A Modular Approach to Heterogeneous Biochemical Model Simulation on an FPGA

Abstract

Mathematical modeling and simulation of cellular systems are important processes in modern life science, to understand the behavior of life as a system. Kinetic model of a biochemical pathways is described as an ordinary differential system, consists of a variety of equations to represent velocity of corresponding chemical reactions. This paper describes a modular and automated approach to synthesize a custom HDL module for given biochemical model, that enables to build an optimal circuit to accelerate its simulation within a limited resource of an FPGA. As the result of evaluation, this method achieved reduction of logic usage by 10-60% while the overheads in frequency and pipeline depth is remaining about 10%.