An FPGA-Based Acceleration Method for Metabolic Simulation.

ArticleinIEICE Transactions on Information and Systems 87-D(8):2029-2037 · August 2004with10 Reads
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.
    • "ReCSiP is an FPGA-based high-throughput biochemical simulation platform. Some prototype modules for biochemical simulations are already implemented on FPGAs[6][10], and they achieved about 10 to 200-fold speedup compared to modern microprocessors. It runs the modules called " solvers " which calculate the velocity of biochemical reactions. "
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