Plasma: versatile e-learning platform powered by The Littlest JupyterHub

Plasma, aka in French "Plateforme d’e-Learning pour l’Analyse de données Scientifiques MAssives", aims at creating an interactive tool to teach computational analysis of massive scientific data. Plasma was born out of the need to offer a reproducible and high-performance analysis environment to our students.

Our previous experiences of teaching genomics at the university were not satisfying. Because of the limited availability of computational resources, studied samples were restricted to very small datasets, far from what is nowadays routinely analyzed in research labs. Furthermore, remote access to computational resources was not always possible and the user experience provided by the classical Unix terminal was somewhat intimidating for the students.

With the help of Jupyter notebooks, we believe Plasma can provide an authentic experience of the actual bioinformatic analyses performed in research labs. We also wanted a web-based solution that could be easily deployed on bare-metal servers or virtual machines, able to handle numerous, simultaneous, and specific analysis environments, with a simple and intuitive management interface.

This project is carried out in collaboration with QuantStack, a company strongly involved in the development of the Jupyter ecosystem. Plasma utilizes tljh-repo2docker, a repo2docker plugin for The Littlest JupyterHub that provides the ability to create multiple user environments in a user-friendly web interface.

The first instance of Plasma is designed for the needs of teachers and students of the European Master of Genetics at Université de Paris. Ultimately, this project is a proof of concept and we plan to collaborate with other institutions to help them adopt Jupyter for teaching.

With this poster, we will provide walkthrough videos showcasing the installation procedure and the creation of user environments for teaching:

• "Installing Plasma on a new server with Ansible".
• "Creating teaching environments".
• "Using the environments".

Plasma has been publicly announced in May 2020: Plasma: A learning platform powered by Jupyter. For more details, you may find interest in:

• the web site of the project,
• Plasma source code,
• Plasma documentation.

We also thank sponsors to the Plasma initiative:

• Région Île-de-France, via the "Trophées franciliens de l’innovation numérique dans le supérieur" (EdTech 2018) grant program,
• Université de Paris, via the Initiative of Excellence (IdEx) Label and its "innovating teaching" grant program,
• EUR G.E.N.E., the graduate school on Genetics and Epigenetics,
• the Université de Paris training program "Création, analyse et valorisation de données biologiques omiques" (DU Omiques).