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 Dec 1
EventInternational Conference on Field Programmable Technology, ICFPT 2007 - Kitakyushu, Japan
Duration: 2007 Dec 122007 Dec 14

Publication series

NameICFPT 2007 - International Conference on Field Programmable Technology

Other

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

ASJC Scopus subject areas

  • Hardware and Architecture
  • Electrical and Electronic Engineering

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  • Cite this

    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 (pp. 193-200). [4439249] (ICFPT 2007 - International Conference on Field Programmable Technology). https://doi.org/10.1109/FPT.2007.4439249