Metadata-Version: 2.4
Name: bigraph-schema
Version: 1.0.1
Summary: A serializable type schema for compositional systems biology
Author: Eran Agmon, Ryan Spangler
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: AUTHORS.md
Requires-Dist: fire
Requires-Dist: ipdb
Requires-Dist: numpy
Requires-Dist: orjson
Requires-Dist: pandas
Requires-Dist: parsimonious
Requires-Dist: pint
Requires-Dist: plum-dispatch
Requires-Dist: pytest
Requires-Dist: requests>=2.31.0
Requires-Dist: setuptools
Requires-Dist: twine>=4.0.2
Dynamic: license-file

# Bigraph-Schema

[![PyPI version](https://img.shields.io/pypi/v/bigraph-schema.svg)](https://pypi.org/project/bigraph-schema/)
[![Tutorial](https://img.shields.io/badge/GitHub%20Pages-Tutorial-brightgreen)](https://vivarium-collective.github.io/bigraph-schema/notebooks/demo.html)

`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:

```console
pip install bigraph-schema
```
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## Getting Started

The following resources provide guided introductions and examples:

- [Type System Overview](https://vivarium-collective.github.io/bigraph-schema/notebooks/core.html) – Demonstrates how to use the `Core` API for schema inference, normalization, and serialization.

- [Bigraph Schema Basics Tutorial](https://vivarium-collective.github.io/bigraph-viz/notebooks/basics.html) – Explains how to compose and visualize schema graphs using the `bigraph-schema` syntax.


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## Related Projects

- [Vivarium](https://vivarium-collective.github.io/) – a compositional framework for hybrid biological simulations.  
- [Bigraph-Viz](https://vivarium-collective.github.io/bigraph-viz/) – visualization tools for bigraph-schema models.  
- [Process-Bigraph](https://github.com/vivarium-collective/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](https://github.com/vivarium-collective/bigraph-schema/blob/main/LICENSE).
