Introduction | Open | Published:
Establishing bioinformatics research in the Asia Pacific
BMC Bioinformaticsvolume 7, Article number: S1 (2006)
In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand) and Busan (South Korea). This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community.
The Asia-Pacific Bioinformatics Network (APBioNet, [1–3]) was established in 1998  to bring together scientists from diverse disciplines, working together in the area of Bioinformatics to champion the advancement of bioinformatics in the Asia Pacific region. After annual meetings held at the Pacific Symposium of Biocomputing (1998–2001), APBioNet executive committee members assisted in organizing InCoB2002 (the International Conference on Bioinformatics, 2002) at Bangkok, Thailand and adopted this meeting as their annual conference. Subsequent conferences followed in Penang, Malaysia (2003); Auckland, New Zealand (2004) and Busan, South Korea (2005). InCoB 2006 was held New Delhi, India.
In the early years, we focused on constructing the network infrastructure capable of supporting the rapid dissemination of bioinformatics databases and computational resources throughout the region such as the BioMirrors initiative . Education and training in bioinformatics in terms of awareness and advocacy amongst the life science community was a key priority, which led to initiatives such as the S* Life Science Informatics Alliance . Today, we are starting to reap the fruits of our collective early labour. Conferences on bioinformatics ranging from the traditional Genome Informatics Workshop (GIW)  based in Japan to the Asia Pacific Bioinformatics Conference (APBC) and the International Life Science Grid Workshop (LSGRID)  are already showcasing the expertise of Asia Pacific bioinformatics research. In recognition of the tremendous growth of bioinformatics in this region, even the International Society for Computational Biology (ISCB) (MG is the current President), to which APBioNet is affiliated, chose to hold the annual flagship ISMB conference in this region in 2003 . High quality research papers from the region have started to appear in bioinformatics publications originating in the region, such as the Journal of Bioinformatics and Computational Biology (World Scientific, Singapore)  and Applied Bioinformatics (originally from New Zealand) .
In recent years, bioinformatics research in the region has reached a standard, requiring international peer-reviewed high-impact factor journal publication. So in 2006, on the occasion of the 5th Annual International Conference on Bioinformatics (InCoB) the APBioNet Executive Committee and the InCoB Steering Committee (chaired by one of the authors, SR) has embarked on establishing international standards in bioinformatics research through this vehicle of a special BMC Bioinformatics issue. Manuscripts were sought from APBioNet members in any area of bioinformatics. The submitted manuscripts span several active research areas, such as the development, organization, mining and integration of data resources; tools for the analysis of sequences, protein structure, transcriptomes, interactomes and genomes; immunoinformatics and the development of informatics resources for large-scale distributed grid computing.
Papers submitted to these proceedings were peer-reviewed by at least two reviewers, from the APBioNet/InCoB editorial board members and external experts as required. The aim of the journal proceedings was to rigorously select only the top 22 high-quality papers originating from more than a dozen Asia Pacific countries, out of 48 manuscripts (acceptance rate of 46%) shortlisted from the 557 abstracts submitted to the scientific organising committee of InCoB 2006. The innovative bioinformatics research in the region is reflected in these accepted papers coauthored from Australia, China, India, Japan, Singapore, South Africa, Taiwan, The Netherlands and USA, which fall into several general themes as described in the following sections.
In the realm of sequence comparisons, Foret et al.  have determined the optimal word size for exact and approximate matches between random sequences. Sprenger et al.  compare available subcellular localization prediction methods. Support vector machine (SVM) approaches have been applied to the prediction of caspase cleavage sites  and the functional class of metal-binding proteins .
New methodologies for fast structure retrieval using spectral graph matching  and domain boundary prediction using a novel interdomain linker index  have been reported. A detailed modelling study of protein dimerization  describes how structural resources and methods can be applied to understand biologically functional quaternary structures.
Transcriptome research is represented by four papers. The first two are novel approaches for predicting microRNA  and selecting effective siRNA  sequences. The application of probabilistic and SVM techniques to splice site identification  is followed by the promoter analysis of antimicrobial peptide-coding genes in three mammalian genomes .
Protein-protein interactions and the networks they form are essential to the fundamental understanding of how biological pathways function. Interactome databases for yeast  and the fruit fly  are reported, to support organism-wide analyses. Mathivanan et al.  have critically evaluated resources available for the human interactome.
Curation and annotation of viral , bacterial  and zebrafish  genomes present interesting challenges, due to the range in genome size, variability and complexity. In the case of zebrafish, Christoffels et al.  have effectively used carp ESTs to facilitate the annotation.
