Stochastic simulation for biochemical reactions on FPGA

M. Yoshimi, Y. Osana, T. Fukushima, Hideharu Amano

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Biological cell simulations generally require high-powered computer resources. A reconfigurable system is a possible solution to the problem as an alternative approach against PC/WS clusters. A stochastic simulation algorithm proposed by Gillespie is implemented on a reconfigurable platform called ReCSiP, and the performance is evaluated. The implemented Lotka system outperforms the software implementation on AthlonXP2800+ by 105.13 times.

Original languageEnglish
Pages (from-to)105-114
Number of pages10
JournalLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3203
Publication statusPublished - 2004

Fingerprint

Reconfigurable Systems
Stochastic Simulation
Field Programmable Gate Array
Field programmable gate arrays (FPGA)
Software
Resources
Alternatives
Cell
Simulation

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

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