10.1371/journal.pcbi.1003317PLoS Computational Biology910

Khan, A.M.

Ranganathan, S.

Schönbach, C.

Tan, T.W.

PLoS Computational Biology

PubMed

Khan, Asif M

Tan, Tin Wee

Schoenbach, Christian

Ranganathan, Shoba

Macquarie University ResearchOnline

APBioNet-transforming bioinformatics in the Asia-Pacific region

ScholarBank@NUS

Message from ISCBAPBioNet—Transforming Bioinformatics in theAsia-Pacific RegionAsif M. Khan1,2", Tin Wee Tan3"*, Christian Scho¨nbach4,5, Shoba Ranganathan6,3*1 Perdana University Graduate School of Medicine, Selangor Darul Ehsan, Malaysia, 2Department of Pharmacology and Molecular Sciences, The Johns Hopkins UniversitySchool of Medicine, Baltimore, Maryland, United States of America, 3Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore,Singapore, 4 School of Science and Technology, Department of Biology and Chemistry, Nazarbayev University, Astana, Republic of Kazakhstan, 5Department ofBioscience and Bioinformatics and Biomedical Informatics R&D Center (BMIRC), Kyushu Institute of Technology, Fukuoka, Japan, 6Department of Chemistry andBiomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, AustraliaIntroductionThe Asia-Pacific Bioinformatics Network(APBioNet; www.apbionet.org) is a nonprof-it, nongovernmental, international organi-zation founded in 1998 that focuses on thepromotion of bioinformatics in the Asia-Pacific region. APBioNet’s mission, since itsinception, has been to pioneer the growthand development of bioinformatics aware-ness, training, education, infrastructure,resources, and research among membercountries and economies. Its work includestechnical coordination, liaison, and/or affil-iation with other international scientificbodies, such as the European MolecularBiology network (EMBnet) and the Interna-tional Society for Computational Biology(ISCB). APBioNet has more than 20organizational and 2,000 individual mem-bers from over 12 countries in the region,from industry, academia, research, govern-ment, investors, and international organiza-tions. APBioNet is spearheading a numberof key bioinformatics initiatives in collabo-ration with international organizations, suchas the Asia-Pacific Advanced Network(APAN), the Association of South-East AsianNations (ASEAN), the Asia-Pacific Econom-ic Cooperation (APEC), and the Asia-PacificInternational Molecular Biology Network(A-IMBN), and industry partners. Many ofthe initiatives and activities have beeninitiated through its flagship conference,the International Conference on Bioinfor-matics (InCoB). In 2012, APBioNet wasincorporated in Singapore as a publiclimited liability company to ensure quality,sustainability, and continuity of its mission toadvance bioinformatics across the regionand beyond. We describe below the keythrust areas of APBioNet.InCoB—Connecting theBioinformatics Community inthe RegionInCoB is a conference series that startedin Bangkok, Thailand in 2002. Since then,APBioNet has adopted InCoB as its annualsignature event (2003: Penang, 2004: Auck-land, 2005: Busan, 2006: New Delhi, 2007:HongKong/Hanoi, 2008: Taipei, 2009:Singapore, 2010: Tokyo, 2011: KualaLumpur, and 2012: Bangkok) and grownit to become one of Asia’s largest bioinfor-matics conferences, targeting practitionersfrom both biology and computing back-grounds (http://bit.ly/10P6CVq). In 2011,InCoB celebrated its tenth anniversary inKuala Lumpur, Malaysia jointly with the 1stISCB-Asia [1] and featured several keyinitiatives, including the launch of theBioDB100 initiative, aimed at gathering100 bioinformatics databases that are Min-imum Information About a Bioinformaticsinvestigation (MIABi)-standards compliantunder one interoperable framework (http://incob.apbionet.org/incob11). InCoB2012(http://incob.apbionet.org/incob12)markedthe homecoming of the conference to