Report on APBioNet Asia Pacific Bioinformatics

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Report on APBioNetReport on APBioNetAsia Pacific BioinformaticsAsia Pacific Bioinformatics

Tan Tin WeeTan Tin WeeFounding SecretariatFounding Secretariat

Asia Pacific Bioinformatics NetworkAsia Pacific Bioinformatics Network

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

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APBioNet objectives:APBioNet objectives:Fostering the Growth of Bioinformatics and Allied Fostering the Growth of Bioinformatics and Allied

Disciplines in the Asia PacificDisciplines in the Asia Pacific

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

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APBioNetAPBioNet(Founded 1998)(Founded 1998)

1997 APEC TEL WG survey – great 1997 APEC TEL WG survey – great disparity of bioinformatics competence; disparity of bioinformatics competence; poor inter-Asian connectivity.poor inter-Asian connectivity.1998 APBioNet formation in PSB’98 1998 APBioNet formation in PSB’98 Hawaii; APBioNet as an APAN projectHawaii; APBioNet as an APAN projectFocussing on country training coursesFocussing on country training coursesNetwork, education, training, international Network, education, training, international conferences, software, database services conferences, software, database services and publicationsand publications

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Achieved Global RecognitionAchieved Global Recognition2005: Official Affiliation with ISCB as Regional 2005: Official Affiliation with ISCB as Regional Affiliate (International Society for Computational Affiliate (International Society for Computational Biology)Biology)2008: Invited Presentation at 202008: Invited Presentation at 20 thth Anniversary of Anniversary of the European Molecular Biology Network 2008, the European Molecular Biology Network 2008, Martina Franca, Italy.Martina Franca, Italy.2009: Invited Presentation at the Inaugural 2009: Invited Presentation at the Inaugural Formation of the IberioAmerican Bioinformatics Formation of the IberioAmerican Bioinformatics Society, RIBio, Mexico.Society, RIBio, Mexico.

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Organisational Comparison with Organisational Comparison with other Regionsother Regions

EU/ECEU/EC

- -

EMBOEMBO

A-IMBNA-IMBN

EMBLEMBL

eIMBLeIMBL

EMBnetEMBnet

APBioNetAPBioNet

ECCB conferenceECCB conference

AASBiAASBi

EMBL DataLibraryEMBL DataLibrary

EMBnet NationalNodes in Europe andOther places

EMBnet NationalNodes in Europe andOther places

Asia Bioinformation Institute ?

Asia Bioinformation Institute ?

EBIEBI

National Nodes? A few who are members of EMBnet

National Nodes? A few who are members of EMBnet

ABCABC

APBC andGIW conf

APBC andGIW conf

InCoB confInCoB conf

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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 Sep 26-28 (Waseda ICC)2010: Tokyo Sep 26-28 (Waseda ICC)

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Top InCoB Papers have been Top InCoB Papers have been published since 2006published since 2006

www.bioinformation.net

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

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Steady Growth of Research Steady Growth of Research output in Asiaoutput in Asia

From Elsevier

IN 2010, at InCoB in Tokyo, we will publish top papers in six journals:BMC BioinformaticsBMC GenomicsImmunomics ResearchIPSJ TransactionsCBI ChemBio journal and 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 – 2010 (TCM ASEAN-China – 2010 (TCM Bioinformatics and Systems Biology Bioinformatics and Systems Biology proposed)proposed)

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APBioNet Partners – East Asia APBioNet Partners – East Asia Bioinformation Network EABNBioinformation Network EABNSponsored by Korean Bioinformation NetworkSponsored by Korean Bioinformation Network

11stst EABN – Busan Korea 2005 EABN – Busan Korea 2005

22ndnd EABN – Thailand (NSTDA) 2007 EABN – Thailand (NSTDA) 2007

33rdrd EABN – Singapore (NUS) 2008 EABN – Singapore (NUS) 2008

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APBioNet PartnersAPBioNet Partners

ASEAN-IndiaASEAN-India– 11stst ASEAN-India Bioinformatics Workshop 2005 ASEAN-India Bioinformatics Workshop 2005– 22ndnd ASEAN-India Workshop 2006 ASEAN-India Workshop 2006

