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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 ([email protected]) ([email protected]) Visiting scientist @ Institute for Infocomm Research (I2R), Singapore Bioinformatics is ….. Bioinformatics is the study of living systems through computation 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 Bioinformatics encompasses Sequences Structures Genomes Transcriptomes Networks, Genetics and pathways populations and systems with input from disciplines/technologies Databases, Data & text ontologies mining Algorithms Maths/Stats Physics/ Chemistry Evolution and phylogenetics Inputs From Different Fields: Biological Scientists Physical Scientists Bioinformatics Computer Scientists Medical Scientists Supporting bioinformatics Internet Access to large biological databases Research, using this data Education and training 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 BitTorrentbased Peer-to-Peer model “Automatic synchronization and distribution of biological databases and software over lowbandwidth networks among developing countries” U Sangket, …. Jong Bhak, … and Tin Wee Tan, Bioinformatics 2008 24(2):299-301 Biological databases Biomirrors biosingapore.org/index.php/BioMirrors 26 databases now updated regularly. Several mirrors in EABN countries Research Applying this data to research problems is key to addressing problems in Biotechnology Medicine Agriculture Veterinary science Biodiversity conservation 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 Publications from this region 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” 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 Education and training Education Undergraduate courses in bioinformatics for life science students Post-graduate programs in bioinformatics PhD programs Workshops on Education in Bioinformatics (WEB) Show that each program has to be tailormade “One size does not fit all” Our region has made considerable progress in commencing formal education Much more needs to be done ...informatics trends Genomics Proteomics Bioinformatics Computational Biology Medical Informatics LIFE SCIENCE INFORMATICS Careers in Bioinformatics Genomics: Genome sequencing of Bacteria, viruses Animals Plants Comparative genomics Annotation and Mapping Gene Discovery Careers in Bioinformatics Functional Genomics (Gene Expression and Regulation): Control Regions Switches Circuits Bypass Feedback loops Environmental Effects Diseased States Chemical Consequences Careers in Bioinformatics Pharmacogenomics: SNPs Regional, ethnic variations Inheritance patterns Radiological/ecological modifications Therapeutic target recognition Correlation of drug and expression effects Pathway Effects Careers in Bioinformatics Proteomics: Protein Profiling Alternate splice variants Orphan genes Cryptic introns Gene Therapy Careers in Bioinformatics Structural Genomics: Experimental Protein structures Apo state Holo state Structural modifications Membrane Proteins Homology Modelling Comparative Modelling Careers in Bioinformatics Drug and Vaccine Design: Screening Natural Products Plants Fungi Bacteria Chemicals In silico modifications of ligands Vaccine design and delivery Job Sectors Academia Research Institutes Biotechnology Bioinformatics Pharmaceutical Agriculture Biodiversity Thank you!