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The AP* Retreat, KLCC, Kuala Lumpur. Feb 28, 2010. Report on APBioNet Asia Pacific Bioinformatics. Tan Tin Wee Founding Secretariat Asia Pacific Bioinformatics Network. APBioNet objectives: Fostering the Growth of Bioinformatics and Allied Disciplines in the Asia Pacific.

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Report on APBioNet Asia Pacific Bioinformatics

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Report on apbionet asia pacific bioinformatics l.jpg

The AP* Retreat, KLCC, Kuala Lumpur. Feb 28, 2010

Report on APBioNetAsia Pacific Bioinformatics

Tan Tin Wee

Founding Secretariat

Asia Pacific Bioinformatics Network

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APBioNet objectives:Fostering the Growth of Bioinformatics and Allied Disciplines in the Asia Pacific

  • Members from Australia, Bangladesh, Brunei Cambodia, China, India, Indonesia, Japan, Korea, Laos, Malaysia, New Zealand, Pakistan, Philippines, Russia, Saudi Arabia, Singapore, Thailand, Vietnam and in North America and Europe.

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APBioNet(Founded 1998)

  • 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

  • Focussing on country training courses

  • Network, education, training, international conferences, software, database services and publications

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Achieved Global Recognition

  • 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, Martina Franca, Italy.

  • 2009: Invited Presentation at the Inaugural Formation of the IberioAmerican Bioinformatics Society, RIBio, Mexico.

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Organisational Comparison with other Regions

EMBL DataLibrary


ECCB conference





EMBnet NationalNodes in Europe and

Other places

InCoB conf

Asia Bioinformation Institute ?






National Nodes? A few who

are members of EMBnet


APBC and

GIW conf

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Regular AGMs at InCoB

  • 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 Sep 26-28 (Waseda ICC)

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Top InCoB Papers have been published since 2006

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Steady Growth of Research output in Asia

From Elsevier

IN 2010, at InCoB in Tokyo, we will publish top papers in six journals:BMC Bioinformatics

BMC Genomics

Immunomics Research

IPSJ Transactions

CBI ChemBio journal and Bioinformation

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  • 1st ASEAN China – 2004 Jingchu Luo Beijing

  • 2nd ASEAN-China – 2008 Singapore

  • 3rd ASEAN-China – 2010 (TCM Bioinformatics and Systems Biology proposed)

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APBioNet Partners – East Asia Bioinformation Network EABN

  • Sponsored by Korean Bioinformation Network

  • 1st EABN – Busan Korea 2005

  • 2nd EABN – Thailand (NSTDA) 2007

  • 3rd EABN – Singapore (NUS) 2008

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APBioNet Partners

  • ASEAN-India

    • 1st ASEAN-India Bioinformatics Workshop 2005

    • 2nd ASEAN-India Workshop 2006

  • Supported by FAOBMB, IUBMB, UNESCO, local inst.

    • APBioNet Workshop in Bogor, Indonesia 2000

    • APBioNet Workshop in Malaysia 2000

    • APBioNet Workshop in Brunei, 2004

    • APBioNet Workhsop in Riyadh, Saudi Arabia 2005

    • APBioNet Workshop in Lahore, Pakistan 2006

    • APBioNet Workshop in Hanoi, Vietnam 2007

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Participation in APAN TEIN2/3 and national RENs

  • 1997 Singapore Research & Education Network (SINGAREN)

  • Today everycountry has NREN of some kind orplans for one

  • Bioinformaticsis a big user

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BioMirror since 1998


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Published paper in top bioinformatics Journal (Gilbert et al, 2004)

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Won Supercomputing SC’2003 Most Geographically Distributed Project


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  • APBioGrid

  • Grid computing installable in three steps

  • Funded by International Development Research Centre IDRC PAN-Asia Grant 2002

  • Azereus P2P database distribution system – Grant funded by IDRC in 2007-2009

  • - Thailand, KOBIC, NUS collaboration.

