Depicted below is the modeling process carried out in the Virtual Cell. It begins with the physiological model being defined in terms of species, structures, reactions, fluxes, and currents. Note, not all models must contain all terms; it will depend on the complexity of the model.

The model is associated with the application component, which allows you to isolate simulation specific assumptions from the rest of the model. This involves mapping the structures to subdomains, which are the image regions defined in either the analytical or experimental geometry, and defining initial conditions, boundary conditions, fast reactions, diffusion protocols and electrical mapping.

Once the application is created, a detailed math description of the model and application is automatically and transparently generated by the software. One can then run a simulation which will include additional model details such as model parameters, mesh size and solver options.

The simulation results can provide information regarding time response, sensitivities and steady state. Such results can be used for analysis, further modeling and for redefining the experimental protocol.

External resources such as pathway databases and information from existing literature are being introduced into the Virtual Cell software. Information from outside sources will be able to be incorporated into the physiological model. Currently reactions from the KEGG Reaction Database can be entered into the Virtual Cell.