itsorigin, Bangkok, as a reputable and majorannual bioinformatics event in the Asia-Pacific region. The 2013 conference washeld recently for the first time in China(http://incob.apbionet.org/incob13), withthe 2014 conference to be held immediatelyprior to and sharing keynote speakers withthe International Union for Pure andApplied Biophysics [IUPAB] 2014 Congress(http://incob.apbionet.org/incob14; July31 to August 2, 2014), in Sydney, Australia.Advancing Standards forBioinformatics ActivitiesIn a multi-stakeholder effort to advancestandards for bioinformatics activities, AP-BioNet has been working since InCoB2009on building 100 exemplar biological andbioinformatics databases (BioDB100) andsoftware tools (BioSW100) [2] that test thefollowing aspects of standardization: i. dataand software persistence and the basis forperpetuity (http://docid.apbionet.org); ii.reinstantiability and reproducibility (http://biodb100.apbionet.org); iii. author and con-tributor identity disambiguation (http://aid.apbionet.org); and iv. Minimum Informa-tion About a Bioinformatics investigation(MIABi) to include basic information neces-sary for an in silico experiment to berepeatable and the results reproducible, aswell as harmonized with community initia-tives in MIBBI [3] and those of theInternational Society for Biocuration (ISB;http://biocurator.org), specifically BioDB-core (http://biocurator.org/biodbcore.shtml). We anticipate that the ongoingtesting efforts [4–7] will help to delineatethe process for standardization and enhancethe implementation of increasingly stan-dardized vocabularies, ontologies, and infra-structural and informational interoperabilityfor the maintenance and sustainability ofCitation: Khan AM, Tan TW, Scho¨nbach C, Ranganathan S (2013) APBioNet—Transforming Bioinformatics inthe Asia-Pacific Region. PLoS Comput Biol 9(10): e1003317. doi:10.1371/journal.pcbi.1003317Published October 31, 2013Copyright:  2013 Khan et al. This is an open-access article distributed under the terms of the CreativeCommons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium,provided the original author and source are credited.Funding: The authors received no specific funding for this article.Competing Interests: AMK and TWT are Nominee Directors of Asia Pacific Bioinformatics Network, Ltd.; SR,CS, and AMK are President, Vice President (Conferences), and Treasurer of APBioNet, respectively. TWT is aboard director of ISCB and former president and current advisor of AMBIS.* E-mail: tinwee@bic.nus.edu.sg (TWT); shoba.ranganathan@mq.edu.au (SR)" AMK and TWT are joint first authors of this work.PLOS Computational Biology | www.ploscompbiol.org 1 October 2013 | Volume 9 | Issue 10 | e1003317knowledge resources of ever-increasing so-phistication.Bioinformatics Education andTrainingAPBioNet has been actively engaged inbridging the bioinformatics capability gap,with emphasis on establishing sustainablebioinformatics education and training [8].APBioNet was represented at the 2001Workshop on Education in Bioinformatics(WEB), a satellite meeting of the Interna-tional Conference on Intelligent Systemsfor Molecular Biology (ISMB) that pro-vided, for the first time, a platform forbioinformatics educators to discuss funda-mental educational and pedagogical issuesfor bioinformatics degree and trainingprograms. APBioNet played a key role inthe third East Asia Bioinformation Net-work meeting (http://eabn.apbionet.org)held in Singapore (2008) that witnessedthe proposal for minimum skills requiredof biologists in bioinformatics and biocom-putation (msrBIC) [8]. APBioNet cooper-ates with organizations, such as the S* LifeScience Informatics Alliance (www.apbionet.org/s-star) [9] and the ASEANVirtual Institute of Science and Technol-ogy (AVIST) (www.avist.org), to facilitateonline/distance