We build Vivarium — an open-source ecosystem for integrative, multi-scale biological modeling, built on the process bigraph formalism: a typed schema system and composition engine that make models easy to define, validate, compose, run, and explore. Everything below is developed openly under the Vivarium Collective.

Start here

The two main entry points into the ecosystem — a browser workbench and an AI-agent toolkit.

• vivarium-workbench — the browser-based workbench for Vivarium workspaces: build, run, and explore composites, simulations, studies, and investigations, and discover the ecosystem through a built-in Marketplace.
• viva-superpowers — a Claude Code plugin of skills and workflows for building and driving Vivarium research projects with AI agents.

Framework

The core of Vivarium 2.0 — the engine and schema system everything else builds on.

• process-bigraph — the composition engine that runs Processes, Steps, and Composites with transparent, typed data flow.
• bigraph-schema — the typed schema system for defining models, state, and interfaces (docs).

For the formal foundation, see Foundations of a Compositional Systems Biology, Process Bigraphs and the Architecture of Compositional Systems Biology, and the Process Bigraph Supplemental Materials.

Tools

Shared tooling for building, sharing, and running composite models.

• viva-template — scaffold for starting a new process-bigraph research workspace.
• viva-marketplace — the ecosystem registry (modules.json) and aggregated artifact index — composites, processes, studies, and investigations across every repo — that powers the workbench Marketplace.
• viva-emitters — interchangeable data emitters (XArray / Zarr / Parquet).
• viva-basic-processes — reusable building blocks such as clocks, interventions, and math expressions.

Models & Applications

Biological models built on the framework.

• v2ecoli — a whole-cell model of E. coli integrating gene regulation, metabolism, and physiology across molecular, cellular, and population scales (live dashboard).
• 3d-ecoli — a spatial, 3D whole-cell model of E. coli (live 3D viewer).
• spatio-flux — spatial flux-balance and reaction–diffusion composites for cells in their environments (demo).
• vivarium-tyssue — process-bigraph integration of tyssue for epithelial tissue mechanics.
• viva-munk — multi-cell simulations with 2D physics, growing and dividing cells in shared chemical environments (demos).
• viva-biomodels — cross-engine comparison of ~900 curated BioModels across multiple simulators (live site).

Browse everything at the Vivarium Collective on GitHub.