A serializable type schema for compositional systems biology
Project description
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.
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
CoreAPI for schema inference, normalization, and serialization. -
Bigraph Schema Basics Tutorial – Explains how to compose and visualize schema graphs using the
bigraph-schemasyntax.
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.
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