The Virtual Cell Software provides 2 environments for defining computational models. BioModels and MathModels allow the user to create models using the tool that best suits their experience. A BioModel consists of a model description (Physiology), and one or more Applications generated using a graphical interface to define model elements. A MathModel is a document defined using the VCell Markup Language (VCML) and is created using VCML 'code'.


The BioModel Physiology includes what is known about the biological system in terms of cellular structures, species and biochemical reactions. Each BioModel Application allows the user to define the quantitative conditions needed to define, run and visualize a Virtual Experiment, i.e. numerical simulation. Thus, an Application includes the Geometry, the Specifications (species, reactions), Protocols (events, electrical mapping), Simulations and Parameter Estimation (if applicable). A single BioModel may have numerous Applications, in which geometries and/or parameters have been changed. Each Application, in turn can have multiple Simulations, in which different numerical methods or conditions are used.


MathModels define Virtual Experiments using VCell Markup Language.