Accelerated analysis of Boolean gene regulatory networks

Abstract

In Systems Biology, Boolean models are gaining popularity in modeling and analysis of qualitative dynamics of gene regulatory mechanisms. With the development of advanced high-throughput technologies, the availability of experimental data on gene-gene, gene-protein interactions is ever increasing. Consequently, modern Boolean models are increasing in size and complexity. Software simulation of Boolean models does not scale for such state-of-the-art complex Boolean models. We propose Field Programmable Gate Arrays (FPGAs) for emulation of Boolean models, exploiting the highly parallel nature of FPGAs. Our emulation framework consists of converting a Boolean model to Verilog, connecting it to an execution core, which runs on an FPGA coherently attached to a POWER8 processor. We report an order of magnitude speed up over a multi-threaded software simulation tool running on the same processor.