Scalable FRM-SSA SoC Design for the Simulation of Networks with Thousands of Biochemical Reactions in Real Time

Simulation of biomolecular networks with thousands of reactions is becoming essential for systems biology. We are presenting the design of a scalable System on Chip parallel architecture that implements Gillespie´s First Reaction Method in reconfigurable FPGA hardware. Our SoC architecture can deliver performance (Mega-Reactions/sec) and throughput (M-Reaction cycles/sec) that is increasing linearly with the number of processors when simulating large biomolecular networks with up to m = 4096 reactions using a moderate size FPGA. We have synthesized and verified various SoC instances with up to N=8 Processing Elements for Xilinx Virtex 5 and Altera Cyclone III FPGAs, reaching clock frequencies up to 180 MHz and delivering simulation performance that is more than 2 order of magnitude higher than that of Intel Core 2 and i7 CPUs running at frequencies above 2GHz.