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Received Grant from IDRC/APNIC Pan Asia Networking Grant and published paper in 2007

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BioWorldWideWorkflowGrid mtg

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Joint Collaboration with WizFolio.comfor bibliographic sharing and management

To manage and share all the scientific papers

you have read, and more, Just sign up and login!

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Bioinformatics on a Disk APBioKnoppix 1 and 2

  • Tim Littlejohn’s BioLateral disks

  • LiveCD – Knoppix-based

  • Extension of BioKnoppix (Puerto Rico)

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BioSLAX virtual desktops

BioSLax on CD

BioSLax on DVD

BioSlax on VMware

BioSlax on USB stick

(BioSlax on Youtube movie)

BioSlax with MokaFive and VMPlayer

BioSlax on Citrix Xen Cloud

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Bioinformatics and Databases in a Box: BioSLAX Server

- 500 to 1Terabyte HDD Boxes

- Plus BioSlax Server LiveCD

- Tested in Institute of Biotechnology

(IBT) Hanoi, 2007/2008

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Institutional Support


  • ASEAN Dialogue Partners – China, India


  • ISCB




  • Many universities

  • Many nationalbioinformatics societies

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S* Life Science Informatics Alliance

  • A thousand trained online

  • Online courses from 2001 to 2005

  • S-star council from Stanford, Sweden (Uppsala/Karolinska), Singapore, Sydney, South Africa, UCSanDiego

  • Mirror sites in 10 places

  • Secretariat in National Univ of Singapore.

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  • Asean Virtual Institute of Science and Technology

  • CanalAVIST will utilize the Trans Eurasia Information Network (TEIN2) to deliver lectures and streaming VDO to members of TEIN2, ASEAN, Europe and Australia with H.263 to DVTS supported by an E-learning platform VCLASS (see by the Internet Education and Research Lab, Asian Institute of Technology

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WEBCB at InCoB2008 and 2009

  • Workshop on Education in Bioinformatics and Computational Biology 23rd Oct 2008 Taipei, Taiwan


  • Curriculum Development

  • Accreditation

  • Testing – India Bioinformatics certification examination system

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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

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What next?

  • Conferences, Workshops, Meetings

  • Training and Education

  • EUAsiaGrid (FP7)

  • Cloud Computing Software

  • BioMirror2 database Services

  • MIABi – Minimum Information about a Bioinformatics Investigation

  • AuthorID, DocID data deposition

  • Asian Bioinformation Centers

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Role of Asian Bioinformation Centers

  • Repository of public knowledge

    • Stimulate private or proprietary knowledge

  • Promotion of standardisation and interoperability

    • Leverage on virtualisation, grid and cloud

  • Champion of bioinformation in our institution, in our city, and in our country

    • Education and awareness

    • Scientific activism with our governments

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APBioNet Historical Milestones

  • 1997: Bioinformatics survey of the region

  • 1998: First Meeting at PSB Hawaii

  • 1998: Endorsement by APEC TEL; APBioNet as first project of APAN

  • 1999: APAN-APBioNet BioMirrors Project

  • 2000: Involvement in S* Alliance; outreach start to Malaysia, Thailand, Brunei

  • 2002: InCoB conference series

  • 2003: IDRC Grant for BioGrid software

  • 2004: APBioKnoppix; later BioSlax (2006)

  • 2004: ASEAN-China Bioinformatics Workshop

  • 2005: Affiliation with ISCB; ASEAN-India Cooperation; KOBIC cooperation

  • 2006: InCoB Conference publishes in BMC Bioinformatics; outreach to Cambodia; Saudi Arabia; Pakistan; Vietnam

  • 2007: IDRC grant for P2P dissemination of biomirror datasets; CanalAVIST project

  • 2008: 2nd ASEAN-China; 3rd East Asia Bioinformation Network; 7th InCoB; BioSlax Server version; Dialogue with EMBnet.

  • 2009: Formation of Asian Bioinformation Centers with A-IMBN

  • 2010: InCoB 2010 conference in Tokyo

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