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PyChaste Tutorials
It is recommended that you follow the tutorials in the order below.
Note
If you are using the docker image, you should see a list of tutorials in your browser on launch.
Demo Problems
These tutorials demonstrate some applications of biological interest, but do not discuss functionality in detail.
- Simulating a Scratch Assay – Setting up a simple cellular automaton, 3D visualization and real-time plotting.
- Simulating Spheroid Growth – Setting up an off-lattice cell population and reaction-diffusion PDEs.
- Simulating an Epithelial Sheet Tensile Test – Setting up a Vertex based cell population and using polymorphism for time varying boundary conditions.
- Simulating Cell Sorting – Setting up a Potts based simulation and labelling cells.
Basic Simulations
These tutorials demonstrate basic functionality. They are based on the C++ versions in Chaste. See the Chaste User Tutorials page for more detailed information.
- Running Mesh Based Simulations – The simplest type of cell-based simulation (also the first to be implemented in Chaste).
- Running Node Based Simulations – Includes details of how to simplify cell-based tests.
- Running Vertex Based Simulations – Includes adding boundary conditions and removing cells from simulations.
- Running Potts Based Simulations – Lattice-based simulations.
- Running Immersed Boundary Simulations – Running simulations using the immersed boundary method.