NRCAM has created a remote user modeling and simulation environment utilizing Java's Remote Method Invocation (RMI). The biologically oriented user interface allows experimentalists to create models, define cellular geometry, specify simulations and analyze the simulation results. The results are run and stored on a remote server and can be reviewed in the software and/or exported in a variety of popular formats.

The design of the biological to mathematical mapping allows for separate use of biological and math components, and includes automatic mathematical simplification using pseudo-steady approximations and mass conservation relationships. This allows for direct specification of mathematical problems, performing simulations and analysis on those systems.

The stand alone mathematics user interface is also a powerful tool for modeling reaction-diffusion systems.

A transparent general purpose solver is used to translate the initial biological description into a set of concise mathematical problems. The solver is transparent to the average user, but is accessible to the theorist as the Math Editor component.

The software is composed of three main components:

1. Modeling Framework
2. Mathematics Framework
3. WWW Interface-Biological Oriented Interface with Integrated Math Editor

1. The modeling framework represents the physiological models of the Virtual Cell and allows for persistence and database support.

2. The mathematics framework transparently solves an important class of mathematical problems encountered in the cellular modeling.

3. The WWW accessible graphical user interface provides access to the technology mentioned above. The user interface has been developed using Java 2 Applets.