{"id":23673779,"url":"https://github.com/carpentries-incubator/managing-computational-projects","last_synced_at":"2026-03-16T22:03:09.647Z","repository":{"id":40234617,"uuid":"398256960","full_name":"carpentries-incubator/managing-computational-projects","owner":"carpentries-incubator","description":"Managing Open and Reproducible Computational Projects","archived":false,"fork":false,"pushed_at":"2024-12-03T01:16:53.000Z","size":10905,"stargazers_count":10,"open_issues_count":19,"forks_count":10,"subscribers_count":11,"default_branch":"main","last_synced_at":"2024-12-06T21:07:22.768Z","etag":null,"topics":["carpentries-incubator","english","lesson","pre-alpha"],"latest_commit_sha":null,"homepage":"https://carpentries-incubator.github.io/managing-computational-projects","language":"R","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/carpentries-incubator.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS","dei":null,"publiccode":null,"codemeta":null},"funding":{"github":["carpentries"],"custom":["https://give.communityin.org/TheCarpentries"]}},"created_at":"2021-08-20T11:41:39.000Z","updated_at":"2024-11-18T06:50:04.000Z","dependencies_parsed_at":"2024-03-19T01:43:15.301Z","dependency_job_id":"6a9a78f1-d3f1-47d5-bdc6-4459735096a0","html_url":"https://github.com/carpentries-incubator/managing-computational-projects","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":"carpentries-incubator/template","purl":"pkg:github/carpentries-incubator/managing-computational-projects","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carpentries-incubator%2Fmanaging-computational-projects","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carpentries-incubator%2Fmanaging-computational-projects/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carpentries-incubator%2Fmanaging-computational-projects/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carpentries-incubator%2Fmanaging-computational-projects/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/carpentries-incubator","download_url":"https://codeload.github.com/carpentries-incubator/managing-computational-projects/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carpentries-incubator%2Fmanaging-computational-projects/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273220117,"owners_count":25066315,"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":"2025-09-02T02:00:09.530Z","response_time":77,"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":["carpentries-incubator","english","lesson","pre-alpha"],"created_at":"2024-12-29T12:56:15.844Z","updated_at":"2026-03-16T22:03:09.600Z","avatar_url":"https://github.com/carpentries-incubator.png","language":"R","funding_links":["https://github.com/sponsors/carpentries","https://give.communityin.org/TheCarpentries"],"categories":[],"sub_categories":[],"readme":"# Data Science for Biomedical Scientists: Managing Open and Reproducible Computational Projects\n\n\u003c!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section --\u003e\n[![All Contributors](https://img.shields.io/badge/all_contributors-13-orange.svg?style=flat-square)](#contributors-)\n\u003c!-- ALL-CONTRIBUTORS-BADGE:END --\u003e\n\n**Thanks for contributing to The Carpentries Incubator!**\nThis repository is part of the **Data Science for Biomedical Scientists: The Turing/Crick partnership project**.\nThis project will facilitate the development of training resources on data science practices for senior researchers, group leaders, late PhD/Postdocs and mid- to late-career biomedical scientists.\nMaterials developed through this project will enable (1) a foundational understanding of AI and data science in the context of biosciences and (2) recommendations for managing (as well as supervising and facilitating) open and reproducible research for the wider biology community.\n\n*This is one of the two masterclasses being developed under **Data Science for Biomedical Scientists: The Turing/Crick partnership project**. For the first masterclass, please visit: [https://github.com/carpentries-incubator/data-science-ai-senior-researchers](https://github.com/carpentries-incubator/data-science-ai-senior-researchers).*\n\nFor details about the project and track management related information, please the [Project Management Repository](https://github.com/alan-turing-institute/data-training-for-bioscience/).\n\n## Developers and Maintainers\n\n- Malvika Sharan\n- Julien Colomb\n\n### Previous developers\n\n- Lydia France was allocated as a developer on this project for six months in 0.5 FTE capacity.\n- Federico Nanni provided supervision for Lydia and contributed to the project planning\n\n**External Reviewer**: Jo Havemann, Access 2 Perspective\n\n## The Carpentries Incubator Programme\n\nThis repository provides a blank starting point for lessons to be developed here.\n\nA member of the Carpentries Curriculum Team will work with you to get your lesson listed on the Community Developed Lessons page and make sure you have everything you need to begin developing your new lesson.