Conference Paper

FPGA Implementation of a Data-Driven Stochastic Biochemical Simulator with the Next Reaction Method

Keio Univ., Yokohama
DOI: 10.1109/FPL.2007.4380656 Conference: Field Programmable Logic and Applications, 2007. FPL 2007. International Conference on
Source: IEEE Xplore

ABSTRACT This paper introduces a scalable FPGA implementation of a stochastic simulation algorithm (SSA) called the next reaction method. There are some hardware approaches of SSAs that obtained high-throughput on reconfigurable devices such as FPGAs, but these works lacked in scalability. The design of this work can accommodate to the increasing size of target biochemical models, or to make use of increasing capacity of FPGAs. Interconnection network between arithmetic circuits and multiple simulation circuits aims to perform a data-driven multi-threading simulation. Approximately 8 times speedup was obtained compared to an execution on Xeon 2.80 GHz.

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