Executable Petri net models for the analysis of metabolic pathways

Abstract

Computer-assisted simulation of biochemical processes is a means to augment the knowledge about the control mechanisms of such processes in particular organisms. This knowledge can be helpful for the goal-oriented design of drugs. Normally, continuous models (differential equations) are chosen for modelling such processes. The application of discrete event systems such as Petri nets has been restricted in the past to low-level modelling and qualitative analysis. To demonstrate that Petri nets are indeed suitable for simulating metabolic pathways, the glycolysis and citric acid cycle are selected as well-understood examples of enzymatic reaction chains (metabolic pathways). The paper discusses the steps that lead from gaining necessary knowledge about the involved enzymes and substances, to establishing and tuning high-level net models, to performing a series of simulations, and finally to analysing the results. We show that the consistent application of the Petri net view to these tasks has certain advantages, and – using advanced net tools – reasonable simulation times can be achieved.