Tutorial: Using CompuCell3D as a Platform to Construct Multi-Scale, Multicellular, Agent-Based Virtual-Tissue Simulations: Exploring the Interactions between Intracellular Pathways, Cell Behaviors, Tissue-Level Signaling, and Whole-Body Context

Organizers:

Professor James Glazier (Indiana University Bloomington), Hayden Fennell, Indiana University Bloomington

Description:

Multi-scale, Multicellular Agent-Based Virtual-Tissue models built using modeling frameworks like CompuCell3D are versatile tools for exploring the complex interactions between intracellular signaling and gene-regulatory networks, inter-cellular signaling through contact and diffusible signals, force generation, cell migration, and shape change. This session will provide a hands-on introduction to using the open-source CompuCell3D modeling environment to construct and execute compact and sharable multiscale, multicellular Virtual-Tissue models for developmental, cancer, toxicology, and infectious-disease applications. Members of the audience will build and explore how CompuCell3D can simplify the construction of complex, extensible and reusable Virtual Tissue models.

Key topics will include: installing and running CompuCell3D, principles of CompuCell3D Physics, representation of cell behaviors and interactions as effective energies and constraints, CC3DML and Python model-specification basics, and representing complex network models in CompuCell3D. Several hands-on exercises will be incorporated to provide practice with the software. For more information or to download, please visit: www.compucell3d.org. CompuCell3d models will be run locally on your machine. Binaries can be found on the website: https://compucell3d.org/SrcBin#MostRecent - please download and install in advance and test one of the Demo models. There is a one-button installer for Windows machines, but be sure to install to a local directory (not a ONE-drive directory) where you have write privileges. Installation takes some time; but if it fails to complete, please run the installer again (don’t delete and reload). Installation on Macs and Linux systems depends on the chip set and operating systems details, so please follow the instructions carefully. If you have difficulty installing CompuCell3D, please contact jaglazier@gmail.com and we will try to arrange to help you. For further help on utilizing CC3D to run your own models please see the documentation at https://compucell3dreferencemanual.readthedocs.io/en/latest/.

You can find slides, exercises and supporting materials for this miniworkshop here: https://drive.google.com/drive/folders/1C3jHkznYtqhnfKPJ7ZQqLa4qqgLQub5I?usp=sharing.

You can find our extensive course on using CompuCell3d at: https://www.youtube.com/playlist?list=PLiEtieOeWbMJ-FtHHo6if-lYOENvRC79J.

Room assignment: Salon 2