Supported by FAOBMB, IUBMB, UNESCO, local Supported by FAOBMB, IUBMB, UNESCO, local inst.inst.– APBioNet Workshop in Bogor, Indonesia 2000APBioNet Workshop in Bogor, Indonesia 2000– APBioNet Workshop in Malaysia 2000APBioNet Workshop in Malaysia 2000– APBioNet Workshop in Brunei, 2004APBioNet Workshop in Brunei, 2004– APBioNet Workhsop in Riyadh, Saudi Arabia 2005APBioNet Workhsop in Riyadh, Saudi Arabia 2005– APBioNet Workshop in Lahore, Pakistan 2006APBioNet Workshop in Lahore, Pakistan 2006– APBioNet Workshop in Hanoi, Vietnam 2007APBioNet Workshop in Hanoi, Vietnam 2007

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Participation in APAN TEIN2/3 Participation in APAN TEIN2/3 and national RENsand national RENs

1997 Singapore Research & Education 1997 Singapore Research & Education Network (SINGAREN)Network (SINGAREN)Today everyToday everycountry has country has NREN of NREN of some kind orsome kind orplans for oneplans for oneBioinformaticsBioinformaticsis a big useris a big user

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BioMirror since 1998BioMirror since 1998

http://www.bio-mirror.nethttp://www.bio-mirror.net//

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

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BioGridBioGrid

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Won Supercomputing SC’2003 Won Supercomputing SC’2003 Most Geographically Distributed Most Geographically Distributed

ProjectProjecthttp://www.psc.edu/publicinfo/sc2003/http://www.psc.edu/publicinfo/sc2003/awards.htmlawards.html

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““BioDataGrid”BioDataGrid”

APBioGridAPBioGridGrid computing installable in Grid computing installable in three stepsthree stepsFunded by International Funded by International Development Research Development Research Centre IDRC PAN-Asia Grant Centre IDRC PAN-Asia Grant 20022002Azereus P2P database Azereus P2P database distribution system – Grant distribution system – Grant funded by IDRC in 2007-2009funded by IDRC in 2007-2009- Thailand, KOBIC, NUS - Thailand, KOBIC, NUS collaboration.collaboration.

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

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BioWorldWideWorkflowGrid mtgBioWorldWideWorkflowGrid mtg

2020

Joint Collaboration with Joint Collaboration with WizFolio.comWizFolio.com

for bibliographic sharing and managementfor bibliographic sharing and management

To manage and share all the scientific papers you have read, and more, Just sign up and login!

2121

Bioinformatics on a Disk Bioinformatics on a Disk APBioKnoppix 1 and 2APBioKnoppix 1 and 2

Tim Littlejohn’s BioLateral disksTim Littlejohn’s BioLateral disks

LiveCD – Knoppix-basedLiveCD – Knoppix-based

Extension of BioKnoppix (Puerto Rico)Extension of BioKnoppix (Puerto Rico)

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BioSLAX virtual desktopsBioSLAX virtual desktopsBioSLax on CDBioSLax on DVDBioSlax on VMwareBioSlax on USB stick(BioSlax on Youtube movie)BioSlax with MokaFive and VMPlayerBioSlax on Citrix Xen Cloud

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Bioinformatics and Bioinformatics and Databases in a Box: BioSLAX Databases in a Box: BioSLAX

ServerServer

- 500 to 1Terabyte HDD Boxes- Plus BioSlax Server LiveCD- Tested in Institute of Biotechnology(IBT) Hanoi, 2007/2008

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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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S* Life Science Informatics AllianceS* Life Science Informatics AllianceA thousand trained onlineA thousand trained online

Online courses from 2001 to 2005Online courses from 2001 to 2005

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

Mirror sites in 10 places Mirror sites in 10 places

Secretariat in National Univ of Singapore.Secretariat in National Univ of Singapore.

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CanalAVIST and AVISTCanalAVIST and AVISTAsean Virtual Institute of Asean Virtual Institute of Science and TechnologyScience and Technology

CanalCanalAVISTAVIST will utilize the  will utilize the Trans Eurasia Information NetTrans Eurasia Information Network (TEIN2)work (TEIN2) to deliver lectures and  to deliver lectures and streaming VDO to members streaming VDO to members of of TEIN2TEIN2, ASEAN, Europe , ASEAN, Europe and Australia with H.263 to and Australia with H.263 to DVTS supported by an E-DVTS supported by an E-learning platform learning platform VCLASSVCLASS (see  (see http://http://www.vclass.netwww.vclass.net) ) by the Internet Education and by the Internet Education and Research Lab, Asian Institute Research Lab, Asian Institute

of Technologyof Technology

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WEBCB at InCoB2008 and 2009WEBCB at InCoB2008 and 2009

