Training material for the CMSO formats and API

This repository contains training material for the formats and API developed by the Cell Migration Standardisation Organisation.

Run using Binder

Binder (see their documentation) allows you to run Jupyter notebooks hosted on Github in an online executable environment. Thus, you do not need to install any libraries if you use this route. Just click in the logo below.

Run locally using Docker

In order to execute the notebooks locally, you can build the Dockerfile stored in the top-level of this repository:

docker build -t cmso-jupyter .
docker run --rm -it -p 8888:8888 cmso-jupyter

Use the URL shown in the startup message, including the token, to access the notebook server from your browser.

For persistence, and to use existing notebooks, you can mount a host directory to /home/jupyter/notebooks in the container:

docker run --rm -it -p 8888:8888 -v $(pwd):/home/jupyter/notebooks cmso-jupyter