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An FPGA-Based, Multi-model Simulation Method for Biochemical Systems


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Title: An FPGA-Based, Multi-model Simulation Method for Biochemical Systems
Authors: Osana, Yasunori / Fukushima, Tomonori / Yoshimi, Masato / Iwaoka, Yow / Shibata, Yuichiro / Kitano, Hiroaki / Funahashi, Akira / Hiroi, Noriko / Amano, Hideharu
Issue Date: 2005
Publisher: IEEE Computer Society Press
Citation: 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) Workshop 3 167a ; 2005
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.
Description: 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05), April 4-8, 2005, Denver, Colorado
Keywords: Biochemical simulation / FPGA / SBML / Multimodel / ODE
URI: http://hdl.handle.net/10069/16326
ISBN: 0769523129
Rights: Copyright(c) 2005 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.
Type: Conference Paper
Text Version: publisher
Appears in Collections:Conference Paper

Citable URI : http://hdl.handle.net/10069/16326

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