Best Practices for Sharing Methods, Protocols, and Code
To ensure that methods, protocols, and code are accessible, reusable, and understandable, researchers should follow these best practices when sharing their work:
Use Version Control:
- Version control (e.g., Git) is essential for tracking changes to protocols and code, ensuring that previous versions are available and that collaborators can contribute without conflicts.
Provide Detailed Documentation:
- For protocols: Include step-by-step instructions for experimental procedures, fieldwork, or data collection, ensuring that all materials, equipment, and conditions are documented.
- For code: Include README files that explain the code’s purpose, usage instructions, dependencies, and installation requirements. Use inline comments to clarify complex code sections.
Ensure Reproducibility:
- Protocols should be described in enough detail that others can replicate the research without ambiguity. Provide exact specifications for equipment, materials, and procedures, and include any contingencies for potential deviations.
- For code, ensure that all dependencies (e.g., specific libraries, software versions) are clearly stated, and include any necessary installation instructions.
Keep Code and Protocols Modular:
- Break protocols and code into smaller, reusable components. This approach makes it easier to update parts of the workflow without affecting the whole, and it facilitates reuse in other projects.
Use Standard Formats and Terminology:
- For protocols, use standardized formats and terminology whenever possible, referencing established procedures or guidelines. This ensures consistency and enables comparison with similar studies.
- For code, use widely recognized programming languages (e.g., Python, R) and avoid proprietary formats that require special software or licenses.
Regularly Update:
- Both methods and protocols may evolve during the course of research. Keep protocols up-to-date, versioning any changes, and ensure that the latest version is always available.