Workshop for MDAnalysis/ML Edinburgh 2022

This repository contains all the materials for the 2022 MDAnalysis/ML workshop taking place at the University of Edinburgh on June 9-10 2022.

Instructors

Irfan Alibay
Matteo Degiacomi
Richard Gowers
Micaela Matta
Antonia Mey

Location

University of Edinburgh, King’s Buildings Campus, Murchison House, room G09 - 10 Max Born Cres, Edinburgh EH9 3BF.

See also accessibility information.

Schedule

Day 1	Session	Materials
9:00-9:30	Registration
9:30-9:40	Opening remarks
9:40-10:45	MDAnalysis
10:45-11:00	:coffee: break :coffee:
11:00-12:30	MDAnalysis
12:30-13:30	Lunch
13:30-14:45	ML Clustering
14:45-15:00	:coffee: break :coffee:
15:00-16:20	ML Dimensionality Reduction
16:20-16:30	Closing remarks
18:00-onwards	Informal social event	Steel Coulson, EH9 1PU

Day 2	Session	Materials
9:00-9:30	Slow start
9:30-9:40	Opening remarks
9:40-10:45	ML Classification
10:45-11:00	:coffee: break :coffee:
11:00-12:30	ML Regression + Neural Networks
12:30-13:30	Lunch
13:30-14:50	Code Clinic
14:50-15:00	Closing remarks

Setting up your python environment before the workshop

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!

Google Colab

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.

Course pre-requisites

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

License

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

Sponsor

We are grateful to the Molecular Graphics and Modelling Society (MGMS) for sponsoring the workshop. The Society was formed in 1981 to bring together scientists working in different fields of study (such as chemistry, physics, biology, mathematics and computer science) who have a common interest in molecular modelling and graphics. The Society’s core activities involve the organising of conferences relevant to its community, as well as developing and encouraging scientists at the start of their careers.

Acknowledgements

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