BAM: BioAmbient machine

In recent years it has become clear that techniques developed for concurrent programming are in fact very useful for the analysis of complex systems in biology. To some level of abstraction, it is possible to regard biological phenomena, such as gene transcription, protein interaction and communication among cells, as concurrent entities that compute according to the rules of chemical reactions. In this paper we present a tool for representing and stochastically simulating complex biological systems with mobile compartments. BAM, our tool, implements a stochastic version of the BioAmbient calculus and helps in understanding and reasoning about the multiple interconnections between components in bioregulatory networks.