Stochastic simulation for biochemical reactions on FPGA

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

doi:10.1007/978-3-540-30117-2_13

Stochastic simulation for biochemical reactions on FPGA

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

Department of Information and Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Chapter

21 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 language	English
Title of host publication	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Editors	Jurgen Becker, Marco Platzner, Serge Vernalde
Publisher	Springer Verlag
Pages	105-114
Number of pages	10
ISBN (Print)	3540229892, 9783540229896
DOIs	https://doi.org/10.1007/978-3-540-30117-2_13
Publication status	Published - 2004 Jan 1

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	3203
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

ASJC Scopus subject areas

Theoretical Computer Science
Computer Science(all)

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10.1007/978-3-540-30117-2_13

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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

Stochastic simulation for biochemical reactions on FPGA. / Yoshimi, M.; Osana, Y.; Fukushima, T. et al.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ed. / Jurgen Becker; Marco Platzner; Serge Vernalde. Springer Verlag, 2004. p. 105-114 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3203).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

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). Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 3203, Springer Verlag, pp. 105-114. https://doi.org/10.1007/978-3-540-30117-2_13

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

Yoshimi, M. ; Osana, Y. ; Fukushima, T. et al. / Stochastic simulation for biochemical reactions on FPGA. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). editor / Jurgen Becker ; Marco Platzner ; Serge Vernalde. Springer Verlag, 2004. pp. 105-114 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Stochastic simulation for biochemical reactions on FPGA

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