{"note":{"id":"nte_x1a4ga39hi","attempt_id":"att_mtm6vrjdpd","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: Plate/well coordinates not recoverable from experiment_id; keep experiment_id as well-level provenance\nkind: dead_end\ntags: [plate-provenance, experiment-id, layout]\nbuilds_on: [nte_uo58m9xewh]\nmodel: claude-opus-5-5\n---\nMethods (main text, \"Automated synthesis\") give the layout per 1920-reaction batch: 6 × 384-well plates, columns 1, 2, 23, 24 empty; initiator along rows A–P (same in all 6 plates); monomers on half plates (cols 3–12 / 13–22, two per plate); terminators along columns (T_k in cols 2+k and 12+k).\n\nI tested whether `experiment_id` enumerates wells in that order (script over Data S1, ids exploded on \"/\"). For the earliest ids (~10578–16000) it does: 20 consecutive ids = one row (10 wells of monomer 1 then 10 of monomer 2, terminator order constant), offset 18 mod 20. But scanning 320-id windows across the whole range, most later windows (offset 5 mod 20, ids ~16k–85k) violate the one-initiator-per-row / one-monomer-per-half rule hundreds of times, so the numbering scheme changed and a global id→well mapping cannot be inferred safely.\n\nDecision: record each well's `experiment_id` (the authors' unique sample id; slash-joined for the 377 de-duplicated replicate wells) as a CUSTOM reaction identifier and in the reaction notes, describe the batch layout in the dataset description, and state that exact plate/well coordinates live in the authors' database (github.com/jugoetz/library-generation `db/`), which this session could not access (GitHub repo access not enabled). No guessed well positions are written.","source":"mcp","created_at":"2026-10-14T04:47:59Z","updated_at":"2026-10-14T04:47:59Z","kind":"working"},"header":{"title":"Plate/well coordinates not recoverable from experiment_id; keep experiment_id as well-level provenance","kind":"dead_end","tags":["plate-provenance","experiment-id","layout"],"builds_on":["nte_uo58m9xewh"],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"Methods (main text, \"Automated synthesis\") give the layout per 1920-reaction batch: 6 × 384-well plates, columns 1, 2, 23, 24 empty; initiator along rows A–P (same in all 6 plates); monomers on half plates (cols 3–12 / 13–22, two per plate); terminators along columns (T_k in cols 2+k and 12+k).\n\nI tested whether `experiment_id` enumerates wells in that order (script over Data S1, ids exploded on \"/\"). For the earliest ids (~10578–16000) it does: 20 consecutive ids = one row (10 wells of monomer 1 then 10 of monomer 2, terminator order constant), offset 18 mod 20. But scanning 320-id windows across the whole range, most later windows (offset 5 mod 20, ids ~16k–85k) violate the one-initiator-per-row / one-monomer-per-half rule hundreds of times, so the numbering scheme changed and a global id→well mapping cannot be inferred safely.\n\nDecision: record each well's `experiment_id` (the authors' unique sample id; slash-joined for the 377 de-duplicated replicate wells) as a CUSTOM reaction identifier and in the reaction notes, describe the batch layout in the dataset description, and state that exact plate/well coordinates live in the authors' database (github.com/jugoetz/library-generation `db/`), which this session could not access (GitHub repo access not enabled). No guessed well positions are written.","attempt":{"id":"att_mtm6vrjdpd","outcome":"completed","ended_at":"2026-10-14T05:14:54Z","problem_id":"prb_b7ur0vjlad","problem_slug":"ord-gotz-2025-three-component-40k","problem_revision_id":"prv_2qz09a9zki","author_handle":"jordan"}}