Performance evaluation of an FPGA-based biochemical simulator ReCSiP

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

研究成果: Conference contribution

4 引用 (Scopus)

抜粋

ReCSiP is an FPGA-based biochemical simulator to accelerate kinetic simulations of biochemical pathways. Biochemical models are described as a set of ordinary differential equations (ODEs). Each equation in the model is called "rate law function", which represents the velocity of corresponding biochemical reaction mechanism. ReCSiP achieves high-throughput simulation with statically pipelined rate law function modules and numerical integration modules on an FPGA. This paper shows the basic structure of ReCSiP, and results of evaluation in 2 aspects: area and throughput. As the summary of evaluation, 1) about 64% of the total circuit area is occupied by floating-point arithmetic units, and 2) with an XC2VP70, ReCSiP at 90MHz can achieve 20x or more speedup compared to Intel's Pentium4 microprocessor at 3.2GHz.

元の言語English
ホスト出版物のタイトルProceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL
ページ845-850
ページ数6
DOI
出版物ステータスPublished - 2006 12 1
イベント2006 International Conference on Field Programmable Logic and Applications, FPL - Madrid, Spain
継続期間: 2006 8 282006 8 30

出版物シリーズ

名前Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL

Other

Other2006 International Conference on Field Programmable Logic and Applications, FPL
Spain
Madrid
期間06/8/2806/8/30

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Electrical and Electronic Engineering

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  • これを引用

    Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Kitano, H., Amano, H., Shibata, Y., & Iwanaga, N. (2006). Performance evaluation of an FPGA-based biochemical simulator ReCSiP. : Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL (pp. 845-850). [4101089] (Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL). https://doi.org/10.1109/FPL.2006.311327