The superstructure toward open bioinformatics grid

  • Authors:

  • Akihiko Konagaya;Fumikazu Konishi;Mariko Hatakeyama;Kenji Satou

  • Affiliations:

  • RIKEN, Genomic Sciences Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan;RIKEN, Genomic Sciences Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan;RIKEN, Genomic Sciences Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan;School of Knowledge Science, Japan Advanced Institute of Science and Technology 1-1, Asahidai, Tatsunokuchi, Ishikawa, 923-1292, Japan

  • Venue:
  • New Generation Computing - Grid systems for life sciences
  • Year:
  • 2004

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Abstract

The grid design strongly depends on not only a network infrastructure but also a superstructure, that is, a social structure of virtual organizations where people trust each other, share resources and work together. Open Bioinformatics Grid (OBIGrid) is a grid aimed at building a cooperative bioinformatics environment for computer sicentists and biologists. In October 2003, OBIGrid consisted of 293 nodes with 492 CPUs provided by 27 sites at universities, laboratories and other enterprises, connected by a virtual private network over the Internet. So many organizations have participated because OBIGrid has been conscious of constructing a superstructure on a grid as well as a grid infrastructure. For the benefit of OBIGrid participants, we have developed a series of life science application services: an open bioinformatics environment (OBIEnv), a scalable genome database (OBISgd), a genome annotation system (OBITco), a biochemical network simulator (OBIYagns), and to name a few.