The design of scalable stochastic biochemical simulator on FPGA

Masato Yoshimi; Yasunori Osana; Yow Iwaoka; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Naoki Iwanaga; Hiroaki Kitano; Hideharu Amano

doi:10.1109/FPT.2005.1568590

The design of scalable stochastic biochemical simulator on FPGA

Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano

Department of Information and Computer Science

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

6 Citations (Scopus)

Abstract

Biochemical simulations including whole-cell models require high performance computing systems. Reconfigurable systems are expected to be an alternative solution for conventional methods by PC clusters or vector computers. This paper shows the implementation of a stochastic biochemical simulation algorithm called Next Reaction Method for Virtex-II PRO, As the result of benchmarking with a small reaction system, the FPGA-based simulator outperforms the software implementation on Xeon 2.40GHz by 17.1 times.

Original language	English
Title of host publication	Proceedings - 2005 IEEE International Conference on Field Programmable Technology
Pages	339-340
Number of pages	2
DOIs	https://doi.org/10.1109/FPT.2005.1568590
Publication status	Published - 2005
Event	2005 IEEE International Conference on Field Programmable Technology - , Singapore Duration: 2005 Dec 11 → 2005 Dec 14

Publication series

Name	Proceedings - 2005 IEEE International Conference on Field Programmable Technology
Volume	2005

Other

Other	2005 IEEE International Conference on Field Programmable Technology
Country/Territory	Singapore
Period	05/12/11 → 05/12/14

ASJC Scopus subject areas

Engineering(all)
Hardware and Architecture
Software

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10.1109/FPT.2005.1568590

Cite this

Yoshimi, M., Osana, Y., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., & Amano, H. (2005). The design of scalable stochastic biochemical simulator on FPGA. In Proceedings - 2005 IEEE International Conference on Field Programmable Technology (pp. 339-340). [1568590] (Proceedings - 2005 IEEE International Conference on Field Programmable Technology; Vol. 2005). https://doi.org/10.1109/FPT.2005.1568590

The design of scalable stochastic biochemical simulator on FPGA. / Yoshimi, Masato; Osana, Yasunori; Iwaoka, Yow et al.

Proceedings - 2005 IEEE International Conference on Field Programmable Technology. 2005. p. 339-340 1568590 (Proceedings - 2005 IEEE International Conference on Field Programmable Technology; Vol. 2005).

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

Yoshimi, M, Osana, Y, Iwaoka, Y, Funahashi, A, Hiroi, N, Shibata, Y, Iwanaga, N, Kitano, H & Amano, H 2005, The design of scalable stochastic biochemical simulator on FPGA. in Proceedings - 2005 IEEE International Conference on Field Programmable Technology., 1568590, Proceedings - 2005 IEEE International Conference on Field Programmable Technology, vol. 2005, pp. 339-340, 2005 IEEE International Conference on Field Programmable Technology, Singapore, 05/12/11. https://doi.org/10.1109/FPT.2005.1568590

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AU - Kitano, Hiroaki

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AB - Biochemical simulations including whole-cell models require high performance computing systems. Reconfigurable systems are expected to be an alternative solution for conventional methods by PC clusters or vector computers. This paper shows the implementation of a stochastic biochemical simulation algorithm called Next Reaction Method for Virtex-II PRO, As the result of benchmarking with a small reaction system, the FPGA-based simulator outperforms the software implementation on Xeon 2.40GHz by 17.1 times.

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The design of scalable stochastic biochemical simulator on FPGA

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