This repository contains the notebook that was used to generate most of the figures of the following article: Contact area–dependent cell communication and the morphological invariance of ascidian embryogenesis
It is important to notice that the notebook will not work without the datasets that should be manually included in the folder Data
The datasets are not included in this repository for space reasons. They can be accessed and downloaded at https://figshare.com/collections/Contact-area_dependent_cell_communications_and_the_morphological_invariance_of_ascidian_embryogenesis/4529990/2.
- ASTEC-JupyterNotebook.ipynb: the notebook which expose some examples on how to handle t
- Data: folder place-holder where the necessary datas to build the figures should be placed
- LICENCE: the licence terms you accept by using the notebook
- README.md: this file
- useful_functions.py: Set of useful functions to handle the data and make figures. Some of them are used in this notebook
In order to be able to run the notebook you need to install several packages:
- python 2.7 or higher, 3.7 or higher (https://www.python.org/)
- numpy,scipy,matplotlib, different scientific packages for python (http://www.numpy.org, http://www.scipy.org, http://matplotlib.org)
- jupyter notebook, a open-source framework to share code (http://jupyter.org)
The code is written in python and can easly be run with a web interface using a Notebook (http://jupyter.org).
You can find a user interface tutorial here (http://jupyter.cs.brynmawr.edu/hub/dblank/public/Jupyter%20Notebook%20Users%20Manual.ipynb)
To start the notebook, open a terminal and run the command jupyter notebook path/to/Package/ASTEC-JupyterNotebook.ipynb