Configuration file syntax

While CMS does not require a configuration file, running a simulation without one uses default settings that will not produce scientifically useful results. As a stochastic model, you must run many realizations in a CMS simulation for statistically significant results. The configuration file uses JSON syntax and a .cfg file extension.

The table below shows the basic parameters used in a minimal configuration.

Parameter Data type Default Description
duration integer 100 The number of time steps to run the realizations for; specified in unitless time relevant to the timescales of the model. The values will correspond to the units specified in the rates used in the model file.
runs integer 1 The number of realizations to run for the simulation.
samples integer 100 The number of samples of the various observables to take over the duration of the simulation.

Besides the parameters listed above, you will likely want to include configuration settings to control the solver that is used, the output created, and the pseudo-random number generator. By default, the Gillespie (SSA) solver is used and the file trajectories.csv is created in the output directory. See the other topics in this section for all available configuration parameters.