ECCOMAS 2024

PyChaste: Python Bindings for Chaste

Amponsah, Kwabena (University of Nottingham)
Grogan, James (Irish Centre for High-End Computing, Dublin,)
Leach, Matthew (University of Sheffield)
Cooper, Fergus (University of Oxford)
Jennings, Jack (University of Sheffield)
Pitt-Francis, Joe (University of Oxford)
Fletcher, Alexander (University of Sheffield)
Mirams, Gary (University of Nottingham)

In session: MS119B - Agent-Based Modelling to simulate cell- and multiscale problems in Biology II

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We present PyChaste, a Python interface for the open source Chaste (Cancer, Heart, and Soft Tissue Environment) simulation package for computational biology. PyChaste has bindings for the subset of Chaste that enables individual-based modelling of cells using a number of approaches such as Cellular Automata (CA), Cellular Potts (CP), Overlapping Spheres (OS) and Vertex Models (VM). PyChaste provides access to this functionality via Python which allows interactive exploration and visualization of cell-based models in Jupyter Notebooks. PyChaste can be installed via a conda package or docker image, which simplifies the process of setting up a number of software dependencies required for running Chaste. We report on the design and implementation of PyChaste and discuss some use cases it enables such as running cell-based modelling tutorials in workshops where participants need only a browser to participate.