supporting a thriving bioinformatics culture in east asia
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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 - PowerPoint PPT PresentationTRANSCRIPT
Supporting a thriving bioinformatics culture
in East AsiaShoba Ranganathan
Professor and Chair – Bioinformatics Dept. of Chemistry and Biomolecular Sciences &Adjunct Professor Biotechnology Research Institute Dept. of BiochemistryMacquarie University Yong Loo Lin School of MedicineSydney, 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
with input from disciplines/technologies
Networks, pathways
and systems
Sequences Genomes Transcriptomes
Databases, ontologies Data & text
miningEvolution andphylogeneticsMaths/StatsAlgorithms Physics/
Chemistry
Genetics and populations
Structures
Inputs From Different Fields:
Bioinformatics
Biological Scientists
Physical Scientists
ComputerScientists
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 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 inBiotechnologyMedicineAgricultureVeterinary scienceBiodiversity 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 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
Genomics Proteomics
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!