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RuleHub

RuleHub is the canonical repository for curated BioNetGen and BNGL model content used across the RuleWorld ecosystem.

It now serves two roles:

  • a human-browsable archive of published, contributed, tutorial, and validation models
  • the machine-readable source of truth for metadata consumed by tools such as BNG Playground

Repository layout

The repository is organized into a few top-level collections:

  • Published/: literature-backed and curated research models
  • Contributed/: contributed model sets, including BNG Playground examples and validation fixtures
  • Tutorials/: tutorial and teaching-oriented BNGL models
  • PyBioNetGen/: PyBioNetGen reference, benchmark, and support model collections

Most model directories contain:

  • one or more .bngl files
  • metadata.yaml
  • README.md

Examples:

  • Published/Faeder2003/
  • Contributed/BNGPlayground_Examples/...
  • Contributed/BNGPlayground_Validation/...
  • Tutorials/General/polymer/
  • Tutorials/NativeTutorials/...

Metadata and manifest

RuleHub now includes a repository-wide metadata and discovery layer:

  • metadata-schema.yaml: schema for per-directory metadata
  • manifest.json: generated manifest describing discoverable model entries
  • scripts/validate-metadata.js: local metadata validator
  • scripts/generate-manifest.js: manifest generator

This metadata is used for:

  • model discovery and indexing
  • gallery visibility and categorization
  • compatibility flags such as bng2_compatible
  • provenance for published, tutorial, test-case, and AI-generated contributed models

BNG Playground integration

BNG Playground no longer keeps its own bundled BNGL corpus as the runtime source of truth.

Instead:

  • RuleHub hosts the model content and metadata
  • BNG Playground resolves models from RuleHub metadata and manifest outputs
  • local playground analysis and migration scripts may use a local RuleHub checkout via RULEHUB_ROOT

That means updates to model metadata, visibility, provenance, and organization should now happen here in RuleHub.

Validation workflow

Before opening a pull request that adds or changes model content, run:

node scripts/validate-metadata.js
node scripts/generate-manifest.js --root . --output manifest.json

The repository also includes CI validation in .github/workflows/validate.yml.

Adding models

For model submission and curation rules, see AddingModels.md.

In general, contributors should:

  1. place models in the appropriate top-level collection
  2. add or update metadata.yaml
  3. add or update README.md
  4. describe multi-file collections with a collection section when applicable
  5. validate metadata and regenerate manifest.json

Notes on migrated content

RuleHub now contains migrated content that previously lived only inside BNG Playground, including:

  • BNG Playground example models
  • validation fixtures
  • tutorial collections
  • runtime-only BNGL models that required explicit preservation

Those migrated entries keep provenance in metadata.yaml, including source-path history where relevant.

Quick links

About

A repository of rule-based models. Could this be the start of something great?

