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Bioinformatics is the application of information technology to the management of biological data. It is the backbone for computational tools and databases that support Genomic and related research.
Bioinformatics is defined as an integration of mathematical, statistical and computer methods to analyze biological, biochemical and biophysical data.
Studies of IDC points out that India will be a potential star in bioscience field in the coming years after considering the factors like bio-diversity, human resources, infrastructure facilities and government’s initiatives. According to IDC, bioscience includes pharma, Bio-IT (bioinformatics), agriculture and R&D. IDC has been reported that the pharmaceutical firms and research institutes in India are looking forward for cost-effective and high-quality research, development, and manufacturing of drugs with more speed.
This sector is the quickest growing field in the country. The vertical growth is because of the linkages between IT and biotechnology, spurred by the human genome project. The promising start-ups are already there in Bangalore, Hyderabad, Pune, Chennai, and Delhi. There are over 200 companies functioning in these places. IT majors such as Intel, IBM, Wipro are getting into this segment spurred by the promises in technological developments.
According to Confederation of Indian Industry(CII), the global bioinformatics industry clocked an estimated turnover of $2 billion in 2000 and is estimated to have done $60 billion by 2005. If the industry and government work together it is possible to achieve a five percent global market share by 2006, i.e., a $3 billion opportunity in India.
The past two years has seen many large multinational pharmaceutical companies acquiring other small companies and developing in the biosciences sector. IDC currently forecasts a compound annual growth rate (from 2001-02 to 2004-05) of about 10 percent in the spending on Information Technology by bioscience organizations. Enterprise applications including data warehousing, knowledge management, and storage are being pursued by these companies as priorities.
IDC data reveals that IT spending in biosciences in India has crossed $138 million by 2005, mainly in the areas of system clusters, storage, application software, and services. Also the governments life science focus provides a great deal of the necessary backbone to develop and deliver innovative products and technologies. This focus will also helps to build fast-growing and lucrative enterprises, attract international investment, and create additional high-value employment opportunities. Hence the focus of the IT sector should be on products and services that aligns with bioscience needs. Demonstrating a true understanding of the IT requirements of biotechnology processes is the key for IT suppliers to bridge the chasm that currently exists between IT and Science.
Science graduates preferably with specialization in Molecular Biology, Biochemistry, Genetics, Microbiology, Medicinal Chemistry,Medical Sciences, Neuroscience’s, Pharmaceutical Science, Veterinary sciences, Food Sciences, Agricultural Sciences, Biotechnology, Physics, Chemistry, Mathematics & Statistics are eligible for the course.
Or B.Es of any discipline
Module I: Introduction to Bioinformatics
- Types of biological data
- The problems associated with the data handling & Need for computational tools
- Fundamental types of bioinformatics analysis
- Major branches of bioinformatics
- Emerging trends, scope and future challenge
Module II: Computer Fundamentals
- Introduction to Computers
- Overview
- Hardware
- Software
- Introduction to Operating Systems
- DOS
- Windows
- Unix and Linux
- Introduction to Networking
- Overview
- Internet
- WWW
- IP/TCP
- FTP
- Linux Commands
- Overview
- User commands
- Application to Bioinformatics
Module III: Option No.1:Programming and Scripting Languages
- Introduction
- Data Types
- Statements
- Loops
- Array
- Structure and Functions
- Points
- Files
- Data Structure
C++
- Introduction
- Class and Objects
- Scope and Variables and Inline Functions
- Constructors and Destructors
- Overloading
- Inheritance
- Virtual Functions Files
- Data structures
- Exception Handling
- Templates
Java Fundamentals
- Introduction
- Class and Objective
- Packages and Interface
- Multi threading
- Applets
- AWT
- JFC and Swings
- JDBC
Perl and Bioperl
- Creating and Running the PERL Programs (Scripts)
- Scalars
- Arrays
- Associated Arrays
- BIO-PERL Modules
- CGI Scripting Using PERL
- File Management
Option 2: Database Management track
- VB (as front end designing tool) & Oracle 9i (as back end RDBMS)
- VB (Visual Basic)
- Introduction to Visual Basic
- Understanding the Integrated Development Environment(IDE)
- Creating Visual Basic project
- Using VB code editor
- Data types, variables and constant in VB
- Using operators
- Control Structures- IF….Then, Select Case, DO….LOOP, FOR……NEXT Working With Forms
- Working with standard controls (Button, Label, Text Box, Picture, Frame, Check Box, List Box etc…..)
