Systems biology - model simulation

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Revision as of 14:59, 18 March 2022 by Ilya Kiselev (Talk | contribs)

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To simulate SBML model, do the following:

  1. Go to the Simulation tab in the right bottom panel. It has two inner tabs: Engine and Plot. First we will need to set variables to plot. Got to Plot tab and set value for default curve.

    Systems biology simulation 0.png

  2. Next step is to go to Engine tab and set simulation properties. Depending on the type of your diagram, the appropriate simulation engine will be set in the Selected engine field. For example, ODE Simulation Engine is used for ordinary differential equation models. For more information on supported simulation engines, see the Simulation section.

    Systems biology simulation 1.png

  3. Select one of the available simulators or use the default one:
    Systems biology simulation 2.png

  4. Set simulation options:
    • Initial time - initial value of the model time. It is strongly recommended to use only the value 0 here.
    • Completion time - the point in model time when the simulation ends.
    • Time increment - the gap between the time points at which the simulation results will be written.

    Systems biology simulation 3.png

  5. Click on the Simulate button Execute icon.png. The window that opens will show the results of simulation of the variables selected to plot.

    Systems biology simulation 4.png

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