mcell - A Multicellular Modeling Framework

mcell is a small set of Python classes that allows the enterprising modeler to:

• Easily create very flexible models of of multicellular dynamics
• Manage the models already created through a simple command-line interface
• Easily change defined parameters in models
• Render the runs of the models in a convenient, simple way
• Analyze the runs of the models through histograms and clustering

mcell is a thin layer on top of the combination of [BionetSolver], which model internal cell states through ODE systems, and [CompuCell3D], which models cell shape dynamics through the Glazier-Graner-Hogeweg. It was created largely in reaction to inconveniences experienced when using BionetSolver and CompuCell3D as detailed [here].

How it works

Model Management

Rendering and Analysis