How to simulate a rule-based model

Once rule-based features are specified in Physiology, a user has mulktiple choices of how to simulate. As standard with Virtual Cell, a Rule-Based BioModel may have numerous Applications, including deterministic and stochastic ( rule-based) applications and special network-free application. Each Application, in turn can have multiple Simulations, in which different numerical methods or conditions are used.

Rule-based Deterministic and Stochastic Applications

If a user chooses to start deterministic or stochastic applications, the BioNetGen network-generation algorithm will be used to generate the complete network of species and reactions that is obtained by applying the set of reaction rules to the set of seed species. Initial amounts of seed species are defined in Network specification tab. Network specification parameters (number of iterations to apply rules and maximal number of molecules per species in generated network) can be used to control the size of the network, which otherwise can become infinite. The generated species and reactions can be seen in Network tab, but not added to the Reaction Diagram view.

After the network is generated, regular determiministic or stochastic simulations can be run.

Network-Free Applications

If a user chooses to start network-free applications, no network-generation attempt will be done and the amounts of model Observables and initially defined species will be simulated using NFSim engine. Simulation parameters can be defined in NFSim Simulation Editor.

Rule-Based MathModel