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 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.

Building the manual

The project includes a 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, 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. 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.

Acknowledgements

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

• Aly Lab Manual
• Getz Lab Manual

TODO

Some outstanding tasks to improve the manual's content, style and accessibility:

• Improve and include public data page
• 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
  • Set up
  • Fix ul, ol and table styling
  • Fix intra-manual links (ending .md)
  • Fix Python code blocks highlighting
  • Build only on tagged versions, not on main