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Bioinformatics Growth in the Asian Region 20 years of Development

Bioinformatics Growth in the Asian Region 20 years of Development. Tan Tin Wee Founding Secretariat Asia Pacific Bioinformatics Network 29 th August 2009 HKU-Pasteur Research Centre - EMBO Bioinformatics and Comparative Genomics Course.

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Bioinformatics Growth in the Asian Region 20 years of Development

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  1. Bioinformatics Growth in the Asian Region20 years of Development Tan Tin Wee Founding Secretariat Asia Pacific Bioinformatics Network 29th August 2009 HKU-Pasteur Research Centre - EMBO Bioinformatics and Comparative Genomics Course

  2. 20 years: European Success StoryEMBO, EMBL, EMBnet, EBI • European Union • European Commission • European Molecular Biology Organisation • European Molecular Biology Laboratories • European Molecular Biology Network • European Bioinformatics Institute

  3. EU/EC funding More than 20 years EMBO – solid history EMBnet – 20yr network of national nodes in over 20 countries. Well interconnected by GEANT2 Long time of high volume data generation and bioinformation creation Know how to share and cooperate No such Asia governmental body; may be APEC or ASEAN GIW nearly 20yrs; A-IMBN 12 yrs; APBioNet 11yrs A-IMBN – recent start 1997 APBioNet – bioinformatics node formation still in progress. Not well connected network. Only national links; last mile problems. Recent growth in data volume and bioinformation creation is still new. Asia still trying to learn how to catch up Europe-Asia ComparisonFunds+Time+Cooperation+Culture

  4. Organisational Comparison 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 National Nodes? Not ready AASBi ABC? APBC and GIW conf

  5. Parallel Growth of Biology and Internet/IT in 20years Mosaic Web browser Web 2.0 World WideWeb started Grid Computing IT Cloud Computing Internet widespread Internet2 ??? Synergy 2020 2000 2010 1990 Genome Project BIO Human Genome completed New Gen Seq Bacterial Genomes Start emerging Human Genome completed

  6. Bioinformatics in Singapore 90’s • 1991 – Biocomputing Interest Group • 1992 – Bioinformatics User Support – first Gopher, WAIS server in Asia; hypertext web interface to bioinformatics software • 1993 – First biological World Wide Web site biomed.nus.sg • 1995 – Planning the formation of the Bioinformatics Centre (BIC) National Univ of Singapore • 1996 – BioKleisli, BioPortal, integration projects • 1997 – Bioinformatics Resource • 1998 – BioMirror1 Project; APBioNet Formed • 1999 – Remote solving of Xray structure of Bucandin

  7. Bioinformatics outreach for Asia in the ‘90s • Limited awareness • Limited recognition • Limited resources • Limited manpower • Mainly in Japan – GIW genome informatics workshop; DDBJ • Sporadic efforts to introduce bioinformatics • Late 90s – emergence of bioinformatics groups in Korea, Malaysia, China, Taiwan • Efforts by WHO (recently TDRs); ICGEBnet formation (Trieste, Delhi); Pasteur’s efforts

  8. Formation of APBioNetHelp ourselves • 1997 APEC TEL WG survey – great disparity of bioinformatics competence; poor inter-Asian connectivity. • 1997 EMBnet nodes in Asia – 2. • 1998 APBioNet formation in PSB’98 Hawaii • 1998 till today – network, education, training, conferences, software, services … awareness low, organisation weak…

  9. 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.

  10. Meetings Members attend InCoB http://incob.apbionet.org • International Conference on Bioinformatics • 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 • 2009: Singapore

  11. Meetings APBioNet-ASEAN-China • 1st ASEAN China – 2004 Jingchu Luo Beijing • 2nd ASEAN-China – 2008 Singapore • 3rd ASEAN-China – 2009 Shanghai (TCM Bioinformatics and Systems Biology)

  12. 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

  13. 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

  14. Outputs Top InCoB Papers have been published since 2006 http://www.biomedcentral.com/bmcbioinformatics/ www.bioinformation.net

  15. Steady Growth of Research output in Asia From Elsevier

  16. Citations

  17. Transformation in 2000s • Build Network • Build Database Resources • Build Computational Services • Develop training software • Hold training courses • Coordinate and organise conferences, workshops, meetings • Inject bioinformatics into curriculum • Policy meetings at governmental and intergovernmental level

  18. Network APAN and national RENs • 1997 Singapore Research & Education Network (SINGAREN) • Today everycountry has NREN of some kind orplans for one

  19. Network TEIN 2 and TEIN 3 • 10M euros • TransEurasian Information Network

  20. Databases BioMirror since 1998 • http://www.bio-mirror.net/

  21. Databases More Asian Databases emerging • Original successful ones: DDBJ, KEGG, wwPDB (PDBj) • Many more emerging but they are not sustainable e.g. ANTIMIC, SPDmod, EXINT, Xdom, etc. • Growth in CJK - China Japan, Korea, Taiwan.

