ReCSiP: An FPGA-based general-purpose biochemical simulator

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

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Mathematical modeling and simulation of cellular systems are essential to modern biological researches. However, simulating with software-based simulators on general-purpose microprocessors cannot provide enough throughput. ReCSiP is an FPGA-based solution for biochemical simulation and parameter scanning. This paper describes its design and hardware implementation. With Xilinx's XC2VP70-5, this method achieved 50-to 80-fold speed-up compared to Intel's Pentium4 processor.

Original languageEnglish
Pages (from-to)1-10
Number of pages10
JournalElectronics and Communications in Japan, Part II: Electronics (English translation of Denshi Tsushin Gakkai Ronbunshi)
Volume90
Issue number7
DOIs
Publication statusPublished - 2007 Jul

Fingerprint

simulators
Field programmable gate arrays (FPGA)
Microprocessor chips
Simulators
Throughput
Scanning
Hardware
microprocessors
central processing units
hardware
simulation
computer programs
scanning

Keywords

  • Biochemical simulations
  • FPGA
  • Ordinary differential equations
  • Rate-law functions
  • Runge-Kutta method

ASJC Scopus subject areas

  • Electrical and Electronic Engineering

Cite this

ReCSiP : An FPGA-based general-purpose biochemical simulator. / Osana, Yasunori; Yoshimi, Masato; Iwaoka, Yow; Kojima, Toshinori; Nishikawa, Yuri; Funahashi, Akira; Hiroi, Noriko; Shibata, Yuichiro; Iwanaga, Naoki; Kitano, Hiroaki; Amano, Hideharu.

In: Electronics and Communications in Japan, Part II: Electronics (English translation of Denshi Tsushin Gakkai Ronbunshi), Vol. 90, No. 7, 07.2007, p. 1-10.

Research output: Contribution to journalArticle

Osana, Yasunori ; Yoshimi, Masato ; Iwaoka, Yow ; Kojima, Toshinori ; Nishikawa, Yuri ; Funahashi, Akira ; Hiroi, Noriko ; Shibata, Yuichiro ; Iwanaga, Naoki ; Kitano, Hiroaki ; Amano, Hideharu. / ReCSiP : An FPGA-based general-purpose biochemical simulator. In: Electronics and Communications in Japan, Part II: Electronics (English translation of Denshi Tsushin Gakkai Ronbunshi). 2007 ; Vol. 90, No. 7. pp. 1-10.
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