One kind of time series which we could generate is the one which interprets the Bio-PEPA model in the continuous, deterministic regime in which the species variables are subject to continuous change and take real number values in each run.
Before we can generate a time series for our Bio-PEPA model we need to set the parameters for the simulation (see Figure 20). The parameters which need to be set, differ from one simulator to another but the simulators for ODE models typically include:
Start time — the start time of the time series (often 0)
Stop time — the stop time of the time series (model dependent)
Step size — the step size of the ODE integrator
Number of data points — the number of data points that you would like to have recorded
Relative error — the relative error of the ODE integrator
Absolute error — the absolute error of the ODE integrator
Once you have selected a solver and entered values for all of the parameters then you can click Finish to run the simulation and plot the results in the Graph View.