Python-based crash course in agent-based modeling
This lecture introduces multicellular systems and agent-based approaches that simulate cells as software objects that "live" in a chemical environment. It then builds a basic agent-based model framework by (1) introducing Python classes, (2) building an Environment class with diffusion/decay, and (3) building a Cell class with basic cell-cell mechanics, birth/death, and coupling to the chemical environment.
- Slides (PDF): click here
- Jupyter notebook: click here (Note: right-click and download the file.)
This lecture turns its attention to PhysiCell, a more developed agent-based modeling framework. After showing some research examples, we perform a hands-on exploration of cloud-hosted PhysiCell models.
- Slides (PDF): click here
- PhysiCell Slack Workspace: click here
- Good place to get technical support
- PhysiCell training course: click here