Workshop 6: Reproducibility and Collaboration

Introduction

In this final workshop, you will focus on making your ancient DNA analysis fully reproducible and ready for collaboration and publication. You will use GitHub, markdown documentation, and workflow best practices to prepare your work for sharing with others. LLMs will assist you in writing clear documentation, collaborative instructions, and reflecting on your computational process. This workshop is designed for students with little prior experience in scientific communication or collaborative coding.

Supporting Materials

• Workshop 6: Intro Slides
• Workshop 6: Background Slides

Problem Statement

Your PI wants your workflow, results, and documentation to be ready for publication and sharing with collaborators. Your job is to:

• Organize your code, workflows, and results in a clear, reproducible structure
• Write clear documentation and usage instructions (README, comments, markdown)
• Prepare your repository for sharing via GitHub Classroom
• Reflect on your computational process and lessons learned

Technical Skills Introduced

• Using git and GitHub for version control and collaboration
• Writing effective documentation (README, markdown, code comments)
• Organizing project files for reproducibility
• Sharing code and results with collaborators
• Prompt engineering for documentation and communication with LLMs

Workshop Structure

1. Repository Organization: Review your files and structure your repository for clarity and reproducibility.
2. Documentation: Use LLMs to help you write a comprehensive README, usage instructions, and code comments.
3. Collaboration: Prepare your repository for sharing with collaborators and instructors via GitHub Classroom.
4. Reflection: Summarize your computational process, challenges, and key lessons learned in a short markdown reflection.
5. Submission: Ensure all files are tracked in git and pushed to GitHub Classroom.

Sample Initial Prompt

I need to prepare my ancient DNA analysis repository for publication and collaboration. Please generate a clear README, usage instructions, and a reflection on the computational process and lessons learned.

Deliverables

By the end of this workshop, you will have created the following artifacts:

1. Organized Repository Structure
   • All code, workflows, and results organized in a clear, logical directory structure
   • Example: data/, scripts/, results/, docs/, Snakefile, README.md
2. Comprehensive Documentation
   • A detailed README file describing the project, usage instructions, workflow, and dependencies
   • Example: README.md
   • Code comments and markdown documentation throughout the repository
3. Collaboration-Ready Repository
   • All files tracked in git and pushed to GitHub Classroom
   • Repository is ready for sharing with collaborators and instructors
4. Reflection Report
   • A short markdown file (1–2 paragraphs) reflecting on your computational process, challenges, and lessons learned
   • Example: reflection.md