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

doi:10.1109/FPL.2008.4630034

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 proceeding › Conference contribution

5 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 language	English
Title of host publication	Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL
Pages	663-666
Number of pages	4
DOIs	https://doi.org/10.1109/FPL.2008.4630034
Publication status	Published - 2008
Event	2008 International Conference on Field Programmable Logic and Applications, FPL - Heidelberg, Germany Duration: 2008 Sept 8 → 2008 Sept 10

Publication series

Name	Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL

Other

Other	2008 International Conference on Field Programmable Logic and Applications, FPL
Country/Territory	Germany
City	Heidelberg
Period	08/9/8 → 08/9/10

ASJC Scopus subject areas

Hardware and Architecture

Access to Document

10.1109/FPL.2008.4630034

Cite this

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 (pp. 663-666). [4630034] (Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL). 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 et al.

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

Research output: Chapter in Book/Report/Conference proceeding › Conference 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, Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL, 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. (Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL). doi: 10.1109/FPL.2008.4630034

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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.",

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AU - Shibata, Yuichiro

AU - Yamada, Hideki

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AB - 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.

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

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