From df5bfb4301ec41bceccaa1f31979cae41f139f99 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Fri, 21 Aug 2026 16:24:15 -0700 Subject: [PATCH] docs: refresh README for tools added since last update The Repository Structure section still described the repo as docs + protocols + manuals + safety docs, missing everything added over the past year. Adds the pieces that were absent and refreshes Quick Start. - Data Catalogs and Web Tools: docs/histology-explorer/, data-portal/, igv_server/ - Automation: .github/workflows/ (Pages deploy, 15-min server probe, URL checker), .github/ISSUE_TEMPLATE/, and scripts/ with a note on why there are two status probers (raven is not in public DNS) - Expand the docs/ bullet to cover onboarding/offboarding, project management, writing and oral presentation guides, agentic coding tools, and the standalone HTML tutorials - Quick Start: add Onboarding, Computing Hardware, and the two data catalogs; point issue reporting at issues/new/choose so the templates are actually used - Note that handbook-navigated protocols live in docs/protocols/, distinct from top-level protocols/ All four new handbook URLs verified to return 200. Co-Authored-By: Claude Opus 5 --- README.md | 32 +++++++++++++++++++++++--------- 1 file changed, 23 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index f310af0dd..3d42d6846 100644 --- a/README.md +++ b/README.md @@ -4,8 +4,10 @@ This repository serves as the central hub for [Roberts Lab](http://faculty.washi ## 📖 Quick Start -- **New to the lab?** Start with the [Roberts Lab Handbook](https://robertslab.github.io/resources/) for comprehensive onboarding information +- **New to the lab?** Start with the [Roberts Lab Handbook](https://robertslab.github.io/resources/) and its [Onboarding](https://robertslab.github.io/resources/Onboarding/) checklist - **Looking for protocols?** Browse our [Lab Protocols](https://github.com/RobertsLab/resources/tree/master/protocols) collection +- **Need computing resources?** See [Computing Hardware](https://robertslab.github.io/resources/Computing-Hardware/), which shows live up/down status for raven, gannet, and klone +- **Looking for data?** Try the [Histology Databank Explorer](https://robertslab.github.io/resources/histology-explorer/) or [Genomic Resources](https://robertslab.github.io/resources/Genomic-Resources/) - **Need help or have questions?** Submit an [issue](https://github.com/RobertsLab/resources/issues) or join the discussion on [Slack](https://genefish.slack.com) - **Major research projects** can be found [here](https://github.com/RobertsLab?utf8=%E2%9C%93&q=project&type=&language=) @@ -17,7 +19,7 @@ This repository serves as the central hub for [Roberts Lab](http://faculty.washi - **Stay updated**: Watch this repository for notifications about important updates ### Contributing and Getting Help: -- **Report issues**: Found something outdated or incorrect? [Submit an issue](https://github.com/RobertsLab/resources/issues/new) +- **Report issues**: Found something outdated or incorrect? [Submit an issue](https://github.com/RobertsLab/resources/issues/new/choose) — templates are available for general lab support, access requests, and coding problems - **Suggest improvements**: Use [GitHub Discussions](https://github.com/RobertsLab/resources/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](https://genefish.slack.com) @@ -37,19 +39,31 @@ This repository serves as the central hub for [Roberts Lab](http://faculty.washi ### Core Documentation: - **`docs/`**: Source files for the [Roberts Lab Handbook](https://robertslab.github.io/resources/) including: - - Lab policies and expectations - - Computing resources and best practices - - Safety protocols and training materials - - Communication guidelines and onboarding information + - 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](https://robertslab.github.io/resources/histology-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](docs/histology-explorer/README.md) +- **`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 +- **`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](scripts/README.md) + ### Administrative: -- **`.readthedocs.yml`**: Configuration for the Roberts Lab Handbook website -- **`mkdocs.yml`**: Configuration file for [MkDocs](https://www.mkdocs.org/) documentation generation +- **`mkdocs.yml`**: Configuration and navigation for the [MkDocs](https://www.mkdocs.org/) 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: