{ "about": { "method": "screening-campaign-observations (controls named, saturation, edge, drift) beside percent inhibition and robust z", "rules": "docs/board/memos/2026-11-07-cso-stage4-assay-campaign.md, rulings 1(a) to 1(g) and 2", "basedOn": { "file": "screening.json", "note": "cases a to k carried with inputs and expected outputs unchanged; the 0.11.0 file stays as published" }, "origin": "Self-constructed plates; cases a to k from screening.py (random.Random(20261013)); l to z from random.Random(20261107) and per-attempt seeds for case n", "markers": "a well whose value is 'marker::' is a reader marker: no value", "tolerances": { "carried a to k": "as screening.json", "percent inhibition, median, MAD (cases l to z)": "1e-9 relative", "robust z (cases l to z, and a to k when re-run with markers)": "1e-12 relative, or 1e-12 absolute when |z| is below 1 (a z near zero is a difference of nearly equal percents)", "calls and ranking": "exact", "control means and SDs, edge means and difference, Welch t and df, F, drift centre, sigma and limits": "1e-9 relative", "p values (Welch, F)": "1e-8 absolute; Pettitt p 1e-9 relative", "shown, m, wells listed, counts, statuses, reasons, outside, Pettitt K and location": "exact" }, "recordedOn": "2026-11-07", "script": "pipeline/assay-analyser/oracles/screening_v2.py", "scriptSha256": "8a9ca9077eaaa2f9379ed4127cb5d411e23f69d74a75a86e0783b031c0f6e19e", "helper": { "script": "pipeline/assay-analyser/oracles/stage_a_oracle.py", "sha256": "492d85ca2fa6750db80b1c64214fd4a0b13cd4c588267244f6262c504c73e3e8" }, "environment": { "image": "ghcr.io/biotechmat/drybench/oracle-env:058a025c3fab26f9@sha256:383cab16fa8cf28a9147b19193eb7d551b39dc3b29def009e3e9268f73d98cd6", "r": "R version 4.4.3 (2025-02-28)", "packages": { "jsonlite": "2.0.0" }, "python": "3.11.15", "numpy": "2.0.2", "scipy": "1.13.1", "recordedOn": "2026-11-07", "cpu": "Intel(R) Xeon(R) Platinum 8370C CPU @ 2.80GHz", "cpuClass": "x86-64-v3", "simd": [ "SSSE3", "SSE41", "POPCNT", "SSE42", "AVX", "F16C", "FMA3", "AVX2" ], "openblasCore": "Haswell", "threads": 1 }, "crossCheck": { "tool": "R stats::median and mad(constant = 1/qnorm(0.75)); t.test(var.equal = FALSE); drop1(lm(y ~ factor(row) + factor(col)), test = \"F\"); qcc::qcc(type = \"xbar.one\"); trend::pettitt.test", "version": "R version 4.4.3 (2025-02-28)", "script": "pipeline/assay-analyser/oracles/r/screening_v2.R", "scriptSha256": "970672eb66e03a991cc5e351151c693c43ac5c01d26ad67325ceebb006d5c880", "ran": true, "packages": { "jsonlite": true, "qcc": false, "trend": false }, "agreement": "every computed median and scaled MAD within 1e-12, Welch t, df and p, type II F, df and p within the tolerances, and, where the package is installed, every qcc centre and limit and every Pettitt K, location and p; the script stops otherwise" } }, "oracle": { "welch": "exact rationals with 60-digit square roots (plate_diagnostics.edge_test) and scipy.stats.ttest_ind(equal_var=False)", "rows and columns": "least squares on the dummy design in NumPy (plate_diagnostics.row_column), type II", "drift": "assay-drift 1.0.0's rule in exact rationals (re-stated from assay_drift.py)", "numpy": "2.0.2", "scipy": "1.13.1" }, "cases": [ { "name": "a-known-controls", "method": "percent", "threshold": 50, "plates": [ { "label": "Plate 1", "format": 96, "wells": [ { "well": "A1", "row": 0, "col": 0, "role": "positive", "value": 990.0, "excluded": false }, { "well": "A2", "row": 0, "col": 1, "role": "sample", "value": 1000.0, "excluded": false }, { "well": "A3", "row": 0, "col": 2, "role": "sample", "value": 550.0, "excluded": false }, { "well": "A4", "row": 0, "col": 3, "role": "sample", "value": 100.0, "excluded": false }, { "well": "A5", "row": 0, "col": 4, "role": "sample", "value": 662.679, "excluded": false }, { "well": "A6", "row": 0, "col": 5, "role": "sample", "value": 312.429, "excluded": false }, { "well": "A7", "row": 0, "col": 6, "role": "sample", "value": 888.434, "excluded": false }, { "well": 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"excluded": false }, { "well": "B7", "row": 1, "col": 6, "role": "sample", "value": 211.872, "excluded": false }, { "well": "B8", "row": 1, "col": 7, "role": "sample", "value": 335.837, "excluded": false }, { "well": "B9", "row": 1, "col": 8, "role": "sample", "value": 760.436, "excluded": false }, { "well": "B10", "row": 1, "col": 9, "role": "sample", "value": 841.981, "excluded": false }, { "well": "B11", "row": 1, "col": 10, "role": "sample", "value": 237.768, "excluded": false }, { "well": "B12", "row": 1, "col": 11, "role": "negative", "value": 105.0, "excluded": false }, { "well": "C1", "row": 2, "col": 0, "role": "positive", "value": 990.0, "excluded": false }, { "well": "C2", "row": 2, "col": 1, "role": "sample", "value": 359.938, "excluded": false }, { "well": "C3", "row": 2, "col": 2, "role": "sample", "value": 258.297, "excluded": false }, { "well": "C4", "row": 2, "col": 3, "role": "sample", "value": 529.535, "excluded": false }, { "well": "C5", "row": 2, "col": 4, "role": 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