Simulating metabolism in Escherichia coli K-12 — A circuit-based approach

Computational methods for describing, understanding, and manipulating biological pathways continue to be a heavily researched area. Many researchers use constructs based in electrical circuit design in the modeling and analysis of biological systems, but few draw on and exploit parallels between electrical circuits and biological circuits for simulation purposes. We develop a biological simulation framework using Xycetrade, a large-scale electrical circuit simulator, that is capable of simulating the complete metabolic system of Escherichia coli K-12. Using our framework we are able to model large-scale hybrid systems as demonstrated in successful simulation of E.coli central metabolism, a system that includes metabolic and corresponding genetic regulatory networks.