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 language | English |
|---|---|
| Pages (from-to) | 2029-2037 |
| Number of pages | 9 |
| Journal | IEICE Transactions on Information and Systems |
| Volume | E87-D |
| Issue number | 8 |
| Publication status | Published - 2004 Aug |
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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 journal › Article
}
TY - JOUR
T1 - An FPGA-based acceleration method for metabolic simulation
AU - Osana, Yasunori
AU - Fukushima, Tomonori
AU - Yoshimi, Masato
AU - Amano, Hideharu
PY - 2004/8
Y1 - 2004/8
N2 - 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.
AB - 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.
KW - FPGA
KW - Metabolic simulation
KW - Ordinary differential equations
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UR - http://www.scopus.com/inward/citedby.url?scp=4344608169&partnerID=8YFLogxK
M3 - Article
AN - SCOPUS:4344608169
VL - E87-D
SP - 2029
EP - 2037
JO - IEICE Transactions on Information and Systems
JF - IEICE Transactions on Information and Systems
SN - 0916-8532
IS - 8
ER -