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 |
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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 |
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