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Supporting
bioinformatics education
in the Asia-Pacific
Shoba Ranganathan
Professor and Chair – Bioinformatics
Dept. of Chemistry and Biomolecular Sciences &
Adjunct Professor
ARC CoE in Bioinformatics
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
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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 (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
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Academia
Research Institutes
Biotechnology
Bioinformatics
Pharmaceutical
Agriculture
Biodiversity
Thank you!