{
 "about": {
  "method": "plate-diagnostics (signal window, SSMD, Z, edge and row/column patterns)",
  "ruling": "docs/board/memos/2026-10-13-cso-plate-diagnostics.md",
  "origin": "Self-constructed plates; seeded generator 20261013 rounded to three decimals, integers for P01",
  "tolerances": {
   "zPrime, signalWindow, ssmd, z, means, differences, spreads and percents": "1e-9 relative",
   "Welch t and df, F": "1e-9 relative",
   "p values": "1e-8 absolute",
   "n, levels, degrees of freedom of F, states and reasons": "exact"
  },
  "thresholds": {
   "minSamplesForZ": 16,
   "minEdgeAndInterior": 4,
   "minResidualDf": 10,
   "edge": "one ring: first and last row and column"
  },
  "recordedOn": "2026-10-13",
  "script": "pipeline/assay-analyser/oracles/plate_diagnostics.py",
  "scriptSha256": "a1d8e69be20b07591ddb0605b262f5180a5c8cea9da5fe936c6f357bb06aadd1",
  "helper": {
   "script": "pipeline/assay-analyser/oracles/stage_a_oracle.py",
   "sha256": "492d85ca2fa6750db80b1c64214fd4a0b13cd4c588267244f6262c504c73e3e8"
  },
  "environment": {
   "image": "ghcr.io/biotechmat/drybench/oracle-env:11b8a5e4456df7eb@sha256:7e69891ca1d9f24838660e0a9887bdb654ce7771d2f2ac7e7275e9b1eb3b6a09",
   "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": "2026-10-13",
   "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::t.test (var.equal = FALSE) and drop1(lm(y ~ factor(row) + factor(col)), test = \"F\"); scipy.stats.ttest_ind (equal_var = False)",
   "version": "R version 4.4.3 (2025-02-28)",
   "script": "pipeline/assay-analyser/oracles/r/plate_diagnostics.R",
   "scriptSha256": "f50ee5ebbd85f930be54fb27d4ac82fde6deabb0a6b3cb8f290deeea9bfc2e92",
   "ran": true,
   "agreement": "every computed Welch t, df and p, and every type II F, df and p, within the tolerances; the script stops otherwise"
  }
 },
 "oracle": {
  "engine": "Python fractions and decimal (hand formulas), NumPy least squares, scipy.stats distributions"
 },
 "plates": [
  {
   "id": "P01",
   "about": "Hand case, integer readings: exact Z', SW, SSMD and Z (16 samples at one concentration)",
   "format": 96,
   "wells": [
    {
     "well": "A1",
     "role": "positive",
     "concentration": null,
     "value": 100,
     "excluded": false
    },
    {
     "well": "B1",
     "role": "positive",
     "concentration": null,
     "value": 104,
     "excluded": false
    },
    {
     "well": "C1",
     "role": "positive",
     "concentration": null,
     "value": 98,
     "excluded": false
    },
    {
     "well": "D1",
     "role": "positive",
     "concentration": null,
     "value": 102,
     "excluded": false
    },
    {
     "well": "E12",
     "role": "negative",
     "concentration": null,
     "value": 10,
     "excluded": false
    },
    {
     "well": "F12",
     "role": "negative",
     "concentration": null,
     "value": 12,
     "excluded": false
    },
    {
     "well": "G12",
     "role": "negative",
     "concentration": null,
     "value": 8,
     "excluded": false
    },
    {
     "well": "H12",
     "role": "negative",
     "concentration": null,
     "value": 10,
     "excluded": false
    },
    {
     "well": "B3",
     "role": "sample",
     "concentration": 1e-05,
     "value": 94,
     "excluded": false
    },
    {
     "well": "B4",
     "role": "sample",
     "concentration": 1e-05,
     "value": 97,
     "excluded": false
    },
    {
     "well": "B5",
     "role": "sample",
     "concentration": 1e-05,
     "value": 91,
     "excluded": false
    },
    {
     "well": "B6",
     "role": "sample",
     "concentration": 1e-05,
     "value": 94,
     "excluded": false
    },
    {
     "well": "C3",
     "role": "sample",
     "concentration": 1e-05,
     "value": 92,
     "excluded": false
    },
    {
     "well": "C4",
     "role": "sample",
     "concentration": 1e-05,
     "value": 95,
     "excluded": false
    },
    {
     "well": "C5",
     "role": "sample",
     "concentration": 1e-05,
     "value": 98,
     "excluded": false
    },
    {
     "well": "C6",
     "role": "sample",
     "concentration": 1e-05,
     "value": 92,
     "excluded": false
    },
    {
     "well": "D3",
     "role": "sample",
     "concentration": 1e-05,
     "value": 90,
     "excluded": false
    },
    {
     "well": "D4",
     "role": "sample",
     "concentration": 1e-05,
     "value": 93,
     "excluded": false
    },
    {
     "well": "D5",
     "role": "sample",
     "concentration": 1e-05,
     "value": 96,
     "excluded": false
    },
    {
     "well": "D6",
     "role": "sample",
     "concentration": 1e-05,
     "value": 90,
     "excluded": false
    },
    {
     "well": "E3",
     "role": "sample",
     "concentration": 1e-05,
     "value": 97,
     "excluded": false
    },
    {
     "well": "E4",
     "role": "sample",
     "concentration": 1e-05,
     "value": 91,
     "excluded": false
    },
    {
     "well": "E5",
     "role": "sample",
     "concentration": 1e-05,
