Network-Free Application

Network-free application is designed to allow simulation of requested quantities (Observables) and initially specified (species) without the generatipon of a network. In cases when the model generated by rules may have an infinite network (such as in filaments) but the number of particles is rather small, this type of application allows a model to make predictions about timecourses of quantities of interest.

Using Network-Free Applications, please be aware of:

• While it can be used for every model obeying limitations below, it is designed to be used to simulate rule-based models.
• This is stochastic simulation, so simulation results will vary by run.
• It operates with particles, so copying deterministic application as NFSim may lead to very large number of particles. This number can be adjusted by changing simulation volume in structure size setting.
• The user is unable to see what species are populated during simulation. To test if reaction rules produce expected species and reactions, the user is advised to generate deterministic rule-based application and test network properties.

• The model must have a single compartment
• All reactions and reaction rules must have mass-action kinetics only
• The number of particles for participating species is limited: the default is 200,000 (it may be increased in NFSim Simulation Editor).