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.
Example#
The following example specifies the Gillespie (SSA) algorithm, 100 realizations, a duration of 730 time units (two years for a model with rates specified in days), and 250 samples of each realization spaced evenly over the 730 time unit duration.
{
"solver" : "SSA",
"runs" : 100,
"duration" : 730,
"samples" : 250
}