Choosing a Client Application

Atlantis provides three client applications. Each one exposes the same end-to-end workflow — the difference is the interface.

Quick Comparison

Client	Launch Command	Best For	Notes
CLI	uv run atlantis	Scripting, automation, quick one-off commands	Fastest for experienced users. Supports --poll for blocking runs.
TUI	uv run atlantis tui	Interactive terminal sessions, SSH environments	Sidebar navigation, tabbed results, file browser. No browser needed.
Web GUI	uv run atlantis gui	Point-and-click in the browser, collaborative demos	Marimo reactive notebook with Tensorboard-style cards.

CLI

The atlantis command-line interface is the primary tool for working with the platform. It supports all workflow steps as subcommands:

uv run atlantis simulator latest       # Build
uv run atlantis simulation run ...     # Run
uv run atlantis simulation outputs ... # Download

Use help as a trailing word on any command (equivalent to --help):

uv run atlantis help
uv run atlantis simulation help
uv run atlantis simulation run help

See CLI Reference for the full command reference.

TUI (Terminal User Interface)

The TUI is a full-screen terminal application built with Textual. It presents the same workflow steps as buttons in a sidebar:

uv run atlantis tui

Features:

• Three domain navigation buttons (Simulations, Simulators, Analyses)

• Auto-listing with per-row status enrichment on click

• Split view: data table (top) + rich log (bottom)

• Double-click a completed simulation to download and browse its output files

• Modal forms for simulation submission

• Animated E. coli banner with green/purple gradient cycling

• Server selector at the bottom

The TUI uses ANSI colors for compatibility with all terminals.

Web GUI (Marimo)

The web GUI is a Marimo reactive notebook that opens in your browser locally or is hosted on the deployed server:

# Local
uv run atlantis gui

# Hosted (no install required)
# https://sms.cam.uchc.edu/ws/Dashboard

Features:

• Tensorboard-style card layout with rounded edges and coloured headers

• Interactive forms with live reactivity

• Auto-refreshing simulation status (30s interval)

• CSS-animated Memphis banner

• Iconify icons throughout the interface

• Status badges with colour-coded states

• Grid layout for compact, dashboard-like arrangement

Workflow Mapping

All three clients map to the same six workflow steps:

Step	Action	CLI	TUI	Web GUI
1–3	Build simulator	simulator latest	Simulators > Build Latest	Simulator card > Build
4	Submit simulation	simulation run	Simulations > Run New	Simulation card > Submit
5	Check status	simulation status	Simulations (auto-listed with status)	Simulation card > Status (auto-refreshes every 30s)
6	Download results	simulation outputs	Double-click completed row	Simulation card > Download
7	Re-run analysis	simulation analysis	Analyses domain	(endpoint available)