1 / 19

Daniel Sze Immediate Past ExCo Member and HK Liaison Representative

The AP* Retreat, Hong Kong. Feb 20, 2011. Report on APBioNet Fostering the Growth of Bioinformatics and Allied Disciplines in the Asia Pacific. Daniel Sze Immediate Past ExCo Member and HK Liaison Representative Asia Pacific Bioinformatics Network. Global & Regional Recognition.

hogan
Download Presentation

Daniel Sze Immediate Past ExCo Member and HK Liaison Representative

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. The AP* Retreat, Hong Kong. Feb 20, 2011 Report on APBioNetFostering the Growth of Bioinformatics and Allied Disciplines in the Asia Pacific Daniel Sze Immediate Past ExCo Member and HK Liaison Representative Asia Pacific Bioinformatics Network

  2. Global & Regional Recognition • 1997 APEC TEL WG survey – great disparity of bioinformatics competence; poor inter-Asian connectivity. • 1998 APBioNet formation in PSB’98 Hawaii; APBioNet as an APAN project • 2005: Official Affiliation with ISCB as Regional Affiliate (International Society for Computational Biology) • 2008: Invited Presentation at 20th Anniversary of the European Molecular Biology Network 2008, Italy. • 2009: Invited Presentation at Inaugural Formation of the IberioAmerican Bioinformatics Society, RIBio, Mexico. • 2010: Participation in the successful EuAsiaGrid 1, a EC FP7 funded project. • 2010: Partnership with the International Society for BioCuration (ISB) • 2011: Conditional offer to host the ISCB-Asia Conference with our flagship InCoB Conference in KL, Malaysia Support by MOSTI, Malaysia • 2012: InCoB conference scheduled for Thailand; in principle support by NSTDA, Thailand.

  3. Meetings Regular AGMs at InCoB http://incob.apbionet.org International Conference on Bioinformatics InCoB • Annually since 2002: Bangkok, Thailand (200) • 2003: Penang, Malaysia (300) • 2004: Auckland, New Zealand (200) • 2005: Busan, South Korea (300) • 2006: New Delhi, India (1,000) • 2007: HongKong, China and Hanoi, Vietnam (300) • 2008: Taipei, Taiwan (300) • 2009: Singapore (400) • 2010: Tokyo (350) (Waseda ICC) • 2011: Kuala Lumpur, Malaysia Nov 27 – Dec 3

  4. Outputs Top InCoB Papers published InCob Publication Statistics BMC Genomics InCoB Supplement Immunome Research InCoB Supplement BMC Bioinformatics InCoB Supplement www.bioinformation.net Number of citations as of Dec 2010.Number of accesses as of Feb 6, 2011.

  5. Steady Growth of Research output in Asia From Elsevier • IN 2011, at InCoB in Malaysia, we will publish top papers in • BMC Bioinformatics • BMC Genomics • Immunomics Research • Journal of Integrative Computational Biosciences (JICB) • Bioinformation

  6. Meetings APBioNet-ASEAN-China • 1st ASEAN China – 2004 Jingchu Luo Beijing • 2nd ASEAN-China – 2008 Singapore • 3rd ASEAN-China – 2011 Suzhou (TCM Bioinformatics and Systems Biology proposed)

  7. Institutional Support • ASEAN • ASEAN Dialogue Partners – China, India • KOBIC • ISCB • FAOBMB • IUBMB • UNESCO • Many universities • Many nationalbioinformatics societies

  8. Transformation in past 10 years • Build on Networks • Build Database Resources • Build Computational Services • Develop training software • Hold training courses • Coordinate and organise conferences, workshops, meetings • Inject bioinformatics into curriculum • Publication of special journal issues in more than 3 different journals • Policy meetings at governmental and intergovernmental level Reported in 2009/2010; all the following in progress • Minimum Information about a Bioinformatics Investigation (MIABI proposed standard) • BioDB100 initiative: 100 miabi-compliant integrated databases • Partnership with International Society for Biocuration • AuthorID, DocID data deposition The Following Completed • EUAsiaGrid 1 Project

  9. The areas that were addressed include • Grid-enabling phylogenetic inference using BEAST • Parameter sweep for parameter optimization using support vector machines (libSVM) • Ligand-receptor docking and molecular dynamics using AutoDock and Gromacs • BLAST/BLAT • Multiple sequence alignment of large datasets using MUSCLE

  10. Bioinformatics Applications (GROningen MAchine for Chemical Simulations) Molecular Dynamics for in silico pharmacological screening of microsomal P450 binding with small molecules such as curcumin from the turmeric plant: Modelling the binding of curcumin to P450

  11. Grid-enabling Gromacs

  12. HIV Phylogenetic Analysis Phylogenetic analysis of HIV proteomes

  13. Large Scale Phylogeography of urban spread of dengue and chikungunya BEAST - Bayesian Evolutionary Analysis Sampling Trees: Cross-platform program for Bayesian MCMC phylogenetic- geospatial evolutionary analysis of molecular sequences Chanditha Hapuarachchi

  14. Enabling Multiple Sequence Comparison by Log-Expectation (MUSCLE) on the Grid Norovirus Research

  15. Support Vector Machineon the Grid Scaling up SVM parameter optimization of caspase cleavage sites prediction of degradome

  16. Other grid bio-apps Grid-enabled Ligand Receptor Docking using AutoDock. Large scale BLAST Searches for prediction of Type 3 Secretion System Effectors in Pathogens such as Burkholderia pseudomallei http://effectors.bic.nus.edu.sg/T3SEdb/ WEKA

  17. Genius Web Portal https://ui.biruni.upm.my • Grid-enabled bioinformatics applications available: • BEAST, MrBayes, Gromacs, GATE, LibSVM, MUSCLE, ProtDist • File uploads and downloads • Customized jobs through JDL files

  18. Collaboration with APBioNet • We need 10 Terabytes of disk space on grid or cloud to host MIABi/BioDB100 initiative • We need full hardware virtualisation platforms for our BioSlaxCloud version for instantiation-on-demand of bioinformatics databases • We need partners who will offer to build interfaces of bioinformatics grid applications and integrate them in workflow management systems Please contact tinwee@bic.nus.edu.sg if you are interested. Thank you!

More Related