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.
Published Version
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