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Supporting bioinformatics education in the Asia-Pacific Shoba Ranganathan Professor and Chair – Bioinformatics Dept. of Chemistry and Biomolecular Sciences &Adjunct Professor ARC CoE in BioinformaticsDept. 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 (I 2 R), Singapore
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Bioinformatics is ….. Bioinformatics is the study of living systems through computation
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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
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Bioinformatics encompasses with input from disciplines/technologies Networks, pathways and systems Sequences Genomes Transcriptomes Databases, ontologies Data & text mining Evolution and phylogenetics Maths/StatsAlgorithms Physics/ Chemistry Genetics and populations Structures
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Inputs From Different Fields: Bioinformatics Biological Scientists Physical Scientists Computer Scientists Medical Scientists
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Supporting bioinformatics Internet Access to large biological databases Research, using this data Education and training
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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
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Biological databases Biomirrors biosingapore.org/index.php/BioMirrors 26 databases now updated regularly. Several mirrors in EABN countries
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Research Applying this data to research problems is key to addressing problems in Biotechnology Medicine Agriculture Veterinary science Biodiversity conservation
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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
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Publications from this region
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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”
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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
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Education and training Education Undergraduate courses in bioinformatics for life science students Post-graduate programs in bioinformatics PhD programs
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Workshops on Education in Bioinformatics (and Computational Biology) (WEB and now WEBCB) 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
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...informatics trends Bioinformatics Computational Biology Medical Informatics LIFE SCIENCE INFORMATICS GenomicsProteomics
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Careers in Bioinformatics Genomics: Genome sequencing of Bacteria, viruses Animals Plants Comparative genomics Annotation and Mapping Gene Discovery
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Careers in Bioinformatics Functional Genomics (Gene Expression and Regulation): Control Regions Switches Circuits Bypass Feedback loops Environmental Effects Diseased States Chemical Consequences
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Careers in Bioinformatics Pharmacogenomics: SNPs Regional, ethnic variations Inheritance patterns Radiological/ecological modifications Therapeutic target recognition Correlation of drug and expression effects Pathway Effects
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Careers in Bioinformatics Proteomics: Protein Profiling Alternate splice variants Orphan genes Cryptic introns Gene Therapy
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Careers in Bioinformatics Structural Genomics: Experimental Protein structures Apo state Holo state Structural modifications Membrane Proteins Homology Modelling Comparative Modelling
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Careers in Bioinformatics Drug and Vaccine Design: Screening Natural Products Plants Fungi Bacteria Chemicals In silico modifications of ligands Vaccine design and delivery
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Job Sectors Academia Research Institutes Biotechnology Bioinformatics Pharmaceutical Agriculture Biodiversity Thank you!
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