A soft IP core generating SoCs for the efficient stochastic simulation of large Biomolecular Networks using FPGAs

A soft IP core, expressed in parametric VHDL, has been developed and used to synthesize different multiprocessor Systems on Chip (SoCs) for the stochastic simulation of large-size biochemical reaction networks based on Gillespie's First Reaction Method (FRM). The SoCs can be configured to have up to N=8 Processing Elements and simulate efficiently in hardware biomolecular networks with up to m=16K reactions. The FPGA implementations of the SoCs are communicating with a host PC via the serial and Ethernet ports for control and data transmission respectively. When mapped to a Virtex-5 Xilinx FPGA the FRM SoCs can deliver simulation performance (in Mega-Reactions/sec) that may exceed by up to two orders of magnitude the performance of well known software simulators running on fast PCs.