CompuCell 3D is an open source software modeling environment and pde solver. It is largely used for cellular modeling (foams, tissues, etc.), however, efforts are being made to include fluid simulation capabilities. Created in collaboration between groups at IU and Notre Dame, CompuCell provides an easy user interface for complex cellular modeling.

The first step in building a CompuCell simulation is to design the cells and their interactions. Properties that you can assign to cells include a target volume or surface area, a response to chemical gradients, secretion of chemicals, differential cell adhesion, etc. . Since the Monte Carlo employed in the GlazierGraner Cellular Potts Model (CPM) method is based on fluctuations, you must also specify the overall amplitude of fluctuations and the degree of deviation allowed from target values, e.g. how much the volume will fluctuate around the target volume.

CompuCell includes some standard initializers that create initial configurations of cells, but you will probably want to create your own. You specify the initial cell configuration in a data file with a simple format. You can create this file with a scripting language or just type it in using a word processor, working from a diagram on some graph paper.

In the future, CompuCell will have graphical tools to help with this process. Once you have written your configuration file, running CompuCell is as simple as playing a movie. You open the player, select the configuration file you want to use (using the command Open from the File dropdown menu) and click the Play button. You can select visualization options and customize the output you wish to store for later analysis. In addition to visualizing (and saving) the cell fields, you can look at chemical fields, pressure fields, velocity fields, etc.

Finally, you can analyze your data with standard techniques for analyzing and visualizing spatial data, e.g. in MatLab or Mathematica. We are currently developing some basic analysis tools to add to the CompuCell player.

Requirements:
* Python

The license of this software is Freeware, you can free download and free use this 3d graphic software.