The design of scalable stochastic biochemical simulator on FPGA

Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano

研究成果: Conference contribution

6 引用 (Scopus)

抜粋

Biochemical simulations including whole-cell models require high performance computing systems. Reconfigurable systems are expected to be an alternative solution for conventional methods by PC clusters or vector computers. This paper shows the implementation of a stochastic biochemical simulation algorithm called Next Reaction Method for Virtex-II PRO, As the result of benchmarking with a small reaction system, the FPGA-based simulator outperforms the software implementation on Xeon 2.40GHz by 17.1 times.

元の言語English
ホスト出版物のタイトルProceedings - 2005 IEEE International Conference on Field Programmable Technology
ページ339-340
ページ数2
DOI
出版物ステータスPublished - 2005 12 1
イベント2005 IEEE International Conference on Field Programmable Technology - , Singapore
継続期間: 2005 12 112005 12 14

出版物シリーズ

名前Proceedings - 2005 IEEE International Conference on Field Programmable Technology
2005

Other

Other2005 IEEE International Conference on Field Programmable Technology
Singapore
期間05/12/1105/12/14

ASJC Scopus subject areas

  • Engineering(all)

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  • これを引用

    Yoshimi, M., Osana, Y., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., & Amano, H. (2005). The design of scalable stochastic biochemical simulator on FPGA. : Proceedings - 2005 IEEE International Conference on Field Programmable Technology (pp. 339-340). [1568590] (Proceedings - 2005 IEEE International Conference on Field Programmable Technology; 巻数 2005). https://doi.org/10.1109/FPT.2005.1568590