The Virtual Cell Software has three primary documents for defining computational models different modeling approaches. Each document can be saved and loaded independently.

• BioModel: a graphical user interface environment to define model elements. A BioModel consists of a model description (Physiology), and one or more Applications that define conditions for exploring computational models of the Physiology.
• MathModel: a mathematical environment that specifies a mathematical model description either automatically generated from a BioModel Application or coded using the VCell Markup Language (VCML).
• Geometry: an explicitly defined 1D, 2D or 3D representation of a spatial structure that a BioModel Application or a MathModel can use for spatially resolved simulations.

The BioModel consists of:

• Physiology – a conceptual representation of the biological system in terms of cellular structures, species and biochemical reactions, including the types of kinetics that govern reactions. Rule-based modeling can also be used, which allows the representation of species as structured objects consisting of Molecules and uses reaction rules to define molecular interactions. The rule-based approach allows one to systematically incorporate site-specific details of molecular interactions into a model and simulate timecourses for model outputs (Observables) that may be functions of a large numbers of species.
• Pathway Information that associates elements of the model with annotated biological
• Applications that each define quantitative conditions needed to simulate and visualize a specific virtual experiment:
  • Specifications for species initial conditions and reactions declarations, as well as network parameters in rule-based approaches
  • Geometries used for simulations. Applications can be compartmental (well-mixed compartments) or can use different types of spatial geometries (see below).
  • Protocols to define experimental events or electrical mapping.
  • Parameter Estimation to estimate exact values of unknown parameters when the model is constrained by known datasets.
  • A mathematical representation is automatically generated for each Application that can be viewed, or edited and run independently as a MathModel.
  • Each Application can have multiple Simulations in which different numerical methods or conditions are used.
    • Simulations with different solvers
    • Simulations with different parameters (length of time, time step, spatial resolution, parameter overrides, etc.).
    • Simulation Results can be viewed and analyzed in VCell or exported to a variety of formats.

 The MathModel is a formalized math description of a BioModel Application. A declarative mathematical language describes processes modeled in the VCell. This language defines parameters, variables, and differential/algebraic systems defined over complex geometry.

• One or more Simulations must be defined for each MathModel to run and produce Results.
• The math from a BioModel Application is a valid MathModel, but a MathModel cannot be converted to a BioModel Application.
• MathModels can be used to override biology-driven limitations of BioModels.

The Geometry is a representation of a spatial structure that a BioModel Application (or a MathModel) can use for spatially resolved simulations.

• A geometry can be 1-D, 2-D, or 3-D.
• Geometry can be defined in multiple ways:
  • Analytically, using mathematical equations
  • Using provided templates for basic shapes
  • Based on an imported image set
  • Created using solid geometry (translate-rotate-scale)