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 1

Keywords

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

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Computer Networks and Communications
  • Electrical and Electronic Engineering

Fingerprint Dive into the research topics of 'ReCSiP: An FPGA-based general-purpose biochemical simulator'. Together they form a unique fingerprint.

  • Cite this