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

• AddingModels.md
• metadata-schema.yaml
• manifest.json
• Published
• Contributed
• Tutorials
• PyBioNetGen