pyVertexModel 1.0.7

A versatile 3D vertex model for modeling tissue and cell mechanics, particularly for tissue repair simulations.

pyVertexModel is versatile 3D vertex model to model tissue and cell mechanics, in particular, regarding tissue repair.

Please, to ensure you use a polished version, use the 'paper' version/branch: https://github.com/Pablo1990/pyVertexModel/tree/paper

Environment

conda create -n pyVertexModel python=3.9
conda activate pyVertexModel
pip install -r requirements.txt

Usage

The first time you run the code, you need to compile the cython code. To do so, run the following commands:

python setup.py build_ext --inplace

To run the code, you can use the following command:

python main.py

To run the tests, we use 'tox':

tox

Changing the parameters

You can change the parameters of the model in the parameters/set.py file. At the moment, you should change it under the 'wing_disc()' function.

Each simulation will be saved in a different folder in the results directory. The name of the folder will be the date and time of the simulation.

Help

For any issues with the code, you can put an issue in the repository. For other matters, you can contact Pablo Vicente Munuera ([e-mail]).