A framework for implementing a network-based stochastic biochemical simulator on an FPGA

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

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

1 Citation (Scopus)

Abstract

This paper studies several designs of network-based FPGA implementation of a stochastic simulation algorithm called the Next Reaction Method, known for its large number of calculattion involved. The procedure is divided into several subdivisions which will be implemented as independent modules, and they are connected with configurable interconnection networks so as to provide high throughput. By performing a multi-threading simulation, 3.6 times speedup was obtained compared with an execution on general purpose processors.

Original languageEnglish
Title of host publicationICFPT 2007 - International Conference on Field Programmable Technology
Pages193-200
Number of pages8
DOIs
Publication statusPublished - 2007
EventInternational Conference on Field Programmable Technology, ICFPT 2007 - Kitakyushu, Japan
Duration: 2007 Dec 122007 Dec 14

Other

OtherInternational Conference on Field Programmable Technology, ICFPT 2007
CountryJapan
CityKitakyushu
Period07/12/1207/12/14

Fingerprint

Field programmable gate arrays (FPGA)
Simulators
Throughput

ASJC Scopus subject areas

  • Hardware and Architecture
  • Electrical and Electronic Engineering

Cite this

Yoshimi, M., Nishikawa, Y., Kojima, T., Osana, Y., Funahashi, A., Hiroi, N., ... Amano, H. (2007). A framework for implementing a network-based stochastic biochemical simulator on an FPGA. In ICFPT 2007 - International Conference on Field Programmable Technology (pp. 193-200). [4439249] https://doi.org/10.1109/FPT.2007.4439249

A framework for implementing a network-based stochastic biochemical simulator on an FPGA. / Yoshimi, Masato; Nishikawa, Yuri; Kojima, Toshlinori; Osana, Yasunori; Funahashi, Akira; Hiroi, Noriko; Shibata, Yuichiro; Yamada, Hideki; Kitano, Hiroaki; Amano, Hideharu.

ICFPT 2007 - International Conference on Field Programmable Technology. 2007. p. 193-200 4439249.

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

Yoshimi, M, Nishikawa, Y, Kojima, T, Osana, Y, Funahashi, A, Hiroi, N, Shibata, Y, Yamada, H, Kitano, H & Amano, H 2007, A framework for implementing a network-based stochastic biochemical simulator on an FPGA. in ICFPT 2007 - International Conference on Field Programmable Technology., 4439249, pp. 193-200, International Conference on Field Programmable Technology, ICFPT 2007, Kitakyushu, Japan, 07/12/12. https://doi.org/10.1109/FPT.2007.4439249
Yoshimi M, Nishikawa Y, Kojima T, Osana Y, Funahashi A, Hiroi N et al. A framework for implementing a network-based stochastic biochemical simulator on an FPGA. In ICFPT 2007 - International Conference on Field Programmable Technology. 2007. p. 193-200. 4439249 https://doi.org/10.1109/FPT.2007.4439249
Yoshimi, Masato ; Nishikawa, Yuri ; Kojima, Toshlinori ; Osana, Yasunori ; Funahashi, Akira ; Hiroi, Noriko ; Shibata, Yuichiro ; Yamada, Hideki ; Kitano, Hiroaki ; Amano, Hideharu. / A framework for implementing a network-based stochastic biochemical simulator on an FPGA. ICFPT 2007 - International Conference on Field Programmable Technology. 2007. pp. 193-200
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