Spatkin

Spatkin: A simulator for rule-based modeling on surfaces. Spatkin implements a direct, lattice-based method, which avoids enumeration of the reaction network implied by a set of rules. Models are specified using an extension of the BioNetGen language, which adds features necessary for characterizing diffusion properties of biomolecules. The tool is capable of simulating biomolecular interactions occurring on or at a two-dimensional surface, such as interactions of the kind commonly involved in receptor signaling.