Advertisement

Implementation of ReCSiP: A ReConfigurable Cell SImulation Platform

  • Yasunori Osana
  • Tomonori Fukushima
  • Hideharu Amano
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2778)

Abstract

A reconfigurable accelerator for cell simulators called "ReCSiP" is proposed. It consists of both reconfigurable hardware and software platform. For high performance simulation, numerical solution of kinetic formulas, which require a large amount of computation, are processed on the reconfigurable hardware. It also provides programming interface for developing cell simulators. In this paper, Michaelis-Menten solver is designed and implemented on ReCSiP. The result of preliminary evaluation shows that ReCSiP is 8 times faster than Intel PentiumIII 1.13GHz when simple metabolic simulations are executed.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Schaff, J., et al.: The virtual cell. In: Proceedings of Pacific Symposium on Biocomputing, vol. 4, pp. 228–239 (1999)Google Scholar
  2. 2.
    Tomita, M., et al.: E-cell: software environment for whole-cell simulation. Bioinformatics 15(1), 72–84 (1999)CrossRefGoogle Scholar
  3. 3.
    Takahashi, K., et al.: Computational challenges in cell simulation: A software engineering approach. In: IEEE Intelligent Systems, October 2002, pp. 64–71 (2002)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Yasunori Osana
    • 1
  • Tomonori Fukushima
    • 1
  • Hideharu Amano
    • 1
  1. 1.Dept. of Computer ScienceKeio UniversityKouhoku-ku, YokohamaJapan

Personalised recommendations