An FPGA-based, multi-model simulation method for biochemical systems

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

Modeling and simulation of a cellular system on computers are now becoming an essential process in biological researches. However, modern PCs can't provide enough performance to simulate large-scale biochemical networks. ReCSiP is the alternative FPGA-based solution for biochemical simulations. In this paper, the novel method of biochemical simulation with multiple reaction models on an FPGA is proposed. The method generates optimal circuit and its optimal schedule for each simulation models written in SBML, the standard markup language in systems biology. ReCSiP has a Xilinx's XC2VP70 and achieved over 20-fold speedup compared to Intel's PentiumIII 1.13GHz.

Original languageEnglish
Title of host publicationProceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005
DOIs
Publication statusPublished - 2005 Dec 1
Event19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005 - Denver, CO, United States
Duration: 2005 Apr 42005 Apr 8

Publication series

NameProceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005
Volume2005

Other

Other19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005
CountryUnited States
CityDenver, CO
Period05/4/405/4/8

Keywords

  • Biochemical simulation
  • FPGA
  • Multimodel
  • ODE
  • SBML

ASJC Scopus subject areas

  • Engineering(all)

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