This is a flat monolayer simulation package for the article:
Yuting Lou1, Jean-Francois Rupprecht1,2, Sophie Theis3, Tetsuya Hiraiwa1, and Timothy E Saunders1,3
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Yuting Lou1, Sophie Theis3, Jean-Francois Rupprecht1,2, Timothy E Saunders1,3, and Tetsuya Hiraiwa1
1Mechanobiology Institute, National University of Singapore
2Aix Marseille Université, Université de Toulon, CNRS,
Centre de Physique Théorique, Turing Centre for Living Systems, Marseille, France
3Warwick Medical School, University of Warwick, Coventry, United Kingdom
This package is based on the tyssue library and its dependencies It recquires a specific version of tyssue that you can find here : tyssue.
The recommanded installation route is to use the conda package manager. You can get a conda distribution for your OS at https://www.anaconda.com/download . Make sure to choose a python 3.6 version. Once you have installed conda, you can install tyssue with:
$ conda install -c conda-forge tyssueYou can then download and install CellPacking from github:
- with git:
$ git clone https://github.com/TimSaundersLab/CellPacking.git
$ cd CellPacking
$ python setup.py install- or by downloading https://github.com/TimSaundersLab/CellPacking/archive/master.zip , uncompressing the archive and running
python setup.py installin the root directory.
Simulation can be run using notebook found in notebooks/PRL or notebooks/PRE folders.
To generate simulation about anisotropic stress and in plane shape index (Fig1B), you can use the following notebook: notebooks/PRE/Simu_Stress_SI.ipynb
To generate simulation about Compression/Extension (Fig1C), you can use the following notebook: notebooks/PRE/Simu_Extension_Compression.ipynb
To generate simulation from the PRL paper, you can use the following notebook: notebooks/PRL/Simulations_Main.ipynb
This work is free software, published under the MPLv2 licence, see LICENCE for details.
© The article authors -- all rights reserved