Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes. Results: We present Cyto-Sim, a stochastic simulator of membrane-enclosed hierarchies of biochemical processes, where the membranes comprise an inner, outer and integral layer. The underlying model is based on formal language theory and has been shown to have decidable properties (Cavaliere and Sedwards, 2006), allowing formal analysis in addition to simulation. The simulator provides variable levels of abstraction via arbitrary chemical kinetics which link to ordinary differential equations. In addition to its compact native syntax, Cyto-Sim currently supports models described as Petri nets, can import all versions of SBML and can export SBML and MATLAB® m-files. Availability: Cyto-Sim is available free, either as an applet or a stand-alone Java program via the web page ( Other versions can be made available upon request.