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
Event2006 International Conference on Field Programmable Logic and Applications, FPL - Madrid, Spain
Duration: 2006 Aug 282006 Aug 30

Other

Other2006 International Conference on Field Programmable Logic and Applications, FPL
CountrySpain
CityMadrid
Period06/8/2806/8/30

Fingerprint

Field programmable gate arrays (FPGA)
Simulators
Throughput
Digital arithmetic
Costs

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Electrical and Electronic Engineering

Cite this

Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., ... 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] https://doi.org/10.1109/FPL.2006.311218

An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems. / Yoshimi, Masato; Osana, Yasunori; Iwaoka, Yow; Nishikawa, Yuri; Kojima, Toshinori; Shibata, Yuichiro; Iwanaga, Naoki; Funahashi, Akira; Hiroi, Noriko; Kitano, Hiroaki; Amano, Hideharu.

Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL. 2006. p. 227-232 4100980.

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

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., 4100980, pp. 227-232, 2006 International Conference on Field Programmable Logic and Applications, FPL, Madrid, Spain, 06/8/28. https://doi.org/10.1109/FPL.2006.311218
Yoshimi M, Osana Y, Iwaoka Y, Nishikawa Y, Kojima T, Shibata Y et al. 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. 2006. p. 227-232. 4100980 https://doi.org/10.1109/FPL.2006.311218
Yoshimi, Masato ; Osana, Yasunori ; Iwaoka, Yow ; Nishikawa, Yuri ; Kojima, Toshinori ; Shibata, Yuichiro ; Iwanaga, Naoki ; Funahashi, Akira ; Hiroi, Noriko ; Kitano, Hiroaki ; Amano, Hideharu. / An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems. Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL. 2006. pp. 227-232
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