The French Institute for Bioinformatics (IFB) offers an infrastructure to deploy learning environments and courses in bioinformatics curricula. In response to the increasing needs for basic skills in Unix, R and Python programming, and the evolution of training modalities, we explore what e-learning has to offer for bioinformatics education.
Who are we?
We are a working group of IFB bioinformatics trainers and university teachers who have been gathering since January 2020 to create innovative solutions for online training of basic concepts in Unix, R and Python. Our common needs were originally to design prerequisite activities for bioinformatics training aimed at biologists, such as the EBAII professional training or university curricula.
List of group members
Hélène Chiapello, Research Engineer - IFB/ELIXIR-FR training coordinator, INRAE (Jouy-en-Josas)
Thomas Denecker, Research Engineer - IFB, CNRS (Paris)
Lucie Khamvongsa Charbonnier, Engineer - IFB, CNRS (Marseille)
Pierre Poulain, Associate Prof. - Université Paris Cité (Paris)
Denis Puthier, Prof. - Aix Marseille Université (Marseille)
Olivier Sand, Research Engineer - IFB/ELIXIR-FR Training Coordinator, CNRS (Lille)
Claire Toffano-Nioche, Researcher - CNRS (Gif-sur-Yvette)
Morgane Thomas-Chollier, Associate Prof. - PSL University - Ecole normale supérieure (Paris)
- Technical survey on digital environments dedicated to self-training resources with practical sessions adapted to our target audiences. We report on the technologies available to create online scenarios for learning and acquiring basic command line and programming skills. This field is actively evolving, especially with in-browser approaches (WebAssembly, Wasm). Our goal is to provide a self-training resource on which biologists wishing to learn bioinformatics could acquire the basics of Unix, R and Python.
- Design of pedagogical content focused on the needs of bioinformatics trainers and teachers, ideally based on the resources deployed on the IFB infrastructure. In 2021, we produced a self-training course on the basics of the Unix command line, a need widely shared by users of IFB services. We implemented this course on the Katacoda platform. This resource composed of 3 scenarios has been successfully used as a prerequisite for several IFB bioinformatics training sessions and university teaching modules. Hundreds of learners have already benefited from this course. Since Katacoda was discontinued in mid-2022, we are currently experimenting with alternative solutions such as KillerCoda and Sandbox.bio.
- Katacoda Unix course: This course was available online until July 2022, when Katacoda changed its business model. Over 200 users, 3 scenarios, content available on https://github.com/IFB-ElixirFr/katacoda-scenarios
- Killercoda Unix course: this course is currently active here : https://killercoda.com/ifb-eformation-linux
Scenarios available here : https://github.com/IFB-ElixirFr/killercoda-scenarios
- A summary of our work was presented at the national JOBIM 2021 conference as a poster.