bioinformatics educationand training. As a result of a researchgrant from the International Developmentand Research Centre (IDRC) of Canadaand subsequent R&D at the NationalUniversity of Singapore (NUS), APBioNetproduced a bioinformatics grid-enabledsoftware, as well as a distributable LiveOScontaining bioinformatics software to fa-cilitate bioinformatics training (http://en.wikipedia.org/wiki/BioSLAX). As part ofits outreach, since 2003 APBioNet haspartnered with various organizations torun bioinformatics workshops in the re-gion (http://bit.ly/12eWyDe). In June2012, APBioNet participated the inaugu-ral Bioinformatics, Biotechnology, Bio-curation and Computational Biology net-works and societies (B3CB) meeting inSweden that led to the establishment of theGlobal Organization for BioinformaticsLearning, Education and Training (GOB-LET; http://mygoblet.org) to coordinatebioinformatics training activities world-wide. All these efforts have contributedto the generation of skilled bioinformati-cians in the region.Database/ComputationalServices and ResourcesOne of the earliest projects that APBioNetset up was a collaboration to build abioinformatics network riding on the ad-vanced network infrastructure of the Asia-Pacific Advanced Network (APAN) (www.apbionet.org/APAN/apan-apbionetMar98.html). This led to the formation of theBioMirrors project (www.bio-mirror.net)[10] and a peer-to-peer (P2P) databasereplication system for low-bandwidth insti-tutions [11]. In response to an increasingdemand for high-performance and high-throughput computational biology, in 2001APBioNet partnered with the NUS Bioin-formatics Centre to promote the concept ofgrid computing in life sciences at theBioGrid’01 symposium (www.bic.nus.edu.sg/biogrid/biogrid01). More recently, AP-BioNet has been actively engaged intracking the progress of advanced network-ing, such as the TransEurasia InformationNetwork (TEIN2), developing cutting-edgeinitiatives, such as the International Work-shop on World Wide Workflow Grid(GridAsia 2007; www.euasiagrid.org), andexploring applications of grid and cloudcomputing for life scientists (EUAsiaGridBioWorkshop 2010; http://trg.apbionet.org/euasiagrid). APBioNet is committedto continuing these efforts to meet thechallenges of big data science in the decadeahead [5].Policy and AwarenessConstructive scientific activism raisesawareness among policy makers for theneed to catalyze the transformation of lifescience research and education in theAsia-Pacific. APBioNet has worked closelywith the ASEAN Committee on Scienceand Technology (COST) to assist indeveloping bioinformatics masterplansand roadmaps for the ten ASEAN mem-ber countries. Through the ASEAN Dia-logue Partner mechanism, APBioNet isalso actively engaging China, India, Japan,and Korea. Beyond these, APBioNet hasalso provided assistance to institutions inPakistan and Saudi Arabia. As a result ofthese extensive, collective, and cooperativeefforts to influence policy and raiseawareness among policy makers andscientific leaders, Asian countries such asSingapore [12], Malaysia [13], Thailand[14], India (http://dbtindia.nic.in/annual05-06/Ch-8-eng.pdf), the Philip-pines, Korea, Pakistan, Indonesia, Brunei,and many others [15] have had stronggrowth of bioinformatics and its allieddisciplines over the last decade [16,17].ConclusionsAPBioNet has come a long way sinceits inception in 1998 at the PacificSymposium for Bioinformatics, Hawaii.Currently, it is the largest regionalbioinformatics organization in the Asia-Pacific, and one of the oldest. It continuesto expand its presence in the region byactively reaching out to the research andeducation community, through its flag-ship conference InCoB. APBioNet is alsotaking steps toward setting standards andinfluencing scientific policy to