Site icon Life Science Trainers

How I Teach Life Scientists…by Using Reproducible and Scalable Learning Environments

The “How I Teach” talk series is an invitation for anyone delivering professional development to life scientists and educators to share their curriculum, tips, technologies, and approaches. Email to participate or complete a submission form to sign up to give a short talk and/or demo of the teaching skill you want to share. See full blog post for details.

Time and Date for Talks

LifeSciTrainers Community Calls May 2022

Register on Zoom for our community call or Join our Slack for more details.

YouTube: Posted after the presentation

How I Teach Life Scientists…by Using Reproducible and Scalable Learning Environments

Geert van Geest, SIB Swiss Institute of Bioinformatics

Format: Short talk and demo

Take home messages


While teaching topics in bioinformatics, setting up a computer learning environments can be challenging. Installing and using required software on the computers of the course participants can be tricky because there is usually a wide range of hardware specs, operating systems, versions, permissions, and settings. In addition, some processes that a teacher would like to run during the course might require a specific operating system or computational resources (e.g., high memory or a GPU). Here, I present an approach to host containers on a cloud service that enables the teacher to: (1) develop a reproducible teaching environment with docker, (2) scale calculations to a wide range of computational requirements on a cloud platform. We have applied this approach to several different courses, including the topics ‘single cell transcriptomics’, ‘variant analysis’ and ‘introduction to NGS’. All containers we have used so far are based on either Rstudio server, jupyterLab or VScode images and are therefore easily approachable by the participants through a web browser. The documentation and scripts to apply this method for teaching can be found at: 


Tutorial Link:

Exit mobile version