FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method

Masato Yoshimi, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hideki Yamada, Hiroaki Kitano, Hideharu Amano

研究成果: Conference contribution

14 引用 (Scopus)

抜粋

This paper introduces a scalable FPGA implementation of a stochastic simulation algorithm (SSA) called the Next Reaction Method. There are some hardware approaches of SSAs that obtained high-through put on reconfigurable devices such as FPGAs, but these works lacked in scalability. The design of this work can accommodate to the increasing size of target biochemical models, or to make use of increasing capacity of FPGAs. Interconnection network between arithmetic circuits and multiple simulation circuits aims to perform a data-driven multi-threading simulation. Approximately 8 times speedup was obtained compared to an execution on Xeon 2.80GHz.

元の言語English
ホスト出版物のタイトルProceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL
ページ254-259
ページ数6
DOI
出版物ステータスPublished - 2007 12 1
イベント2007 International Conference on Field Programmable Logic and Applications, FPL - Amsterdam, Netherlands
継続期間: 2007 8 272007 8 29

出版物シリーズ

名前Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL

Other

Other2007 International Conference on Field Programmable Logic and Applications, FPL
Netherlands
Amsterdam
期間07/8/2707/8/29

ASJC Scopus subject areas

  • Computer Science Applications
  • Electrical and Electronic Engineering

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  • これを引用

    Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Yamada, H., Kitano, H., & Amano, H. (2007). FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method. : Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL (pp. 254-259). [4380656] (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL). https://doi.org/10.1109/FPL.2007.4380656