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Contributing to Organoid Intelligence Repository

Thank you for your interest in contributing to the open-source companion repository for "Organoid Intelligence: Biological Computing In Living Systems". We welcome contributions from researchers, educators, engineers, and students.

Code of Conduct

By participating in this project, you agree to abide by our Code of Conduct. Please read it before contributing.

How to Contribute

Reporting Issues

  • Use the GitHub Issues tracker.
  • Search existing issues before opening a new one.
  • Use the appropriate issue template if available.
  • Include sufficient detail: what you expected, what happened, how to reproduce.

Suggesting Enhancements

  • Open an issue with the label enhancement.
  • Describe the motivation and use case clearly.
  • If proposing new content, describe the scientific basis.

Submitting Pull Requests

  1. Fork the repository.
  2. Create a feature branch: git checkout -b feature/your-feature-name
  3. Make your changes following the style guidelines below.
  4. Commit with descriptive messages: git commit -m "feat: add chapter on X"
  5. Push and open a Pull Request against main.
  6. Fill in the PR template completely.
  7. Request a review from a maintainer.

Style Guidelines

Markdown / Textbook Content

  • Use ATX-style headers (##, ###)
  • Keep line lengths under 120 characters
  • Use LaTeX-style math in $$...$$ blocks for equations
  • Include figure placeholders for any referenced visuals
  • Cite primary literature; avoid self-referential claims without evidence
  • Maintain consistent terminology with the glossary in Appendix A

Python Code

  • Follow PEP 8 style
  • Use type hints for function signatures
  • Document all public functions with docstrings (Google style)
  • Ensure code runs under Python 3.9+
  • Include if __name__ == '__main__': blocks in executable scripts
  • Test your code before submitting

Lab Protocols

  • Follow the existing LP-00X template format
  • Include version numbers, BSL levels, and dates
  • Use generic catalog numbers or clearly label them as examples
  • Have all safety information in Section 2

Development Setup

git clone https://github.com/DaScientist/Organoid-Intelligence.git
cd Organoid-Intelligence
pip install -r visualizations/python/requirements.txt
pip install python-docx  # for generate_docx.py

Review Process

All pull requests are reviewed by maintainers. Reviews focus on:

  • Scientific accuracy
  • Clarity and accessibility
  • Code correctness and style
  • Consistency with the rest of the repository

Attribution

Contributors will be acknowledged in the repository's Contributors section. Significant contributions to textbook content may be noted in the Acknowledgments of future editions.

Questions?

Open a GitHub Discussion or contact the maintainers through the Issues tracker.