Quickstart

This page takes you from zero to downloaded simulation results in three commands. For a deeper walkthrough, see End-to-End Workflow.

The End-to-End Workflow

Every simulation follows the same three-step pattern, regardless of which client application you use:

  1. Build a simulator container image from the vEcoli source code

  2. Run a simulation workflow using that simulator

  3. Download the results

CLI Quickstart

# 1. Build the latest simulator (polls until the build finishes)
uv run atlantis simulator latest

# 2. Run a simulation (replace 11 with your Simulator ID from step 1)
uv run atlantis simulation run my_experiment 11 \
  --generations 1 --seeds 1 --run-parca --poll

# 3. Download results (replace 35 with your Simulation ID from step 2)
uv run atlantis simulation outputs 35 --dest ./results

That’s it. Your results are in ./results/.

TUI Quickstart

uv run atlantis tui

The TUI opens an interactive terminal with a sidebar. Use the navigation buttons to:

  1. Click Build Latest under SIMULATORS

  2. Click Run New under SIMULATIONS, fill in the form, and submit

  3. Click Download Outputs and enter the simulation ID

Web GUI Quickstart

uv run atlantis gui

This opens a Marimo notebook in your browser with interactive card-based sections for each workflow step. Fill in the forms and click the run buttons in order.

What Happens During a Run

When you submit a simulation with --run-parca, the platform runs a multi-step pipeline on the HPC cluster:

  1. Parca (parameter calculator) — generates the simulation dataset from the vEcoli model (~5–8 min)

  2. Simulation — runs the whole-cell simulation for the specified number of generations and seeds (~5–7 min per gen per seed)

  3. Analysis — post-processes simulation outputs into TSV data files and plots (~3–5 min)

Without --run-parca, step 1 is skipped and a pre-existing parca dataset is used.

Next Steps