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

Author

Osana, Yasunori ; Fukushima, Tomonori ; Yoshimi, Masato ; Iwaoka, Yow ; Funahashi, Akira ; Hiroi, Noriko ; Shibata, Yuichiro ; Kitano, Hiroaki ; Amano, Hideharu

Author_Institution

Keio Univ., Yokohama, Japan

fYear

2005

fDate

4-8 April 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 Pentiumlll 1.13GHz.

Keywords

biochemistry; biology computing; digital simulation; field programmable gate arrays; FPGA; SBML; biochemical simulation; biochemical system; cellular system; multimodel simulation; optimal circuit; standard markup language; systems biology; Biological system modeling; Biology computing; Circuit simulation; Computational modeling; Computer simulation; Field programmable gate arrays; Large-scale systems; Markup languages; Optimal scheduling; Personal communication networks; Biochemical simulation; FPGA; Multimodel; ODE; SBML;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel and Distributed Processing Symposium, 2005. Proceedings. 19th IEEE International

Print_ISBN

0-7695-2312-9

Type

conf

DOI

10.1109/IPDPS.2005.103

Filename

1420035