PBG Live Sandbox

Available since v0.9.3

The PBG Live Sandbox is a self-contained Marimo app that lets you explore and operate every part of the Atlantis compose subsystem live from your browser — no local process-bigraph installation required.

Launch

# Install Atlantis (if not already — one-time setup)
git clone https://github.com/vivarium-collective/sms-api.git
cd sms-api
uv sync

# Launch sandbox in app mode (recommended for demos)
uv run atlantis compose sandbox

# Notebook/edit mode — see and modify source cells
uv run atlantis compose sandbox --mode edit

Your browser opens automatically at http://localhost:2718. All five tabs call the live Atlantis API at https://sms.cam.uchc.edu.

The Five Tabs

⚗️ Process Runtime

Demonstrates the full stateful instance lifecycle from the Process Runtime endpoints.

Walkthrough (no SBML needed):

  1. Select MSEComparison from the process dropdown

  2. The config editor pre-fills with the live schema from the API: {"ignore_nans": false, "columns_of_interest": []}

  3. Click Initialize → → API calls POST /compose/v1/process/MSEComparison/initialize, returns a UUID

  4. Live inputs and outputs schemas appear automatically:

    • inputs: {"results": "numeric_results"}

    • outputs: {"comparison_result": "map[map[map[float]]]"}

  5. Click End Process → instance released from memory and marked ended in DB

Button

REST call

rest-process equivalent

Initialize →

POST /process/{name}/initialize

POST /process/{name}

(auto)

GET /process/{name}/inputs/{id}

GET /process/{name}/inputs/{id}

(auto)

GET /process/{name}/outputs/{id}

GET /process/{name}/outputs/{id}

End Process

POST /process/{name}/end/{id}

DELETE /process/{name}/{id}

🧬 BioModels

Full EBI BioModels → SLURM simulation pipeline:

  1. Click Fetch IDs from EBI → retrieves BIOMD0000000001–005 etc.

  2. Enter a model ID → Get Metadata → shows SBML files, authors, format

  3. Select a simulator (copasi or tellurium) → Submit Run → SLURM

    • API fetches SBML from EBI

    • Extracts UniformTimeCourse from SED-ML

    • Builds a process-bigraph document (CopasiUTCStep or TelluriumUTCStep)

    • Dispatches SLURM job on UCONN CCAM HPC

    • Returns a simulation ID

See BioModels for the full integration guide.

🦠 v2ecoli

Submit a whole-cell E. coli simulation directly from the browser:

  1. Set Duration (seconds of biological time), Seed, Interval

  2. Click Submit v2ecoli → SLURM → calls POST /compose/v1/curated/ecoli?duration=10&seed=0&interval=1.0

  3. Returns a simulation ID — poll with atlantis compose status <id> --base-url https://sms.cam.uchc.edu

See v2ecoli for full simulation options.

📋 Registry

Live table of all 11 link_registry entries with package origin, SBML requirement, and config field names. This is the ground-truth view of what allocate_core() discovers on the deployed API pod.

🔷 Types

Fetches all 42 bigraph-schema primitive types live from GET /compose/v1/types — the same types used in all config_schema, inputs, and outputs definitions across the compose system.

Prerequisites

Only the Atlantis CLI is needed. Install from source:

git clone https://github.com/vivarium-collective/sms-api.git
cd sms-api
uv sync

No local process-bigraph, pbsim-common, or v2ecoli installation required. All computation runs on the Atlantis server and UCONN CCAM HPC.