CompuCell3D: multicellular agent-based virtual tissue modelling with CompuCell3D

Trainer: James Glazier

Overview:  This section introduces the open-source multicellular virtual-tissue modeling framework CompuCell3D (CC3D). The materials provide just a taste of CompuCell3D, you can find more information about it and learn more on the CompuCell3D website.

Learning outcomes:

By the end of the section you will be able to:

• Develop simple multicellular virtual tissue models in CompuCell3D using the simulation-specification GUI Wizard and the Twedit++ model editor
• Explain how CompuCell3D represents multicellular systems through a combination of the CC3DML and Python programming languages
• Integrate dynamic network models specified using SBML/Tellurium/Antimony and other languages into a multicellular context and interconnect them through CC3D/Python
• Use these methods to build a simple model of chemotaxis-driven vasculogenesis and of Delta-Notch patterning during embryonic development

Relevant webpages:

• CompuCell3D home page
• You can download and install the software on your local machine. Binary versions for Windows, Mac, and Linux are available at https://compucell3d.org/SrcBin.
• CompuCell3D GitHub repository

Materials:

• Using CompuCell3D as a platform to construct multiscale multicellular agent-based virtual-tissue simulations of development and disease – slides
• Angiogenesis demo files
• Delta-Notch demo files
• CompuCell3D support material
• Manuals and Tutorials
• CompuCell3D demos