Batch Means

This page provides the accompanying material of the IFM 2017 paper, where we extended MultiVeStA with steady state analysis capabilities. he main page of MultiVeStA

Download

A command-line version of Bio-PEPA integrated with MultiVeStA is available here.

Transient analysis

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

 

MultiVeStA’s homepage

Is here.