https://github.com/warelab/sorghum-marker-dashboard
Making markers accesible with dashboard
https://github.com/warelab/sorghum-marker-dashboard
Last synced: 11 days ago
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Making markers accesible with dashboard
- Host: GitHub
- URL: https://github.com/warelab/sorghum-marker-dashboard
- Owner: warelab
- Created: 2026-04-14T18:37:54.000Z (2 months ago)
- Default Branch: main
- Last Pushed: 2026-05-22T17:27:37.000Z (about 1 month ago)
- Last Synced: 2026-05-22T21:31:33.490Z (about 1 month ago)
- Language: JavaScript
- Size: 3.57 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Sorghum Marker Review
Open `index.html` in a browser to review collaborator marker counts, curated marker filters, chromosome distribution, annotation summaries, and marker-level feedback.
## Share with collaborators
This is a static web app. It can be hosted from any static file host, including GitHub Pages, Vercel, Netlify, an institutional web server, or a shared internal HTTP server.
GitHub Pages is configured by `.github/workflows/deploy-dashboard-pages.yml`. After this branch is merged to `main`, enable Pages with source set to `GitHub Actions` in the repository settings. The dashboard will publish at:
```text
https://warelab.github.io/sorghum_100k_marker_panel/
```
You can also run the workflow manually from the GitHub Actions tab with `Deploy marker dashboard to GitHub Pages`.
For a quick local preview:
```sh
cd dashboard
python3 -m http.server 8080
```
Then open `http://localhost:8080`.
## Feedback workflow
Share `CURATOR_REVIEW_INSTRUCTIONS.md` with collaborators for step-by-step marker validation instructions.
1. Ask collaborators to choose their group from the `Group` dropdown.
2. They can search/filter the review queue and inspect markers in the current-marker panel.
3. They select one marker, several markers, or all visible markers.
4. They choose a decision, add an optional comment, and submit feedback.
5. If Google Forms is configured, one response row is sent per selected marker.
6. The dashboard also keeps a browser-local CSV backup.
Google Forms setup is documented in `GOOGLE_FORM_SETUP.md`. Until `feedback-config.js` is connected to a real form, feedback is stored locally and can be exported as `sorghum_marker_feedback.csv`.
## Refresh the data bundle
Run this from the repository root after updating the marker catalog or summary TSV files:
```sh
python3 dashboard/scripts/build_dashboard_data.py
```
The dashboard uses `data.js`, which is generated from:
- `marker_catalog_304_corrected.tsv`
- `marker_extraction_report.md`
- `results/summary_region_class.tsv`
- `results/summary_per_chromosome.tsv`
- `results/summary_per_gene.tsv`
The generator repairs the 8 concatenated Jura/SbMATE rows for dashboard display using the coordinate block documented in `marker_extraction_report.md`.
The generator also writes `normalized_marker_catalog.tsv`, which adds a stable `canonicalId` for every curated marker while keeping the collaborator-provided name in `originalName`. See `marker_nomenclature.md` for the naming rules.