{"id":24959273,"url":"https://github.com/inscidar/analysis-notebooks","last_synced_at":"2025-04-10T20:12:07.067Z","repository":{"id":205338910,"uuid":"559019003","full_name":"inscidar/analysis-notebooks","owner":"inscidar","description":"The accessibility evaluation of life science resources","archived":false,"fork":false,"pushed_at":"2024-10-21T16:35:22.000Z","size":537958,"stargazers_count":2,"open_issues_count":2,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-06T06:35:18.258Z","etag":null,"topics":["hidivelab"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/inscidar.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-10-28T20:51:05.000Z","updated_at":"2024-12-10T17:32:25.000Z","dependencies_parsed_at":"2024-10-21T22:17:34.077Z","dependency_job_id":null,"html_url":"https://github.com/inscidar/analysis-notebooks","commit_stats":null,"previous_names":["hms-dbmi/bio-accessibility-evaluation","hms-dbmi/life-sciences-a11y-evaluation","inscidar/analysis-notebooks"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inscidar%2Fanalysis-notebooks","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inscidar%2Fanalysis-notebooks/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inscidar%2Fanalysis-notebooks/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inscidar%2Fanalysis-notebooks/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/inscidar","download_url":"https://codeload.github.com/inscidar/analysis-notebooks/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248288361,"owners_count":21078903,"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":["hidivelab"],"created_at":"2025-02-03T07:46:41.525Z","updated_at":"2025-04-10T20:12:07.038Z","avatar_url":"https://github.com/inscidar.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Life Sciences Accessibility Evaluation [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/hms-dbmi/life-sciences-a11y-evaluation/blob/main/notebooks/99-Google-Colab-Playground.ipynb)\n\nThis repository contains source code for surveying the accessibility of life sciences data resources and journals and visualizing results.\n\n## Development\n\nSet up environments using Conda:\n\n```sh\nconda env create -f environment.yml\n```\n\nStart Jupyter with the Python kernel:\n\n```sh\nconda activate life-sciences-a11y-evaluation\njupyter lab notebooks\n```\n\nUnzip accessibility results (`accessibility-status.csv.zip`) that you want to use and analyze.\n\n## Troubleshooting\n\nTo add or remove a conda package, update the environment file. Then run\n\n```sh\nconda env update -f environment.yml\n```\n\nIf you cannot find the Python kernel you created, the following solution may work:\n\nhttps://stackoverflow.com/a/71040470/2499810\n\n## Data\n\nWebpages to data portals are selected from Database Commons (https://ngdc.cncb.ac.cn/databasecommons), which is a site recommended by Cell Press and Bioinformatics Advances. \n\n```\nhttps://ngdc.cncb.ac.cn/databasecommons/database/browse?term=\u0026q=\u0026draw=1\u0026columns%5B0%5D.data=0\u0026columns%5B0%5D.name=\u0026columns%5B0%5D.searchable=false\u0026columns%5B0%5D.orderable=false\u0026columns%5B0%5D.search.value=\u0026columns%5B0%5D.search.regex=false\u0026columns%5B1%5D.data=zindex\u0026columns%5B1%5D.name=\u0026columns%5B1%5D.searchable=true\u0026columns%5B1%5D.orderable=true\u0026columns%5B1%5D.search.value=\u0026columns%5B1%5D.search.regex=false\u0026columns%5B2%5D.data=citation\u0026columns%5B2%5D.name=\u0026columns%5B2%5D.searchable=true\u0026columns%5B2%5D.orderable=true\u0026columns%5B2%5D.search.value=\u0026columns%5B2%5D.search.regex=false\u0026columns%5B3%5D.data=shortName\u0026columns%5B3%5D.name=\u0026columns%5B3%5D.searchable=true\u0026columns%5B3%5D.orderable=true\u0026columns%5B3%5D.search.value=\u0026columns%5B3%5D.search.regex=false\u0026columns%5B4%5D.data=foundedYear\u0026columns%5B4%5D.name=\u0026columns%5B4%5D.searchable=true\u0026columns%5B4%5D.orderable=true\u0026columns%5B4%5D.search.value=\u0026columns%5B4%5D.search.regex=false\u0026order%5B0%5D.column=1\u0026order%5B0%5D.dir=desc\u0026order%5B1%5D.column=4\u0026order%5B1%5D.dir=DESC\u0026start=0\u0026length=10000\u0026search.value=\u0026search.regex=false\u0026_=1667231167872\n```\n\n## Cite\n\nPlease cite the [following paper](https://osf.io/5v98j/):\n\n```\nSehi L'Yi, Thomas C Smits, Alexander Lex, Nils Gehlenborg, \nDigital Accessibility of Life Sciences Data Portals and Journal Websites, \nOSF Preprints, 10.31219/osf.io/5v98j\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finscidar%2Fanalysis-notebooks","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finscidar%2Fanalysis-notebooks","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finscidar%2Fanalysis-notebooks/lists"}