Text mining approaches allow the integration of the scientific literature with genomic and high-throughput experiments. Tsai et al.  present improvements in identifying biological terms, a key step in this process.
In the global fight against disease, Khan et al.  discuss sequence-based immunogenic epitope prediction strategies for the dengue virus, while Tong et al.  describe a structure-based docking approach to define HLA Class II autoantigenic peptides.
As computational problems in biology evolve in size, resource requirements and complexity, grid computing has emerged as a viable solution in many instances. Konagaya  reviews currently available grid computing resources and applications, while providing a futuristic extension from a computing to a knowledge grid.
This special issue of BMC Bioinformatics is a milestone in Asia Pacific bioinformatics research. The breadth and depth of research activity in the region, as reflected by the submitted papers, underscores the rapid development of bioinformatics amongst our institutions of higher learning and research. It demonstrates that the bioinformatics resource infrastructure set up in the past forms a strong foundation for meeting the demands of the research community. The success of regional bioinformatics education programs is highlighted by the increasing number of papers with graduate research students as first authors.
As bioinformatics starts to mature in the Asia Pacific region, research leaders, such as those in the recently formed Asian Association for Societies in Bioinformatics (AASBi)  and administrators of our respective institutions must plan for the network and resource infrastructure of the next decade, the so-called cyberinfrastructure for biology (CIBIO) . Indeed, policy meetings such as the East Asia Bioinformatics Networking (EABN) , first held at InCoB2005 in Busan, and ASEAN human resource development in bioinformatics, held in India and China are already in place to address these issues. We are well placed "to foster the growth of Bioinformatics and its allied disciplines in the Asia Pacific" . This growth is a key element in the development of a new generation of researchers who can lead in developing the new Biology of the twenty-first century.
The Asia-Pacific Bioinformatics Network[http://apbionet.org]
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Ranganathan S, Subbiah S, Tan TW: APBioNet: the Asia-Pacific regional consortium for bioinformatics. Appl Bioinformatics 2002, 1: 101–105.
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Gilbert D, Ugawa Y, Buchhorn M, Tan TW, Mizushima A, Kim H, Chon K, Weon S, Ma J, Ichiyanagi Y, Liou DM, Keretho S, Napis S: Bio-Mirror project for public bio-data distribution. Bioinformatics 2004, 20: 3238–3240. 10.1093/bioinformatics/bth219
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Genome Informatics Workshop[http://giw.ims.u-tokyo.ac.jp/giw/index.html]
International Life Science Grid Workshop (LSGRID)[http://www.lsgrid.org/]
11th International Conference on Intelligent Systems for Molecular Biology (ISMB), Brisbane, Australia, June 29–July 3, 2003[http://www.iscb.org/ismb2003/]
Journal of Bioinformatics and Computational Biology (JBCB)[http://www.worldscinet.com/jbcb/jbcb.shtml]
Foret S, Kantorovitz MR, Burden C: Asymptotic behavior and optimal word size for exact and approximate k-word matches between random sequences. BMC Bioinformatics 2006, 7(Suppl 5):S20. 10.1186/1471-2105-7-S5-S21
Sprenger J, Fink JL, Teasdale RD: Evaluation and comparison of mammalian subcellular localization prediction methods. BMC Bioinformatics 2006, 7(Suppl 5):S3. 10.1186/1471-2105-7-S5-S3
Wee LJK, Tan TW, Ranganathan S: SVM-based prediction of caspase substrate cleavage sites. BMC Bioinformatics 2006, 7(Suppl 5):S14. 10.1186/1471-2105-7-S5-S14
Lin HH, Han LY, Zhang HL, Zheng CJ, Xie B, Chen YZ: Prediction of the Functional Class of Metal-Binding Proteins from Sequence Derived Physicochemical Properties by Support Vector Machine Approach. BMC Bioinformatics 2006, 7(Suppl 5):S13. 10.1186/1471-2105-7-S5-S13
