https://github.com/mdanalysis/mdanalysisworkshop-intermediate1day
Materials for 1-day intermediate workshop
https://github.com/mdanalysis/mdanalysisworkshop-intermediate1day
Last synced: about 1 year ago
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Materials for 1-day intermediate workshop
- Host: GitHub
- URL: https://github.com/mdanalysis/mdanalysisworkshop-intermediate1day
- Owner: MDAnalysis
- License: other
- Created: 2024-09-04T07:41:27.000Z (almost 2 years ago)
- Default Branch: ccpbiosim-24
- Last Pushed: 2024-09-05T13:59:22.000Z (almost 2 years ago)
- Last Synced: 2025-04-06T08:28:23.317Z (about 1 year ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 12 MB
- Stars: 4
- Watchers: 6
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.md
- Authors: AUTHORS.md
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README
# MDAnalysis Workshop - 2024 CCPBioSim Training Week
Materials for the Sep 5, 2024 MDAnalysis hybrid workshop at the University of Sheffield and online.
## Instructors
(online) Richard Gowers - [@richardjgowers](https://github.com/richardjgowers)
(in person) Micaela Matta - [@micaela-matta](https://github.com/micaela-matta)
## Location
#### Workshop Lectures and Tutorials:
Lecture Theatre D
Hicks Building, Department of Physics and Astronomy
University of Sheffield, S3 7RH
United Kingdom
See also [accessibility information](https://www.accessable.co.uk/university-of-sheffield/access-guides/hicks-building-lecture-theatre-block).
## Schedule
| Time (BST) | Session | Materials |
|---------------|----------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 9:30-9:35 | Opening Remarks and Introductions | |
| 9:35-10:30 | **Session 1:** System Manipulation | [Lecture 1](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Lecture1_MDAnalysisBasics.ipynb), [Tutorial 1](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial1_System_Manipulation.ipynb) |
| 10:30-10:45 | :coffee: break :coffee: | |
| 10:45-12:30 | **Session 2:** Distances and Trajectories | [Lecture 2](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Lecture2_Distance_calculations.ipynb), [Tutorial 2](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial2_Distances_Trajectories.ipynb) |
| 12:30-14:00 | Lunch | |
| 14:00-15:30 | **Session 3:** Analysis Tools 1 | [Tutorial 3](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial3_Analysis1.ipynb) |
| 15:30-15:45 | :coffee: break :coffee: | |
| 15:45-16:45 | **Session 4:** Analysis Tools 2 | [Tutorial 4](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial4_Analysis2.ipynb) |
| 16:45-16:50 | 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-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial1_System_Manipulation.ipynb) |
| **Session 2:** Distances and Trajectories | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial2_Distances_Trajectories.ipynb) |
| **Session 3:** Analysis Tools | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial3_Analysis1.ipynb) |
| **Session 4:** Advanced Tips and Requests | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial4_Analysis2.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 our partner for this workshop, [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/