CECAM 2023

This repository includes slides, recordings, source code, and resources for the CECAM 2023 workshop (March 2023).

Setup Materials

PhysiCell set-up guides

MacOS Setup

• Slides: click here
• Video: click here

Windows Setup

• Slides: click here
• Video: click here

Linux Setup

Linux users can most likely skip setup g++ and Python setup, but they should download PhysiCell 1.10.4 (or later) to test that they can compile and run the sample projects. See either the Windows or MacOS guide for details.

Further help

You can get setup help in our dedicated PhysiCell Slack workspace.

PhysiMESS set-up guide

With PhysiCell setup you should be ready to run PhysiMESS

• Source code: click here
• Setup guide: click here

You can get setup help in our CECAM Slack workspace.

Helpful tutorials

Working with PhysiCell Projects

• Slides: click here
• Video: click here

Key components in code

If you look in the code directory, you'll see:

• PhysiCell - this is a sneak peak of the upcoming 1.11.0 release, which we'llk use throughout the workshop.
  • You may want to refer to the release notes
• PhysiCell Model Builder - This is an integrated environment for setting up, running, and visualizing PhysiCell simulations.
• PhysiMESS - This is a snapshot of the PhysiMESS extension to PhysiCell, which is tailored to ECM modeling.

We will run most of our tutorials and sessions within these directories, and we'll rely upon this relative pathing.

Other suggested tools.

The setup guides should already suggest ImageMagick. We also recommend Microsoft VS Code as a good, cross-platform code editor.

Sessions

Monday

Plenary (11.30-12.30)

Detangling complex multicellular systems with agent-based modeling - Paul Macklin

• Slides: click here
• Recording: click here

Tutorial Session 1 (First PhysiCell model) (12.30-13.30)

An hands-on tutorial that introduces the model builder GUI - Lead by Paul Macklin

• Slides: click here
• Basic Modelling Workflow Recording: click here
• Intermediate Modelling Workflow Recording: click here
• Source code: Use make load PROJ=demo1 to load the full source.

Tutorial Session 2 (Full modeling workflow) (14.30-16.00)

An introduction to signals, behaviours, functions, and a full modelling example - Lead by Paul Macklin

• Slides: click here
• Full Modelling Workflow Recording: click here
• Source code: Use make load PROJ=demo2 to load the full source.

Tuesday

Tutorial Session 3 (Modelling the ECM as a substrate) (11.30-12.30)

An introduction to substrates and ECM continuum approaches in PhysiCell - Lead by Robyn Shuttleworth

• Slides: click here
• Recording click here
• Source code: required files pyMCDS.py and Simulation_Printing.ipynb

Tutorial Session 4 (Introducing PhysiMESS) (13.30-15.00)

An introduction to PhysiMESS and modelling the ECM components as additional agents - Lead by Cicely Macnamara

This tutorial will follow on from intial setup as per setup guide

• Slides click here
• Recording click here
• Source Code click here