Bhattacharya S, Chiranjib Bhattacharyya C, Chandra NR: Projections for Fast Retrieval of Protein Structures. BMC Bioinformatics 2006, 7(Suppl 5):S5. 10.1186/1471-2105-7-S5-S5
Sikder AR, Zomaya AY: Improving the performance of DomainDiscovery of Protein Domain Boundary Assignment Using inter-domain Linker index. BMC Bioinformatics 2006, 7(Suppl 5):S6. 10.1186/1471-2105-7-S5-S6
Suresh A, Verma C: Modelling study of dimerization in mammalian defensins. BMC Bioinformatics 2006, 7(Suppl 5):S17. 10.1186/1471-2105-7-S5-S17
Thadani R, Tammi MT: MicroTar: predicting microRNA targets from RNA duplexes. BMC Bioinformatics 2006, 7(Suppl 5):S21. 10.1186/1471-2105-7-S5-S20
Takasaki S, Kawamura Y, Konagaya A: Selecting Effective siRNA Sequences by using Radial Basis Function Network and Decision Tree Learning. BMC Bioinformatics 2006, 7(Suppl 5):S20. 10.1186/1471-2105-7-S5-S22
Baten AKMA, Chang BCH, Halgamuge SK, Li J: Splice site identification using probabilistic parameters and SVM classification. BMC Bioinformatics 2006, 7(Suppl 5):S15. 10.1186/1471-2105-7-S5-S15
Brahmachary M, Schönbach C, Yang L, Huang E, Tan SL, Chowdhary R, Krishnan SPT, Lin CY, Hume DA, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB: Computational Promoter Analysis of Mouse, Rat and Human Antimicrobial Peptide-coding Genes. BMC Bioinformatics 2006, 7(Suppl 5):S8. 10.1186/1471-2105-7-S5-S8
Wu X, Zhu L, Guo J, Fu C, Zhou H, Dong D, Li Z, Zhang DY, Lin K: SPIDer: Saccharomyces Protein-protein Interaction Database. BMC Bioinformatics 2006, 7(Suppl 5):S16. 10.1186/1471-2105-7-S5-S16
Lin CY, Cho CS, Chen CL, Lin FK, Lin CH, Chen SH, Chen PY, Lo CZ, Hsiung CA: Fly-DPI: Database of Protein Interactomes for D. melanogaster in the Approach of Systems Biology. BMC Bioinformatics 2006, 7(Suppl 5):S18. 10.1186/1471-2105-7-S5-S18
Mathivanan S, Periaswamy B, Gandhi TKB, Kandasamy K, Suresh S, Mohmood R, Ramachandra YL, Pandey A: An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics 2006, 7(Suppl 5):S19. 10.1186/1471-2105-7-S5-S19
Kulkarni-Kale U, Bhosle SG, Manjari GS, Joshi M, Bansode S, Kolaskar AS: Curation of viral genomes: Challenges, applications and the way forward. BMC Bioinformatics 2006, 7(Suppl 5):S12. 10.1186/1471-2105-7-S5-S12
Ranjan S, Gundu RK, Ranjan A: MycoperonDB: A database of computationally identified operons and transcriptional units in Mycobacteria. BMC Bioinformatics 2006, 7(Suppl 5):S9. 10.1186/1471-2105-7-S5-S9
Christoffels A, Bartfai R, Srinivasan H, Komen H, Orban L: Comparative genomics in cyprinids: Common carp ESTs help the annotation of the zebrafish genome. BMC Bioinformatics 2006, 7(Suppl 5):S2. 10.1186/1471-2105-7-S5-S2
Tsai RTH, Sung CL, Dai HJ, Hung HC, Sung TY, Hsu WL: NERBio: using selected word conjunction, term normalization, and global patterns to improve biomedical named entity recognition. BMC Bioinformatics 2006, 7(Suppl 5):S11. 10.1186/1471-2105-7-S5-S11
Khan AM, Heiny AT, Lee KX, Srinivasan KN, Tan TW, August JT, Brusic V: Large-scale sequence analysis of genetic and T-cell epitope antigenic diversity in dengue virus. BMC Bioinformatics 2006, 7(Suppl 5):S4. 10.1186/1471-2105-7-S5-S4
Tong JC, Tan TW, Sinha AA, Ranganathan S: Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris. BMC Bioinformatics 2006, 7(Suppl 5):S7. 10.1186/1471-2105-7-S5-S7
Konagaya A: Trends in Life Science Grid: From Computing Grid to Knowledge Grid. BMC Bioinformatics 2006, 7(Suppl 5):S10. 10.1186/1471-2105-7-S5-S10
The Association of Asian Societies for Bioinformatics[http://www.aasbi.org/]
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East Asia Bioinformatics Network (EABN)[http://biocc.ngic.re.kr/Biomeeting/Mediawiki/index.php?title=EABN&redirect=no]
We thank the referees for their dedication and effort in reviewing the manuscripts submitted for this supplement. We also thank the BMC Bioinformatics Editorial Office for their support and encouragement in making this issue possible.
This article has been published as part of BMC Bioinformatics Volume 7, Supplement 5, 2006: APBioNet – Fifth International Conference on Bioinformatics (InCoB2006). The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2105-7?issue=S5.