The rule-set can either be translated into a model such as Markov chains or differential equations, or be treated using tools that directly work on the rule-set in place of a translated model, as the latter is typically much bigger.
An important domain where this is often the case is biochemical models of living organisms.
Where: With the above line of code, BioNetGen will automatically create an ODE for each model species with the correct mass balance.
Early efforts to use rule-based modeling in simulation of biochemical systems include the stochastic simulation systems StochSim[2] A widely used tool for rule-based modeling of biochemical networks is BioNetGen [3] It is released under the GNU GPL, version 3.
The biochemical modeling framework Virtual Cell includes a BioNetGen interpreter.