A command-line version of Bio-PEPA integrated with MultiVeStA is available here.
The experiment depicted in Figure 2, consisting in the transient analysis of the query in Listing 2 can be executed by running:
java -jar MultiVeStABioPepa.jar client -sd uk.ac.ed.inf.biopepa.multivesta.BioPEPAState \ -m input/models/camp-pka-mapk.biopepa -f input/MultiQuaTEx/ACFractionTransient.quatex \ -l 1 -vp true -a 0.05 -d1 0.01 -sots 1 -bs 30
where we specified the following options:
- -sd: the simulator to be used;
- -m: the model;
- -f: the query;
- -l: the local parallelism, useful to distribute the simulations across the cores of the used machine
- -vp: if the result has to be shown in an interactive plot;
- -a and -d1: the confidence interval;
- -sots the random seed to be used to generate all seeds necessary to the analysis (useful to reproducibility);
- -bs: the number of simulations to be performed at each iteration before checking the confidence interval, and at every iteration.
Steady state analysis
Instead, the query in Listing 3 can be analysed at steady state by running:
java -jar MultiVeStABioPepa.jar client -sd uk.ac.ed.inf.biopepa.multivesta.BioPEPAState \ -m input/models/camp-pka-mapk.biopepa -f input/MultiQuaTEx/ACFractionSteady.quatex \ -vp true -a 0.05 -d1 0.01 -sots 1