{"id":24780664,"url":"https://github.com/rendeirolab/lab-manual","last_synced_at":"2025-04-10T04:03:32.396Z","repository":{"id":274478898,"uuid":"922970981","full_name":"rendeirolab/lab-manual","owner":"rendeirolab","description":"The Rendeiro lab manual","archived":false,"fork":false,"pushed_at":"2025-04-07T11:19:24.000Z","size":911,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-10T04:02:36.474Z","etag":null,"topics":["academia","documentation","lab-manual","research"],"latest_commit_sha":null,"homepage":"http://rendeiro.group/lab-manual/","language":"CSS","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/rendeirolab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":null,"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":"2025-01-27T12:24:52.000Z","updated_at":"2025-04-07T11:19:28.000Z","dependencies_parsed_at":"2025-03-24T05:13:34.806Z","dependency_job_id":"e9758772-f5c9-46ef-8c18-4b351a5bc9eb","html_url":"https://github.com/rendeirolab/lab-manual","commit_stats":null,"previous_names":["rendeirolab/lab-manual"],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rendeirolab%2Flab-manual","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rendeirolab%2Flab-manual/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rendeirolab%2Flab-manual/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rendeirolab%2Flab-manual/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rendeirolab","download_url":"https://codeload.github.com/rendeirolab/lab-manual/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248154981,"owners_count":21056543,"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":["academia","documentation","lab-manual","research"],"created_at":"2025-01-29T10:50:23.055Z","updated_at":"2025-04-10T04:03:32.359Z","avatar_url":"https://github.com/rendeirolab.png","language":"CSS","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cdiv style=\"page-break-after: always;\"\u003e\u003c/div\u003e\n\n# Lab manual\n\nWelcome to the Rendeiro Lab Manual.\n\nThis manual provides comprehensive information about the lab's culture, procedures, and workflows to ensure a collaborative and efficient research environment.\n\nThe manual is hosted in the [`lab-manual`](https://github.com/rendeirolab/lab-manual/) repository on GitHub. It is written in [Markdown](https://daringfireball.net/projects/markdown/) and can be converted to HTML and PDF using [Pandoc](https://pandoc.org/).\n\nThis manual is open source and maintained collaboratively. Anyone on GitHub can propose changes.\n\n## Building the manual\n\nThe project includes a [Makefile](https://github.com/rendeirolab/lab-manual/blob/main/Makefile) to streamline the development process.\n\nKey targets include:\n\n- **`format`**: Formats Markdown files consistently using `mdformat`.\n- **`build`**: Converts the manual into a single HTML file using `pandoc` and generates a PDF file using `wkhtmltopdf`.\n- **`clean`**: Removes generated files to ensure a fresh build.\n\nStyling for the manual is controlled by a custom [CSS file](assets/style.css), which ensures a nice appearance in both HTML and PDF formats.\n\n## Editing content\n\nTo contribute:\n1. Edit or create files directly on GitHub or locally on your system.\n2. Submit a pull request with a clear, one-line description of the changes made.\n3. Follow best practices by adding reviewers and referencing related issues, if applicable.\n\nFor adding a table of contents to any document, use [mdformat-toc](https://github.com/hukkin/mdformat-toc). Insert ```\u003c!-- mdformat-toc start --\u003e``` where the table of contents should appear, and run `mdformat \u003cfile.md\u003e` on the edited file, or `make format` to format all.\n\n## Acknowledgements\n\nWe thank the following labs for sharing their open-source lab manuals, which inspired this project:\n\n- [Aly Lab Manual](https://github.com/alylab/labmanual)\n- [Getz Lab Manual](https://github.com/getzlab/getzlab.github.io)\n\n\n## TODO\n\nSome outstanding tasks to improve the manual's content, style and accessibility:\n\n- [ ] Improve and include [public data page](source/public_data.md)\n- [ ] Add additional resources on project planning\n- [ ] Add section on 'Developing a project'\n- [ ] Add section on 'Publications'\n- [ ] Add section on 'Authorship'\n- [ ] Add section on 'Engaging in new projects'\n- [ ] Add proper `href` for all links\n- [ ] Align all file names with `h1` heading (for easy linking and easier website deploy)\n- [ ] Remove hackaton ideas section from 'Communication'\n- [ ] Updat build and dependencies docs\n- [ ] Website deployment\n    - [x] Set up\n    - [x] Fix `ul`, `ol` and `table` styling\n    - [x] Fix intra-manual links (ending .md)\n    - [x] Fix Python code blocks highlighting\n    - [ ] Build only on tagged versions, not on `main`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frendeirolab%2Flab-manual","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frendeirolab%2Flab-manual","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frendeirolab%2Flab-manual/lists"}