In the following, we describe how to reproduce simulation traces of the Petri net models presented in the paper entitled "Petri Nets for Modeling Cholesterol Metabolism and Hypercholesterolemia Therapy."

Prerequisites:

    To load the Petri net models (continuous, hybrid, and fuzzy continuous Petri nets), you need to have Snoopy Tool installed on your machine.
    If Snoopy is not installed, please follow this link to obtain the Snoopy installation package: https://www-dssz.informatik.tu-cottbus.de/DSSZ/Software/Snoopy.

Workflow:

    - You can load the PN model directly by double-clicking a Snoopy PN file (e.g., .cpn), which will trigger Snoopy to run and load the corresponding file immediately. Alternatively, you can run Snoopy and then load the PN model file by clicking on the File menu -> Open command and then choosing the Snoopy PN document.
    - To run a simulation of the loaded PN model, please navigate to the View menu -> Start Simulation Mode.
    - The simulation configuration window will appear as a result of the previous step. In this window, you can do the following:
        - Change the model configuration (e.g., value sets of the used constants such as kinetic parameters).
        - Change the default simulation configuration (e.g., simulation time, the corresponding ODE solver for continuous simulation).
        - Configure the corresponding simulator to produce simulation traces to the local drive on the machine via the Import/Export section.
    - After you finish the configuration sections (optional), you can start the model simulation by clicking on the Start Simulation button.
    - Once the simulation progress reaches 100%, you can view the simulation results by clicking on the default view.

Please note that we used the Gnuplot tool to produce the simulation traces presented in our paper. For plotting fence plots presented in the fuzzy continuous Petri net model, we developed our Gnuplot script for this purpose, which is attached as well. In this case, you need to export simulation traces to the CSV format and then feed the results .csv to the .plt script.

Dr. George Assaf
Cottbus, 18.03.2023