Training and Documentation
We divide PhysiCell's training curriculum into several short courses:
- Essentials:
- A hands-on primer to introduce agent-based modeling and simulation with PhysiCell Studio. All PhysiCell users and developers should start here. No software installlation is required.
- Boolean Networks with PhysiBoSS
- A hands-on introduction to adding Boolean networks to cell agents with PhysiBoSS in PhysiCell Studio. PhysiCell and PhysiBoSS users should continue here only after completing PhysiCell Essentials training. Some C++ may be required.
- Advanced PhysiCell Modeling
- Learn to develop custom model components and visualizations in C++. Learn to use C++ extensions for ODEs (via libRoadrunner), ECM fibers (via PhysiMeSS), and more. PhysiCell and PhysiBoSS users and developers should complete Essentials and PhysiBoSS training first. C++ (including a PhysiCell C++ developement environment) are required.
- PhysiCell for Developers
- Learn about the PhysiCell core C++ structure and APIs, and how to contribute to C++ core and extensions. PhysiCell and PhysiBoSS users and developers should complete Essentials, PhysiBoSS, and Advanced Modeling training first. C++ (including a PhysiCell C++ developement environment) are required.
Training Courses
PhysiCell Essentials
This short course is the place to start, whether new to modeling, planning serious models in PhysiCell, or preparing for more advanced C++ based customizations. We'll introduce agent-based modeling (and PhysiCell), and lead you through several hands-on exercises to create models, without need for coding.
The work can be done in a web browser or in PhysiCell Studio, and no background coding (or deep knowledge of biology) is required.
Prerequisites
- Background knowledge: Basic knowledge of biology, and concepts of mathematical functions.
- Software setup: Web browser, or optional PhysiCell Studio Desktop
Sessions
Session 1: Introduction to Agent-Based Modeling and PhysiCell
- Slides: Click Here
- Recording:
Optional: Desktop Installation of PhysiCell Studio
- Slides: (in development)
- Recording:
Session 2: Hands-on work Part 1: Getting Started, and Villager/Zombie Model
- Slides: Click here
- Code: Zombies & Villagers example (unzip in user_projects)
- Recording:
Session 3: Hands-on work Part 2: Cancer Chemotherapy & Immunology Models
- Slides: Click here
- Code: Cancer-immune example (unzip in user_projects)
- Recording:
Optional: Notes and Tips on Parameter Estimates
- Slides: (in development)
- Recording:
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Integration of Boolean Networks with PhysiBoSS
This short course builds upon the PhysiCell Essentials training to introduce Boolean signaling models, and how to add them to cell agents using PhysiBoSS. Early readers can get started by reading the excellent guide in Ruscone et al. (2024).
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Advanced PhysiCell Modeling
This short course builds upon the training in Essentials and PhysiBoSS to help users learn how to build custom code and visualization in C++. It also introduces C++ based extensions including libRoadrunner (for ODE models) and PhysiMeSS (for ECM fiber modeling).
This course requires a working PhysiCell C++ development environment.
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PhysiCell for Developers
This short course further builds off of the Advanced Modeling training to introduce PhysiCell's core C++ structure, with a focus on how to contribute to the core C++ libraries, as well as community extensions.
This course requires a working PhysiCell C++ development environment.
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Other Guides
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