A serializable type schema for compositional systems biology

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for eagmon from gravatar.com eagmon Avatar for youdonotexist from gravatar.com youdonotexist

Unverified details

These details have not been verified by PyPI
Meta
  • Author: Eran Agmon, Ryan Spangler
  • Requires: Python >=3.9
Report project as malware

Project description

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

Verified details

These details have been verified by PyPI
Maintainers
Avatar for eagmon from gravatar.com eagmon Avatar for youdonotexist from gravatar.com youdonotexist

Unverified details

These details have not been verified by PyPI
Meta
  • Author: Eran Agmon, Ryan Spangler
  • Requires: Python >=3.9

Release history Release notifications | RSS feed

1.4.2

1.4.1

1.3.4

This version

1.3.3

1.3.2

1.3.1

1.3.0

1.2.17

1.2.16

1.2.15

1.2.14

1.2.12

1.2.11

1.2.10

1.2.9

1.2.8

1.2.7

1.2.6

1.2.5

1.2.4

1.2.3

1.2.1

1.1.6

1.1.5

1.1.4

1.1.3

1.1.2

1.1.1

1.0.15

1.0.14

1.0.13

1.0.12

1.0.11

1.0.5

1.0.4

1.0.3

1.0.2

1.0.1

1.0.0

0.0.77

0.0.75

0.0.74

0.0.73

0.0.72

0.0.71

0.0.68

0.0.65

0.0.64

0.0.63

0.0.62

0.0.60

0.0.59

0.0.58

0.0.57

0.0.56

0.0.55

0.0.54

0.0.53

0.0.52

0.0.51

0.0.50

0.0.49

0.0.48

0.0.47

0.0.46

0.0.45

0.0.44

0.0.43

0.0.42

0.0.41

0.0.38

0.0.37

0.0.35

0.0.32

0.0.31

0.0.30

0.0.29

0.0.28

0.0.27

0.0.22

0.0.21

0.0.19

0.0.18

0.0.17

0.0.15

0.0.14

0.0.13

0.0.12

0.0.11

0.0.9

0.0.8

0.0.7

0.0.6

0.0.5

0.0.4

0.0.3

0.0.2

0.0.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

bigraph_schema-1.3.3.tar.gz (123.7 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

bigraph_schema-1.3.3-py3-none-any.whl (139.3 kB view details)

Uploaded Python 3

File details

Details for the file bigraph_schema-1.3.3.tar.gz.

File metadata

  • Download URL: bigraph_schema-1.3.3.tar.gz
  • Upload date:
  • Size: 123.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for bigraph_schema-1.3.3.tar.gz
Algorithm Hash digest
SHA256 2372c4ae16b1017f8565dcfbff6391e0df95c8d6738e49fa66c49638b9239a9e
MD5 c15aa0db1e6fd25a62e08507452925fe
BLAKE2b-256 654d2837273109d41f210161c7f8f7cd9ffdd2807fb0090d6e700fb1b41515e6

See more details on using hashes here.

Provenance

The following attestation bundles were made for bigraph_schema-1.3.3.tar.gz:

Publisher: release.yml on vivarium-collective/bigraph-schema

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file bigraph_schema-1.3.3-py3-none-any.whl.

File metadata

  • Download URL: bigraph_schema-1.3.3-py3-none-any.whl
  • Upload date:
  • Size: 139.3 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for bigraph_schema-1.3.3-py3-none-any.whl
Algorithm Hash digest
SHA256 8d96b38c9aeb2ac500edcfeb3c82778ced434898a1003cee7bb458059bd0f855
MD5 63691c072f1a3afdc07f89a2ec5adf15
BLAKE2b-256 2c805087a0e0d07c430cc1d21f1c4473c986455f6d53847c993ef1ee065ee6f8

See more details on using hashes here.

Provenance

The following attestation bundles were made for bigraph_schema-1.3.3-py3-none-any.whl:

Publisher: release.yml on vivarium-collective/bigraph-schema

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page