CompuCell3D

Friday, Sept. 6th, afternoon

Hands-on introduction to using the open-source CompuCell3D modeling environment to construct and execute compact and sharable multiscale, multicellular Virtual-Tissue models.

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, and force generation, cell migration and shape change. Among other applications the open-source modeling environment CompuCell3D has been used successfully to build models of vascular tumor growth and therapy, embryonic development, liver and developmental toxicology, lung infection, immune response and anti-viral therapies. This workshop will explore how CompuCell3D can simplify the construction of complex, extensible and reusable Virtual Tissue models. Members of the audience will build and explore models by downloading the software from (www.compucell3d.org) or run it on-line at (https://nanohub.org/resources/cc3dbase4x; free with required registration). .

Speaker(s): Joel Vanin and Prof. James A. Glazier, Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47408, USA

Workshop Schedule:

• Introduction to CompuCell3D—Installing and Running CompuCell3D. Exercise—Angiogenesis simulation.
• Principles of CompuCell3D Physics—Cells as spatially-extended computational agents. CPM/GGH Representation of cells, Representation of cell behaviors and interactions as Effective Energies and Constraints. Modified Metropolis Dynamics.
• Representing CPM/GGH Models in CompuCell3D Scripts—CC3DML and Python model-specification basics.
• Representing and solving complex networks in CompuCell3D. Loading network models into individual cells, specified in SBML, CellML, Antimony or MaBoSS. Coupling subcellular models between cells. Exercise—Cell-Cycle models.
• Exercise—Exploring the interaction between subcellular networks and dynamic spatial organization. Building a simulation of Delta-Notch intracellular and juxtacrine signaling. Coupling to Cell-Cycle Models.
• Introduction to chemical fields, diffusion, decay, secretion, absorption.
• Coupling cells to chemical Fields. Exercise—Chemotaxis and nutrient-limited growth
• Compartmental Cells and Links—Building Epithelia and Spatially Complex Cells
• Using CompuCell3D as a Callable component in complex modeling workflows
• Principles of Model Building and Debugging

Audience: Anyone interested in multicellular Virtual-Tissue modeling or in coupling network models to cell behaviors and dynamic spatial organization. Background: Some experience with basic Python programming helpful.

Learning Outcomes: Ability to use CompuCell3D to design, execute and explore Virtual-Tissue simulations integrating cells, networks and external chemical fields.

For more information: see www.compucell3d.org or contact jaglazier@gmail.com or joelvanin@gmail.com.

After the workshop we provide support for user’s further model development.

Computer Requirements: Any Windows or Mac computer. CompuCell3D is open-source and free. It also runs on many LINUX deployments (see www.compucell3d.org for details). CompuCell3D can also be run in a browser-based deployment on the nanoHUB public servers without a local installation.