README.md

Roberts Lab Resources

This repository serves as the central hub for Roberts Lab members, containing comprehensive documentation, protocols, and guidance for all aspects of lab operations. Whether you're a new member getting started or an experienced researcher looking for specific protocols, this repository provides the resources you need.

📖 Quick Start

• New to the lab? Start with the Roberts Lab Handbook and its Onboarding checklist
• Looking for protocols? Browse our Lab Protocols collection
• Need computing resources? See Computing Hardware, which shows live up/down status for raven, gannet, and klone
• Looking for data? Try the Histology Databank Explorer or Genomic Resources
• Need help or have questions? Submit an issue or join the discussion on Slack
• Major research projects can be found here

🤝 How to Interact with This Repository

For All Lab Members:

• Browse resources: Navigate through folders and files to find what you need
• Search: Use GitHub's search function to quickly locate specific information
• Stay updated: Watch this repository for notifications about important updates

Contributing and Getting Help:

• Report issues: Found something outdated or incorrect? Submit an issue — templates are available for general lab support, access requests, and coding problems
• Suggest improvements: Use GitHub Discussions for ideas and feedback
• Make edits: Click the pencil icon (✏️) on any page to edit directly, or submit a pull request
• Join conversations: Connect with lab members on Slack

Communication Channels:

• GitHub Issues: For troubleshooting, requests, and lab meeting topics
• GitHub Discussions: For broader conversations and feedback
• Slack: For day-to-day lab communication (genefish.slack.com)

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📁 Repository Structure

Core Documentation:

• docs/: Source files for the Roberts Lab Handbook including:
  • Lab culture: onboarding and offboarding, code of conduct, expectations, safety
  • How we work: communication, project management, lab notebooks, data management
  • Guides: scientific writing, oral presentations, outreach slides
  • Computing and code: best practices, agentic coding tools, hardware, Klone and Raven guides
  • Bioinformatic workflows: annotation, DNA methylation, gene expression, transcriptome assembly
  • Self-directed tutorials (standalone HTML): bash-tutorial.html, github-tutorial.html, agentic-ai-bootcamp.html, bivalve-histology-tutorial/

Data Catalogs and Web Tools:

• docs/histology-explorer/: Histology Databank Explorer — static site for searching the histology databank by species, project, year, tissue, and researcher, with links to slide images on owl. Includes the build scripts that regenerate its data (build/build_index.py, build/make_derivatives.py) — see its README
• data-portal/: Self-contained portal for browsing the lab's sequencing libraries (Nightingales) and reference genomes. build.py regenerates nightingales.json from the Nightingales sheet export and genomes.json from docs/Genomic-Resources.md
• igv_server/: IGV genome registry and annotation files for the lab's IGV server

Lab Resources:

• protocols/: Comprehensive collection of lab protocols, including both custom procedures and commercial kit protocols. Note that protocols surfaced in the handbook navigation live in docs/protocols/
• equipment_manuals/: Equipment documentation and user manuals
• lab_safety_docs/: Safety training materials and documentation

Automation:

• .github/workflows/: Deploys the handbook to GitHub Pages on push to master, probes server status every 15 minutes, and checks for broken links in Markdown files
• .github/ISSUE_TEMPLATE/: Issue templates for lab support requests, access requests, and coding issues
• scripts/: Server status probers (check_servers.py, publish_status.sh) that power the status lights on the Computing Hardware page. Results are published to the orphan server-status branch by both a GitHub Action and an in-network cron job, since raven is not reachable from outside the UW network — see scripts/README.md

Administrative:

• mkdocs.yml: Configuration and navigation for the MkDocs handbook site
• .readthedocs.yml: Read the Docs build configuration (the live handbook is deployed to GitHub Pages by the workflow above)
• histology_request_form_2019.pdf: Histology sample submission form for consultation services

Additional Resources:

• archive/: Historical documents and archived materials
• img/: Images and media files used throughout the documentation