https://github.com/mdanalysis/mdanalysisworkshop-intro0.5day
Materials for 0.5-day MDAnalysis workshops
https://github.com/mdanalysis/mdanalysisworkshop-intro0.5day
Last synced: 12 months ago
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Materials for 0.5-day MDAnalysis workshops
- Host: GitHub
- URL: https://github.com/mdanalysis/mdanalysisworkshop-intro0.5day
- Owner: MDAnalysis
- License: other
- Created: 2023-07-21T11:43:50.000Z (almost 3 years ago)
- Default Branch: feb24-ws
- Last Pushed: 2024-05-03T10:05:05.000Z (about 2 years ago)
- Last Synced: 2024-10-29T17:39:37.274Z (over 1 year ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 21.7 MB
- Stars: 7
- Watchers: 9
- Forks: 7
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
- Authors: AUTHORS.md
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README
# Online Workshop: Introduction to MDAnalysis and Molecular Nodes, February 2024
Materials for the February 28, 2024 MDAnalysis and Molecular Nodes workshop. The [recording](https://www.youtube.com/watch?v=3zKBjnRnAMg) of this workshop is available on the [MDAnalysis YouTube channel](https://www.youtube.com/@mdanalysis3040).
## Schedule
Each section will consist of a **lecture** component, introducing relevant concepts,
and a guided **tutorial** component which you can follow along with the instructor
(or at your own pace).
Moderators: [Lily Wang](https://github.com/lilyminium) and [Brady Johnston](https://github.com/BradyAJohnston)
| Time | Topic | Instructor |
|-----|-----|-----|
|03:00 - 03:05 UTC | Introduction | |
|03:05 - 04:15 UTC | **MDAnalysis Part 1 (basics, system manipulation)** [Lecture ,1](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Lecture1_MDAnalysisBasics.ipynb) / [Tutorial 1](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Tutorial1_System_Manipulation.ipynb) | [Fiona Naughton](https://github.com/fiona-naughton) |
|04:15 - 04:20 UTC | Q&A / Break| |
|04:20 - 05:30 UTC | **MDAnalysis Part 2 (distances, trajectories)** [Lecture 2](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Lecture2_Distance_calculations.ipynb) / [Tutorial 2](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Tutorial2_Distances_Trajectories.ipynb) | [Lily Wang](https://github.com/lilyminium) |
|05:30 - 05:35 UTC | Q&A / Break ||
|05:35 - 06:45 UTC | [Molecular Nodes Tutorial](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/blender/MolecularNodes.md) / [Blender Notebook Tutorial](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/blender/Interactive_Blender_Notebook.ipynb) | [Brady Johnston](https://github.com/BradyAJohnston), [Yuxuan Zhuang](https://github.com/yuxuanzhuang) |
|06:45 - 06:50 UTC | Final Announcements ||
|06:50 - 07:00 UTC | Final Q&A ||
## Workshop pre-requisites
The workshop assumes that attendees have a working knowledge of MD (molecular dynamics) simulation workflows, [Jupyter notebooks][1], Python (especially the [NumPy library][2]), and the bash shell.
## Google Colab
If for any reason you cannot set up a local environment with all required packages as explained below, you can use Google Colab to run the MDAnalysis workshop notebooks directly from your browser, no installation required.
| Session | Materials |
|-------------------------|-----------|
| Lecture 1: MDAnalysis Basics| [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Lecture1_MDAnalysisBasics.ipynb) |
| Tutorial 1: System Manipulation and Atom Selection | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Tutorial1_System_Manipulation.ipynb) |
| Lecture 2: Distance Calculations | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Lecture2_Distance_calculations.ipynb) |
| Tutorial 2: Distances and Trajectories | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Tutorial2_Distances_Trajectories.ipynb) |
## 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.
## 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](https://creativecommons.org/licenses/by-nd/3.0/deed.en).
## Acknowledgements
Please see [`AUTHORS.md`](AUTHORS.md) for a list of contributors to the workshop
materials.
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](https://chanzuckerberg.com/) DAF, an advised fund of Silicon Valley Community Foundation (funder DOI 10.13039/100014989). MDAnalysis also thanks [NumFOCUS](https://numfocus.org/) for its continued support as our fiscal sponsor.
##
[1]: https://jupyter-notebook.readthedocs.io/en/stable/
[2]: https://numpy.org/