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

研究成果: Conference contribution

4 引用 (Scopus)

抜粋

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.

元の言語English
ホスト出版物のタイトルProceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005
DOI
出版物ステータスPublished - 2005 12 1
イベント19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005 - Denver, CO, United States
継続期間: 2005 4 42005 4 8

出版物シリーズ

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

Other

Other19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005
United States
Denver, CO
期間05/4/405/4/8

ASJC Scopus subject areas

  • Engineering(all)

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  • これを引用

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