ReCSiP: An FPGA-based general-purpose biochemical simulator

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

doi:10.1002/ecjb.20370

ReCSiP: An FPGA-based general-purpose biochemical simulator

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

Department of Information and Computer Science

Research output: Contribution to journal › Article › peer-review

10 Citations (Scopus)

Abstract

Mathematical modeling and simulation of cellular systems are essential to modern biological researches. However, simulating with software-based simulators on general-purpose microprocessors cannot provide enough throughput. ReCSiP is an FPGA-based solution for biochemical simulation and parameter scanning. This paper describes its design and hardware implementation. With Xilinx's XC2VP70-5, this method achieved 50-to 80-fold speed-up compared to Intel's Pentium4 processor.

Original language	English
Pages (from-to)	1-10
Number of pages	10
Journal	Electronics and Communications in Japan, Part II: Electronics (English translation of Denshi Tsushin Gakkai Ronbunshi)
Volume	90
Issue number	7
DOIs	https://doi.org/10.1002/ecjb.20370
Publication status	Published - 2007 Jul

Keywords

Biochemical simulations
FPGA
Ordinary differential equations
Rate-law functions
Runge-Kutta method

ASJC Scopus subject areas

Physics and Astronomy(all)
Computer Networks and Communications
Electrical and Electronic Engineering

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10.1002/ecjb.20370

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Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., & Amano, H. (2007). ReCSiP: An FPGA-based general-purpose biochemical simulator. Electronics and Communications in Japan, Part II: Electronics (English translation of Denshi Tsushin Gakkai Ronbunshi), 90(7), 1-10. https://doi.org/10.1002/ecjb.20370

Osana, Y, Yoshimi, M, Iwaoka, Y, Kojima, T, Nishikawa, Y, Funahashi, A, Hiroi, N, Shibata, Y, Iwanaga, N, Kitano, H & Amano, H 2007, 'ReCSiP: An FPGA-based general-purpose biochemical simulator', Electronics and Communications in Japan, Part II: Electronics (English translation of Denshi Tsushin Gakkai Ronbunshi), vol. 90, no. 7, pp. 1-10. https://doi.org/10.1002/ecjb.20370

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AU - Nishikawa, Yuri

AU - Funahashi, Akira

AU - Hiroi, Noriko

AU - Shibata, Yuichiro

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AU - Kitano, Hiroaki

AU - Amano, Hideharu

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AB - Mathematical modeling and simulation of cellular systems are essential to modern biological researches. However, simulating with software-based simulators on general-purpose microprocessors cannot provide enough throughput. ReCSiP is an FPGA-based solution for biochemical simulation and parameter scanning. This paper describes its design and hardware implementation. With Xilinx's XC2VP70-5, this method achieved 50-to 80-fold speed-up compared to Intel's Pentium4 processor.

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KW - Ordinary differential equations

KW - Rate-law functions

KW - Runge-Kutta method

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ReCSiP: An FPGA-based general-purpose biochemical simulator

Abstract

Keywords

ASJC Scopus subject areas

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