enable anew generation of scientists to embracethe new biology of today that is increas-ingly information- and technology-driven,with knowledge generation dependent onapplications of physical and computersciences.AcknowledgmentsThe authors thank Ms. Hadia Syahirah ofPerdana University for help with preparation ofthe manuscript.References1. Scho¨nbach C, Tan TW, Kelso J, Rost B, NathanS, et al. (2011) InCoB celebrates its tenthanniversary as first joint conference with ISCB-Asia. BMC Genomics 12 Suppl 3: S1.2. Tan TW, Tong JC, Khan AM, de Silva M, LimKS, et al. (2010) Advancing standards forbioinformatics activities: persistence, reproduc-ibility, disambiguation and Minimum Informa-tion About a Bioinformatics investigation(MIABi). BMC Genomics 11 Suppl 4: S27.3. Taylor CF, Field D, Sansone SA, Aerts J,Apweiler R, et al. (2008) Promoting coherentminimum reporting guidelines for biological andbiomedical investigations: the MIBBI project. NatBiotechnol 26: 889–896.4. Ranganathan S, Eisenhaber F, Tong JC, TanTW (2009) Extending Asia Pacific bioinformaticsinto new realms in the ‘‘-omics’’ era. BMCGenomics 10 Suppl 3: S1.5. Ranganathan S, Scho¨nbach C, Kelso J, RostB, Nathan S, et al. (2011) Towards big datascience in the decade ahead from ten yearsof InCoB and the 1st ISCB-Asia Joint Con-ference. BMC Bioinformatics 12 Suppl 13:S1.6. Ranganathan S, Scho¨nbach C, Nakai K, TanTW (2010) Challenges of the next decade for theAsia Pacific region: 2010 International Confer-ence in Bioinformatics (InCoB 2010). BMCGenomics 11 Suppl 4: S1.7. Scho¨nbach C, Tongsima S, Chan J, Brusic V, TanTW, et al. (2012) InCoB2012 Conference: frombiological data to knowledge to technological break-throughs. BMC Bioinformatics 13 Suppl 17: S1.8. Tan TW, Lim SJ, Khan AM, Ranganathan S(2009) A proposed minimum skill set for univer-sity graduates to meet the informatics needs andchallenges of the ‘‘-omics’’ era. BMC Genomics10 Suppl 3: S36.9. Lim YP, Ho¨o¨g JO, Gardner PS, Ranganathan S,Andersson S, et al. (2003) The S-Star trialbioinformatics course: an on-line learning success.Biochem Mol Biol Edu 31: 20–23.10. Gilbert D, Ugawa Y, Buchhorn M, Wee TT,Mizushima A, et al. (2004) Bio-Mirror project forPLOS Computational Biology | www.ploscompbiol.org 2 October 2013 | Volume 9 | Issue 10 | e1003317public bio-data distribution. Bioinformatics 20:3238–3240.11. Sangket U, Phongdara A, ChotigeatW, Nathan D,Kim WY, et al. (2008) Automatic synchronizationand distribution of biological databases andsoftware over low-bandwidth networks amongdeveloping countries. Bioinformatics 24: 299–301.12. Eisenhaber F, Kwoh CK, Ng S-K, Sung W-K,Wong L (2009) Brief overview of bioinformaticsactivities in Singapore. PLoS Comput Biol 5:e1000508. doi:10.1371/journal.pcbi.1000508.13. Zeti AMH, Shamsir MS, Tajul-Arifin K, MericanAF, Mohamed R, et al. (2009) Bioinformatics inMalaysia: hope, initiative, effort, reality, andchallenges. PLoS Comput Biol 5: e1000457.doi:10.1371/journal.pcbi.1000457.14. TongsimaW,TongsimaS,PalittapongarnpimP(2008)Outlook on Thailand’s genomics and computationalbiologyresearchanddevelopment.PLoSComputBiol4: e1000115. doi:10.1371/journal.pcbi.1000115.15. Miyano S, Ranganathan S (2001) The Asia-Pacific regional perspective on bioinformatics.IEEE Intelligent Systems 16: 19–61.16. Tan TW (2006) Fostering growth of bioinfor-matics and allied disciplines in the Asia Pacific.Asia Pacific Biotech News (APBN): WorldScientific. pp. 1497–1499.17. Ranganathan S, Hsu WL, Yang UC, Tan TW(2008) Emerging strengths in Asia Pacific bioin-formatics. BMC Bioinformatics 9 Suppl 12: S1.PLOS Computational Biology | www.ploscompbiol.org 3 October 2013 | Volume 9 | Issue 10 | e1003317

APBioNet-Transforming Bioinformatics in the Asia-Pacific Region

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