README.md

CellPacking

This is a flat monolayer simulation package for the article:

Curvature-induced cell rearrangements in biological tissues

Yuting Lou¹, Jean-Francois Rupprecht^1,2, Sophie Theis³, Tetsuya Hiraiwa¹, and Timothy E Saunders^1,3

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

Installation

This package is based on the tyssus 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 tyssue

You can then download and install CellPacking from github:

• with git:

$ git clone https://github.com/TimSaundersLab/CellPacking.git
$ cd invagination
$ python setup.py install

• or by downloading https://github.com/TimSaundersLab/CellPacking/archive/master.zip , uncompressing the archive and running python setup.py install in the root directory.

Licence

This work is free software, published under the MPLv2 licence, see LICENCE for details.

© The article authors -- all rights reserved