Supporting bioinformatics education in the Asia-Pacific Shoba Ranganathan Professor and Chair – Bioinformatics Dept. of Chemistry and Biomolecular Sciences & Adjunct Professor ARC Co. E in Bioinformatics 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 (I 2 R), 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 Bit. Torrentbased 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
Biological databases § Biomirrors § biosingapore. org/index. php/Bio. Mirrors § 26 databases now updated regularly. § Several mirrors in EABN countries
Research § Applying this data to research problems is key to addressing problems in v. Biotechnology v. Medicine v. Agriculture v. Veterinary science v. Biodiversity conservation
Forum for presenting research results § EABN meetings § APBio. Net’s International Conference in Bioinformatics (In. Co. B) v. Taipei, Taiwan: Oct. 20 -23, 2008 § Other international conferences in 2008 § RECOMB 2008 at Singapore: Mar/Apr § ISMB 2008 at Toronto, Canada: July § GIW 2008 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, 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 § Ph. D programs
Workshops on Education in Bioinformatics (and Computational Biology) (WEB and now WEBCB) § 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!
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