Process-Bigraph
Process-Bigraph is a compositional runtime and protocol for building and executing multiscale biological models from interoperable processes.
It provides a shared architectural layer for:
- declaring process interfaces
- wiring processes through typed shared state
- orchestrating execution across heterogeneous timescales
- supporting dynamic structure (workflows, division, graph rewrites)
Process-Bigraph is the execution core of Vivarium 2.0, designed to integrate models built with different formalisms—including ODEs, FBA, agent-based models, spatial solvers, and machine-learning components—into a single coherent simulation.
🧩 What is a Process Bigraph?
A process bigraph combines:
- Typed stores — hierarchical, schema-validated state defined with bigraph-schema
- Processes — executable components with explicit input/output ports
- Composites — encapsulated sub-simulations with their own internal structure
- Orchestration patterns — multi-timestepping, directed workflows, and event-driven rewrites
Processes do not mutate state directly. Instead, they emit typed deltas that are merged by the runtime.
This allows:
- numerical updates
- structural rewrites
- scheduling and orchestration
to coexist under a single execution semantics.
In this sense, Process-Bigraph is a composition protocol, not a domain-specific simulator.
📄 Paper reference
The conceptual framework and formal semantics of process bigraphs are introduced in:
Agmon, E. & Spangler, R. K.
Process Bigraphs and the Architecture of Compositional Systems Biology
https://arxiv.org/abs/2512.23754
🚀 Getting Started
Installation
pip install process-bigraph
📘 Tutorials
The Process-Bigraph tutorials are executable Jupyter notebooks, rendered to HTML and published automatically on GitHub Pages.
- 📚 Tutorial Index (all tutorials)
https://vivarium-collective.github.io/process-bigraph/notebooks/index.html
Learning Path (Featured Tutorials)
-
Tutorial 1 — Process-Bigraph Basics
Processes, Steps, ports, Composites, workflows, and emitters
https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_1.html -
Tutorial 2 — Wrapping an ODE Solver (
odeint)
How to expose an existing scientific API as a Process
https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_2.html -
Tutorial 3 — Declarative Math
Defining mathematical relationships, signal pipelines, and events usingMathExpressionStep
https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_3.html -
Tutorial 4 — Composing a Biological Model
The central dogma from four small processes: composition over shared molecular state, biological units in the port types, and adding regulation by adding a wire
https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_4.html
More tutorials are added continuously and appear automatically in the index.
Architecture
- The framework, end to end — start here to understand the whole system:
what the objects are (documents, sites, handles), how they compose, the
higher-order DAG, templates and gating, content-addressed artifacts, the
git:protocol, and the laws everything else follows from. doc/architecture.md
Topic Guides
-
Emitters — Recording Simulation Results Built-in emitters (RAM, console, JSON, SQLite), how to wire them, retrieve results, store runs long-term, and write your own. doc/emitters.md
-
Tick lifecycle — how a step network is ordered and advanced, and how a protocol runtime batches remote dispatch. doc/tick_lifecycle.md
-
Distributed lifecycles — running parts of a composite off-process. doc/distributed_lifecycles.md
🧪 Reference Implementation: spatio-flux
Process-Bigraph is exercised end-to-end in spatio-flux, a multiscale reference model built entirely using the process-bigraph protocol.
spatio-flux composes spatial fields, particle dynamics, and metabolic processes using typed shared state and declarative orchestration.
GitHub: https://github.com/vivarium-collective/spatio-flux
Live test report: https://vivarium-collective.github.io/spatio-flux/report/index.html
🔗 Related Resources
-
Bigraph Schema Basics
https://vivarium-collective.github.io/bigraph-viz/notebooks/basics.html
Introduction to the schema language underlying Process-Bigraph -
Visualization of Bigraph Document — diagramming and rendering with bigraph-viz
https://vivarium-collective.github.io/bigraph-viz/notebooks/format.html -
E. coli Whole-Cell Wiring Diagram
https://raw.githubusercontent.com/vivarium-collective/bigraph-viz/main/doc/_static/ecoli.png -
Claude Code skills — wrap simulators, compose
pbg-*packages, and scaffold process-bigraph research workspaces with the pbg-superpowers Claude Code plugin (install with/plugin install pbg-superpowers).
📜 License
Process-Bigraph is open-source software released under the
Apache 2 License.
2 maintainers
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