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Khan AM, Tan TW, Schönbach C, Ranganathan S. APBioNet-transforming bioinformatics in the Asia-Pacific region. PLoS Comput Biol 2013; 9:e1003317. [PMID: 24204244 PMCID: PMC3814852 DOI: 10.1371/journal.pcbi.1003317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Asif M. Khan
- Perdana University Graduate School of Medicine, Selangor Darul Ehsan, Malaysia
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- * E-mail: (TWT); (SR)
| | - Christian Schönbach
- School of Science and Technology, Department of Biology and Chemistry, Nazarbayev University, Astana, Republic of Kazakhstan
- Department of Bioscience and Bioinformatics and Biomedical Informatics R&D Center (BMIRC), Kyushu Institute of Technology, Fukuoka, Japan
| | - Shoba Ranganathan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia
- * E-mail: (TWT); (SR)
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Tan TW, Xie C, De Silva M, Lim KS, Patro CPK, Lim SJ, Govindarajan KR, Tong JC, Choo KH, Ranganathan S, Khan AM. Simple re-instantiation of small databases using cloud computing. BMC Genomics 2013; 14 Suppl 5:S13. [PMID: 24564380 PMCID: PMC3852246 DOI: 10.1186/1471-2164-14-s5-s13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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.
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Nwose EU, Bwititi PT. Can Computer Meridian Diagnostic be useful in diagnosis and management of diseases? Med Hypotheses 2013; 81:564-7. [PMID: 23896216 DOI: 10.1016/j.mehy.2013.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 06/30/2013] [Accepted: 07/02/2013] [Indexed: 11/28/2022]
Abstract
The need for the development of appropriate guidelines for effective or safe use of antioxidants and herbs has always been a concern, especially for the alternative medicine practices. Computer Meridian Diagnostic (CMD) is one of emerging computer-based diagnostic technologies available to alternative medicine practitioners. However, case report of the agents monitored with CMD is uncommon; and concerted effort to bring this into conventional medical practice is yet to be. This hypothesis builds on an anecdotal observation of anti-stress effect monitored with CMD, with a view to highlight a potential tool that requires expatiation, as well as proof of concept and validation studies for possible integration in conventional and traditional medicine practices for therapeutic monitoring.
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Affiliation(s)
- E U Nwose
- School of Psychological & Clinical Sciences, Charles Darwin University, Australia.
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Schönbach C, Tongsima S, Chan J, Brusic V, Tan TW, Ranagathan S. InCoB2012 Conference: from biological data to knowledge to technological breakthroughs. BMC Bioinformatics 2012; 13 Suppl 17:S1. [PMID: 23281929 PMCID: PMC3521245 DOI: 10.1186/1471-2105-13-s17-s1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Ten years ago when Asia-Pacific Bioinformatics Network held the first International Conference on Bioinformatics (InCoB) in Bangkok its theme was North-South Networking. At that time InCoB aimed to provide biologists and bioinformatics researchers in the Asia-Pacific region a forum to meet, interact with, and disseminate knowledge about the burgeoning field of bioinformatics. Meanwhile InCoB has evolved into a major regional bioinformatics conference that attracts not only talented and established scientists from the region but increasingly also from East Asia, North America and Europe. Since 2006 InCoB yielded 114 articles in BMC Bioinformatics supplement issues that have been cited nearly 1,000 times to date. In part, these developments reflect the success of bioinformatics education and continuous efforts to integrate and utilize bioinformatics in biotechnology and biosciences in the Asia-Pacific region. A cross-section of research leading from biological data to knowledge and to technological applications, the InCoB2012 theme, is introduced in this editorial. Other highlights included sessions organized by the Pan-Asian Pacific Genome Initiative and a Machine Learning in Immunology competition. InCoB2013 is scheduled for September 18-21, 2013 at Suzhou, China.
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Affiliation(s)
- Christian Schönbach
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
- Biomedical Informatics Research and Development Center, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Jonathan Chan
- School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Republic of Singapore
- Computational Resource Centre (A*CRC), A*STAR, Singapore 138632, Republic of Singapore
| | - Shoba Ranagathan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Republic of Singapore
- Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, NSW 2109, Australia
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New Progress of Glycan as Receptors for Influenza Virus*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ozdemir V, Muljono DH, Pang T, Ferguson LR, Manamperi A, Samper S, Someya T, Tassé AM, Tsai SJ, Zhou HH, Lee EJD. Asia-Pacific Health 2020 and Genomics without Borders: Co-Production of Knowledge by Science and Society Partnership for Global Personalized Medicine. ACTA ACUST UNITED AC 2011; 9:1-5. [PMID: 21490881 DOI: 10.2174/187569211794728841] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Vural Ozdemir
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
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Ranganathan S, Schönbach C, Nakai K, Tan TW. Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010). BMC Genomics 2010; 11 Suppl 4:S1. [PMID: 21143792 PMCID: PMC3005919 DOI: 10.1186/1471-2164-11-s4-s1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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.
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Affiliation(s)
- Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia.
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Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi). BMC Genomics 2010; 11 Suppl 4:S27. [PMID: 21143811 PMCID: PMC3005918 DOI: 10.1186/1471-2164-11-s4-s27] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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.
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Schönbach C, Nakai K, Tan TW, Ranganathan S. InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. BMC Bioinformatics 2010; 11 Suppl 7:S1. [PMID: 21106116 PMCID: PMC2957677 DOI: 10.1186/1471-2105-11-s7-s1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The International Conference on Bioinformatics (InCoB), the annual conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted in one of countries of the Asia-Pacific region. The 2010 conference was awarded to Japan and has attracted more than one hundred high-quality research paper submissions. Thorough peer reviewing resulted in 47 (43.5%) accepted papers out of 108 submissions. Submissions from Japan, R.O. Korea, P.R. China, Australia, Singapore and U.S.A totaled 43.8% and contributed to 57.4% of accepted papers. Manuscripts originating from Taiwan and India added up to 42.8% of submissions and 28.3% of acceptances. The fifteen articles published in this BMC Bioinformatics supplement cover disease informatics, structural bioinformatics and drug design, biological databases and software tools, signaling pathways, gene regulatory and biochemical networks, evolution and sequence analysis.
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Affiliation(s)
- Christian Schönbach
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
| | - Kenta Nakai
- Laboratory of Functional Analysis in silico, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597
| | - Shoba Ranganathan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597
- Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia
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Abstract
The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation from 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 9-11, 2009 at Biopolis, Singapore. InCoB has actively engaged researchers from the area of life sciences, systems biology and clinicians, to facilitate greater synergy between these groups. To encourage bioinformatics students and new researchers, tutorials and student symposium, the Singapore Symposium on Computational Biology (SYMBIO) were organized, along with the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and the Clinical Bioinformatics (CBAS) Symposium. However, to many students and young researchers, pursuing a career in a multi-disciplinary area such as bioinformatics poses a Himalayan challenge. A collection to tips is presented here to provide signposts on the road to a career in bioinformatics. An overview of the application of bioinformatics to traditional and emerging areas, published in this supplement, is also presented to provide possible future avenues of bioinformatics investigation. A case study on the application of e-learning tools in undergraduate bioinformatics curriculum provides information on how to go impart targeted education, to sustain bioinformatics in the Asia-Pacific region. The next InCoB is scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010.
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