Chaste Tutorial at 2025 SMB Meeting

A directory of materials for the July 2025 Chaste Tutorial at the OPEN VT workshop in Edmundton, Canada.

The main Chaste repository can be found here.

Prerequesites

Before the workshop you will need to download and install Docker (and other useful tools), and download the chaste docker container (this contains the source code you will need).

• Install Docker and allocate it at least 4GB RAM
• On the command line run the following: docker run -it --init --rm -v chaste_data:/home/chaste chaste/release (or one of the commands below to view output)
• This is your terminal on Chaste we will work in here in the workshop.
• To make things easier you should also Install
• VSCode for editing code and
• Paraview for visualisation.

Mounting output in Windows

docker run -it --init --rm -v chaste_data:/home/chaste -v C:\Projects\output:/home/chaste/output chaste/release

Mountung output in macOS

docker run -it --init --rm -v chaste_data:/home/chaste -v "${PWD}"/output:/home/chaste/output chaste/release

Visualising with Paraview

UserTutorials/VisualizingWithParaview

Tasks

• https://chaste.github.io/docs/user-tutorials/
  • Where to start with cell-based simulations:
    • UserTutorials/CellBasedDemo - a quick introduction to the basics of cell-based simulations in Chaste.
    • UserTutorials/VisualizingWithParaview
  • Running basic simulation types:
    • UserTutorials/RunningMeshBasedSimulations - the first type of cell-based simulation included in Chaste, start here!
    • UserTutorials/RunningNodeBasedSimulations - includes details of how to simplify cell-based tests
    • UserTutorials/RunningVertexBasedSimulations - includes adding boundary conditions and removing cells from simulations
    • UserTutorials/RunningPottsBasedSimulations - lattice-based simulations
    • UserTutorials/RunningImmersedBoundarySimulations - immersed boundary simulations