process-bigraph 1.4.5

protocol and execution for compositional systems biology

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.

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🧩 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.

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📄 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

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🚀 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 using MathExpressionStep
  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_3.html

More tutorials are added continuously and appear automatically in the index.

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

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🧪 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

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🔗 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

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📜 License

Process-Bigraph is open-source software released under the
Apache 2 License.