ATLAS

ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data converted to the OMOP Common Data Model V5. Researchers can create cohorts by defining groups of people based on an exposure to a drug or diagnosis of a particular condition using healthcare claims data. ATLAS has vocabulary searching of medical concepts to identify people with specific conditions, drug exposures etc. Patient profiles can be viewed within a specific cohort allowing visualization of a particular subject's health care records. Population effect level estimation analyses allows for comparison of two different cohorts and leverages R packages.

Resources

• Atlas Demo (ohdsi.org)
• Documentation
• Releases

Technology

ATLAS is built using HTML, CSS and Knockout JavaScript. For more information on using Atlas, please refer to the setup guide.

Dependencies

• WebAPI — a running WebAPI instance is required; Atlas is a client that talks to it over HTTP.

Development

npm install
npm run dev      # Vite dev server, default http://localhost:5173/atlas/
npm run build    # production build, output to js/assets/bundle/
npm test         # Node's built-in test runner
npm run lint     # eslint/neostandard

Configuration

Atlas is a browser app (Vite + Knockout.js), so configuration happens in two different places depending on when it takes effect:

Build time (npm run dev / npm run build, and the Docker builder stage) — set environment variables before running the command, e.g. via a gitignored .env.local file (Vite loads this automatically) or direnv/.envrc:

Variable	Purpose
VITE_WEBAPI_URL	WebAPI instance the app talks to, e.g. http://localhost:8080/webapi/
VITE_WEBAPI_NAME	Display name for that instance

js/config.js reads these directly (import.meta.env.VITE_*) — there's no separate config file to create.

Container runtime (a pre-built Docker image, no rebuild) — set env vars on docker run -e ... or in a compose file's environment: block. The entrypoint substitutes them into a small file the running app fetches on load, so the same image can be pointed at different WebAPI instances without rebuilding:

Variable	Purpose
WEBAPI_URL	WebAPI instance the app talks to
ATLAS_INSTANCE_NAME	Display name for that instance
ATLAS_*	Feature flags and auth-provider settings — see the full list of ENV defaults in Dockerfile

Building the container image

build.sh produces a multi-arch (linux/amd64 + linux/arm64) image with podman, so a build on an Apple Silicon machine runs on the AMD64 deployment hosts. It tags three names — the package.json version, that version plus the short git SHA, and latest — and pushes only when asked:

./build.sh            # build only; nothing leaves this machine
PUSH=1 ./build.sh     # build and push to chi-tools.uc.edu

Pushing needs a one-time podman login chi-tools.uc.edu. Pushes from a dirty working tree are refused (override with FORCE=1), since a latest built from uncommitted code can't be reproduced. Overrides: REGISTRY, PLATFORMS (e.g. PLATFORMS=linux/arm64 for a fast local-only build).

The Vite build runs natively on the build host rather than under emulation — its output is architecture-neutral, so both architectures share it. Only the nginx runtime layer differs.

Running with Docker

podman run --rm -p 8080:8080 \
  -e WEBAPI_URL=http://my-webapi-host:8080/WebAPI/ \
  -e ATLAS_INSTANCE_NAME="My Instance" \
  chi-tools.uc.edu/atlas:latest

Atlas is served under the /atlas/ path prefix, so the URL is http://localhost:8080/atlas/.

For deployment, deploy/compose.yaml and deploy/.env.example are the files to copy to /srv/atlas on the target host.

Getting Involved

• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

License

ATLAS is licensed under Apache License 2.