A serializable type schema for compositional systems biology

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  • Author: Eran Agmon, Ryan Spangler
  • Requires: Python >=3.9
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Bigraph-Schema

PyPI version Tutorial Units Demo

bigraph-schema provides a serializable type schema for compositional and multiscale modeling.
It defines a compact, extensible language for describing hierarchical data structures — the foundation of the Vivarium 2.0 simulation framework.

The library offers a unified interface for representing, validating, and transforming schemas and data in structured simulations.
By standardizing schema definitions, it enables interoperability between models, extensibility across frameworks, and reproducibility of computational experiments.

Installation

Install directly from PyPI:

pip install bigraph-schema

Getting Started

The following resources provide guided introductions and examples:

  • Type System Overview – Demonstrates how to use the Core API for schema inference, normalization, and serialization.

  • Bigraph Schema Basics Tutorial – Explains how to compose and visualize schema graphs using the bigraph-schema syntax.

  • Units Demo – Demonstrates Quantity, Number._units, and wire-level unit conversion.

Related Projects

  • Vivarium – a compositional framework for hybrid biological simulations.
  • Bigraph-Viz – visualization tools for bigraph-schema models.
  • Process-Bigraph – process composition and orchestration built on bigraph-schema.

License

bigraph-schema is open-source software released under the Apache 2.0 License.

Project details

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  • Author: Eran Agmon, Ryan Spangler
  • Requires: Python >=3.9

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