An FPGA-based acceleration method for metabolic simulation

Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Hideharu Amano

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Computer simulation of cellular process is one of the most important applications in bioinformatics. Since such simulators need huge computational resources, many biologists must use expensive PC/WS clusters. ReCSiP is an FPGA-based, reconfigurable accelerator which aims to realize economical high-performance simulation environment on desktop computers. It can exploit fine-grain parallelism in the target applications by small hardware modules in the FPGA which work in parallel manner. As the first step to implement a simulator of cellular process on ReCSiP, a solver to perform a basic simulation of metabolism was implemented. The throughput of the solver was about 29 times faster than the software on Intel's PentiumIII operating at 1.13 GHz.

Original languageEnglish
Pages (from-to)2029-2037
Number of pages9
JournalIEICE Transactions on Information and Systems
VolumeE87-D
Issue number8
Publication statusPublished - 2004 Aug

Fingerprint

Field programmable gate arrays (FPGA)
Simulators
Bioinformatics
Metabolism
Personal computers
Particle accelerators
Throughput
Hardware
Computer simulation

Keywords

  • FPGA
  • Metabolic simulation
  • Ordinary differential equations

ASJC Scopus subject areas

  • Information Systems
  • Computer Graphics and Computer-Aided Design
  • Software

Cite this

An FPGA-based acceleration method for metabolic simulation. / Osana, Yasunori; Fukushima, Tomonori; Yoshimi, Masato; Amano, Hideharu.

In: IEICE Transactions on Information and Systems, Vol. E87-D, No. 8, 08.2004, p. 2029-2037.

Research output: Contribution to journalArticle

Osana, Y, Fukushima, T, Yoshimi, M & Amano, H 2004, 'An FPGA-based acceleration method for metabolic simulation', IEICE Transactions on Information and Systems, vol. E87-D, no. 8, pp. 2029-2037.
Osana, Yasunori ; Fukushima, Tomonori ; Yoshimi, Masato ; Amano, Hideharu. / An FPGA-based acceleration method for metabolic simulation. In: IEICE Transactions on Information and Systems. 2004 ; Vol. E87-D, No. 8. pp. 2029-2037.
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