MDAnalysis + Machine Learning Workshops

In collaboration with CCPBioSim, 3 MDAnalysis core devs (@ialibay, @micaela-matta, @richardjgowers) together with @ppxasjsm (University of Edinburgh) and @degiacom (University of Durham) organised and ran a 2-day hybrid (in person/online) workshop titled “MDAnalysis and Machine Learning for Molecular Simulations” on June 9-10 2022, immediately following the 8th Annual CCPBioSim Conference. The workshop received generous funding from the MGMS Early Career Workshop Initiative.

The topics covered included:

• The fundamentals and basics of MDAnalysis
• How to get started with machine learning and tools such as scikit-learn
• How to use MDAnalysis in conjunction with machine learning
• Applying these tools to your own research projects

The workshop was hosted at the University of Edinburgh and consisted of 4 half days in a hybrid format, with over 40 in person attendees and over 30 attendees online at any point in time. A special thank you to Jasmin Güven (PhD student in the group of Antonia Mey) who moderated questions from online participants!

The teaching materials can be run on Google Colab and are found on GitHub.

The workshop style was massively adapted from Software carpentries, using a mixture of life coding, walking through Jupyter notebooks and problem sections. We used the post-it system for instant feedback from participants, and also ran a post-workshop survey, collecting overwhelmingly good feedback.

Thanks to this success, @micaela-matta, @degiacom and @ppxasjsm will be running the workshop again at the CCP5 Summer School on July 26-27 2022, in Durham!

We are glad to see such a high demand for training resources and events from the molecular simulation community. We look forward to continuing to deliver these workshops in the future.

— the MDAnalysis team