An Integrated System for Distributed Bioinformatics Environment on Grids

  • Kenji Satou
  • Yasuhiko Nakashima
  • Shin’ichi Tsuji
  • Xavier Defago
  • Akihiko Konagaya
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3370)


In this paper, an integrated system called OBIEnv, which has been developed on OBIGrid, is described. In addition to automatic database transfer and deployment, it provides various functionalities for transparent and fault-tolerant processing of bioinformatics tasks on Grid. A feasibility study on the analysis of horizontal gene transfer was done using 119 heterogeneous Linux nodes in 5 different sites, and OBIEnv proved its applicability to practical problems in bioinformatics.


Horizontal Gene Transfer Virtual Private Network Globus Toolkit Japan Advance Institute Transparent Computing 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Imoto, S., Goto, T., Miyano, S.: Estimation of genetic networks and functional structures between genes by using Bayesian network and nonparametric regression. In: Pacific Symposium on Biocomputing, vol. 7, pp. 175–186 (2002)Google Scholar
  2. 2.
    Ogata, H., Goto, S., Fujibuchi, W., Kanehisa, M.: Computation with the KEGG pathway database. BioSystems 47, 119–128 (1998)CrossRefGoogle Scholar
  3. 3.
  4. 4.
    Foster, I., Kesselman, C.: The Globus Project: A Status Report. In: Proc. IPPS/SPDP 1998 Heterogeneous Computing Workshop, pp. 4–18 (1998)Google Scholar
  5. 5.
  6. 6.
    Hoppe, H.-C., Mallmann, D.: EUROGRID — European Testbed for GRID Applications, GRIDSTART Technical Bulletin (October 2002)Google Scholar
  7. 7.
    Foster, I.: What is the Grid? A Three Point Checklist. In: GRID Today, July 20 (2002)Google Scholar
  8. 8.
    Konagaya, A.: OBIGrid: Towards a New Distributed Platform for Bioinformatics. In: 21st IEEE Symposium on Reliable Distributed Systems (SRDS 2002), pp. 380–381 (2002)Google Scholar
  9. 9.
    Konagaya, A., Konishi, F., Hatakeyama, M., Satou, K.: The Superstructure Toward Open Bioinformatics Grid. Journal of New Generation Computing 22(2), 167–176 (2004)zbMATHCrossRefGoogle Scholar
  10. 10.
    Sugawara, H.: Gene Trek in Procaryote Space powered by a GRID environment. In: Konagaya, A., Satou, K. (eds.) LSGRID 2004. LNCS (LNBI), vol. 3370, pp. 1–2. Springer, Heidelberg (2005)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Kenji Satou
    • 1
    • 2
  • Yasuhiko Nakashima
    • 3
  • Shin’ichi Tsuji
    • 3
  • Xavier Defago
    • 4
    • 5
  • Akihiko Konagaya
    • 6
  1. 1.School of Knowledge ScienceJapan Advanced Institute of Science and Technology 
  2. 2.BIRDJapan Science and Technology Agency (JST) 
  3. 3.NEC Software Hokuriku, Ltd. 
  4. 4.School of Information ScienceJapan Advanced Institute of Science and Technology 
  5. 5.PRESTOJapan Science and Technology Agency (JST) 
  6. 6.Riken Genomic Sciences Center Computer Science 

Personalised recommendations