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Genome Informatics 13: 484–485 (2002)
OBIGrid: A New Computing Platform for Bioinformatics Fumikazu Konishi
1
Akinobu Fukuzaki
1
[email protected]
[email protected]
Tomoyuki Yamamoto2
Xavier Defago2
[email protected]
[email protected]
1 2
Kenji Satou2
[email protected]
Akihiko Konagaya
1,2
[email protected]
The Institute of Physcal and Chemical Research (RIKEN) Genomeic Sciences Center W520, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan Japan Advanced Institute of Science and Technology Graduate School of Knowledge Science, 1-1 Asahidai, Tatsunokuchi, Ishikawa 923-1292, Japan
Keywords: grid computing, virtual private network
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Introduction
Recently, bioinformatics requires high performance computing facilities for homology search, molecular simulation, cell simulation etal. Grid computing [1] has a potential for expansion in computing performance by connecting a large number of computers or PC clusters with high performance networks. Along with this line, we have designed and developed the Open Bioinformatics Grid (OBIGrid [2] http://www.obigrid.org/ ) in corporation with Japan Committee on High-Performance Computing for Bioinformatics and Initiative for Parallel Bioinformatics Processing (IPAB). On designing OBIGrid, we emphasize the importance of network transparency and security policy issues rather than the performance at the early development stage. Therefore, we adopt a virtual private network (VPN) to protect a Grid system from/to the outer world. As for bioinformatics environment, we set the following design goals to provide: 1. Open bioinformatics platform for both computer scientists and biologists. 2. Well-known genome related databases with daily updating. 3. Basic bioinformatics applications such as homology search and molecular simulation. 4. Network transparent language environment portable to any computers on the Grid. 5. High performance computer resources for research purpose. 6. Prototype software tools for research purpose. 7. Biological experimental data for research purpose. In order to achieve those goals, we have designed an open bioinformatics environment (OBIEnv [3]) , genomic XML databases [4], distributed parallel BLAST search systems, molecular dynamics simulation system on molecular dynamics machine (MDM), and bioinformatics script programming environment such as BioPerl, BioJava and BioPython. In preparing such environment, a network transparency supported by secure authentication with encryption technology is the most important feature for grid users to share data and/or programs among organizations.
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OBIGrid: A New Computing Platform for Bioinformatics
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Figure 1: The connected sites on OBIGrid.
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Current Status
In the present time, the OBIGrid has connected 19 sites with a Globus Toolkit 2.0 over the Internet using a virtual private network (VPN) with hub and spoke topology.
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Discussion
So far we have outlined the design philosophy of OBIGrid. It is too early to derive any conclusion at this stage, but the OBIGrid system has a good potential to bring fruitful results to both computer scientists and biologists in the following points: For computer scientists, OBIGrid can work as bioinformatics environment with genomic databases and applications without management overhead. For biologists, OBIGrid would work as a network to distribute biological experimental data to those who are interested in the data. In either way, the most essential factor of the OBIGrid system is to accelerate humanto-human communication.
Acknowledgments The authours give special thanks to the members of Japan Committee on High-performance Computing for Bioinformatics and Initiative for Parallel Bioinformatics for their fruitful discussion about Grid technologies, special thanks also to those who participate to the OBIGrid project. This work was partly supported by Grant-in-aid for Scientific Research on Priority Areas (C) Genome Information Science from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
References [1] Foster, I. and Kesselman, K., The Grid: Blueprint for a New Computing Infrastructure, Morgan Kaufmann, 1998. [2] Fumikazu, K., Hiroyuki, U., Kenji, S., and Akihiko K., A network design for Open Bioinformatics Grid (OBIGrid), Proc. The 3rd Annual Meeting ’02, Chem-Bio Informatics Society, 192–193, 2002. [3] Kenji, S., Yasuhiko, N., Shinichi, T., Xavier, D., Tomoyuki, Y., and Akihiko, K., Proc. The 3rd Annual Meeting ’02, Chem-Bio Informatics Society, 188–189, 2002. [4] Shinichi T., Yasuhiko, N., Xavier, D., Tomoyuki, Y., Kenji, S., Fumikazu, K., and Akihiko, K., Distributed parallel implementation of DDBJ XML using scalable genome, Proc. The 3rd Annual Meeting ’02, Chem-Bio Informatics Society, 194–195, 2002.
