Practical implementation of a network-based Stochastic biochemical simulation system on an FPGA

Masato Yoshimi, Yuri Nishikawa, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Hideki Yamada, Hiroaki Kitano, Hideharu Amano

研究成果: Conference contribution

5 引用 (Scopus)

抜粋

Stochastic simulation of biochemical reaction networks are widely focused by life scientists to represent stochastic behaviors in cellular processes. Stochastic algorithm has loop-and thread-level parallelism, and it is suitable for running on application specific hardware to achieve high performance with low cost. We have implemented and evaluated the FPGA-based stochastic simulator according to theoretical research of the algorithm. This paper introduces an improved architecture for accelerating a stochastic simulation algorithm called the Next Reaction Method. This new architecture has scalability to various size of FPGA. As the result with a middle-range FPGA, 5.38 times higher throughput was obtained compared to software running on a Core 2 Quad Q6600 2.40GHz.

元の言語English
ホスト出版物のタイトルProceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL
ページ663-666
ページ数4
DOI
出版物ステータスPublished - 2008 11 3
イベント2008 International Conference on Field Programmable Logic and Applications, FPL - Heidelberg, Germany
継続期間: 2008 9 82008 9 10

出版物シリーズ

名前Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL

Other

Other2008 International Conference on Field Programmable Logic and Applications, FPL
Germany
Heidelberg
期間08/9/808/9/10

ASJC Scopus subject areas

  • Hardware and Architecture

フィンガープリント Practical implementation of a network-based Stochastic biochemical simulation system on an FPGA' の研究トピックを掘り下げます。これらはともに一意のフィンガープリントを構成します。

  • これを引用

    Yoshimi, M., Nishikawa, Y., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Yamada, H., Kitano, H., & Amano, H. (2008). Practical implementation of a network-based Stochastic biochemical simulation system on an FPGA. : Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL (pp. 663-666). [4630034] (Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL). https://doi.org/10.1109/FPL.2008.4630034