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Soufiene Benkirane

Stirling's software

I have developed a software that allows can:

• Translate a PEPA model with information about compartments into a valid PEPA model: I have developed a grammar that allows compartments in PEPA model. A draft of the description of the grammar can be found here. Further biologically inspired PEPA models with compartments can be found here and there
.
• Performs stochastic simulation and derives ODEs: the stochastic simulations are performed by the tool develop by the University of Edinburgh (though it might not be the most up to date version of the tool) and derives ODEs from the PEPA model using the Stirling Amendment algorithm described in this paper. A Mathematica file is then generated, explicitely containing the ODEs, the average of the simulations performed, as well as the standard deviation.

The software can be downloaded here. The version of the tool developed by the University of Edinburgh can be downloaded here and needs to be in the folder the software is in. All the java and javacc code used for this software is available in the jar. Feel free to modify it to suit your needs, and let me know if you have any question, or if you find a bug in the software. Apologies for any french used in the code. I tried to avoid, but old habits are sometimes hard to get rid of.