{"id":18524303,"url":"https://github.com/mdanalysis/mdanalysisworkshop-intro0.5day","last_synced_at":"2025-06-30T08:34:45.478Z","repository":{"id":182800214,"uuid":"669119648","full_name":"MDAnalysis/MDAnalysisWorkshop-Intro0.5Day","owner":"MDAnalysis","description":"Materials for 0.5-day MDAnalysis workshops","archived":false,"fork":false,"pushed_at":"2024-05-03T10:05:05.000Z","size":22756,"stargazers_count":7,"open_issues_count":5,"forks_count":7,"subscribers_count":9,"default_branch":"feb24-ws","last_synced_at":"2024-10-29T17:39:37.274Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MDAnalysis.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.md","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-07-21T11:43:50.000Z","updated_at":"2024-10-21T12:51:05.000Z","dependencies_parsed_at":null,"dependency_job_id":"74b4d9ba-fe20-49e5-a68f-bc57f5a7a487","html_url":"https://github.com/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day","commit_stats":{"total_commits":61,"total_committers":12,"mean_commits":5.083333333333333,"dds":0.6557377049180328,"last_synced_commit":"fffe41578f9d56d871abe3bcfa3b5166180b5a7d"},"previous_names":["mdanalysis/mdanalysisworkshop2023","mdanalysis/mdanalysisworkshop-intro0.5day","mdanalysis/mdanalysisworkshop-ucl24"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysisWorkshop-Intro0.5Day","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysisWorkshop-Intro0.5Day/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysisWorkshop-Intro0.5Day/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysisWorkshop-Intro0.5Day/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MDAnalysis","download_url":"https://codeload.github.com/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/tar.gz/refs/heads/feb24-ws","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248031640,"owners_count":21036446,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-06T17:40:30.617Z","updated_at":"2025-04-09T11:32:00.692Z","avatar_url":"https://github.com/MDAnalysis.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Online Workshop: Introduction to MDAnalysis and Molecular Nodes, February 2024\nMaterials 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).\n\n## Schedule\n\nEach section will consist of a **lecture** component, introducing relevant concepts, \nand a guided **tutorial** component which you can follow along with the instructor \n(or at your own pace).\n\nModerators: [Lily Wang](https://github.com/lilyminium) and [Brady Johnston](https://github.com/BradyAJohnston)\n\n| Time | Topic | Instructor |\n|-----|-----|-----|\n|03:00 - 03:05 UTC | Introduction | |\n|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) |\n|04:15 - 04:20 UTC | Q\u0026A / Break| |\n|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) | \n|05:30 - 05:35 UTC | Q\u0026A / Break ||\n|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) |\n|06:45 - 06:50 UTC | Final Announcements ||\n|06:50 - 07:00 UTC | Final Q\u0026A ||\n\n## Workshop pre-requisites\n\nThe 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.\n\n\n## Google Colab\n\n\nIf 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. \n\n| Session                 | Materials |\n|-------------------------|-----------|\n| Lecture 1: MDAnalysis Basics| [![MDA Part 1 Lecture](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Lecture1_MDAnalysisBasics.ipynb) |\n| Tutorial 1: System Manipulation and Atom Selection  | [![MDA Part 1 Tutorial](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Tutorial1_System_Manipulation.ipynb) |\n| Lecture 2: Distance Calculations | [![MDA Part 2 Lecture](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Lecture2_Distance_calculations.ipynb) |\n| Tutorial 2: Distances and Trajectories | [![MDA Part 2 Tutorial](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intro0.5Day/blob/feb24-ws/notebooks/Tutorial2_Distances_Trajectories.ipynb) |\n\n\n## Setting up your Python environment *before the workshop*\n\n\u003c!--The workshop will be in a blended learning environment and hands-on. You will need a working installation of MDAnalysis and related packages including data to analyze in order to participate. The full installation may take up to about 1 GB of space (mostly for data, which you can delete after the workshop).--\u003e \n\nInstructions for setting up your environment to run this workshop locally\nare provided in [`INSTALL.md`](INSTALL.md).\n\nA full list of the required Python packages can be seen inside [`environment.yml`](environment.yml).\n\nAs 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!\n\n**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.\n\n\n## Code of Conduct\n\nAll 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/).\n\n## License\n\nWritten materials are provided under the [CC-BY-4.0 SA license](LICENSE.md).\n\nThe 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).\n\n## Acknowledgements\n\nPlease see [`AUTHORS.md`](AUTHORS.md) for a list of contributors to the workshop\nmaterials.\n\nThis 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.\n\n##\n[1]: https://jupyter-notebook.readthedocs.io/en/stable/\n[2]: https://numpy.org/\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fmdanalysisworkshop-intro0.5day","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmdanalysis%2Fmdanalysisworkshop-intro0.5day","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fmdanalysisworkshop-intro0.5day/lists"}