An FPGA-Based Acceleration Method for Metabolic Simulation

Yasunori OSANA  Tomonori FUKUSHIMA  Masato YOSHIMI  Hideharu AMANO  

IEICE TRANSACTIONS on Information and Systems   Vol.E87-D   No.8   pp.2029-2037
Publication Date: 2004/08/01
Online ISSN: 
Print ISSN: 0916-8532
Type of Manuscript: Special Section PAPER (Special Section on Reconfigurable Systems)
Category: Recornfigurable Systems
metabolic simulation,  ordinary differential equations,  FPGA,  

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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.