Resources

Readme
MIT license
Activity
Custom properties

Stars

2 stars

Watchers

17 watching

Forks

7 forks
Report repository

Releases

Packages

Contributors

Languages

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GitHub - RuleWorld/RuleHub: A repository of rule-based models. Could this be the start of something great? · GitHub
Skip to content
BranchesTags
Repository files navigation
RuleHub
RuleHub is the canonical repository for curated BioNetGen and BNGL model content used across the RuleWorld ecosystem.
It now serves two roles:
  • a human-browsable archive of published, contributed, tutorial, and validation models
  • the machine-readable source of truth for metadata consumed by tools such as BNG Playground
Repository layout
The repository is organized into a few top-level collections:
  • Published/: literature-backed and curated research models
  • Contributed/: contributed model sets, including BNG Playground examples and validation fixtures
  • Tutorials/: tutorial and teaching-oriented BNGL models
  • PyBioNetGen/: PyBioNetGen reference, benchmark, and support model collections
Most model directories contain:
  • one or more .bngl files
  • metadata.yaml
  • README.md
Examples:
  • Published/Faeder2003/
  • Contributed/BNGPlayground_Examples/...
  • Contributed/BNGPlayground_Validation/...
  • Tutorials/General/polymer/
  • Tutorials/NativeTutorials/...
Metadata and manifest
RuleHub now includes a repository-wide metadata and discovery layer:
  • metadata-schema.yaml: schema for per-directory metadata
  • manifest.json: generated manifest describing discoverable model entries
  • scripts/validate-metadata.js: local metadata validator
  • scripts/generate-manifest.js: manifest generator
This metadata is used for:
  • model discovery and indexing
  • gallery visibility and categorization
  • compatibility flags such as bng2_compatible
  • provenance for published, tutorial, test-case, and AI-generated contributed models
BNG Playground integration
BNG Playground no longer keeps its own bundled BNGL corpus as the runtime source of truth.
Instead:
  • RuleHub hosts the model content and metadata
  • BNG Playground resolves models from RuleHub metadata and manifest outputs
  • local playground analysis and migration scripts may use a local RuleHub checkout via RULEHUB_ROOT
That means updates to model metadata, visibility, provenance, and organization should now happen here in RuleHub.
Validation workflow
Before opening a pull request that adds or changes model content, run:
node scripts/validate-metadata.js
node scripts/generate-manifest.js --root . --output manifest.json
The repository also includes CI validation in .github/workflows/validate.yml.
Adding models
For model submission and curation rules, see AddingModels.md.
In general, contributors should:
  1. place models in the appropriate top-level collection
  2. add or update metadata.yaml
  3. add or update README.md
  4. describe multi-file collections with a collection section when applicable
  5. validate metadata and regenerate manifest.json
Notes on migrated content
RuleHub now contains migrated content that previously lived only inside BNG Playground, including:
  • BNG Playground example models
  • validation fixtures
  • tutorial collections
  • runtime-only BNGL models that required explicit preservation
Those migrated entries keep provenance in metadata.yaml, including source-path history where relevant.
Quick links
About
A repository of rule-based models. Could this be the start of something great?
Resources
Readme
MIT license
Activity
Custom properties
Stars
2 stars
Watchers
17 watching
Forks
7 forks
Report repository
Releases
Packages
Contributors
Languages

