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Stochastic Simulation for Biochemical Reactions on FPGA

  • M. Yoshimi
  • Y. Osana
  • T. Fukushima
  • H. Amano
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3203)

Abstract

Biological cell simulations generally require high-powered computer resources. A reconfigurable system is a possible solution to the problem as an alternative approach against PC/WS clusters. A stochastic simulation algorithm proposed by Gillespie is implemented on a reconfigurable platform called ReCSiP, and the performance is evaluated. The implemented Lotka system outperforms the software implementation on AthlonXP2800+ by 105.13 times.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • M. Yoshimi
    • 1
  • Y. Osana
    • 1
  • T. Fukushima
    • 1
  • H. Amano
    • 1
  1. 1.Dept. of Computer ScienceKeio UniversityYokohamaJapan

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