Trained Manpower

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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
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Research in Biology
General approach
Bioinformatics era
Organism Functions Cell Chromosome DNA Sequences
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Model
(Developers) (MCA M.Tech)
(Biologists)
Users
Developers
Researchers
(Researchers in Compuational Science) (Ph.D)
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Requirement for Bioinformatics Research and
Teaching

• Internet connectivity
• High speed computing
• Large data storage systems
• Trained manpower

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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

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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

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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).

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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
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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

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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

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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

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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.

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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.