{"note":{"id":"nte_w61u5iant4","attempt_id":"att_yb51atz4ja","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: Source inventory and scope plan\nkind: approach\ntags: [inventory, scope, dedup]\nmodel: claude-opus-5-5\n---\nRan a pandas inventory over every sheet (scripts/inventory.py) and ran pdftotext on the SI.\n\n- **MOESM3.xlsx** is a superset workbook. It contains every MOESM9 (ED Fig. 6) screen sheet, the Fig. 3 library sheets (`Report - Variable Conditions`, 1,536 rows; `Report - tBuXphos + P2-Et`, 384 rows; `Nucleophile Plate Map`; `Coupling Library` with product SMILES; `Reaction Conditions`), ASMS sheets (List/Expt/PIVOT/ALIS/Affinity — out of scope) and `Scale Up Synthesis + Activity`.\n- MOESM9 duplicates MOESM3's screen sheets. MOESM4 and MOESM12 are identical (PCA + big-library csv). MOESM5/6/7(=8) duplicate the Fig. 2A/2B/2C sheets inside MOESM2. MOESM10 is the scale-up table. MOESM11 holds IC50 curves (out of scope).\n- `Compiled Yield Data` and `prelim-screening-csv` are concatenations of the per-screen sheets (2,110 rows ≈ 672+162+384+360... minus some). I will **not** use them, to avoid double counting. I build from the per-screen sheets only.\n- SI §3.1 general HTE conditions: 1 µL reactions (0.1 M core, 100 nmol), 1.5 equiv building block (0.6 M stock), 10 mol% Pd G2/G3 precatalyst (0.04 M stock), 2 equiv base (0.8 M stock), N2 glovebox, ambient temperature, 18–24 h. Quench with 3×1 µL 0.5 M AcOH/DMSO containing a biphenyl (PhPh) internal standard, then UPLC-MS/UV.\n- Plan, priority order: (1) the five §3 optimisation screens; (2) the §8.2/§8.3 384-member CHK1 library (1,536 variable-condition + 384 single-condition reactions); (3) the §5.2/§6.2/§7.2 Fig. 2 libraries and the bench-scale syntheses, as time allows. Everything goes in one Dataset, with the description listing which part came from which sheet.\n","source":"mcp","created_at":"2026-10-14T04:12:34Z","updated_at":"2026-10-14T04:12:34Z","kind":"working"},"header":{"title":"Source inventory and scope plan","kind":"approach","tags":["inventory","scope","dedup"],"builds_on":[],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"Ran a pandas inventory over every sheet (scripts/inventory.py) and ran pdftotext on the SI.\n\n- **MOESM3.xlsx** is a superset workbook. It contains every MOESM9 (ED Fig. 6) screen sheet, the Fig. 3 library sheets (`Report - Variable Conditions`, 1,536 rows; `Report - tBuXphos + P2-Et`, 384 rows; `Nucleophile Plate Map`; `Coupling Library` with product SMILES; `Reaction Conditions`), ASMS sheets (List/Expt/PIVOT/ALIS/Affinity — out of scope) and `Scale Up Synthesis + Activity`.\n- MOESM9 duplicates MOESM3's screen sheets. MOESM4 and MOESM12 are identical (PCA + big-library csv). MOESM5/6/7(=8) duplicate the Fig. 2A/2B/2C sheets inside MOESM2. MOESM10 is the scale-up table. MOESM11 holds IC50 curves (out of scope).\n- `Compiled Yield Data` and `prelim-screening-csv` are concatenations of the per-screen sheets (2,110 rows ≈ 672+162+384+360... minus some). I will **not** use them, to avoid double counting. I build from the per-screen sheets only.\n- SI §3.1 general HTE conditions: 1 µL reactions (0.1 M core, 100 nmol), 1.5 equiv building block (0.6 M stock), 10 mol% Pd G2/G3 precatalyst (0.04 M stock), 2 equiv base (0.8 M stock), N2 glovebox, ambient temperature, 18–24 h. Quench with 3×1 µL 0.5 M AcOH/DMSO containing a biphenyl (PhPh) internal standard, then UPLC-MS/UV.\n- Plan, priority order: (1) the five §3 optimisation screens; (2) the §8.2/§8.3 384-member CHK1 library (1,536 variable-condition + 384 single-condition reactions); (3) the §5.2/§6.2/§7.2 Fig. 2 libraries and the bench-scale syntheses, as time allows. Everything goes in one Dataset, with the description listing which part came from which sheet.\n","attempt":{"id":"att_yb51atz4ja","outcome":"completed","ended_at":"2026-10-14T04:31:20Z","problem_id":"prb_kduq00682f","problem_slug":"ord-gesmundo-2018-nanoscale-synthesis-affinity","problem_revision_id":"prv_agtapqkymx","author_handle":"jordan"}}