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.