Practical implementation of a network-based Stochastic biochemical simulation system on an FPGA

Masato Yoshimi, Yuri Nishikawa, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Hideki Yamada, Hiroaki Kitano, Hideharu Amano

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

Stochastic simulation of biochemical reaction networks are widely focused by life scientists to represent stochastic behaviors in cellular processes. Stochastic algorithm has loop-and thread-level parallelism, and it is suitable for running on application specific hardware to achieve high performance with low cost. We have implemented and evaluated the FPGA-based stochastic simulator according to theoretical research of the algorithm. This paper introduces an improved architecture for accelerating a stochastic simulation algorithm called the Next Reaction Method. This new architecture has scalability to various size of FPGA. As the result with a middle-range FPGA, 5.38 times higher throughput was obtained compared to software running on a Core 2 Quad Q6600 2.40GHz.

Original languageEnglish
Title of host publicationProceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL
Pages663-666
Number of pages4
DOIs
Publication statusPublished - 2008
Event2008 International Conference on Field Programmable Logic and Applications, FPL - Heidelberg, Germany
Duration: 2008 Sep 82008 Sep 10

Other

Other2008 International Conference on Field Programmable Logic and Applications, FPL
CountryGermany
CityHeidelberg
Period08/9/808/9/10

Fingerprint

Field programmable gate arrays (FPGA)
Scalability
Simulators
Throughput
Hardware
Costs

ASJC Scopus subject areas

  • Hardware and Architecture

Cite this

Yoshimi, M., Nishikawa, Y., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., ... Amano, H. (2008). Practical implementation of a network-based Stochastic biochemical simulation system on an FPGA. In Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL (pp. 663-666). [4630034] https://doi.org/10.1109/FPL.2008.4630034

Practical implementation of a network-based Stochastic biochemical simulation system on an FPGA. / Yoshimi, Masato; Nishikawa, Yuri; Osana, Yasunori; Funahashi, Akira; Hiroi, Noriko; Shibata, Yuichiro; Yamada, Hideki; Kitano, Hiroaki; Amano, Hideharu.

Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL. 2008. p. 663-666 4630034.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Yoshimi, M, Nishikawa, Y, Osana, Y, Funahashi, A, Hiroi, N, Shibata, Y, Yamada, H, Kitano, H & Amano, H 2008, Practical implementation of a network-based Stochastic biochemical simulation system on an FPGA. in Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL., 4630034, pp. 663-666, 2008 International Conference on Field Programmable Logic and Applications, FPL, Heidelberg, Germany, 08/9/8. https://doi.org/10.1109/FPL.2008.4630034
Yoshimi M, Nishikawa Y, Osana Y, Funahashi A, Hiroi N, Shibata Y et al. Practical implementation of a network-based Stochastic biochemical simulation system on an FPGA. In Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL. 2008. p. 663-666. 4630034 https://doi.org/10.1109/FPL.2008.4630034
Yoshimi, Masato ; Nishikawa, Yuri ; Osana, Yasunori ; Funahashi, Akira ; Hiroi, Noriko ; Shibata, Yuichiro ; Yamada, Hideki ; Kitano, Hiroaki ; Amano, Hideharu. / Practical implementation of a network-based Stochastic biochemical simulation system on an FPGA. Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL. 2008. pp. 663-666
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