Compose living models.
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Vivarium is a framework for building multiscale biological models by composing independently-written simulators into one executable whole — and for turning the runs into auditable scientific evidence. Independent formalisms (ODEs, flux-balance analysis, PDEs, agent-based models) are wrapped as typed Processes and wired together through explicit, checkable interfaces, so new science is a new study, not a patch to the model.
The comprehensive guide to the whole ecosystem — foundations, building & running models, turning runs into evidence, and a full reference. Includes a quick start, an interactive bigraph explorer, and a searchable module catalog.
| Package | What it is |
|---|---|
| bigraph-schema | The type system beneath every store — types, ports, and the apply law that merges deltas so independent processes compose. |
| process-bigraph | The engine and the composite / process / step / template primitives — the tick scheduler and the emitters that record state. |
| vivarium-workbench | The AI-free dashboard server — investigations, studies, runs, analyses, and report cards, with every change committed to git. |
| viva-superpowers | The /viva-* Claude Code skills that author and run everything through the Workbench. All AI lives here, so the tool stays auditable. |
The framework is described in Agmon & Spangler, Process bigraphs and the architecture of compositional systems biology (arXiv:2512.23754), which introduces Vivarium 2.0 as the open-source implementation, demonstrated with the Spatio-Flux microbial-ecosystem library.
