An approach to carry out research and teaching in Bioinformatics in remote areas

1. An approach to carry out research and teaching in Bioinformatics in remote areas Alok Bhattacharya Alok Bhattacharya Centre for Computational Biology & Bioinformatics JAWAHARLAL NEHRU UNIVERSITY, NEW DELHI

2. Research in Biology General approach Bioinformatics era Organism Functions Cell Chromosome DNA Sequences

3. Model (Developers) (MCA & M.Tech) (Biologists) Users Developers Researchers (Researchers in Compuational Science) (Ph.D)

6. Requirement for Bioinformatics Research and Teaching • Internet connectivity • High speed computing • Large data storage systems • Trained manpower

7. Trained Manpower • Trained manpower is difficult to get particularly in remote areas • These is a need to think about • Remote teaching • Remote maintenance of hardware and software • Remote guidance of research • High degree of mobility is important

8. High Speed Computing • Desktop PCs quite often do not meet the need for large scale computing • Large cluster of CPU are needed • One solution is to put individual desktops on a GRID • Using open-source software

9. Appropriate Bioinformatics Research and Teaching in smaller universities and Institutions • The areas should be decided based on local needs • Low technology solutions may be explored • Open source software running on local machines can be used for all teaching and research • All data can be periodically downloaded locally or in major centres and distributed to all around the country • Large population of students in these universities are our asset and should be made use of (“cottage industry approach”).

10. There is a need to think ab initio regarding the kind of research and teaching on bioinformatics to be conducted in a smaller Universities and Institutes

11. BROAD RESEARCH AREA Computational Genomics • Genome Annotation • Sequence Comparison, pattern motif, profiles • Comparative Genomics • Gene segmentation Structural Bioinformatics • Protein structure and topology • Structure prediction and modeling • In silico drug discovery • Structure manipulation

12. Continue.... Systems Biology • Biochemical network • Metabolic and Gene Regulatory Network • Systems approach to understand cellular process  Large Scale Date Analysis • Gene expression array Database Management • Genome & Proteome databases

13. SPECIFIC PROBLEMS • ANNOTATION • Manual annotation of genomes following a set of rules. • -Students can be given a gene each and the annotation can be part of a class exercise • -Large number of students can be involved in the process generating a large amount of data • 2. Checking the quality of automated annotation • -There are errors in many annotated genome data deposited at NCBI • -Large number of students can be involved in this exercise • What do we need? • Genome data and some specific softwares can be written in a CD and distributed to the students for working locally

14. SPECIFIC PROBLEMS (2) • MANUALLY CURATED DATABASES • Generation of manually curated promoter database. • 2. Enzyme, activities, kinetics etc • What do we need? • Research papers can be written in a CD and distributed to the students for working locally. Major Institutes can cooperate to get these CDs made.

15. CONCLUSION Lets make use of our strength (large number of bright students) and overcome the weaknesses (lack of infrastructure and facilities). We need to plan properly and work together.