This repository contains all the materials for the MDAnalysis/Machine Learning tutorials that form part of the CCP5 Biomolecular Simulation Advance Course taking place on July 26-27th at Durham University.

Matteo Degiacomi
Micaela Matta
Antonia Mey

Durham University
Room: W414

W414 is on the fourth floor of the Geography ("West") building. Enter at the northeast corner of the building at 54.767675, -1.573041. We've been asked not to use the "staff" toilets near W414, but rather to use the facilities on the ground floor. I shall be putting up some signage.

Day	Session	Materials
26th PM	Introduction to the MDAnalysis package (Micaela Matta)
26th PM	MDAnalysis: advanced topics (Micaela Matta)
27th AM	Dimensionality reduction, part 1 (Antonia Mey)
27th AM	Dimensionality reduction, part 2 (Matteo Degiacomi)
27th PM	Data clustering (Antonia Mey)
27th PM	Data classification (Matteo Degiacomi)

Instructions for setting up your environment to run this workshop locally are provided in INSTALL.md.

A full list of the required Python packages can be seen inside environment.yml.

As downloading and installing everything will take a little while, ideally you should follow these steps before the workshop starts. If you encounter any issues during installation, we can help!

If for any reason you cannot set up a local environment with all required packages, you can use Google Colab to run all workshop notebooks directly from your browser, no installation required.

The course assumes that attendees have a working knowledge of Jupyter notebooks, Python (especially the NumPy library), and the bash shell.

The MDAnalysis logo and its derivatives are licensed under the Creative Commons Attribution-NoDerivs 3.0 Unported License.

The MDAnalysis material is licences under CC-BY 4.0

The ML material is licenced under CC-BY-SA 4.0.

See here for the details of the licence

Please see AUTHORS.md for a list of contributors to the workshop materials.