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 proceedingConference 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 languageEnglish
Title of host publicationReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs
Pages125-130
Number of pages6
DOIs
Publication statusPublished - 2009
Event2009 International Conference on ReConFigurable Computing and FPGAs, ReConFig'09 - Cancun, Mexico
Duration: 2009 Dec 92009 Dec 11

Other

Other2009 International Conference on ReConFigurable Computing and FPGAs, ReConFig'09
CountryMexico
CityCancun
Period09/12/909/12/11

Fingerprint

Field programmable gate arrays (FPGA)
Chemical reactions
Pipelines
Kinetics
Networks (circuits)

Keywords

  • Biochemistry
  • Design automation
  • FPGA
  • Kinetic simulation

ASJC Scopus subject areas

  • Hardware and Architecture
  • Software

Cite this

Yamada, H., Osana, Y., Ishimori, T., Ooya, T., Yoshimi, M., Nishikawa, 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] 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; Ooya, Tomonori; Yoshimi, Masato; Nishikawa, Yuri; Funahashi, Akira; Hiroi, Noriko; Amano, Hideharu; Shibata, Yuichiro; Oguri, Kiyoshi.

ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs. 2009. p. 125-130 5382039.

Research output: Chapter in Book/Report/Conference proceedingConference 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, 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 https://doi.org/10.1109/ReConFig.2009.55
Yamada, Hideki ; Osana, Yasunori ; Ishimori, Tomoya ; Ooya, Tomonori ; Yoshimi, Masato ; Nishikawa, Yuri ; Funahashi, Akira ; Hiroi, Noriko ; Amano, Hideharu ; Shibata, Yuichiro ; Oguri, Kiyoshi. / A modular approach to heterogeneous biochemical model simulation on an FPGA. ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs. 2009. pp. 125-130
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