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GitHub - RuleWorld/RuleHub: A repository of rule-based models. Could this be the start of something great? · GitHub
Skip to content
BranchesTags
Repository files navigation
RuleHub
RuleHub is the canonical repository for curated BioNetGen and BNGL model content used across the RuleWorld ecosystem.
It now serves two roles:
  • a human-browsable archive of published, contributed, tutorial, and validation models
  • the machine-readable source of truth for metadata consumed by tools such as BNG Playground
Repository layout
The repository is organized into a few top-level collections:
  • Published/: literature-backed and curated research models
  • Contributed/: contributed model sets, including BNG Playground examples and validation fixtures
  • Tutorials/: tutorial and teaching-oriented BNGL models
  • PyBioNetGen/: PyBioNetGen reference, benchmark, and support model collections
Most model directories contain:
  • one or more .bngl files
  • metadata.yaml
  • README.md
Examples:
  • Published/Faeder2003/
  • Contributed/BNGPlayground_Examples/...
  • Contributed/BNGPlayground_Validation/...
  • Tutorials/General/polymer/
  • Tutorials/NativeTutorials/...
Metadata and manifest
RuleHub now includes a repository-wide metadata and discovery layer:
  • metadata-schema.yaml: schema for per-directory metadata
  • manifest.json: generated manifest describing discoverable model entries
  • scripts/validate-metadata.js: local metadata validator
  • scripts/generate-manifest.js: manifest generator
This metadata is used for:
  • model discovery and indexing
  • gallery visibility and categorization
  • compatibility flags such as bng2_compatible
  • provenance for published, tutorial, test-case, and AI-generated contributed models
BNG Playground integration
BNG Playground no longer keeps its own bundled BNGL corpus as the runtime source of truth.
Instead:
  • RuleHub hosts the model content and metadata
  • BNG Playground resolves models from RuleHub metadata and manifest outputs
  • local playground analysis and migration scripts may use a local RuleHub checkout via RULEHUB_ROOT
That means updates to model metadata, visibility, provenance, and organization should now happen here in RuleHub.
Validation workflow
Before opening a pull request that adds or changes model content, run:
node scripts/validate-metadata.js
node scripts/generate-manifest.js --root . --output manifest.json
The repository also includes CI validation in .github/workflows/validate.yml.
Adding models
For model submission and curation rules, see AddingModels.md.
In general, contributors should:
  1. place models in the appropriate top-level collection
  2. add or update metadata.yaml
  3. add or update README.md
  4. describe multi-file collections with a collection section when applicable
  5. validate metadata and regenerate manifest.json
Notes on migrated content
RuleHub now contains migrated content that previously lived only inside BNG Playground, including:
  • BNG Playground example models
  • validation fixtures
  • tutorial collections
  • runtime-only BNGL models that required explicit preservation
Those migrated entries keep provenance in metadata.yaml, including source-path history where relevant.
Quick links
About
A repository of rule-based models. Could this be the start of something great?
Resources
Readme
MIT license
Activity
Custom properties
Stars
2 stars
Watchers
17 watching
Forks
7 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
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GitHub - RuleWorld/RuleHub: A repository of rule-based models. Could this be the start of something great? · GitHub
Skip to content
BranchesTags
Repository files navigation
RuleHub
RuleHub is the canonical repository for curated BioNetGen and BNGL model content used across the RuleWorld ecosystem.
It now serves two roles:
  • a human-browsable archive of published, contributed, tutorial, and validation models
  • the machine-readable source of truth for metadata consumed by tools such as BNG Playground
Repository layout
The repository is organized into a few top-level collections:
  • Published/: literature-backed and curated research models
  • Contributed/: contributed model sets, including BNG Playground examples and validation fixtures
  • Tutorials/: tutorial and teaching-oriented BNGL models
  • PyBioNetGen/: PyBioNetGen reference, benchmark, and support model collections
Most model directories contain:
  • one or more .bngl files
  • metadata.yaml
  • README.md
Examples:
  • Published/Faeder2003/
  • Contributed/BNGPlayground_Examples/...
  • Contributed/BNGPlayground_Validation/...
  • Tutorials/General/polymer/
  • Tutorials/NativeTutorials/...
Metadata and manifest
RuleHub now includes a repository-wide metadata and discovery layer:
  • metadata-schema.yaml: schema for per-directory metadata
  • manifest.json: generated manifest describing discoverable model entries
  • scripts/validate-metadata.js: local metadata validator
  • scripts/generate-manifest.js: manifest generator
This metadata is used for:
  • model discovery and indexing
  • gallery visibility and categorization
  • compatibility flags such as bng2_compatible
  • provenance for published, tutorial, test-case, and AI-generated contributed models
BNG Playground integration
BNG Playground no longer keeps its own bundled BNGL corpus as the runtime source of truth.
Instead:
  • RuleHub hosts the model content and metadata
  • BNG Playground resolves models from RuleHub metadata and manifest outputs
  • local playground analysis and migration scripts may use a local RuleHub checkout via RULEHUB_ROOT
That means updates to model metadata, visibility, provenance, and organization should now happen here in RuleHub.
Validation workflow
Before opening a pull request that adds or changes model content, run:
node scripts/validate-metadata.js
node scripts/generate-manifest.js --root . --output manifest.json
The repository also includes CI validation in .github/workflows/validate.yml.
Adding models
For model submission and curation rules, see AddingModels.md.
In general, contributors should:
  1. place models in the appropriate top-level collection
  2. add or update metadata.yaml
  3. add or update README.md
  4. describe multi-file collections with a collection section when applicable
  5. validate metadata and regenerate manifest.json
Notes on migrated content
RuleHub now contains migrated content that previously lived only inside BNG Playground, including:
  • BNG Playground example models
  • validation fixtures
  • tutorial collections
  • runtime-only BNGL models that required explicit preservation
Those migrated entries keep provenance in metadata.yaml, including source-path history where relevant.
Quick links
About
A repository of rule-based models. Could this be the start of something great?
Resources
Readme
MIT license
Activity
Custom properties
Stars
2 stars
Watchers
17 watching
Forks
7 forks
Report repository
Releases
Packages
Contributors
Languages

