Stochastic simulation for biochemical reactions on FPGA

M. Yoshimi, Y. Osana, T. Fukushima, H. Amano

Research output: Chapter in Book/Report/Conference proceedingChapter

19 Citations (Scopus)

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.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
EditorsJurgen Becker, Marco Platzner, Serge Vernalde
PublisherSpringer Verlag
Pages105-114
Number of pages10
ISBN (Print)3540229892, 9783540229896
DOIs
Publication statusPublished - 2004 Jan 1

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3203
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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    Yoshimi, M., Osana, Y., Fukushima, T., & Amano, H. (2004). Stochastic simulation for biochemical reactions on FPGA. In J. Becker, M. Platzner, & S. Vernalde (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (pp. 105-114). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3203). Springer Verlag. https://doi.org/10.1007/978-3-540-30117-2_13