What is git?
Git(hub) has tow main purposes:
- Version control: Track changes in your own files, code etc.
- Collaboration: Contribute to someone else’s files, code etc.
In addition it allows for:
- Efficient workflows
- Massive resource of information, ideas, books, code, etc.
- Publishing and hosting of code and material, websites etc.
Git in a rsearch context
Background:
Dr. Alice is a computational biologist working on a collaborative research project aimed at understanding the genetic factors influencing a specific disease. Her team comprises researchers from different institutions, and they need a centralized platform for data analysis and collaboration.
How GitHub can be used:
Code Repository:
Dr. Alice creates a GitHub repository to host the research project’s codebase. This repository contains analysis scripts, data preprocessing pipelines, and documentation. Collaborators can clone the repository to access the latest code and contribute to it.
Data Sharing:
The team collects and curates extensive genetic data. Using Git Large File Storage (LFS) on GitHub, they store the data files in the same repository, ensuring version-controlled access to the data. The data is well-organized and documented in the repository’s README.
Collaborative Analysis:
Collaborators, including Dr. Bob and Dr. Carol, fork Dr. Alice’s repository and create feature branches for specific analysis tasks. They make changes, run experiments, and submit pull requests back to the main repository for review.
Issue Tracking:
Dr. Alice uses GitHub’s issue tracking system to create tasks for different aspects of the project. For example, they may have tasks for data preprocessing, statistical analysis, and visualization. This ensures that everyone on the team knows what needs to be done and helps manage their progress.
Peer Review:
Dr. Alice and her team use the pull request feature for peer review. They can comment on specific lines of code, suggest improvements, and discuss the results directly in the pull request. This transparent and collaborative process ensures the quality of the analysis.
Project Management:
Dr. Alice creates a project board on GitHub to track the progress of different analysis components. They can move tasks across different columns, such as “To Do,” “In Progress,” and “Done,” to visualize the status of each task.
Documentation:
Dr. Alice maintains comprehensive project documentation in Markdown format within the repository. This includes explanations of the data sources, analysis methods, and results. Collaborators can contribute to and refine this documentation over time.
Reproducibility:
With the code, data, and documentation all in one place on GitHub, Dr. Alice’s team ensures that their research is highly reproducible. Other researchers can access the repository to replicate and validate the findings.
Data Citations:
As the project progresses, Dr. Alice obtains a DOI for the GitHub repository, making it citable in research papers. This promotes recognition of their work and encourages other researchers to use and build upon their findings.
By using GitHub for this collaborative research project, Dr. Alice and her team streamline their data analysis, foster transparency, and maintain an organized and reproducible research workflow. The platform facilitates teamwork, enabling researchers from different institutions to work together effectively.