Establishing bioinformatics research in the Asia Pacific

Abstract

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 5^th 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.

Introduction

The Asia-Pacific Bioinformatics Network (APBioNet, [1–3]) was established in 1998 [4] 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 [5]. 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 [6]. Today, we are starting to reap the fruits of our collective early labour. Conferences on bioinformatics ranging from the traditional Genome Informatics Workshop (GIW) [7] based in Japan to the Asia Pacific Bioinformatics Conference (APBC) and the International Life Science Grid Workshop (LSGRID) [8] 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 [9]. 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) [10] and Applied Bioinformatics (originally from New Zealand) [11].

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 5^th 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.

Proceedings summary

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.

Sequence analysis

In the realm of sequence comparisons, Foret et al. [12] have determined the optimal word size for exact and approximate matches between random sequences. Sprenger et al. [13] compare available subcellular localization prediction methods. Support vector machine (SVM) approaches have been applied to the prediction of caspase cleavage sites [14] and the functional class of metal-binding proteins [

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Acknowledgements

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.

Author information

Authors and Affiliations

1. Department of Chemistry and Biomolecular Sciences and Biotechnology Research Institute, Macquarie University, Sydney, NSW 2109, Australia

   Shoba Ranganathan

2. Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore

   Shoba Ranganathan, Martti Tammi & Tin Wee Tan

3. Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore

   Martti Tammi

4. Department of Biological Sciences, Purdue University, Lilly Hall of Life Sciences 915 W. State Street, West Lafayette, IN47907-2054, USA

   Michael Gribskov

Corresponding author

Correspondence to Shoba Ranganathan.

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Ranganathan, S., Tammi, M., Gribskov, M. et al. Establishing bioinformatics research in the Asia Pacific. BMC Bioinformatics 7 (Suppl 5), S1 (2006). https://doi.org/10.1186/1471-2105-7-S5-S1

• Published: 18 December 2006

• DOI: https://doi.org/10.1186/1471-2105-7-S5-S1