Vivarium Workbench

What is Vivarium?

Vivarium is a framework for integrative, multi-scale modeling. Instead of one monolithic model, you write small, self-contained Processes — each describing one mechanism (metabolism, gene expression, physics, transport) — and wire them together into Composites that share state through a typed bigraph. Processes advance in time (Temporal) or transform state as dataflow (Steps), and any composite can itself be used as a process inside a larger one. This makes models modular, reusable, and composable across scales — from molecules to whole cells to colonies.

Built on process-bigraph and bigraph-schema.

What is the Workbench?

The Workbench is a web UI over a Vivarium workspace — a directory of composites, studies, investigations, and data. It reads and writes that workspace, committing every action to a git branch so you get a full audit trail. From here you can browse the registry, configure and run simulations, explore a composite's wiring, organize work into studies and investigations, and view the resulting reports and visualizations.

How to use it

• Resources — the datasets, references, and expert notes your work draws on.
• Catalog / Processes — browse every Composite and Process. Open a card to Configure its parameters, choose Observables and an emitter, Explore its bigraph, and Run it — the run's progress and figures appear under Outputs.
• Studies — organize runs into investigations that pose a question and gate on an expected result.
• Runs — every simulation you've launched, with its results and artifacts.
• Analysis — tools and viewers matched to what your runs produced.

Tip: start on Catalog → Composites, open ecoli_baseline (or any composite), set Steps, and hit ▶ Run.