An FPGA-Based Acceleration Method for Metabolic Simulation.

Keio University, Edo, Tokyo, Japan
IEICE Transactions on Information and Systems (Impact Factor: 0.21). 08/2004; 87-D(8):2029-2037.
Source: DBLP


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.

5 Reads
Show more