  22. Compute BioGrid

  23. Compute BioGrid • 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.

  24. Compute APBioGrid Computing

  25. Research BioWorldWideWorkFlow

  26. Research BioWorldWideWorkFlow

  27. BioWorldWideWorkflowGrid mtg

  28. Coming Soon Introducing WizFolio.comfor bibliographic sharing and management To manage and share all the scientific papers you have read, and more, Just sign up and login!

  29. Import From Clipboard Direct PDF Upload Colleagues Online Search Highly optimized to PubMed Manual Entry Get Match Import from RIS WizAdd Direct Export from Webpages WizFolio Web 2.0 Organize Folder, Flags, Tags, Filters WizCite Seamless citation generation with live preview Sharing of References Locate Full-Text Articles (PDF) Word 2003 Word 2007

  30. Compute Bioinformatics on a Disk APBioKnoppix 1 and 2 • Tim Littlejohn’s BioLateral disks • LiveCD – Knoppix-based • Extension of BioKnoppix (Puerto Rico)

  31. Compute 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

  32. Compute 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

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

  34. 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.

  35. Education LAMS Learning Activity Management System

  36. Education CENTRA for online PBL

  37. 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

  38. 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

  39. APBioNet Historical Milestones • 1997: Bioinformatics survey of the region • 1998: First Meeting at PSB Hawaii • 1998: Endorsement by APEC TEL • 1998: 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.

  40. What next? • Conferences, Workshops, Meetings • Training and Education • Network Infrastructure • Software • Mirror Services • … • Future?

  41. Challenges ahead • Lack of curriculum transformation some Tier 1 universities and none in Tier 2 and lower. • Lack of bioinformatics-enabled professors • Lack of institutional resources (network, expertise) • Lack of professional career framework • Lack of recognition and organisational support • Lack of recurrent or established financial support • Lack of bandwidth of older people, and lack of young people and volunteers • Stimulate high impact research • Stimulate high impact resources and databases • Stimulate high impact software and services • Stimulate high quality education and graduates

  42. What can we do strategically? • Be more actively involved in ISCB • Seek membership for our members in EMBnet or its enlarged entity E”xtended”MBnet • Facilitation of Research Grant funding • Support the ABC initiative • Support our colleagues in AASBi, APBC, GIW etc.

  43. Today’s Challenges for Asia andPersonal Genomics • BioInformation have and have-nots – big disparity in capacities in different institutions and cities of Asia • Lack of interoperability and standardisation • Lack of Asia repositories – over reliance on Western sources • Low to high level of knowledge in Asian life scientists – big disparity

  44. Personal Genomics • In 10 to 20 years, it will be common in the West. • Asia will lag by at least 10 years • What will improve it? • Education • Positive Publicity • Information infrastructure • Standards and best practice

  45. 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

  46. New initiatives • Minimum Bioinformatics Skillsets for Life science undergraduates/graduates • Minimum Information about a Bioinformatics Investigation MIABi • AuthorID disambiguation • Deposition of datasets • What new areas of Research can we compete in?

  47. Origin of Species 200th Anniversary of Darwin’s birth 150th Anniversary of the “Origin of Species” Alfred Russel Wallace Malay Archipelago

  48. Origin of Life

  49. From Religion: Logos • Old Testament of the Holy Bible: • Genesis 1:1 In the beginning God created the heavens and the earth. • New Testament of the Holy Bible: • John 1: 1 In the beginning was the Word, and the Word was with God, and the Word was God. • Logos (Greek, "word,""reason,""ratio"), in ancient and especially in medieval philosophy and theology, the divine reason that acts as the ordering principle of the universe.

  50. Tao (道, pinyin: dào (help·info) ) is a concept found in Taoism, Confucianism, and more generally in ancient Chinese philosophy. While the character itself translates as 'way', 'path', or 'route', or sometimes more loosely as 'doctrine' or 'principle', it is used philosophically to signify the fundamental or true nature of the world. The concept of Tao differs from Western ontology, however; it is an active and holistic conception of the world, rather than a static, atomistic one.

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