Codex-generated pull request

[Psuedonerd]

Codex generated this pull request, but encountered an unexpected error after generation. This is a placeholder PR message.

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Codex Task

[chatgpt-codex-connector]

💡 Codex Review

RuleHub/data/summaries/Barua2007_aigenerated.md

Line 31 in 16a8114

The readouts distinguish free receptor, receptor bound to SHP2, multiply engaged receptor-SHP2 complexes, open SHP2, and phosphorylated receptor. They show how receptor scaffolding and SHP2 conformational opening control the amount of active phosphatase complex.

Align Barua 2007 readouts with the BNGL observable

For this generated summary, I checked Published/Barua2007/Barua_2007.bngl; its begin observables block defines only pYR (R(Y1~P!?)). It does not output free receptor, receptor-bound SHP2, multiply engaged complexes, or open SHP2, so users reading the summary or choosing plots from it will look for measurements the model never produces.

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RuleHub/data/summaries/Blinovegfr_aigenerated.md

Line 31 in 16a8114

The readouts follow receptor or ligand-containing patterns and show how much receptor is free, ligand-associated, or complexed over time.

Include EGFR phosphorylation and Shc readouts

For Published/Blinovegfr/Blinov_egfr.bngl, the observables include Y1068_phosp, Y1173_phosp, Total_phosp, and ShcP_Cyt, and the rules phosphorylate EGFR and Shc. Describing the measurements as only free/ligand-associated/complexed receptor hides half of the actual outputs and leads users to treat this as binding-only when the model also reports adaptor phosphorylation.

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RuleHub/data/ai_summaries.json

Line 213 in 16a8114

"model_id": "lac_operon_dreisigmeyer2008",

Use the manifest model id in the summary index

The repository's manifest uses Dreisigmeyer_2008 for this single-BNGL model (see manifest.json / scripts/generate-manifest.js, which uses metadata.id when modelFiles.length === 1), but this index stores the BNGL filename stem. Any site code that joins data/ai_summaries.json to the manifest by model_id will fail to attach this summary; the same mismatch appears for Gardner, Goldstein, Harmon, Hlavacek 1999, and Hlavacek 2001.

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