- Properties and methods of Objects in VB
- Building a Menu in VB
- Error trapping
- Working with Data controls
- ADO database programming with connection to oracle
- Manipulating the Data from VB forms
- Oracle 9i (RDBMS)
- Introduction to DBMS and RDBMS
- Writing a basic SQL statement
- Restricting and Sorting the data
- Single row function
- Displaying data from multiple function
- Using group function
- Writing sub queries
- Manipulating Data
- Creating and Managing tables
- Including constrains
- Crating Views
- Other Database objects
- Controlling user access
- SQL Workshop
- Using Set Operations
- Oracle 9i Date time function
- Enhancement to the GROUP BY clause
- Advance sub queries
Module IV
- Biological sequence databases & sequencing methodologies
- Introduction & requirement for Biological databases
- Basic classification – Primary, Secondary & Aggregated databases
- DNA sequencing – Principles & methodologies
- Automated sequencing machines
- Nucleotide Sequence databases
- Protein sequencing – Principles & methodologies
- Protein sequence databases
- Concept of secondary databases – PROSITE & other secondary databases
- Protein Structure databases – Detailed account of PDB
- Secondary structure databases
- Associated Software & other online resources:
- NCBI Server, Entrez, GenBank, EMBL & DDBJ, SWISSPROT, PIR & UNIPROT, Scan PROSITE, PDB, MMDB & CDD
Module V
- Sequence analysis & its applications
- Basic principles of Sequence analysis
- Sequence alignment – Pairwise & Multiple sequence alignments
- Global & Local alignment algorithms: Needleman & Wunsch, Smith waterman
- MSA – Progressive Alignment
- Sequence similarity searches
- FASTA & BLAST – Algorithms & Applications
- Practical applications of sequence analysis
- Phylogenetic analysis – Basic steps involved
- Predictive methods using nucleotide sequences
- Gene prediction – Principles & methods
- Predicting other regions of interest
Associated Software & other online resources
- Emboss Align, Clustal – W, MultAlign, Sequence retrieval from databases – ENTREZ & SRS
- Similarity searching using BLAST & Fasta
- Restriction analysis – NebCutter, RestrictionMapper, Webcutter, etc
- Primer design- Primer3, OMEGA, etc
- Tools in Phylogenetic analysis – PHYLIP, PAUP, McClade
Module VI: Structure analysis
- Overview of Structure determination methods
- Structural complexity associated with proteins
- Structure visualization methods – Rasmol, Pymol, SWISSPDB viewer, etc
- Structure alignment methods – VAST, SSAP, DALI
- Structure superimposition methods & Associated tools
- Sequence to structure dogma
- Predicting physical properties of proteins using sequence data
- Structure prediction methods
- Comparative/homology modeling
- ab initio methods
- Fold recognition
- Applications of HMMs, Neural networking & Threading methods
Associated Software & other online resources
- Structure visualization tools – Rasmol, Pymol, SWISSPDB viewer, etc
- Structure alignment tools – VAST, SSAP, DALI
- Secondary structure prediction tools: NNPREDICT, PredictProtein, SOPMA, etc
- Quaternary structure & other prediction tools: WHAT-IF, LOOK, SWISS-MODEL, 3Dee, FSSP, PHD, PHDhtm, TMpred, etc
Module VII: Structural & Functional Genomics
- Introduction – The science of 'omics'
- Genome sequencing strategies – Clone-contig & shotgun approaches
- Genome projects: Human genome project – Detailed account
- Microbial genome projects – E.coli, Haemophilus, etc.
- Plant genome projects – Arabidopsis thaliana, Rice genome project, etc.
- Other genome projects – Worm genome project, Mouse genome project, etc.
- Post genomic era – Functional genomics
- Comparative genomics – Whole genome comparisons & associated technologies
- Principles, construction & applications of Microarray technology including GEO database & problems associated with microarray image analysis
- Expressed Sequence Tags (ESTs) – Detailed account, dbEST, Applications
- Single nucleotide polymorphisms (SNPs) - Detailed account, dbSNP, Applications
- Pharmacogenomics
- Transcriptomics – The link between the genomics and proteomics
Associated Software & other online resources
- Genomic databases (Entrez genome, Flybase, etc.), dbEST, dbSNP, GEO
Module VIII: Proteomics, Metabolomics, Interactomics & Systems Biology
- Introduction
- Methods of protein sequencing
- Mass spectrometry - Methods and applications in proteomics including peptide mass fingerprinting
- Analysis of proteome data
- Associated tools
- Protein chips
- Metabolomics – Introduction, principles, applications & databases associated with it etc
- Interactomics – Interaction studies
- Systems Biology – holistic approach to tackle biological problems
Associated Software & other online resources
- KEGG, BRENDA, PFBP, WIT, BIND, COMPEC, DIP, FIMM, etc
Module IX: Principles of Molecular modeling, Protein engineering, in silico drug designing & Informatics
- Introduction to Molecular modeling
- Construction of initial model
- Refining the model
- Manipulation of structures
- Deriving pharmacophores
- Visualization methods & tools
- Protein engineering: Introduction
- Protein design principles
- Comparative & ab intio methods
- Manipulation at genic level
- Role of computational tools
- Iterative cycle of protein engineering
- Examples of engineered proteins
- In silico drug designing & Pharmacoinformatics: Introduction
- Rational drug designing procedure & CADD
- Drug discovery & development cycle
- Target discovery & characterization
- Chemical space & High Throughput Screening procedures
- Identification of Candidate drugs
- Molecular Docking studies – Principles & applications
- Clinical trials & approval
- Example drugs
Associated Software & other online resources
- Chem-X, CombiLibMaker, Dock, Autodock, CombiDock, LIGIN, FTDock, GRAMM, FlexX,
Module IX:
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