An FPGA-based acceleration method for metabolic simulation

Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Hideharu Amano

Research output: Contribution to journalReview article

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

Keywords

  • FPGA
  • Metabolic simulation
  • Ordinary differential equations

ASJC Scopus subject areas

  • Software
  • Hardware and Architecture
  • Computer Vision and Pattern Recognition
  • Electrical and Electronic Engineering
  • Artificial Intelligence

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