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Report on APBioNetReport on APBioNet

Fostering the Growth of Bioinformatics and Fostering the Growth of Bioinformatics and Allied Disciplines in the Asia PacificAllied Disciplines in the Asia Pacific

Daniel SzeDaniel SzeImmediate Past ExCo Member and HK Liaison Immediate Past ExCo Member and HK Liaison

RepresentativeRepresentativeAsia Pacific Bioinformatics NetworkAsia Pacific Bioinformatics Network

The AP* Retreat, Hong Kong. Feb 20, 2011

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Global & Regional RecognitionGlobal & Regional Recognition1997 1997 APEC TEL WG survey – great disparity of bioinformaticsAPEC TEL WG survey – great disparity of bioinformatics

competence; poor inter-Asian connectivity.competence; poor inter-Asian connectivity.1998 1998 APBioNet formation in PSB’98 Hawaii; APBioNet formation in PSB’98 Hawaii;

APBioNet as an APAN project APBioNet as an APAN project 2005: 2005: Official Affiliation with ISCB as Regional Affiliate Official Affiliation with ISCB as Regional Affiliate

(International Society for Computational Biology)(International Society for Computational Biology)2008: 2008: Invited Presentation at 20Invited Presentation at 20thth Anniversary of the Anniversary of the

European Molecular Biology Network 2008, Italy.European Molecular Biology Network 2008, Italy.2009: 2009: Invited Presentation at Inaugural Formation of theInvited Presentation at Inaugural Formation of the

IberioAmerican Bioinformatics Society, RIBio, IberioAmerican Bioinformatics Society, RIBio, Mexico.Mexico.2010: 2010: Participation in the successful EuAsiaGrid 1, Participation in the successful EuAsiaGrid 1,

a EC FP7 funded project.a EC FP7 funded project.2010: 2010: Partnership with the International Society Partnership with the International Society

for BioCuration (ISB)for BioCuration (ISB)2011: 2011: Conditional offer to host the ISCB-Asia Conference Conditional offer to host the ISCB-Asia Conference

with our flagship InCoB Conference in KL, Malaysiawith our flagship InCoB Conference in KL, MalaysiaSupport by MOSTI, MalaysiaSupport by MOSTI, Malaysia

2012:2012: InCoB conference scheduled for Thailand; in principleInCoB conference scheduled for Thailand; in principlesupport by NSTDA, Thailand.support by NSTDA, Thailand.

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Regular AGMs at InCoB Regular AGMs at InCoB http://incob.apbionet.orghttp://incob.apbionet.org

International Conference on Bioinformatics InCoBInternational Conference on Bioinformatics InCoB

Annually since 2002: Bangkok, Thailand (200)Annually since 2002: Bangkok, Thailand (200)

2003: Penang, Malaysia (300)2003: Penang, Malaysia (300)

2004: Auckland, New Zealand (200)2004: Auckland, New Zealand (200)

2005: Busan, South Korea (300)2005: Busan, South Korea (300)

2006: New Delhi, India (1,000)2006: New Delhi, India (1,000)

2007: HongKong, China and Hanoi, Vietnam (300)2007: HongKong, China and Hanoi, Vietnam (300)

2008: Taipei, Taiwan (300)2008: Taipei, Taiwan (300)

2009: Singapore (400)2009: Singapore (400)

2010: Tokyo (350) (Waseda ICC)2010: Tokyo (350) (Waseda ICC)

2011: Kuala Lumpur, Malaysia Nov 27 – Dec 32011: Kuala Lumpur, Malaysia Nov 27 – Dec 3

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Top InCoB Papers publishedTop InCoB Papers published

www.bioinformation.netBMC Bioinformatics InCoB Supplement

InCob Publication StatisticsBMC Genomics InCoB SupplementYear   Articles Total accessed Oct 2010 cited 

2010 Vol 11 Supp 4  20 N/A N/A N/A

2009 Vol 10 Supp 3  36 25,683 2,501   45

Immunome Research InCoB SupplementYear   Articles   accessed in total Oct 2010 cited 

2010Vol 6 Supp 1

6 1,175   1,175 N/A

Year    Articles  Total accessed Oct 2010 cited 

2010 Vol 11 Supp 7  16 3,126 3,126 N/A

2009 Vol 10 Supp 15 12 11,630 1,165 19

2008 Vol 9 Supp 12  25 43,607   1,596 121

2007 Vol 9 Supp 1  23 45,109 1,143 133

2006 Vol 7 Supp 5  22 78,761 2,315 270

Number of citations as of Dec 2010.Number of accesses as of Feb 6, 2011.

