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Supporting a thriving bioinformatics culture in East Asia

Supporting a thriving bioinformatics culture in East Asia. Shoba Ranganathan Professor and Chair – Bioinformatics Dept. of Chemistry and Biomolecular Sciences & Adjunct Professor Biotechnology Research Institute Dept. of Biochemistry

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Supporting a thriving bioinformatics culture in East Asia

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  1. Supporting a thriving bioinformatics culture in East Asia Shoba Ranganathan Professor and Chair – Bioinformatics Dept. of Chemistry and Biomolecular Sciences & Adjunct Professor Biotechnology Research Institute Dept. of Biochemistry Macquarie University Yong Loo Lin School of Medicine Sydney, Australia National University of Singapore, Singapore (shoba.ranganathan@mq.edu.au) (shoba@bic.nus.edu.sg) Visiting scientist @ Institute for Infocomm Research (I2R), Singapore

  2. Bioinformatics is ….. • Bioinformatics is the study of living systems through computation

  3. Essential elements of Bioinformatics ...We must hook our individual computers into the worldwide network that gives us access to daily changes in the databases and also makes immediate our communications with each other. The programs that display and analyze the material for us must be improved - and we must learn to use them more effectively. Like the purchased kits, they will make our life easier, but also like the kits, we must understand enough of how they work to use them effectively… Walter Gilbert (1991) “Towards a paradigm shift in biology” Nature News and Views 349:99

  4. Sequences Networks, pathways and systems Structures Genetics and populations Genomes Transcriptomes Bioinformatics encompasseswith input from disciplines/technologies Databases, ontologies Data & text mining Algorithms Maths/Stats Physics/ Chemistry Evolution and phylogenetics

  5. Inputs From Different Fields: Biological Scientists Physical Scientists Bioinformatics Computer Scientists Medical Scientists

  6. Supporting bioinformatics • Internet • Access to large biological databases • Research, using this data • Education and training

  7. Internet • Internet: Currently available though the APAN (Asia-Pacific Advanced Network) project • However, connectivity and access to large biological databases remain an issue • Creative solutions are now available using BitTorrent-based Peer-to-Peer model • “Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries” U Sangket, …. Jong Bhak, … and Tin Wee Tan, Bioinformatics 2008 24(2):299-301

  8. Biological databases • Biomirrors • biosingapore.org/index.php/BioMirrors • 26 databases now updated regularly. • Several mirrors in EABN countries

  9. Research • Applying this data to research problems is key to addressing problems in • Biotechnology • Medicine • Agriculture • Veterinary science • Biodiversity conservation

  10. Forum for presenting research results • EABN meetings • APBioNet’s International Conference in Bioinformatics (InCoB) • Taipei, Taiwan: Oct. 20-23, 2008 • Other international conferences in 2008 • RECOMB2008 at Singapore: Mar/Apr • ISMB2008 at Toronto, Canada: July • GIW2008 at Gold Coast, Australia: Dec

  11. Publications from this region

  12. Research-related issues • Lack of researchers in bioinformatics for discussion • Issue of “critical mass” • Communication gap • Biologists, biochemists, chemists, computer scientists, information technologists, statisticians…. • Need for a virtual “Mentor Group”

  13. Education and training • Training • Quick solution to lack of trained bioinformatics personnel • Tutorials, workshops, short-term courses, research internships • Distance education or face-to-face

  14. Education and training • Education • Undergraduate courses in bioinformatics for life science students • Post-graduate programs in bioinformatics • PhD programs

  15. Workshops on Education in Bioinformatics (WEB) • Show that each program has to be tailor-made • “One size does not fit all” • Our region has made considerable progress in commencing formal education • Much more needs to be done

  16. ...informatics trends Genomics Proteomics Bioinformatics Computational Biology Medical Informatics LIFE SCIENCE INFORMATICS

  17. Careers in Bioinformatics • Genomics: • Genome sequencing of • Bacteria, viruses • Animals • Plants • Comparative genomics • Annotation and Mapping • Gene Discovery

  18. Careers in Bioinformatics • Functional Genomics (Gene Expression and Regulation): • Control Regions • Switches • Circuits • Bypass • Feedback loops • Environmental Effects • Diseased States • Chemical Consequences

  19. Careers in Bioinformatics • Pharmacogenomics: • SNPs • Regional, ethnic variations • Inheritance patterns • Radiological/ecological modifications • Therapeutic target recognition • Correlation of drug and expression effects • Pathway Effects

  20. Careers in Bioinformatics • Proteomics: • Protein Profiling • Alternate splice variants • Orphan genes • Cryptic introns • Gene Therapy

  21. Careers in Bioinformatics • Structural Genomics: • Experimental Protein structures • Apo state • Holo state • Structural modifications • Membrane Proteins • Homology Modelling • Comparative Modelling

  22. Careers in Bioinformatics • Drug and Vaccine Design: • Screening Natural Products • Plants • Fungi • Bacteria • Chemicals • In silico modifications of ligands • Vaccine design and delivery

  23. Job Sectors • Academia • Research Institutes • Biotechnology • Bioinformatics • Pharmaceutical • Agriculture • Biodiversity Thank you!

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