GitHub is an effective platform for collaborative and reproducible laboratory research

Area of Science:

• Molecular Biology
• Computational Biology
• Scientific Workflow Management

Background:

• Laboratory research faces challenges in reproducibility and data sharing, particularly in early stages.
• Existing solutions for integrating reproducibility into research workflows are limited.
• Modern software development practices offer potential solutions for scientific research.

Purpose of the Study:

• To propose and demonstrate a framework for enhancing reproducibility and collaboration in laboratory research.
• To adapt the GitHub platform for organizing and documenting the entire research project lifecycle.
• To provide a practical, three-step approach for integrating GitHub into molecular biology lab workflows.

Main Methods:

• Utilizing GitHub issues and project boards for experimental design and organization.
• Implementing version control systems for documenting experiments and data analyses.
• Employing containerized packages to ensure reproducible software environments for data analysis and writing.

Main Results:

• Demonstrated the effective adaptation of GitHub for comprehensive research project management.
• Outlined a scalable, versatile, and affordable three-step integration approach.
• Provided example repositories for practical implementation.

Conclusions:

• Adopting a software development workflow, specifically using GitHub, can significantly enhance research reproducibility and collaboration.
• This framework is suitable for diverse research settings, from small groups to large collaborations.
• Early adoption of this approach improves knowledge transfer efficiency and fidelity within and across laboratories.