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

doi:10.1109/IPDPS.2005.103

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

Department of Information and Computer Science

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

5 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 language	English
Title of host publication	Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005
DOIs	https://doi.org/10.1109/IPDPS.2005.103
Publication status	Published - 2005
Event	19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005 - Denver, CO, United States Duration: 2005 Apr 4 → 2005 Apr 8

Publication series

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

Other

Other	19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005
Country/Territory	United States
City	Denver, CO
Period	05/4/4 → 05/4/8

Keywords

Biochemical simulation
FPGA
Multimodel
ODE
SBML

ASJC Scopus subject areas

Engineering(all)

Access to Document

10.1109/IPDPS.2005.103

Cite this

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 Article 1420035 (Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005; Vol. 2005). https://doi.org/10.1109/IPDPS.2005.103

An FPGA-based, multi-model simulation method for biochemical systems. / Osana, Yasunori; Fukushima, Tomonori; Yoshimi, Masato et al.
Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005. 2005. 1420035 (Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005; Vol. 2005).

Research output: Chapter in Book/Report/Conference proceeding › Conference 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., 1420035, Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005, vol. 2005, 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. 2005. 1420035. (Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005). doi: 10.1109/IPDPS.2005.103

@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",

series = "Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005",

booktitle = "Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005",

note = "19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005 ; Conference date: 04-04-2005 Through 08-04-2005",

}

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 - 9780769523125

T3 - Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005

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

T2 - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005

Y2 - 4 April 2005 through 8 April 2005

ER -

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

Abstract

Publication series

Other

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this