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 Visiting 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 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

Inputs From Different Fields: Bioinformatics Biological Scientists Physical Scientists 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 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 (2):

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 , 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 (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

...informatics trends Bioinformatics Computational Biology Medical Informatics LIFE SCIENCE INFORMATICS GenomicsProteomics

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!