Add AI-generated model summaries, coder-facing explanations, and explanation skills

[Psuedonerd]

Motivation

• Provide machine-generated, biologist- and coder-facing explanations for RuleHub models to support site integration and curator workflows.
• Index the produced summaries in a JSON index to enable programmatic consumption by the website and tools.
• Add skill descriptions and agent interface metadata so the repository can generate consistent summaries for different audiences.

Description

• Added a machine-readable index data/ai_summaries.json containing summary metadata for many models.
• Added biologist-facing Markdown summaries under data/summaries/*.md that follow the required human-readable structure for each model.
• Added coder-facing, technical Markdown explanations under data/summaries_coders/*.md that enumerate molecule types, rules, observables, and actions.
• Introduced new skill definitions and agent metadata under skills/ (explain-rulehub-model-coders, explain-rulehub-model-simple) including SKILL.md guidance and an openai.yaml agent interface, and removed the deprecated skills/explain-rulehub-model/SKILL.md file.

Testing

• Validated the new JSON with jq to ensure it is syntactically valid (success).
• Spot-checked several new Markdown files in a local Markdown viewer to confirm they render and the required sections are present (success).
• No automated unit tests were added for this change; there are no failing test runs associated with these content additions.

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Codex Task

[chatgpt-codex-connector]

💡 Codex Review

RuleHub/data/ai_summaries.json

Line 213 in 731c07f

"model_id": "lac_operon_dreisigmeyer2008",

Use metadata ids in the summary index

For entries like this one, model_id is the BNGL basename, but yaml_path points to metadata whose id is Dreisigmeyer_2008, and the generated manifest uses metadata.id as the model id in scripts/generate-manifest.js:87-90. In consumers that join data/ai_summaries.json to manifest/gallery records by id, these entries will not match and the summaries for Dreisigmeyer, Gardner, Goldstein, Harmon, Hlavacek 1999, and Hlavacek 2001 will be hidden. Please populate model_id from the metadata id consistently.

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RuleHub/skills/explain-rulehub-model-simple/SKILL.md

Line 1 in 731c07f

# Explain RuleHub Model

Add frontmatter to the simple skill

In environments that load Codex skills from skills/*/SKILL.md, this file will not be discoverable because it starts directly with a Markdown heading instead of the required YAML frontmatter. The adjacent coder skill has name and description frontmatter, but this replacement simple skill does not, so the biologist-facing explanation skill cannot be selected by its trigger description. Please add name: explain-rulehub-model-simple and a description before the heading.

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