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Steady Growth of Research Steady Growth of Research output in Asiaoutput 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

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APBioNet-ASEAN-ChinaAPBioNet-ASEAN-China11stst ASEAN China – 2004 Jingchu Luo Beijing ASEAN China – 2004 Jingchu Luo Beijing

22ndnd ASEAN-China – 2008 Singapore ASEAN-China – 2008 Singapore

33rdrd ASEAN-China – 2011 Suzhou (TCM ASEAN-China – 2011 Suzhou (TCM Bioinformatics and Systems Biology Bioinformatics and Systems Biology proposed)proposed)

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Institutional SupportInstitutional Support

ASEANASEANASEAN Dialogue Partners – China, IndiaASEAN Dialogue Partners – China, IndiaKOBICKOBICISCBISCBFAOBMBFAOBMBIUBMBIUBMBUNESCOUNESCOMany universitiesMany universitiesMany nationalMany nationalbioinformatics societiesbioinformatics societies

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Transformation Transformation in past 10 yearsin past 10 years

Build on NetworksBuild on NetworksBuild Database ResourcesBuild Database ResourcesBuild Computational ServicesBuild Computational ServicesDevelop training softwareDevelop training softwareHold training coursesHold training coursesCoordinate and organise conferences, workshops, meetingsCoordinate and organise conferences, workshops, meetingsInject bioinformatics into curriculumInject bioinformatics into curriculumPublication of special journal issues in more than 3 different journalsPublication of special journal issues in more than 3 different journalsPolicy meetings at governmental and intergovernmental levelPolicy meetings at governmental and intergovernmental level

Reported in 2009/2010; all the following in progressReported in 2009/2010; all the following in progressMinimum Information about a Bioinformatics Investigation (MIABI proposed Minimum Information about a Bioinformatics Investigation (MIABI proposed standard)standard)BioDB100 initiative: 100 miabi-compliant integrated databasesBioDB100 initiative: 100 miabi-compliant integrated databasesPartnership with International Society for BiocurationPartnership with International Society for BiocurationAuthorID, DocID data depositionAuthorID, DocID data deposition

The Following CompletedThe Following CompletedEUAsiaGrid 1 ProjectEUAsiaGrid 1 Project

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The areas that were addressed include The areas that were addressed include i.i. Grid-enabling phylogenetic Grid-enabling phylogenetic

inference using BEASTinference using BEAST

ii.ii. Parameter sweep for parameter Parameter sweep for parameter optimization using support vector optimization using support vector machines (libSVM)machines (libSVM)

iii.iii. Ligand-receptor docking and Ligand-receptor docking and molecular dynamics using molecular dynamics using AutoDock and GromacsAutoDock and Gromacs

iv.iv. BLAST/BLAT BLAST/BLAT

v.v. Multiple sequence alignment of Multiple sequence alignment of large datasets using MUSCLElarge datasets using MUSCLE

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Bioinformatics Bioinformatics ApplicationsApplications

(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

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Grid-enabling GromacsGrid-enabling Gromacs

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HIV Phylogenetic HIV Phylogenetic AnalysisAnalysis

Phylogenetic analysis of HIV proteomes

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Large Scale Phylogeography Large Scale Phylogeography of urban spreadof urban spread of dengue and chikungunya of dengue and chikungunya

Chanditha Hapuarachchi

BEAST - Bayesian Evolutionary Analysis Sampling Trees:Cross-platform programfor Bayesian MCMC phylogenetic-geospatial evolutionary analysis of

molecular sequences

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Norovirus Research

Enabling Multiple Sequence Comparison by Log-Expectation (MUSCLE) on the Grid

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Support Vector MachineSupport Vector Machine onon the Grid the Grid

Scaling up SVM parameter optimization of caspase cleavage Scaling up SVM parameter optimization of caspase cleavage

sites prediction of degradomesites prediction of degradome

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Other grid bio-appsOther grid bio-apps

Grid-enabled Ligand Receptor Docking Grid-enabled Ligand Receptor Docking using AutoDock.using AutoDock.

Large scale BLAST Searches for prediction Large scale BLAST Searches for prediction of Type 3 Secretion System Effectors in of Type 3 Secretion System Effectors in Pathogens such as Pathogens such as Burkholderia Burkholderia pseudomalleipseudomallei– http://effectors.bic.nus.edu.sg/T3SEdb/http://effectors.bic.nus.edu.sg/T3SEdb/– WEKAWEKA

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• Grid-enabled bioinformatics applications available:• BEAST, MrBayes, Gromacs, GATE, LibSVM, MUSCLE, ProtDist

• File uploads and downloads

• Customized jobs through JDL files

Genius Web Portalhttps://ui.biruni.upm.my

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Collaboration with APBioNetCollaboration with APBioNet

We need We need 10 Terabytes10 Terabytes of disk space on grid or of disk space on grid or cloud to host MIABi/BioDB100 initiativecloud to host MIABi/BioDB100 initiativeWe need We need full hardware virtualisation platforms full hardware virtualisation platforms for our BioSlaxCloud versionfor our BioSlaxCloud version for instantiation-on- for instantiation-on-demand of bioinformatics databasesdemand of bioinformatics databasesWe need partners who will offer to We need partners who will offer to build interfacesbuild interfaces of bioinformatics grid applications and of bioinformatics grid applications and integrate integrate them in workflowthem in workflow management systems management systems

Please contact tinwee@bic.nus.edu.sg if you are Please contact tinwee@bic.nus.edu.sg if you are interested.interested.

Thank you!Thank you!