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try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
GitHub - RuleWorld/RuleHub: A repository of rule-based models. Could this be the start of something great? · GitHub
Skip to content
BranchesTags
Repository files navigation
RuleHub
RuleHub is the canonical repository for curated BioNetGen and BNGL model content used across the RuleWorld ecosystem.
It now serves two roles:
  • a human-browsable archive of published, contributed, tutorial, and validation models
  • the machine-readable source of truth for metadata consumed by tools such as BNG Playground
Repository layout
The repository is organized into a few top-level collections:
  • Published/: literature-backed and curated research models
  • Contributed/: contributed model sets, including BNG Playground examples and validation fixtures
  • Tutorials/: tutorial and teaching-oriented BNGL models
  • PyBioNetGen/: PyBioNetGen reference, benchmark, and support model collections
Most model directories contain:
  • one or more .bngl files
  • metadata.yaml
  • README.md
Examples:
  • Published/Faeder2003/
  • Contributed/BNGPlayground_Examples/...
  • Contributed/BNGPlayground_Validation/...
  • Tutorials/General/polymer/
  • Tutorials/NativeTutorials/...
Metadata and manifest
RuleHub now includes a repository-wide metadata and discovery layer:
  • metadata-schema.yaml: schema for per-directory metadata
  • manifest.json: generated manifest describing discoverable model entries
  • scripts/validate-metadata.js: local metadata validator
  • scripts/generate-manifest.js: manifest generator
This metadata is used for:
  • model discovery and indexing
  • gallery visibility and categorization
  • compatibility flags such as bng2_compatible
  • provenance for published, tutorial, test-case, and AI-generated contributed models
BNG Playground integration
BNG Playground no longer keeps its own bundled BNGL corpus as the runtime source of truth.
Instead:
  • RuleHub hosts the model content and metadata
  • BNG Playground resolves models from RuleHub metadata and manifest outputs
  • local playground analysis and migration scripts may use a local RuleHub checkout via RULEHUB_ROOT
That means updates to model metadata, visibility, provenance, and organization should now happen here in RuleHub.
Validation workflow
Before opening a pull request that adds or changes model content, run:
node scripts/validate-metadata.js
node scripts/generate-manifest.js --root . --output manifest.json
The repository also includes CI validation in .github/workflows/validate.yml.
Adding models
For model submission and curation rules, see AddingModels.md.
In general, contributors should:
  1. place models in the appropriate top-level collection
  2. add or update metadata.yaml
  3. add or update README.md
  4. describe multi-file collections with a collection section when applicable
  5. validate metadata and regenerate manifest.json
Notes on migrated content
RuleHub now contains migrated content that previously lived only inside BNG Playground, including:
  • BNG Playground example models
  • validation fixtures
  • tutorial collections
  • runtime-only BNGL models that required explicit preservation
Those migrated entries keep provenance in metadata.yaml, including source-path history where relevant.
Quick links
About
A repository of rule-based models. Could this be the start of something great?
Resources
Readme
MIT license
Activity
Custom properties
Stars
2 stars
Watchers
17 watching
Forks
7 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - RuleWorld/RuleHub: A repository of rule-based models. Could this be the start of something great? · GitHub
Skip to content
BranchesTags
Repository files navigation
RuleHub
RuleHub is the canonical repository for curated BioNetGen and BNGL model content used across the RuleWorld ecosystem.
It now serves two roles:
  • a human-browsable archive of published, contributed, tutorial, and validation models
  • the machine-readable source of truth for metadata consumed by tools such as BNG Playground
Repository layout
The repository is organized into a few top-level collections:
  • Published/: literature-backed and curated research models
  • Contributed/: contributed model sets, including BNG Playground examples and validation fixtures
  • Tutorials/: tutorial and teaching-oriented BNGL models
  • PyBioNetGen/: PyBioNetGen reference, benchmark, and support model collections
Most model directories contain:
  • one or more .bngl files
  • metadata.yaml
  • README.md
Examples:
  • Published/Faeder2003/
  • Contributed/BNGPlayground_Examples/...
  • Contributed/BNGPlayground_Validation/...
  • Tutorials/General/polymer/
  • Tutorials/NativeTutorials/...
Metadata and manifest
RuleHub now includes a repository-wide metadata and discovery layer:
  • metadata-schema.yaml: schema for per-directory metadata
  • manifest.json: generated manifest describing discoverable model entries
  • scripts/validate-metadata.js: local metadata validator
  • scripts/generate-manifest.js: manifest generator
This metadata is used for:
  • model discovery and indexing
  • gallery visibility and categorization
  • compatibility flags such as bng2_compatible
  • provenance for published, tutorial, test-case, and AI-generated contributed models
BNG Playground integration
BNG Playground no longer keeps its own bundled BNGL corpus as the runtime source of truth.
Instead:
  • RuleHub hosts the model content and metadata
  • BNG Playground resolves models from RuleHub metadata and manifest outputs
  • local playground analysis and migration scripts may use a local RuleHub checkout via RULEHUB_ROOT
That means updates to model metadata, visibility, provenance, and organization should now happen here in RuleHub.
Validation workflow
Before opening a pull request that adds or changes model content, run:
node scripts/validate-metadata.js
node scripts/generate-manifest.js --root . --output manifest.json
The repository also includes CI validation in .github/workflows/validate.yml.
Adding models
For model submission and curation rules, see AddingModels.md.
In general, contributors should:
  1. place models in the appropriate top-level collection
  2. add or update metadata.yaml
  3. add or update README.md
  4. describe multi-file collections with a collection section when applicable
  5. validate metadata and regenerate manifest.json
Notes on migrated content
RuleHub now contains migrated content that previously lived only inside BNG Playground, including:
  • BNG Playground example models
  • validation fixtures
  • tutorial collections
  • runtime-only BNGL models that required explicit preservation
Those migrated entries keep provenance in metadata.yaml, including source-path history where relevant.
Quick links
About
A repository of rule-based models. Could this be the start of something great?
Resources
Readme
MIT license
Activity
Custom properties
Stars
2 stars
Watchers
17 watching
Forks
7 forks
Report repository
Releases
Packages
Contributors
Languages

