The Virtual Cell project.

The Virtual Cell is a modular computational framework that permits construction of models, application of numerical solvers to perform simulations, and analysis of simulation results. A key feature of the Virtual Cell is that it permits the incorporation of realistic experimental geometries within full 3D spatial models. An intuitive JAVA interface allows access via a web browser and includes options for database access, geometry definition (including directly from microscope images), specification of compartment topology, species definition and assignment, chemical reaction input and computational mesh. The system is designed for cell biologists to aid both the interpretation and the planning of experiments. It also contains sophisticated modelling tools that are appropriate for the needs of mathematical biologists. Thus, communication between these traditionally separate scientific communities can be facilitated. This paper will describe the status of the project and will survey several applications to cell biological problems.