IEICE TRANSACTIONS on Information
An FPGA-Based Acceleration Method for Metabolic Simulation
Summary :
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.
- Publication
- IEICE TRANSACTIONS on Information Vol.E87-D No.8 pp.2029-2037
- Publication Date
- 2004/08/01
- Publicized
- Online ISSN
- DOI
- Type of Manuscript
- Special Section PAPER (Special Section on Reconfigurable Systems)
- Category
- Recornfigurable Systems
Authors
Keyword
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Yasunori OSANA, Tomonori FUKUSHIMA, Masato YOSHIMI, Hideharu AMANO, "An FPGA-Based Acceleration Method for Metabolic Simulation" in IEICE TRANSACTIONS on Information,
vol. E87-D, no. 8, pp. 2029-2037, August 2004, doi: .
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.
URL: https://global.ieice.org/en_transactions/information/10.1587/e87-d_8_2029/_p
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@ARTICLE{e87-d_8_2029,
author={Yasunori OSANA, Tomonori FUKUSHIMA, Masato YOSHIMI, Hideharu AMANO, },
journal={IEICE TRANSACTIONS on Information},
title={An FPGA-Based Acceleration Method for Metabolic Simulation},
year={2004},
volume={E87-D},
number={8},
pages={2029-2037},
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.},
keywords={},
doi={},
ISSN={},
month={August},}
Copy
TY - JOUR
TI - An FPGA-Based Acceleration Method for Metabolic Simulation
T2 - IEICE TRANSACTIONS on Information
SP - 2029
EP - 2037
AU - Yasunori OSANA
AU - Tomonori FUKUSHIMA
AU - Masato YOSHIMI
AU - Hideharu AMANO
PY - 2004
DO -
JO - IEICE TRANSACTIONS on Information
SN -
VL - E87-D
IS - 8
JA - IEICE TRANSACTIONS on Information
Y1 - August 2004
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.
ER -
English
