{"id":18524253,"url":"https://github.com/mdanalysis/mdanalysisworkshop-intermediate1day","last_synced_at":"2025-04-09T11:31:59.335Z","repository":{"id":255521045,"uuid":"852084734","full_name":"MDAnalysis/MDAnalysisWorkshop-Intermediate1Day","owner":"MDAnalysis","description":"Materials for 1-day intermediate workshop","archived":false,"fork":false,"pushed_at":"2024-09-05T13:59:22.000Z","size":12557,"stargazers_count":4,"open_issues_count":1,"forks_count":1,"subscribers_count":6,"default_branch":"ccpbiosim-24","last_synced_at":"2025-04-06T08:28:23.317Z","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":"CHANGELOG.md","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":"2024-09-04T07:41:27.000Z","updated_at":"2025-02-01T15:01:01.000Z","dependencies_parsed_at":"2024-09-05T22:56:03.465Z","dependency_job_id":"dff957e3-6388-4bd1-9a42-483f345b9d98","html_url":"https://github.com/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day","commit_stats":null,"previous_names":["mdanalysis/mdanalysisworkshop-intermediate1day"],"tags_count":0,"template":false,"template_full_name":"MDAnalysis/MDAnalysisWorkshop-Intro1Day","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysisWorkshop-Intermediate1Day","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysisWorkshop-Intermediate1Day/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysisWorkshop-Intermediate1Day/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysisWorkshop-Intermediate1Day/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MDAnalysis","download_url":"https://codeload.github.com/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/tar.gz/refs/heads/ccpbiosim-24","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248031634,"owners_count":21036442,"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":"2024-11-06T17:40:13.077Z","updated_at":"2025-04-09T11:31:59.308Z","avatar_url":"https://github.com/MDAnalysis.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MDAnalysis Workshop - 2024 CCPBioSim Training Week \nMaterials for the Sep 5, 2024 MDAnalysis hybrid workshop at the University of Sheffield and online.\n\n## Instructors\n\n(online) Richard Gowers - [@richardjgowers](https://github.com/richardjgowers)\n\n(in person) Micaela Matta  - [@micaela-matta](https://github.com/micaela-matta)\n\n## Location\n\n\n#### Workshop Lectures and Tutorials:\n\nLecture Theatre D\nHicks Building, Department of Physics and Astronomy\n\nUniversity of Sheffield, S3 7RH\nUnited Kingdom\n\nSee also [accessibility information](https://www.accessable.co.uk/university-of-sheffield/access-guides/hicks-building-lecture-theatre-block).\n\n\n## Schedule\n\n| Time (BST)    | Session                                                  | Materials                                                                                                                                                                |\n|---------------|----------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| 9:30-9:35     | Opening Remarks and Introductions\t                       |   \t                                                                                                                                                                      |\n| 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)                                                       \t                                                                    |\n| 10:30-10:45   | :coffee: break :coffee:          \t                       |   \t                                                                                                                                                                      |\n| 10:45-12:30   | **Session 2:** Distances and Trajectories  \t             | [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)                                                                                                                         |\n| 12:30-14:00   | Lunch                 \t                                 |   \t                                                                                                                                                                      |\n| 14:00-15:30   | **Session 3:** Analysis Tools 1                           | [Tutorial 3](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial3_Analysis1.ipynb)                                                |\n| 15:30-15:45   | :coffee: break  :coffee:         \t                       |   \t                                                                                                                                                                      |\n| 15:45-16:45   | **Session 4:**  Analysis Tools 2                | [Tutorial 4](https://github.com/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial4_Analysis2.ipynb)                                                |\n| 16:45-16:50   | Closing Remarks    \t                                     |     \t                                                                                                                                                                    |\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## Google Colab\n\nIf 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.\n\n| Session                                                  | Materials                                                                                                                                                                        |\n|----------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| **Session 1:** MDAnalysis Basics and System Manipulation |[![MDA Part 1](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial1_System_Manipulation.ipynb)  \t                                                                                                              |\n| **Session 2:** Distances and Trajectories  \t             | [![MDA Part 2](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial2_Distances_Trajectories.ipynb)                                                                                                               |\n| **Session 3:** Analysis Tools                            | [![MDA Part 3](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial3_Analysis1.ipynb)                                                                                                                                                                                 | \n| **Session 4:** Advanced Tips and Requests                | [![MDA Part 4](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/MDAnalysisWorkshop-Intermediate1Day/blob/ccpbiosim-24/notebooks/Tutorial4_Analysis2.ipynb)                                                                                                                                                                                 |\n\n## Workshop pre-requisites\n\nThe workshop assumes that attendees have a working knowledge of [Jupyter notebooks][1], Python (especially the [NumPy library][2]), and the bash shell.\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.\n\n## Acknowledgements\n\nPlease see [`AUTHORS.md`](AUTHORS.md) for a list of contributors to the workshop materials.\n\nWe would like to give a special thanks  our partner for this workshop, [CCPBioSim](https://www.ccpbiosim.ac.uk/).\n\n\u003cimg\nsrc=\"/logos/CCPBioSim_Logo.jpeg\"\ntitle=\"CCPBioSim Logo\" alt=\"CCPBioSim Logo\"\nstyle=\"float: left; height: 5em; \" /\u003e\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 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.\n\n\u003cimg\nsrc=\"/logos/CZI_Logo.jpg\"\ntitle=\"Chan Zuckerberg Initiative Logo\" alt=\"Chan Zuckerberg Initiative Logo\"\nstyle=\"float: left; height: 5em; \" /\u003e\n\n\u003cimg\nsrc=\"/logos/numfocus-sponsored.png\"\ntitle=\"NumFOCUS Sponsored Project Logo\" alt=\"NumFOCUS Sponsored Project Logo\"\nstyle=\"float: left; height: 5em; \" /\u003e\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-intermediate1day","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmdanalysis%2Fmdanalysisworkshop-intermediate1day","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fmdanalysisworkshop-intermediate1day/lists"}