https://github.com/rendeirolab/lab-manual
The Rendeiro lab manual
https://github.com/rendeirolab/lab-manual
academia documentation lab-manual research
Last synced: about 1 year ago
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The Rendeiro lab manual
- Host: GitHub
- URL: https://github.com/rendeirolab/lab-manual
- Owner: rendeirolab
- Created: 2025-01-27T12:24:52.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-04-07T11:19:24.000Z (about 1 year ago)
- Last Synced: 2025-04-10T04:02:36.474Z (about 1 year ago)
- Topics: academia, documentation, lab-manual, research
- Language: CSS
- Homepage: http://rendeiro.group/lab-manual/
- Size: 890 KB
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
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README
# Lab manual
Welcome to the Rendeiro Lab Manual.
This manual provides comprehensive information about the lab's culture, procedures, and workflows to ensure a collaborative and efficient research environment.
The 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/).
This manual is open source and maintained collaboratively. Anyone on GitHub can propose changes.
## Building the manual
The project includes a [Makefile](https://github.com/rendeirolab/lab-manual/blob/main/Makefile) to streamline the development process.
Key targets include:
- **`format`**: Formats Markdown files consistently using `mdformat`.
- **`build`**: Converts the manual into a single HTML file using `pandoc` and generates a PDF file using `wkhtmltopdf`.
- **`clean`**: Removes generated files to ensure a fresh build.
Styling for the manual is controlled by a custom [CSS file](assets/style.css), which ensures a nice appearance in both HTML and PDF formats.
## Editing content
To contribute:
1. Edit or create files directly on GitHub or locally on your system.
2. Submit a pull request with a clear, one-line description of the changes made.
3. Follow best practices by adding reviewers and referencing related issues, if applicable.
For adding a table of contents to any document, use [mdformat-toc](https://github.com/hukkin/mdformat-toc). Insert `````` where the table of contents should appear, and run `mdformat ` on the edited file, or `make format` to format all.
## Acknowledgements
We thank the following labs for sharing their open-source lab manuals, which inspired this project:
- [Aly Lab Manual](https://github.com/alylab/labmanual)
- [Getz Lab Manual](https://github.com/getzlab/getzlab.github.io)
## TODO
Some outstanding tasks to improve the manual's content, style and accessibility:
- [ ] Improve and include [public data page](source/public_data.md)
- [ ] Add additional resources on project planning
- [ ] Add section on 'Developing a project'
- [ ] Add section on 'Publications'
- [ ] Add section on 'Authorship'
- [ ] Add section on 'Engaging in new projects'
- [ ] Add proper `href` for all links
- [ ] Align all file names with `h1` heading (for easy linking and easier website deploy)
- [ ] Remove hackaton ideas section from 'Communication'
- [ ] Updat build and dependencies docs
- [ ] Website deployment
- [x] Set up
- [x] Fix `ul`, `ol` and `table` styling
- [x] Fix intra-manual links (ending .md)
- [x] Fix Python code blocks highlighting
- [ ] Build only on tagged versions, not on `main`