\n\nA member of the [Carpentries Curriculum Team](https://carpentries.org/team/)\nwill work with you to get your lesson listed on the\n[Community Developed Lessons page][community-lessons]\nand make sure you have everything you need to begin developing your new lesson.\n\n## What to do next\n\n- [ ] If you're going to contribute to developing lesson material for the first time\naccording to our design principles,\nconsider reading the [Carpentries Curriculum Development Handbook][cdh]\n- [ ] Consult the [Lesson Example][lesson-example] website to find out more about\nworking with the lesson template\n\n## Contributing\n\nWe welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any\nquestions, concerns, or experience any difficulties along the way.\n\nWe'd like to ask you to familiarize yourself with our [Contribution Guide](CONTRIBUTING.md) and have a look at\nthe [more detailed guidelines][workbench] on proper formatting, ways to render the lesson locally, and even\nhow to write new episodes. Note that we are using the new workbench templates and tooling. Rendering of the lessons is now based on R, via `sandpaper::serve()` while the package is not (yet) on CRAN.\n\nPlease see the current list of [issues][FIXME] for ideas for contributing to this\nrepository. For making your contribution, we use the GitHub flow, which is\nnicely explained in the chapter [Contributing to a Project](http://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) in Pro Git\nby Scott Chacon.\nLook for the tag ![good\\_first\\_issue](https://img.shields.io/badge/-good%20first%20issue-gold.svg). This indicates that the maintainers will welcome a pull request fixing this issue.\n\n## Citation\n\nThis lesson will be realeased on Zenodo for DOI (digital object identifier). Meanwhile, please cite this repository as:\n*Data Science for Biomedical Scientists: Managing Open and Reproducible Computational Projects, 2022, [https://github.com/carpentries-incubator/managing-computational-projects](https://github.com/carpentries-incubator/managing-computational-projects)*\n\n## Contributors ✨\n\nThanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):\n\n\u003c!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section --\u003e\n\u003c!-- prettier-ignore-start --\u003e\n\u003c!-- markdownlint-disable --\u003e\n\u003ctable\u003e\n  \u003ctbody\u003e\n    \u003ctr\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"http://malvikasharan.github.io/\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/5370471?v=4?s=100\" width=\"100px;\" alt=\"Malvika Sharan\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eMalvika Sharan\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#content-malvikasharan\" title=\"Content\"\u003e🖋\u003c/a\u003e \u003ca href=\"https://github.com/carpentries-incubator/managing-computational-projects/pulls?q=is%3Apr+reviewed-by%3Amalvikasharan\" title=\"Reviewed Pull Requests\"\u003e👀\u003c/a\u003e \u003ca href=\"https://github.com/carpentries-incubator/managing-computational-projects/commits?author=malvikasharan\" title=\"Documentation\"\u003e📖\u003c/a\u003e \u003ca href=\"#fundingFinding-malvikasharan\" title=\"Funding Finding\"\u003e🔍\u003c/a\u003e \u003ca href=\"#ideas-malvikasharan\" title=\"Ideas, Planning, \u0026 Feedback\"\u003e🤔\u003c/a\u003e \u003ca href=\"#mentoring-malvikasharan\" title=\"Mentoring\"\u003e🧑‍🏫\u003c/a\u003e \u003ca href=\"#projectManagement-malvikasharan\" title=\"Project Management\"\u003e📆\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/LydiaFrance\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/85945427?v=4?s=100\" width=\"100px;\" alt=\"Lydia France\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eLydia France\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#content-LydiaFrance\" title=\"Content\"\u003e🖋\u003c/a\u003e \u003ca href=\"#ideas-LydiaFrance\" title=\"Ideas, Planning, \u0026 Feedback\"\u003e🤔\u003c/a\u003e \u003ca href=\"#example-LydiaFrance\" title=\"Examples\"\u003e💡\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/EstherPlomp\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/46314469?v=4?s=100\" width=\"100px;\" alt=\"Esther Plomp\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eEsther Plomp\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#content-EstherPlomp\" title=\"Content\"\u003e🖋\u003c/a\u003e \u003ca href=\"https://github.com/carpentries-incubator/managing-computational-projects/pulls?q=is%3Apr+reviewed-by%3AEstherPlomp\" title=\"Reviewed Pull Requests\"\u003e👀\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"http://concarneau.mnhn.fr/\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/7910679?v=4?s=100\" width=\"100px;\" alt=\"Yvan Le Bras\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eYvan Le Bras\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/carpentries-incubator/managing-computational-projects/issues?q=author%3Ayvanlebras\" title=\"Bug reports\"\u003e🐛\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/fedenanni\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/8415204?v=4?s=100\" width=\"100px;\" alt=\"Federico Nanni\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eFederico