Extending Asia Pacific bioinformatics into new realms in the

BMC Genomics (Impact Factor: 3.99). 12/2009; 10 Suppl 3(Suppl 3):S1. DOI: 10.1186/1471-2164-10-S3-S1
Source: PubMed


The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 7-11, 2009 at Biopolis, Singapore. Besides bringing together scientists from the field of bioinformatics in this region, InCoB has actively engaged clinicians and researchers from the area of systems biology, to facilitate greater synergy between these two groups. InCoB2009 followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India), Hong Kong and Taipei (Taiwan), with InCoB2010 scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. The Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and symposia on Clinical Bioinformatics (CBAS), the Singapore Symposium on Computational Biology (SYMBIO) and training tutorials were scheduled prior to the scientific meeting, and provided ample opportunity for in-depth learning and special interest meetings for educators, clinicians and students. We provide a brief overview of the peer-reviewed bioinformatics manuscripts accepted for publication in this supplement, grouped into thematic areas. In order to facilitate scientific reproducibility and accountability, we have, for the first time, introduced minimum information criteria for our pubilcations, including compliance to a Minimum Information about a Bioinformatics Investigation (MIABi). As the regional research expertise in bioinformatics matures, we have delineated a minimum set of bioinformatics skills required for addressing the computational challenges of the "-omics" era.

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Available from: Frank Eisenhaber, Jul 28, 2015
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    • "Recently, in 2009, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics network and pioneer of the annual International Conference on Bioinformatics (InCoB) now in its twelfth year, initiated the effort for Minimum Information about a Bioinformatics Investigation (MIABi), building on earlier ideas [4]. The standards for transparency, provenance and scientific reproducibility amongst the bioinformatics and computational biology community were drafted and published a year later [5]. "
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    ABSTRACT: Background Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. Results We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Conclusions Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear.
    BMC Genomics 10/2013; 14(5). DOI:10.1186/1471-2164-14-S5-S13 · 3.99 Impact Factor
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    • "Over the past eight years of InCoB conferences (Bangkok, Thailand (2002); Penang, Malaysia (2003); Auckland, New Zealand (2004); Busan, South Korea (2005); New Delhi, India (2006) [2]; Hong Kong (2007) [3]; Taipei, Taiwan (2008) [4] and Singapore (2009) [5,6]) and associated satellite workshops and meetings, we have seen a healthy growth in the development and advancement of bioinformatics, commensurate with an increase in the number of scientists who moved into bioinformatics from other fields and the number of students who have taken an interest in bioinformatics. Consequently, there has been a significant growth in the number of publications in bioinformatics, as well in "wetlab" biology, containing computational techniques. "
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    ABSTRACT: The 2010 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation formed in 1998, was organized as the 9th International Conference on Bioinformatics (InCoB), Sept. 26-28, 2010 in Tokyo, Japan. Initially, APBioNet created InCoB as forum to foster bioinformatics in the Asia Pacific region. Given the growing importance of interdisciplinary research, InCoB2010 included topics targeting scientists in the fields of genomic medicine, immunology and chemoinformatics, supporting translational research. Peer-reviewed manuscripts that were accepted for publication in this supplement, represent key areas of research interests that have emerged in our region. We also highlight some of the current challenges bioinformatics is facing in the Asia Pacific region and conclude our report with the announcement of APBioNet's 100 BioDatabases (BioDB100) initiative. BioDB100 will comply with the database criteria set out earlier in our proposal for Minimum Information about a Bioinformatics and Investigation (MIABi), setting the standards for biocuration and bioinformatics research, on which we will report at the next InCoB, Nov. 27 - Dec. 2, 2011 at Kuala Lumpur, Malaysia.
    BMC Genomics 12/2010; 11 Suppl 4(Suppl 4):S1. DOI:10.1186/1471-2164-11-S4-S1 · 3.99 Impact Factor
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    • "Developed through a joint effort by the Asia-Pacific Bioinformatics Network (APBioNet) (http://www.apbionet.org/) and the wider bioinformatics community [21], the MIABi initiative arises from a response to the growing need for transparency, provenance and scientific reproducibility amongst the bioinformatics and computational biology community. Currently, it is increasingly common for computational tools to be applied to ever larger datasets in order to generate output with little commensurate effort to review objectively the quality of the process undertaken, or the quality of the input data, analytical process, or the conclusions drawn. "
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    ABSTRACT: The 2010 International Conference on Bioinformatics, InCoB2010, which is the annual conference of the Asia-Pacific Bioinformatics Network (APBioNet) has agreed to publish conference papers in compliance with the proposed Minimum Information about a Bioinformatics investigation (MIABi), proposed in June 2009. Authors of the conference supplements in BMC Bioinformatics, BMC Genomics and Immunome Research have consented to cooperate in this process, which will include the procedures described herein, where appropriate, to ensure data and software persistence and perpetuity, database and resource re-instantiability and reproducibility of results, author and contributor identity disambiguation and MIABi-compliance. Wherever possible, datasets and databases will be submitted to depositories with standardized terminologies. As standards are evolving, this process is intended as a prelude to the 100 BioDatabases (BioDB100) initiative whereby APBioNet collaborators will contribute exemplar databases to demonstrate the feasibility of standards-compliance and participate in refining the process for peer-review of such publications and validation of scientific claims and standards compliance. This testbed represents another step in advancing standards-based processes in the bioinformatics community which is essential to the growing interoperability of biological data, information, knowledge and computational resources.
    BMC Genomics 12/2010; 11 Suppl 4(Suppl 4):S27. DOI:10.1186/1471-2164-11-S4-S27 · 3.99 Impact Factor
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