A Network-free application is designed to allow simulation of requested quantities of Observables and initially specified species without the generatipon of a network. In cases where the network generated by rules may be infinitely large (such as with filaments) but the number of particles is rather small, a network-free application allows a model to make predictions about timecourses of only the quantities of interest. Network-Free Applications use the NFSim simulator.
When using Network-Free Applications, it is important to be aware that:
Using a Network-Free application has the following limitations:
- While NRSim can be used with any model that obeys the limitations described below, it is designed to be used to simulate rule-based models.
- NFSim performs a stochastic simulation, so simulation results will vary by run.
- NFSim operates with particles, so copying a deterministic application as a Network-Free simulation may lead to very large numbers of particles. This number can be adjusted by changing the simulation volume in the structure size setting.
- The user is unable to see what species are populated during the simulation. To test if the reaction rules produce the expected species and reactions, the user is advised to generate a deterministic rule-based application
and test the network properties.
- The model must have a single compartment
- All reactions and reaction rules must have mass-action kinetics.
- The number of particles for participating species is limited: the default is 200,000 (it may be increased using the
NFSim Simulation Editor).