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

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9 Author(s)
Y. Osana ; Keio Univ., Yokohama, Japan ; T. Fukushima ; M. Yoshimi ; Y. Iwaoka
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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 Pentiumlll 1.13GHz.

Published in:

19th IEEE International Parallel and Distributed Processing Symposium

Date of Conference:

4-8 April 2005