Supporting bioinformatics education

in the Asia-PacificShoba Ranganathan

Professor and Chair – Bioinformatics Dept. of Chemistry and Biomolecular Sciences &Adjunct Professor ARC CoE in Bioinformatics Dept. of BiochemistryMacquarie University Yong Loo Lin School of MedicineSydney, Australia National University of Singapore, Singapore(shoba.ranganathan@mq.edu.au) (shoba@bic.nus.edu.sg)

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 (and ComputationalBiology) (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

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 ProfilingAlternate splice variants

Orphan genesCryptic introns

Gene Therapy

Careers in Bioinformatics

Structural Genomics:

Experimental Protein structuresApo stateHolo stateStructural modifications

Membrane Proteins Homology Modelling Comparative Modelling

Careers in Bioinformatics

Drug and Vaccine Design:

Screening Natural ProductsPlantsFungiBacteria

Chemicals In silico modifications of ligands Vaccine design and delivery

Job Sectors Academia Research Institutes Biotechnology Bioinformatics Pharmaceutical Agriculture Biodiversity

Thank you!