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Contributing to the CBD Two-Pathway Model

Thank you for your interest in contributing to this research. This project is an open-science effort, and we welcome contributions from computational biologists, pharmacologists, mitochondrial researchers, and anyone with relevant expertise.

How to Contribute

Reporting Issues

  • Model discrepancies: If simulation outputs conflict with published experimental data, please open an issue with the relevant citation.
  • Parameter challenges: If you believe a kinetic parameter (Kd, scavenging capacity, etc.) should be recalibrated, provide the source data or reference.
  • Bug reports: For code issues (dependency errors, numerical instability, plotting bugs), use the Bug Report issue template.

Proposing Changes

  1. Fork the repository.
  2. Create a feature branch (git checkout -b improvement/your-description).
  3. Make your changes with clear commit messages.
  4. Ensure all simulations still run: python simulation/simulation_v4_honest.py
  5. Open a Pull Request describing what changed and why.

Research Collaboration

If you are interested in:

  • Wet-lab validation of the falsifiable hypotheses (H1--H3)
  • Extending the ODE model (e.g., adding ATP dynamics, calcium handling)
  • Cross-species parameterization (rodent vs. human hepatocyte data)
  • Clinical data integration (CBD trial datasets with liver function markers)

Please open an issue using the Research Collaboration template, or contact the corresponding author directly.

Code Standards

  • Python 3.9+ with dependencies listed in requirements.txt.
  • Simulation scripts should save output to figures/ using path-relative resolution.
  • Use descriptive variable names that map to the biological quantities they represent.
  • Include printed numerical summaries alongside any generated figures.

Scientific Standards

  • All parameter values must be traceable to published literature or clearly labeled as estimated.
  • Synthetic or simulated data must never be presented as experimental results.
  • New model versions should be added as separate scripts (e.g., simulation_v5_*.py), preserving the existing version history.

License

By contributing, you agree that your contributions will be licensed under the same CC BY 4.0 license that covers this project.