The Virtual Cell Modeling and Simulation Framework (VCell) was developed by the National Resource for Cell Analysis and Modeling. This unique software platform has been designed to model cell biological processes. Biochemical and electrophysiological data describing individual reactions are associated with experimental microscopic image data describing their subcellular locations. Cell physiological events can then be simulated within the empirically derived geometries, thus facilitating the direct comparison of model predictions with experiment.

VCell consists of a biological and mathematical framework. As decscribed in the Overview , users can create biological models from which the software will generate the mathematical code needed to run simulations. Mathematicians may opt to use the math framework, based on the Virtual Cell Markup Language, for creating their own mathematical descriptions.

Models can be reused, updated and published so they are available to the scientific community. In addition, models may also be privately shared amongst collaborating groups. The data from simulations are stored on the Virtual Cell database server and are easily exported in a variety of formats. Access to the Virtual Cell modeling software is available via the internet using a JAVA based interface. The Virtual Cell has been developed using the latest supported Java technology.

Virtual Cell also supports rule-based modeling, which allows the representation of species as structured objects consisting of molecules and uses reaction rules to define molecular interactions that transform the attributes of species. The rule-based approach allows one to systematically incorporate site-specific details of molecular interactions into a model.