Report on apbionet asia pacific bioinformatics
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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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The AP* Retreat, KLCC, Kuala Lumpur. Feb 28, 2010

Report on APBioNetAsia 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

  • 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.


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


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.


Organisational Comparison with other Regions

EMBL DataLibrary

EBI

ECCB conference

EU/EC

EMBO

EMBL

EMBnet

EMBnet NationalNodes in Europe and

Other places

InCoB conf

Asia Bioinformation Institute ?

-

A-IMBN

eIMBL

APBioNet

ABC

National Nodes? A few who

are members of EMBnet

AASBi

APBC and

GIW conf


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 Sep 26-28 (Waseda ICC)


Outputs

Top InCoB Papers have been published since 2006

http://www.biomedcentral.com/bmcbioinformatics/

www.bioinformation.net


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


Meetings

APBioNet-ASEAN-China

  • 1st ASEAN China – 2004 Jingchu Luo Beijing

  • 2nd ASEAN-China – 2008 Singapore

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


Meetings

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


Training

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


Network

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


Databases

BioMirror since 1998

  • http://www.bio-mirror.net/


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


Compute

BioGrid


Won Supercomputing SC’2003 Most Geographically Distributed Project

  • http://www.psc.edu/publicinfo/sc2003/awards.html


Compute

“BioDataGrid”

  • 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.


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


BioWorldWideWorkflowGrid mtg


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!


Bioinformatics on a Disk APBioKnoppix 1 and 2

  • Tim Littlejohn’s BioLateral disks

  • LiveCD – Knoppix-based

  • Extension of BioKnoppix (Puerto Rico)


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


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


Institutional Support

  • ASEAN

  • ASEAN Dialogue Partners – China, India

  • KOBIC

  • ISCB

  • FAOBMB

  • IUBMB

  • UNESCO

  • Many universities

  • Many nationalbioinformatics societies


Education

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.


Education

CanalAVIST and AVIST

  • 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 http://www.vclass.net) by the Internet Education and Research Lab, Asian Institute of Technology


Education

WEBCB at InCoB2008 and 2009

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

  • http://trg.apbionet.org/webcb/

  • Curriculum Development

  • Accreditation

  • Testing – India Bioinformatics certification examination system


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


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


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


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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