bigraph-schema 1.0.14

A serializable type schema for compositional systems biology

Bigraph-Schema

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.

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Installation

Install directly from PyPI:

pip install bigraph-schema

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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.

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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.

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License

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