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GitHub - RuleWorld/RuleHub: A repository of rule-based models. Could this be the start of something great? · GitHub
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RuleHub
RuleHub is the canonical repository for curated BioNetGen and BNGL model content used across the RuleWorld ecosystem.
It now serves two roles:
  • a human-browsable archive of published, contributed, tutorial, and validation models
  • the machine-readable source of truth for metadata consumed by tools such as BNG Playground
Repository layout
The repository is organized into a few top-level collections:
  • Published/: literature-backed and curated research models
  • Contributed/: contributed model sets, including BNG Playground examples and validation fixtures
  • Tutorials/: tutorial and teaching-oriented BNGL models
  • PyBioNetGen/: PyBioNetGen reference, benchmark, and support model collections
Most model directories contain:
  • one or more .bngl files
  • metadata.yaml
  • README.md
Examples:
  • Published/Faeder2003/
  • Contributed/BNGPlayground_Examples/...
  • Contributed/BNGPlayground_Validation/...
  • Tutorials/General/polymer/
  • Tutorials/NativeTutorials/...
Metadata and manifest
RuleHub now includes a repository-wide metadata and discovery layer:
  • metadata-schema.yaml: schema for per-directory metadata
  • manifest.json: generated manifest describing discoverable model entries
  • scripts/validate-metadata.js: local metadata validator
  • scripts/generate-manifest.js: manifest generator
This metadata is used for:
  • model discovery and indexing
  • gallery visibility and categorization
  • compatibility flags such as bng2_compatible
  • provenance for published, tutorial, test-case, and AI-generated contributed models
BNG Playground integration
BNG Playground no longer keeps its own bundled BNGL corpus as the runtime source of truth.
Instead:
  • RuleHub hosts the model content and metadata
  • BNG Playground resolves models from RuleHub metadata and manifest outputs
  • local playground analysis and migration scripts may use a local RuleHub checkout via RULEHUB_ROOT
That means updates to model metadata, visibility, provenance, and organization should now happen here in RuleHub.
Validation workflow
Before opening a pull request that adds or changes model content, run:
node scripts/validate-metadata.js
node scripts/generate-manifest.js --root . --output manifest.json
The repository also includes CI validation in .github/workflows/validate.yml.
Adding models
For model submission and curation rules, see AddingModels.md.
In general, contributors should:
  1. place models in the appropriate top-level collection
  2. add or update metadata.yaml
  3. add or update README.md
  4. describe multi-file collections with a collection section when applicable
  5. validate metadata and regenerate manifest.json
Notes on migrated content
RuleHub now contains migrated content that previously lived only inside BNG Playground, including:
  • BNG Playground example models
  • validation fixtures
  • tutorial collections
  • runtime-only BNGL models that required explicit preservation
Those migrated entries keep provenance in metadata.yaml, including source-path history where relevant.
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A repository of rule-based models. Could this be the start of something great?
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