We build Vivarium — an open-source ecosystem for integrative, multi-scale biological modeling. The current framework is organized around the process bigraph formalism: a typed schema system and composition engine that make models easy to define, validate, compose, and visualize. Everything below is developed openly under the Vivarium Collective.
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).
- bigraph-viz — visualization of composite models and how their parts are wired together.
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, running, and exploring composite models.
- vivarium-dashboard — interactive dashboard for workspaces, composites, simulations, and investigations.
- pbg-template — scaffold for starting a new process-bigraph research workspace.
- pbg-superpowers — skills and workflows for authoring and driving workspaces.
- pbg-emitters — interchangeable data emitters (XArray / Zarr / Parquet).
- pbg-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).
- vivatyssue — 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).
- biomodels-comparison — cross-engine comparison of ~900 curated BioModels across multiple simulators (live site).
Browse everything at the Vivarium Collective on GitHub.