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19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 3
An FPGA-Based, Multi-model Simulation Method for Biochemical Systems
Denver, Colorado
April 04-April 08
ISBN: 0-7695-2312-9
ASCII Text
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Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Yow Iwaoka, Yuichiro Shibata, Hiroaki Kitano, Akira Funahashi, Noriko Hiroi, Hideharu Amano, "An FPGA-Based, Multi-model Simulation Method for Biochemical Systems," Parallel and Distributed Processing Symposium, International, vol. 4, pp. 167a, 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 3, 2005.
 
 
BibTex
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@article{ 10.1109/IPDPS.2005.103,
author = {Yasunori Osana and Tomonori Fukushima and Masato Yoshimi and Yow Iwaoka and Yuichiro Shibata and Hiroaki Kitano and Akira Funahashi and Noriko Hiroi and Hideharu Amano},
title = {An FPGA-Based, Multi-model Simulation Method for Biochemical Systems},
journal ={Parallel and Distributed Processing Symposium, International},
volume = {4},
year = {2005},
issn = {1530-2075},
pages = {167a},
doi = {http://doi.ieeecomputersociety.org/10.1109/IPDPS.2005.103},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
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TY - CONF
JO - Parallel and Distributed Processing Symposium, International
TI - An FPGA-Based, Multi-model Simulation Method for Biochemical Systems
SN - 1530-2075
SP
EP
A1 - Yasunori Osana,
A1 - Tomonori Fukushima,
A1 - Masato Yoshimi,
A1 - Yow Iwaoka,
A1 - Yuichiro Shibata,
A1 - Hiroaki Kitano,
A1 - Akira Funahashi,
A1 - Noriko Hiroi,
A1 - Hideharu Amano,
PY - 2005
KW - Biochemical simulation
KW - FPGA
KW - SBML
KW - Multimodel
KW - ODE
VL - 4
JA - Parallel and Distributed Processing Symposium, International
ER -
 
Yasunori Osana, Keio University, Yokohama, Japan
Tomonori Fukushima, Keio University, Yokohama, Japan
Masato Yoshimi, Keio University, Yokohama, Japan
Yow Iwaoka, Keio University, Yokohama, Japan
Yuichiro Shibata, Nagasaki University, Japan
Hiroaki Kitano, ERATO-SORST, JST, Japan
Akira Funahashi, ERATO-SORST, JST, Japan
Noriko Hiroi, ERATO-SORST, JST, Japan
Hideharu Amano, Keio University, Japan
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.
Index Terms:
Biochemical simulation, FPGA, SBML, Multimodel, ODE
Citation:
Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Yow Iwaoka, Yuichiro Shibata, Hiroaki Kitano, Akira Funahashi, Noriko Hiroi, Hideharu Amano, "An FPGA-Based, Multi-model Simulation Method for Biochemical Systems," ipdps, vol. 4, pp.167a, 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 3, 2005
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