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Practical implementation of a network-based stochastic biochemical simulation system on an FPGA

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9 Author(s)

Stochastic simulation of biochemical reaction networks are widely focused by life scientists to represent stochastic behaviors in cellular processes. Stochastic algorithm has loop-and thread-level parallelism, and it is suitable for running on application specific hardware to achieve high performance with low cost. We have implemented and evaluated the FPGA-based stochastic simulator according to theoretical research of the algorithm. This paper introduces an improved architecture for accelerating a stochastic simulation algorithm called the Next Reaction Method. This new architecture has scalability to various size of FPGA. As the result with a middle-range FPGA, 5.38 times higher throughput was obtained compared to software running on a Core 2 Quad Q6600 2.40 GHz.

Published in:

Field Programmable Logic and Applications, 2008. FPL 2008. International Conference on

Date of Conference:

8-10 Sept. 2008