{"id":18524302,"url":"https://github.com/mdanalysis/workshopmdmledinburgh2022","last_synced_at":"2025-09-03T09:38:21.712Z","repository":{"id":38094481,"uuid":"497868196","full_name":"MDAnalysis/WorkshopMDMLEdinburgh2022","owner":"MDAnalysis","description":null,"archived":false,"fork":false,"pushed_at":"2025-07-25T07:17:22.000Z","size":71929,"stargazers_count":65,"open_issues_count":7,"forks_count":14,"subscribers_count":11,"default_branch":"main","last_synced_at":"2025-08-28T23:25:44.768Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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.CC-BY-SA","code_of_conduct":"CODE_OF_CONDUCT.md","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,"zenodo":null}},"created_at":"2022-05-30T09:09:56.000Z","updated_at":"2025-07-25T07:17:29.000Z","dependencies_parsed_at":"2025-08-28T18:43:26.421Z","dependency_job_id":null,"html_url":"https://github.com/MDAnalysis/WorkshopMDMLEdinburgh2022","commit_stats":{"total_commits":110,"total_committers":9,"mean_commits":"12.222222222222221","dds":0.7727272727272727,"last_synced_commit":"fb0112bce6526d7d5c3d9501c35dc1de6df64adc"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/MDAnalysis/WorkshopMDMLEdinburgh2022","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FWorkshopMDMLEdinburgh2022","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FWorkshopMDMLEdinburgh2022/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FWorkshopMDMLEdinburgh2022/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FWorkshopMDMLEdinburgh2022/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MDAnalysis","download_url":"https://codeload.github.com/MDAnalysis/WorkshopMDMLEdinburgh2022/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FWorkshopMDMLEdinburgh2022/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273423610,"owners_count":25103143,"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","status":"online","status_checked_at":"2025-09-03T02:00:09.631Z","response_time":76,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2024-11-06T17:40:30.538Z","updated_at":"2025-09-03T09:38:21.187Z","avatar_url":"https://github.com/MDAnalysis.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Workshop for MDAnalysis/ML Edinburgh 2022\n\nThis repository contains all the materials for the 2022 MDAnalysis/ML workshop taking place at the University of Edinburgh on June 9-10 2022.\n\n## Instructors\nIrfan Alibay    \nMatteo Degiacomi   \nRichard Gowers   \nMicaela Matta   \nAntonia Mey   \n\n## Location\n\nUniversity of Edinburgh, King’s Buildings Campus, [Murchison House, room G09](https://www.ed.ac.uk/timetabling-examinations/timetabling/room-bookings/bookable-rooms3/room/0654_00_G.09) - 10 Max Born Cres, Edinburgh EH9 3BF. \n\nSee also [accessibility information](https://www.accessable.co.uk/the-university-of-edinburgh/king-s-buildings/access-guides/murchison-house#d2279e8b-6141-084a-857c-3d756f3983bb).\n\n\n## Schedule\n\n|  Day 1 \t        | Session                 | Materials |\n|---------------\t|-------------------------|-----------|\n| 9:00-9:30     \t| Registration          \t|   \t|\n| 9:30-9:40     \t| Opening remarks       \t|   \t|\n| 9:40-10:45    \t| MDAnalysis            \t|  [![MDA Part 1](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/WorkshopMDMLEdinburgh2022/blob/main/MD/MD_01_System_Manipulation.ipynb)  \t|\n| 10:45-11:00   \t| :coffee: break  :coffee:              \t|   \t|\n| 11:00-12:30   \t| MDAnalysis            \t| [![MDA Part 2](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/WorkshopMDMLEdinburgh2022/blob/main/MD/MD_02_Distances_Trajectories.ipynb)   \t|\n| 12:30-13:30   \t| Lunch                 \t|   \t|\n| 13:30-14:45   \t| ML Clustering          \t| [![ML Clustering](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/WorkshopMDMLEdinburgh2022/blob/main/ML/ML_clustering_01.ipynb)  \t|  \n| 14:45-15:00   \t| :coffee: break   :coffee:             \t|   \t| \n| 15:00-16:20   \t| ML Dimensionality Reduction          \t| [![ML DR](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/WorkshopMDMLEdinburgh2022/blob/main/ML/ML_DR_02.ipynb)  \t|\n| 16:20-16:30   \t| Closing remarks       \t|   \t|\n| 18:00-onwards \t| Informal social event \t| [Steel Coulson, EH9 1PU](https://goo.gl/maps/ZNGPp9ZS1ag2ovFV9) \t|\n\n\n|  Day 2 \t        | Session                 | Materials |\n|--- |--- |--- |\n| 9:00-9:30\t|  Slow start \t| |\n| 9:30-9:40    \t| Opening remarks  | |\n| 9:40-10:45   \t| ML Classification\t| [![ML DR](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/WorkshopMDMLEdinburgh2022/blob/main/ML/ML_RF_03.ipynb)|\n| 10:45-11:00  \t| :coffee: break :coffee:\t| |\n| 11:00-12:30 \t| ML Regression + Neural Networks\t| [![ML_NN](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MDAnalysis/WorkshopMDMLEdinburgh2022/blob/main/ML/ML_NN_04.ipynb)|\n| 12:30-13:30 \t| Lunch | |\n| 13:30-14:50 \t|  Code Clinic \t| |\n| 14:50-15:00  | Closing remarks |\n\n## Setting up your python environment *before the workshop*\n\n\u003c!--The workshop will be 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## 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## Course pre-requisites\n\nThe course assumes that attendees have a working knowledge of [Jupyter notebooks][1], Python (especially the [NumPy library][2]), and the bash shell.\n\n\n## License\n\n\u003c!--TBA--\u003e\nThe MDAnalysis logo and its derivatives are licensed under the Creative Commons Attribution-NoDerivs 3.0 Unported License.\n\n## Sponsor \n\n![logo](assets/cropped-mgms_logo_clean_2014_square.png)\n\nWe are grateful to the [Molecular Graphics and Modelling Society (MGMS)](https://www.mgms.org/WordPress/about/) for sponsoring the workshop.\nThe Society was formed in 1981 to bring together scientists working in different fields of study (such as chemistry, physics, biology, mathematics and computer science) who have a common interest in molecular modelling and graphics. The Society’s core activities involve the organising of conferences relevant to its community, as well as developing and encouraging scientists at the start of their careers.\n\n\n## Acknowledgements\n\nPlease see [`AUTHORS.md`](AUTHORS.md) for a list of contributors to the workshop\nmaterials.\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%2Fworkshopmdmledinburgh2022","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmdanalysis%2Fworkshopmdmledinburgh2022","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fworkshopmdmledinburgh2022/lists"}