A custom FPGA for the simulation of gene regulatory networks

Abstract

We present a unique FPGA that uses a mix of digital and large-signal analog computation for the simulation of gene regulatory networks. The prototype IC consists of a 4x5 array of configurable logic blocks along with programmable interconnect. It can simulate a network of pathways involving up to 20 genes and their associated proteins. The circuit design takes advantage of a number of analogies between CMOS circuits and gene networks. For example, a capacitor charge is used to represent a protein concentration, currents represent protein production, and a transistor switch network is used to compute the influences of activator and repressor proteins on gene expression. A simulation shows how the chip can predict oscillatory behavior in a particular well-known three-gene system.