Workshop on Education in Bioinformatics Workshop on Education in Bioinformatics and Computational Biology 23and Computational Biology 23rdrd Oct 2008 Oct 2008 Taipei, TaiwanTaipei, Taiwan

http://trg.apbionet.org/webcb/http://trg.apbionet.org/webcb/

Curriculum DevelopmentCurriculum Development

AccreditationAccreditation

Testing – India Bioinformatics certification Testing – India Bioinformatics certification examination systemexamination system

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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, Coordinate and organise conferences, workshops, meetingsmeetingsInject bioinformatics into curriculumInject bioinformatics into curriculumPublication of special journal issues in more than 3 Publication of special journal issues in more than 3 different journalsdifferent journalsPolicy meetings at governmental and intergovernmental Policy meetings at governmental and intergovernmental levellevel

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What next?What next?

Conferences, Workshops, MeetingsConferences, Workshops, Meetings

Training and EducationTraining and Education

EUAsiaGrid (FP7)EUAsiaGrid (FP7)

Cloud Computing SoftwareCloud Computing Software

BioMirror2 database ServicesBioMirror2 database Services

MIABi – Minimum Information about a MIABi – Minimum Information about a Bioinformatics InvestigationBioinformatics Investigation

AuthorID, DocID data depositionAuthorID, DocID data deposition

Asian Bioinformation CentersAsian Bioinformation Centers

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Role of Asian Bioinformation Role of Asian Bioinformation CentersCenters

Repository of public knowledgeRepository of public knowledge– Stimulate private or proprietary knowledgeStimulate private or proprietary knowledge

Promotion of standardisation and Promotion of standardisation and interoperabilityinteroperability– Leverage on virtualisation, grid and cloudLeverage on virtualisation, grid and cloud

Champion of bioinformation in our Champion of bioinformation in our institution, in our city, and in our countryinstitution, in our city, and in our country– Education and awarenessEducation and awareness– Scientific activism with our governmentsScientific activism with our governments

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APBioNet Historical MilestonesAPBioNet Historical Milestones1997: Bioinformatics survey of the region1997: Bioinformatics survey of the region1998: First Meeting at PSB Hawaii1998: First Meeting at PSB Hawaii1998: Endorsement by APEC TEL; APBioNet as first project of APAN1998: Endorsement by APEC TEL; APBioNet as first project of APAN1999: APAN-APBioNet BioMirrors Project1999: APAN-APBioNet BioMirrors Project2000: Involvement in S* Alliance; outreach start to Malaysia, Thailand, Brunei2000: Involvement in S* Alliance; outreach start to Malaysia, Thailand, Brunei2002: InCoB conference series2002: InCoB conference series2003: IDRC Grant for BioGrid software2003: IDRC Grant for BioGrid software2004: APBioKnoppix; later BioSlax (2006)2004: APBioKnoppix; later BioSlax (2006)2004: ASEAN-China Bioinformatics Workshop2004: ASEAN-China Bioinformatics Workshop2005: Affiliation with ISCB; ASEAN-India Cooperation; KOBIC cooperation2005: Affiliation with ISCB; ASEAN-India Cooperation; KOBIC cooperation2006: InCoB Conference publishes in BMC Bioinformatics; outreach to Cambodia; 2006: InCoB Conference publishes in BMC Bioinformatics; outreach to Cambodia; Saudi Arabia; Pakistan; VietnamSaudi Arabia; Pakistan; Vietnam2007: IDRC grant for P2P dissemination of biomirror datasets; CanalAVIST 2007: IDRC grant for P2P dissemination of biomirror datasets; CanalAVIST projectproject2008: 22008: 2ndnd ASEAN-China; 3 ASEAN-China; 3rdrd East Asia Bioinformation Network; 7 East Asia Bioinformation Network; 7thth InCoB; BioSlax InCoB; BioSlax Server version; Dialogue with EMBnet.Server version; Dialogue with EMBnet.2009: Formation of Asian Bioinformation Centers with A-IMBN2009: Formation of Asian Bioinformation Centers with A-IMBN2010: InCoB 2010 conference in Tokyo2010: InCoB 2010 conference in Tokyo