An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems

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

研究成果: Conference contribution

6 被引用数 (Scopus)

抄録

Stochastic simulation of biochemical systems has become one of major approaches to study life processes as system, yet is a computational challenge to run the simulation due to its vast calculation cost. This paper shows the implementation and evaluation of a stochastic simulation algorithm (SSA) called "First Reaction Method" on an FPGA-based biochemical simulator. It achieves high throughput by (1) consecutively throwing data into deeply-pipelined floating point arithmetic units, and (2) by distruibuting multiple simulators for parallel execution. As the result of evaluation on an FPGA-based simulation platform called ReC-SiP2, the simulator outperforms execution on Xeon 2.80 GHz by approximately 80 times, even with large-scale biochemical systems.

本文言語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227-232
ページ数6
DOI
出版ステータス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
CountrySpain
CityMadrid
Period06/8/2806/8/30

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Electrical and Electronic Engineering

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