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Stochastic Simulation for Biochemical Reactions on FPGA

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Field Programmable Logic and Application (FPL 2004)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 3203))

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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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References

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Author information

Authors and Affiliations

  1. Dept. of Computer Science, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, #223-8522, Japan

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

Authors
  1. M. Yoshimi
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  2. Y. Osana
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  3. T. Fukushima
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  4. H. Amano
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Editor information

Editors and Affiliations

  1. ITIV - Universitaet Karlsruhe (TH),  

    Jürgen Becker

  2. University of Paderborn,  

    Marco Platzner

  3. IMEC, Kapeldreef 75, Leuven, Leuven, Belgium

    Serge Vernalde

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© 2004 Springer-Verlag Berlin Heidelberg

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Yoshimi, M., Osana, Y., Fukushima, T., Amano, H. (2004). Stochastic Simulation for Biochemical Reactions on FPGA. In: Becker, J., Platzner, M., Vernalde, S. (eds) Field Programmable Logic and Application. FPL 2004. Lecture Notes in Computer Science, vol 3203. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30117-2_13

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  • DOI: https://doi.org/10.1007/978-3-540-30117-2_13

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-22989-6

  • Online ISBN: 978-3-540-30117-2

  • eBook Packages: Springer Book Archive

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