This repository contains code to simulate a center-based model of cartilage formation and growth. This code was used to generate results and figures for the manuscript "Contributions of cell behavior to geometric order in embryonic cartilage".

The code is organized as a user project for the simulation software Chaste. In particular, it works with Chaste version 2019.1.

Once Chaste is set up, this repository can be cloned and linked into the projects folder in the Chaste source, i.e. at /path/to/Chaste/projects/. (Re-)configuring Chaste using

ccmake path/to/Chaste

inside the Chaste build folder should then enable generation of the relevant executables using

cd chaste_build/
make MesenchymalCondensationSimulation
make CartilageSheetSimulation
make MissingColumnSimulation

The jupyter notebook files found in the experiments folders show how to run the simulations.

The simulation data used to generate the result figures (~2GB) can be downloaded from figshare at https://doi.org/10.6084/m9.figshare.21731804. If unpacked and copied to experiments/data, the jupyter notebooks can be used to generate the figures found in the Results section of the article. The notebooks also list the exact commands used to generate the data including all parameter settings.