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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Citations (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationProceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL
Pages227-232
Number of pages6
DOIs
Publication statusPublished - 2006 Dec 1
Event2006 International Conference on Field Programmable Logic and Applications, FPL - Madrid, Spain
Duration: 2006 Aug 282006 Aug 30

Publication series

NameProceedings - 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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    Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., & Amano, H. (2006). An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems. In Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL (pp. 227-232). [4100980] (Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL). https://doi.org/10.1109/FPL.2006.311218