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
Volume2005
DOIs
Publication statusPublished - 2005
Event19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005 - Denver, CO, United States
Duration: 2005 Apr 42005 Apr 8

Other

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

Fingerprint

Field programmable gate arrays (FPGA)
Markup languages
Networks (circuits)
Systems Biology

Keywords

  • Biochemical simulation
  • FPGA
  • Multimodel
  • ODE
  • SBML

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Osana, Y., Fukushima, T., Yoshimi, M., Iwaoka, Y., Funahashi, A., Hiroi, N., ... Amano, H. (2005). An FPGA-based, multi-model simulation method for biochemical systems. In Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005 (Vol. 2005). [1420035] https://doi.org/10.1109/IPDPS.2005.103

An FPGA-based, multi-model simulation method for biochemical systems. / Osana, Yasunori; Fukushima, Tomonori; Yoshimi, Masato; Iwaoka, Yow; Funahashi, Akira; Hiroi, Noriko; Shibata, Yuichiro; Kitano, Hiroaki; Amano, Hideharu.

Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005. Vol. 2005 2005. 1420035.

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

Osana, Y, Fukushima, T, Yoshimi, M, Iwaoka, Y, Funahashi, A, Hiroi, N, Shibata, Y, Kitano, H & Amano, H 2005, An FPGA-based, multi-model simulation method for biochemical systems. in Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005. vol. 2005, 1420035, 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005, Denver, CO, United States, 05/4/4. https://doi.org/10.1109/IPDPS.2005.103
Osana Y, Fukushima T, Yoshimi M, Iwaoka Y, Funahashi A, Hiroi N et al. An FPGA-based, multi-model simulation method for biochemical systems. In Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005. Vol. 2005. 2005. 1420035 https://doi.org/10.1109/IPDPS.2005.103
Osana, Yasunori ; Fukushima, Tomonori ; Yoshimi, Masato ; Iwaoka, Yow ; Funahashi, Akira ; Hiroi, Noriko ; Shibata, Yuichiro ; Kitano, Hiroaki ; Amano, Hideharu. / An FPGA-based, multi-model simulation method for biochemical systems. Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005. Vol. 2005 2005.
@inproceedings{0eb3eea65f9b425f81b42bc9265165fe,
title = "An FPGA-based, multi-model simulation method for biochemical systems",
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.",
keywords = "Biochemical simulation, FPGA, Multimodel, ODE, SBML",
author = "Yasunori Osana and Tomonori Fukushima and Masato Yoshimi and Yow Iwaoka and Akira Funahashi and Noriko Hiroi and Yuichiro Shibata and Hiroaki Kitano and Hideharu Amano",
year = "2005",
doi = "10.1109/IPDPS.2005.103",
language = "English",
isbn = "0769523129",
volume = "2005",
booktitle = "Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005",

}

TY - GEN

T1 - An FPGA-based, multi-model simulation method for biochemical systems

AU - Osana, Yasunori

AU - Fukushima, Tomonori

AU - Yoshimi, Masato

AU - Iwaoka, Yow

AU - Funahashi, Akira

AU - Hiroi, Noriko

AU - Shibata, Yuichiro

AU - Kitano, Hiroaki

AU - Amano, Hideharu

PY - 2005

Y1 - 2005

N2 - 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.

AB - 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.

KW - Biochemical simulation

KW - FPGA

KW - Multimodel

KW - ODE

KW - SBML

UR - http://www.scopus.com/inward/record.url?scp=33746321090&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33746321090&partnerID=8YFLogxK

U2 - 10.1109/IPDPS.2005.103

DO - 10.1109/IPDPS.2005.103

M3 - Conference contribution

AN - SCOPUS:33746321090

SN - 0769523129

SN - 0769523129

SN - 9780769523125

VL - 2005

BT - Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005

ER -