CompuCell3D is conducive for experimentation and testing biological models by providing a flexible and extensible package, with many different levels of control.

High-level steering is possible through CompuCell Player, an interactive GUI built upon Qt threads which execute in parallel with the computational back end.

Functionality such as zooming, rotation, playing and pausing simulations, setting colors and viewing cross sections is available through the player, with a sample screenshot shown below.

Extending the back end is possible through an XML-based domain-specific language Biologo, which after lexical analysis and generation transparently converts to C++ extensions which can be compiled and dynamically loaded at runtime.

The back end uses object-oriented design patterns which contribute to extensibility, reducing coupling between independently operating modules.