Difference between revisions of "Systems biology - model simulation"

Revision as of 15:02, 18 March 2022

To simulate SBML model, do the following:

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.
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.
Select one of the available simulators or use the default one:
- Euler
- Dormand-Prince
- Imex
- Descrete
- Radau V
- JVode (default)
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.
- Absolute tolerance, Relative Tolerance - tolerances for simulation. For example model we use 1.0E-8 values for both tolerances.
Click on the Simulate button . The window that opens will show the results of simulation of the variables selected to plot.

@@ Line 25: / Line 25: @@
 *'''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.
+*'''Absolute tolerance''', '''Relative Tolerance''' - tolerances for simulation. For example model we use 1.0E-8 values for both tolerances.
 <br>[[File:systems_biology_simulation_3.png]]<br><br>