Dashboards

The GenSpectrum dashboards are interactive dashboards for the analysis of pathogen genomic data.

Visit it: https://genspectrum.org

The dashboards visualize genomic data obtained from several LAPIS instances. They utilize the Dashboard Components library.

Currently, we support the following organisms:

• SARS-CoV-2
• Influenza A
• Influenza A/H5N1
• Influenza A/H3N2
• Influenza A/H1N1pdm
• Influenza B
• Influenza B/Victoria
• West Nile Virus
• RSV-A
• RSV-B
• Mpox
• Ebola Sudan
• Ebola Zaire
• Crimean-Congo Hemorrhagic Fever (CCHF)

The dashboards also allow users to create subscriptions to receive notifications when there is new data above a configurable threshold for certain variant of an organism.

Contents

This monorepo contains the following packages:

• backend/: The backend for additional features of the dashboard website, currently the notification features.

• website/: The dashboard website: delivery of the (basically static, via Astro) HTML pages with the embedded Dashboard Components (which are included via npm), which retrieve data from LAPIS instances directly, and some additional client side features accessing the backend.

• example-data/: A Node.js seeder script and Dockerfile that populate the backend with example collections (resistance mutation data for 3CLpro, RdRp, and Spike).

Local setup

Check the Docker compose file for an example on how to run the dashboards Docker images.

Use Docker Compose to run the dashboards:

BACKEND_TAG=latest WEBSITE_TAG=latest SEEDER_TAG=latest docker compose up

Seeding example data

The example-data-seeder service seeds the backend with example collections.

BACKEND_TAG=latest WEBSITE_TAG=latest SEEDER_TAG=latest docker compose up

The seeder is idempotent — running it multiple times will not create duplicate collections. Collections are owned by the example-data-seeder user and can be inspected via:

GET /collections?userId=example-data-seeder&organism=covid

Deleting data

docker compose down won't delete the postgres volume. Use ... down -v to also delete the DB volume.