Once a biological model has been defined in the physiology view, an Application in the Virtual Cell software is used to set up a virtual experiment. Setting up an application includes deciding the type of mathematical model (deterministic or stochastic) to be created, mapping relationships between the physiological objects, their values and geometries, and setting initial conditions for the species and reactions. The Specifications item in an 'Application' involves setting initial conditions for species and reactions for that particular virtual experiment.
Specifications can be accessed by clicking the Specifications item under any Application in the 'Navigation' panel tree structure. This selects the Specifications tab for the application in the 'View' panel on the right. The 'Specifications' tab has the following 3 sub-tabs: