Rendeiro group

Lab manual

DOI

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 repository on GitHub. It is written in Markdown and can be converted to HTML and PDF using Pandoc.

This manual is open source and maintained collaboratively. Anyone on GitHub can propose changes.

Editing the manual

To contribute an addition or change to the manual:

  1. Edit or create files directly on GitHub, or locally on your computer.
  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.

Tip: to add a table of contents to a new document, use mdformat-toc. Insert <!-- mdformat-toc start --> where the table of contents should appear, and run mdformat <file.md> on the edited file, or make format to format all.

Building the manual locally

To preview changes locally before committing to GitHub and deploying on the lab website, you can build the manual locally using the provided tools. Ensure you have the necessary dependencies installed:

On Debian/Ubuntu, make requirements installs them.

To streamline the development process the project includes a Makefile. 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, which ensures a nice appearance in both HTML and PDF formats.

Releases

Versions are named by date (YYYY-MM-DD). To make a release, update CHANGELOG.md and the version and date-released fields in CITATION.cff, then create a GitHub release with a tag of the same name. The build workflow attaches the HTML and PDF versions of the manual to the release, and Zenodo archives it with a DOI, using the metadata in .zenodo.json. When the list of authors changes, update both .zenodo.json and CITATION.cff.

Citing the manual

If you use or adapt this manual, please cite it:

Rendeiro, A. F., Zheng, Y., Moustafa, S., Abila, E., Buljan, I., & Veres, T. Rendeiro lab manual. Zenodo. https://doi.org/10.5281/zenodo.23398121

This DOI always resolves to the latest version; each release also has its own DOI, listed on Zenodo. Citation metadata is in CITATION.cff, and the "Cite this repository" button on the GitHub page exports it in common formats.

License

The manual is licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). See LICENSE.

Acknowledgements

We thank the following labs for sharing their open-source lab manuals, which inspired this project:

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