https://github.com/mdanalysis/mdanalysisworkshop-intro1day
Materials for 1-day MDAnalysis workshops
https://github.com/mdanalysis/mdanalysisworkshop-intro1day
Last synced: about 1 year ago
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Materials for 1-day MDAnalysis workshops
- Host: GitHub
- URL: https://github.com/mdanalysis/mdanalysisworkshop-intro1day
- Owner: MDAnalysis
- License: other
- Created: 2024-05-03T10:51:48.000Z (about 2 years ago)
- Default Branch: may24-ws
- Last Pushed: 2024-05-10T12:56:49.000Z (about 2 years ago)
- Last Synced: 2024-05-22T16:24:12.092Z (about 2 years ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 3.48 MB
- Stars: 1
- Watchers: 0
- Forks: 1
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.md
- Authors: AUTHORS.md
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README
# MDAnalysisWorkshop UCL 2024
Materials for the May 10, 2024 MDAnalysis workshop at University College London.
## Instructors
Richard Gowers - [@richardjgowers](https://github.com/richardjgowers)
Micaela Matta - [@micaela-matta](https://github.com/micaela-matta)
Harry Lewin (Teaching Assistant)
## Location
#### Workshop Lectures and Tutorials:
G15 Public Cluster, DMS Watson Building
University College London
Gower Street, London, WC1E 6BT
United Kingdom
See also [accessibility information](https://www.accessable.co.uk/ucl/access-guides/dms-watson-building-public-cluster-g15).
#### Coffee Breaks and Lunch:
Garden Room, Wilkins Building
University College London
Gower Street, London, WC1E 6BT
United Kingdom
See also [accessibility information](https://www.accessable.co.uk/ucl/access-guides/wilkins-building-garden-room-meeting-room).
## Schedule
| Time (BST) | Session | Materials |
|---------------|----------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 9:00-9:15 | Check-In/Registration | |
| 9:15-9:25 | Opening Remarks and Introductions | |
| 9:25-10:45 | **Session 1:** MDAnalysis Basics and System Manipulation | [Lecture 1](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro1.0Day/blob/may24-ws/notebooks/Lecture1_MDAnalysisBasics.ipynb), [Tutorial 1](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro1.0Day/blob/may24-ws/notebooks/Tutorial1_System_Manipulation.ipynb) |
| 10:45-11:10 | :coffee: break :coffee: | |
| 11:10-12:30 | **Session 2:** Distances and Trajectories | [Lecture 2](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro1.0Day/blob/may24-ws/notebooks/Lecture2_Distance_calculations.ipynb), [Tutorial 2](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro1.0Day/blob/may24-ws/notebooks/Tutorial2_Distances_Trajectories.ipynb) |
| 12:30-13:45 | Lunch | |
| 13:45-15:05 | **Session 3:** Analysis Tools | [Tutorial 3](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro1Day/blob/may24-ws/notebooks/Tutorial3_Analysis.ipynb) |
| 15:05-15:30 | :coffee: break :coffee: | |
| 15:30-16:50 | **Session 4:** Advanced Tips and Requests | [Tutorial 4](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro1Day/blob/may24-ws/notebooks/Tutorial4_Advanced.ipynb) |
| 16:50-17:00 | 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`](INSTALL.md).
A full list of the required Python packages can be seen inside [`environment.yml`](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!
**Note:** Materials may change between now and the time of the workshop, so while we ask you to install ahead of time, also make sure to `git pull` just prior to the start of the workshop.
## 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.
| Session | Materials |
|----------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| **Session 1:** MDAnalysis Basics and System Manipulation |[](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro1Day/blob/may24-ws/notebooks/Tutorial1_System_Manipulation.ipynb) |
| **Session 2:** Distances and Trajectories | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro1Day/blob/may24-ws/notebooks/Tutorial2_Distances_Trajectories.ipynb) |
| **Session 3:** Analysis Tools | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro1Day/blob/may24-ws/notebooks/Tutorial3_Analysis.ipynb) |
| **Session 4:** Advanced Tips and Requests | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro1Day/blob/may24-ws/notebooks/Tutorial4_Advanced.ipynb) |
## Workshop pre-requisites
The workshop assumes that attendees have a working knowledge of [Jupyter notebooks][1], Python (especially the [NumPy library][2]), and the bash shell.
## Code of Conduct
All members of the MDAnalysis community and participants in MDAnalysis workshops are expected to abide by the MDAnalysis [Code of Conduct](https://www.mdanalysis.org/pages/conduct/).
## License
Written materials are provided under the [CC-BY-4.0 SA license](LICENSE.md).
The MDAnalysis logo and its derivatives are licensed under the Creative Commons Attribution-NoDerivs 3.0 Unported License.
## Acknowledgements
Please see [`AUTHORS.md`](AUTHORS.md) for a list of contributors to the workshop materials.
We would like to give a special thanks to our partners for this workshop, the [Thomas Young Centre](https://thomasyoungcentre.org/), the [JCMaxwell Node of CECAM](https://uk-jcmaxwell.cecam.org/), and [CCPBioSim](https://www.ccpbiosim.ac.uk/).
This workshop has been made possible in part by a [grant](https://chanzuckerberg.com/eoss/proposals/mdanalysis-outreach-and-project-manager/) from the Chan Zuckerberg Initiative DAF, a donor advised fund of Silicon Valley Community Foundation (funder DOI 10.13039/100014989). MDAnalysis also thanks NumFOCUS for its continued support as our fiscal sponsor.
##
[1]: https://jupyter-notebook.readthedocs.io/en/stable/
[2]: https://numpy.org/