Simulations

You can run a simulation once you have defined your physiology and created an Application in a BioModel The model will be automatically saved upon running a simulation.

The Virtual Cell automatically converts the biological description defined in a BioModel into a corresponding mathematical system of math equations (e.g. ordinary and/or partial differential). The Virtual Cell will then solve the equations by applying numerical solvers to perform and analyze simulations. Afterwards Results can be displayed and analyzed on-line or downloaded to the userís computer in a variety of formats.

The Virtual Cell supports 5 categories of simulations.

The appropriate solver will automatically be chosen when a simulation is created. Additional solver choices may be available as dropdown menu. For more details about numerics solvers used in these simulations, refer to Numerical Solvers.



On the Simulation panel, you create, edit and run your simulations as well as view the results. Simulations that have been created are listed in the table. In this table, one can view some of the simulation parameters among which some can be changed in place.

Once a simulation is selected in the table, the properties of the selected simulation is displayed in the "Object Properties" Pane at the bottom. This provides a quick review of simulation settings. Most parameters can be changed by editing the simulation.

Simulation Toolbar:

On the left are the controls that create/edit/delete the simulations. on the right are the controls that run/stop simulations and view the results. Note most of buttons are only enabled when one or more simulations are selected. One can edit the name of a simulation by double-clicking on the Name field to select for editing. Pressing enter commits any edits to the simulation name.

On the left:

On the Right: