Discrete event systems specification in systems biology - a discussion of stochastic pi calculus and DEVS

The goal of systems biology is to analyze the behavior and interrelationships between entities of entire functional biological systems. Discrete event approaches are of particular interest if small numbers of entities, like DNA molecules, shall be modeled. Two general approaches toward discrete event modeling and simulation are presented. They provide rather different perspectives on the system to be modeled, as is illustrated based on a model of the Trypophan Operon. Whereas in Devs distinctions are emphasized, e.g. between system and its environment, between structural and non structural changes, between properties attributed to a system and the system itself, these distinctions become fluent in the compact description of the π-calculus. However, both share the problem that in order to support a comfortable modeling, adaptations and extensions according to the concrete requirements of this challenging application area are needed.