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.