 4
2.9 ➢ Protein Structure databases – Detailed account of PDB 2
2.1 ➢ Secondary structure databases 3
2.11 ➢ Associated Software & other online resources:
2.12  NCBI Server, Entrez, GenBank, EMBL & DDBJ, SWISSPROT, PIR & UNIPROT, Scan PROSITE, PDB, MMDB & CDD 14
3 Sequence analysis & its applications 45
3.1 ➢ Basic principles of Sequence analysis 1
3.2 ➢ Sequence alignment – Pairwise & Multiple sequence alignments 1
3.3 ➢ Global & Local alignment algorithms: Needleman & Wunsch, Smith waterman 4
3.4 ➢ MSA – Progressive Alignment 1
3.5 ➢ Sequence similarity searches
3.6 ➢ FASTA & BLAST – Algorithms & Applications 4
3.7 ➢ Practical applications of sequence analysis 2
3.8 ➢ Phylogenetic analysis – Basic steps involved 4
3.9 ➢ Predictive methods using nucleotide sequences: 2
3.1 ➢ Gene prediction – Principles & methods 2
3.11 ➢ Predicting other regions of interest 2
3.12 ➢ Associated Software & other online resources:
3.13 ➢ Emboss Align, Clustal – W, MultAlign, Sequence retrieval from databases – ENTREZ & SRS 5
3.14 ➢ Similarity searching using BLAST & Fasta 4
3.15 ➢ Restriction analysis – NebCutter, RestrictionMapper, Webcutter, etc 5
3.16 ➢ Primer design- Primer3, OMEGA, etc 3
3.17 ➢ Tools in Phylogenetic analysis – PHYLIP, PAUP, McClade, 5
4 Module VI: Structure analysis 45
4.1 ➢ Overview of Structure determination methods 2
4.2 ➢ Structural complexity associated with proteins 1
4.3 ➢ Structure visualization methods – Rasmol, Pymol, SWISSPDB viewer, etc 4
4.4 ➢ Structure alignment methods – VAST, SSAP, DALI 4
4.5 ➢ Structure superimposition methods & Associated tools 2
4.6 ➢ Sequence to structure dogma 1
4.7 ➢ Predicting physical properties of proteins using sequence data 2
4.8 ➢ Structure prediction methods –
4.9 ➢ Comparative/homology modeling 2
4.1 ➢ ab initio methods 2
4.11 ➢ Fold recognition 2
4.12 ➢ Applications of HMMs, Neural networking & Threading methods 2
4.13 ➢ Associated Software & other online resources:
4.14  Role of ExPASy server in protein analysis 4
4.15  Structure visualization tools – Rasmol, Pymol, SWISSPDB viewer, etc 4
4.16  Structure alignment tools – VAST, SSAP, DALI 2
4.17  Secondary structure prediction tools: NNPREDICT, PredictProtein, SOPMA, etc 4
4.18  Quaternary structure & other prediction tools: WHAT-IF, LOOK, SWISS-MODEL, 3Dee, FSSP, PHD, PHDhtm, TMpred, etc 7
5 Module VII: Structural & Functional Genomics 45
5.1 ➢ Introduction – The science of 'omics' 1
5.2 ➢ Genome sequencing strategies – Clone-contig & shotgun approaches 4
5.3 ➢ Genome projects: Human genome project – Detailed account 2
5.4 ➢ Microbial genome projects – E.coli, Haemophilus, etc. 4
5.5 ➢ Plant genome projects – Arabidopsis thaliana, Rice genome project, etc. 4
5.6 ➢ Other genome projects – Worm genome project, Mouse genome project, etc. 4
5.7 ➢ Post genomic era – Functional genomics 2
5.8 ➢ Comparative genomics – Whole genome comparisons & associated technologies 2
5.9 ➢ Principles, construction & applications of Microarray technology including GEO database & problems associated with microarray image analysis 5
5.1 ➢ Expressed Sequence Tags (ESTs) – Detailed account, dbEST, Applications 2
5.11 ➢ Single nucleotide polymorphisms (SNPs) - Detailed account, dbSNP, Applications 2
5.12 ➢ Pharmacogenomics 2
5.13 ➢ Transcriptomics – The link between the genomics and proteomics 2
5.14 ➢ Associated Software & other online resources:
5.15  Genomic databases (Entrez genome, Flybase, etc.), dbEST, dbSNP, GEO 9
6 Module VIII: Proteomics, Metabolomics, Interactomics & Systems Biology 45
6.1 ➢ Introduction 1
6.2 ➢ Methods of protein sequencing 2
6.3 ➢ Mass spectrometry - Methods and applications in proteomics including peptide mass fingerprinting 5
6.4 ➢ Analysis of proteome data 8
6.5 ➢ Associated tools 5
6.6 ➢ Protein chips 2
6.7 ➢ Metabolomics – Introduction, principles, applications & databases associated with it etc 4
6.8 ➢ Interactomics – Interaction studies 4
6.9 ➢ Systems Biology – holistic approach to tackle biological problems 4
6.1 ➢ Associated Software & other online resources:
6.11  KEGG, BRENDA, PFBP, WIT, BIND, COMPEC, DIP, FIMM.. 10
7 Module IX: Principles of Molecular modeling, Protein engineering, in silico drug designing & Informatics 55
7.1 ➢ Introduction to Molecular modeling 1
7.2 ➢ Construction of initial model 2
7.3 ➢ Refining the model 2
7.4 ➢ Manipulation of structures 2
7.5 ➢ Deriving pharmacophores 2
7.6 ➢ Visualization methods & tools 2
7.7 ➢ Protein engineering: Introduction 1
7.8 ➢ Protein design principles 2
7.9 ➢ Comparative & ab intio methods 2
7.1 ➢ Manipulation at genic level 2
7.11 ➢ Role of computational tools 1
7.12 ➢ Iterative cycle of protein engineering 1
7.13 ➢ Examples of engineered proteins 2
7.14 ➢ in silico drug designing & Pharmacoinformatics: Introduction 1
7.15 ➢ Rational drug designing procedure & CADD 2
7.16 ➢ Drug discovery & development cycle 2
7.17 ➢ Target discovery & characterization 2
7.18 ➢ Chemical space & High Throughput Screening procedures 2
7.19 ➢ Identification of Candidate drugs 2
7.2 ➢ Molecular Docking studies – Principles & applications 2
7.21 ➢ Clinical trials & approval 1
7.22 ➢ Example drugs 2
7.23 ➢ Associated Software & other online resources:
7.24  Chem-X, CombiLibMaker, Dock, Autodock, CombiDock, LIGIN, FTDock, GRAMM, FlexX, 17
Module X: Project work (one month)
TOTAL(hrs.) 275

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