A modular approach to heterogeneous biochemical model simulation on an FPGA

Hideki Yamada; Yasunori Osana; Tomoya Ishimori; Tomonori Ooya; Masato Yoshimi; Yuri Nishikawa; Akira Funahashi; Noriko Hiroi; Hideharu Amano; Yuichiro Shibata; Kiyoshi Oguri

doi:10.1109/ReConFig.2009.55

A modular approach to heterogeneous biochemical model simulation on an FPGA

Hideki Yamada, Yasunori Osana, Tomoya Ishimori, Tomonori Ooya, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata, Kiyoshi Oguri

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

1 Citation (Scopus)

Abstract

Mathematical modeling and simulation of cellular systems are important processes in modern life science, to understand the behavior of life as a system. Kinetic model of a biochemical pathways is described as an ordinary differential system, consists of a variety of equations to represent velocity of corresponding chemical reactions. This paper describes a modular and automated approach to synthesize a custom HDL module for given biochemical model, that enables to build an optimal circuit to accelerate its simulation within a limited resource of an FPGA. As the result of evaluation, this method achieved reduction of logic usage by 10-60% while the overheads in frequency and pipeline depth is remaining about 10%.

Original language	English
Title of host publication	ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs
Pages	125-130
Number of pages	6
DOIs	https://doi.org/10.1109/ReConFig.2009.55
Publication status	Published - 2009 Dec 1
Event	2009 International Conference on ReConFigurable Computing and FPGAs, ReConFig'09 - Cancun, Mexico Duration: 2009 Dec 9 → 2009 Dec 11

Publication series

Name	ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs

Other

Other	2009 International Conference on ReConFigurable Computing and FPGAs, ReConFig'09
Country/Territory	Mexico
City	Cancun
Period	09/12/9 → 09/12/11

Keywords

Biochemistry
Design automation
FPGA
Kinetic simulation

ASJC Scopus subject areas

Hardware and Architecture
Software

Access to Document

10.1109/ReConFig.2009.55

Cite this

Yamada, H., Osana, Y., Ishimori, T., Ooya, T., Yoshimi, M., Nishikawa, Y., Funahashi, A., Hiroi, N., Amano, H., Shibata, Y., & Oguri, K. (2009). A modular approach to heterogeneous biochemical model simulation on an FPGA. In ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs (pp. 125-130). [5382039] (ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs). https://doi.org/10.1109/ReConFig.2009.55

A modular approach to heterogeneous biochemical model simulation on an FPGA. / Yamada, Hideki; Osana, Yasunori; Ishimori, Tomoya et al.
ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs. 2009. p. 125-130 5382039 (ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs).

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

Yamada, H, Osana, Y, Ishimori, T, Ooya, T, Yoshimi, M, Nishikawa, Y, Funahashi, A, Hiroi, N, Amano, H, Shibata, Y & Oguri, K 2009, A modular approach to heterogeneous biochemical model simulation on an FPGA. in ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs., 5382039, ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs, pp. 125-130, 2009 International Conference on ReConFigurable Computing and FPGAs, ReConFig'09, Cancun, Mexico, 09/12/9. https://doi.org/10.1109/ReConFig.2009.55

Yamada H, Osana Y, Ishimori T, Ooya T, Yoshimi M, Nishikawa Y et al. A modular approach to heterogeneous biochemical model simulation on an FPGA. In ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs. 2009. p. 125-130. 5382039. (ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs). doi: 10.1109/ReConFig.2009.55

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AU - Funahashi, Akira

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A modular approach to heterogeneous biochemical model simulation on an FPGA

Abstract

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Keywords

ASJC Scopus subject areas

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