Nanni\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#mentoring-fedenanni\" title=\"Mentoring\"\u003e🧑‍🏫\u003c/a\u003e \u003ca href=\"#projectManagement-fedenanni\" title=\"Project Management\"\u003e📆\u003c/a\u003e \u003ca href=\"#ideas-fedenanni\" title=\"Ideas, Planning, \u0026 Feedback\"\u003e🤔\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://tbyhdgs.info\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/9694524?v=4?s=100\" width=\"100px;\" alt=\"Toby Hodges\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eToby Hodges\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#infra-tobyhodges\" title=\"Infrastructure (Hosting, Build-Tools, etc)\"\u003e🚇\u003c/a\u003e \u003ca href=\"#question-tobyhodges\" title=\"Answering Questions\"\u003e💬\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"http://lisanna.github.io\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/8490781?v=4?s=100\" width=\"100px;\" alt=\"Lisanna Paladin\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eLisanna Paladin\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#ideas-Lisanna\" title=\"Ideas, Planning, \u0026 Feedback\"\u003e🤔\u003c/a\u003e \u003ca href=\"#example-Lisanna\" title=\"Examples\"\u003e💡\u003c/a\u003e\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"http://www.mboalab.africa\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/70091210?v=4?s=100\" width=\"100px;\" alt=\"JAFSIA Elisee\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eJAFSIA Elisee\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#ideas-jafsia\" title=\"Ideas, Planning, \u0026 Feedback\"\u003e🤔\u003c/a\u003e \u003ca href=\"#content-jafsia\" title=\"Content\"\u003e🖋\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://orcid.org/0000-0002-3127-5520\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/1876667?v=4?s=100\" width=\"100px;\" alt=\"Julien Colomb\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eJulien Colomb\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#ideas-jcolomb\" title=\"Ideas, Planning, \u0026 Feedback\"\u003e🤔\u003c/a\u003e \u003ca href=\"https://github.com/carpentries-incubator/managing-computational-projects/pulls?q=is%3Apr+reviewed-by%3Ajcolomb\" title=\"Reviewed Pull Requests\"\u003e👀\u003c/a\u003e \u003ca href=\"#content-jcolomb\" title=\"Content\"\u003e🖋\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/mlagisz\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/13009327?v=4?s=100\" width=\"100px;\" alt=\"Malgorzata Lagisz\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eMalgorzata Lagisz\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#ideas-mlagisz\" title=\"Ideas, Planning, \u0026 Feedback\"\u003e🤔\u003c/a\u003e \u003ca href=\"https://github.com/carpentries-incubator/managing-computational-projects/pulls?q=is%3Apr+reviewed-by%3Amlagisz\" title=\"Reviewed Pull Requests\"\u003e👀\u003c/a\u003e \u003ca href=\"#content-mlagisz\" title=\"Content\"\u003e🖋\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/SaraVilla\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/43204602?v=4?s=100\" width=\"100px;\" alt=\"Sara Villa\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eSara Villa\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#ideas-SaraVilla\" title=\"Ideas, Planning, \u0026 Feedback\"\u003e🤔\u003c/a\u003e \u003ca href=\"https://github.com/carpentries-incubator/managing-computational-projects/pulls?q=is%3Apr+reviewed-by%3ASaraVilla\" title=\"Reviewed Pull Requests\"\u003e👀\u003c/a\u003e \u003ca href=\"#content-SaraVilla\" title=\"Content\"\u003e🖋\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"http://@yalahowy\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/23166543?v=4?s=100\" width=\"100px;\" alt=\"Sara\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eSara\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#ideas-selgebali\" title=\"Ideas, Planning, \u0026 Feedback\"\u003e🤔\u003c/a\u003e \u003ca href=\"#content-selgebali\" title=\"Content\"\u003e🖋\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://access2perspectives.org\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/13553996?v=4?s=100\" width=\"100px;\" alt=\"Jo Havemann\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eJo Havemann\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#content-johav\" title=\"Content\"\u003e🖋\u003c/a\u003e\u003c/td\u003e\n    \u003c/tr\u003e\n  \u003c/tbody\u003e\n\u003c/table\u003e\n\n\u003c!-- markdownlint-restore --\u003e\n\u003c!-- prettier-ignore-end --\u003e\n\n\u003c!-- ALL-CONTRIBUTORS-LIST:END --\u003e\n\nThis project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!\n\n[community-lessons]: https://carpentries.org/community-lessons\n[cdh]: https://cdh.carpentries.org\n[lesson-example]: https://carpentries.github.io/lesson-example\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcarpentries-incubator%2Fmanaging-computational-projects","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcarpentries-incubator%2Fmanaging-computational-projects","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcarpentries-incubator%2Fmanaging-computational-projects/lists"}