Configuration¶

Server Connection¶

All client applications connect to an Atlantis API server. The default is http://localhost:8080.

Override per-command (CLI):

uv run atlantis simulator latest --base-url https://sms.cam.uchc.edu

Override for your session:

export API_BASE_URL=https://sms.cam.uchc.edu

In the TUI, Desktop GUI, and Web GUI, use the server selector dropdown to switch servers at any time.

Available Servers¶
Server	URL	Notes
Production	`https://sms.cam.uchc.edu`	Main deployment
Development	`https://sms-dev.cam.uchc.edu`	Staging / test
Local	`http://localhost:8080`	Default; typically a port-forward to a remote cluster

Simulation Configuration Presets¶

Available config filenames are discovered dynamically from the simulator’s vEcoli repository. Different simulators (different commits, repos, branches) may have different configs available. Use the discovery command to see what’s available for a given simulator:

uv run atlantis simulation configs SIMULATOR_ID

The default is api_simulation_default.json. If the config file doesn’t exist in the repo, the server falls back to an embedded default template.

Analysis Module Discovery¶

Analysis modules available for --analysis-options depend on what exists in the simulator’s vEcoli repo under ecoli/analysis/{category}/. Discover available modules before submitting:

uv run atlantis simulation analyses SIMULATOR_ID

Or via the REST API:

curl http://localhost:8080/api/v1/simulations/discovery?simulator_id=16

Analysis defaults are repo-aware: private vEcoli repo simulators get cd1_* modules by default; public repo simulators get no default analyses. User-specified --analysis-options always overrides the defaults.

Environment Variables¶

These environment variables affect client behavior:

Variable	Description
`API_BASE_URL`	Default API server URL (overrides `http://localhost:8080`)