CompuCell3D

What is CompuCell3D?

CompuCell3D is an open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms.

It uses Cellular Potts Model to model cell behavior. For technical details about modeling please refer Multi-Scale Modeling of Tissues Using CompuCell3D paper.

This project is funded by the NIH and EPA.

Goal of this manual

The goal of this manual is to teach biomodelers how to effectively use multi-scale, multi-cell simulation environment CompuCell3D to build, test, run and post-process simulations of biological phenomena occurring at single cell, tissue or even up to single organism levels.

Contents

• 1. Introduction
• 2. GGH Applications
• 3. GGH Simulation Overview
  • 3.1. Effective Energy
  • 3.2. Dynamics
  • 3.3. Algorithmic Implementation of Effective-Energy Calculations
• 4. CompuCell3D
• 5. Building CC3DML-Based Simulations Using CompuCell3D
  • 5.1. Short Introduction to XML
  • 5.2. Cell Sorting Simulation
  • 5.3. Angiogenesis Model
  • 5.4. Bacterium-and-Macrophage Simulation
• 6. References

Need More

For more information please visit CompuCell3D website. If you have any question please feel free to ask us at CompuCell3D User Forum.