     "value": 94,
     "excluded": false
    },
    {
     "well": "E6",
     "role": "sample",
     "concentration": 1e-05,
     "value": 97,
     "excluded": false
    }
   ],
   "expected": {
    "zPrime": {
     "status": "computed",
     "value": 0.8610445474947122,
     "nPositive": 4,
     "nNegative": 4
    },
    "signalWindow": {
     "status": "computed",
     "value": 30.346781854386467,
     "nPositive": 4,
     "nNegative": 4
    },
    "ssmd": {
     "status": "computed",
     "value": 29.78674201721296,
     "nPositive": 4,
     "nNegative": 4
    },
    "controlSpan": 91.0,
    "z": {
     "status": "computed",
     "value": 0.8461997778992676,
     "nSamples": 16,
     "nNegative": 4,
     "concentration": 1e-05
    },
    "pattern": [
     {
      "group": "positive",
      "n": 4,
      "edge": {
       "status": "withheld",
       "reason": "too-few-wells",
       "nEdge": 4,
       "nInterior": 0
      },
      "rows": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      },
      "columns": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      }
     },
     {
      "group": "negative",
      "n": 4,
      "edge": {
       "status": "withheld",
       "reason": "too-few-wells",
       "nEdge": 4,
       "nInterior": 0
      },
      "rows": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      },
      "columns": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      }
     },
     {
      "group": "samples",
      "n": 16,
      "edge": {
       "status": "withheld",
       "reason": "too-few-wells",
       "nEdge": 0,
       "nInterior": 16
      },
      "rows": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 16,
       "rows": 4,
       "columns": 4,
       "residualDf": 9
      },
      "columns": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 16,
       "rows": 4,
       "columns": 4,
       "residualDf": 9
      }
     }
    ]
   }
  },
  {
   "id": "P02",
   "about": "One vehicle and one kill well: Z', SW, SSMD and Z withheld",
   "format": 96,
   "wells": [
    {
     "well": "A1",
     "role": "positive",
     "concentration": null,
     "value": 100,
     "excluded": false
    },
    {
     "well": "H12",
     "role": "negative",
     "concentration": null,
     "value": 5,
     "excluded": false
    },
    {
     "well": "C3",
     "role": "sample",
     "concentration": 1e-05,
     "value": 97.824,
     "excluded": false
    },
    {
     "well": "C4",
     "role": "sample",
     "concentration": 1e-05,
     "value": 98.807,
     "excluded": false
    },
    {
     "well": "C5",
     "role": "sample",
     "concentration": 1e-05,
     "value": 93.347,
     "excluded": false
    },
    {
     "well": "C6",
     "role": "sample",
     "concentration": 1e-05,
     "value": 99.105,
     "excluded": false
    },
    {
     "well": "C7",
     "role": "sample",
     "concentration": 1e-05,
     "value": 94.224,
     "excluded": false
    },
    {
     "well": "D3",
     "role": "sample",
     "concentration": 1e-05,
     "value": 95.741,
     "excluded": false
    },
    {
     "well": "D4",
     "role": "sample",
     "concentration": 1e-05,
     "value": 96.42,
     "excluded": false
    },
    {
     "well": "D5",
     "role": "sample",
     "concentration": 1e-05,
     "value": 89.411,
     "excluded": false
    },
    {
     "well": "D6",
     "role": "sample",
     "concentration": 1e-05,
     "value": 100.641,
     "excluded": false
    },
    {
     "well": "D7",
     "role": "sample",
     "concentration": 1e-05,
     "value": 99.114,
     "excluded": false
    },
    {
     "well": "E3",
     "role": "sample",
     "concentration": 1e-05,
     "value": 91.824,
     "excluded": false
    },
    {
     "well": "E4",
     "role": "sample",
     "concentration": 1e-05,
     "value": 91.859,
     "excluded": false
    },
    {
     "well": "E5",
     "role": "sample",
     "concentration": 1e-05,
     "value": 99.573,
     "excluded": false
    },
    {
     "well": "E6",
     "role": "sample",
     "concentration": 1e-05,
     "value": 88.366,
     "excluded": false
    },
    {
     "well": "E7",
     "role": "sample",
     "concentration": 1e-05,
     "value": 94.704,
     "excluded": false
    },
    {
     "well": "F3",
     "role": "sample",
     "concentration": 1e-05,
     "value": 99.289,
     "excluded": false
    },
    {
     "well": "F4",
     "role": "sample",
     "concentration": 1e-05,
     "value": 101.214,
     "excluded": false
    },
    {
     "well": "F5",
     "role": "sample",
     "concentration": 1e-05,
     "value": 92.67,
     "excluded": false
    },
    {
     "well": "F6",
     "role": "sample",
     "concentration": 1e-05,
     "value": 86.79,
     "excluded": false
    },
    {
     "well": "F7",
     "role": "sample",
     "concentration": 1e-05,
     "value": 97.623,
     "excluded": false
    }
   ],
   "expected": {
    "zPrime": {
     "status": "withheld",
     "reason": "too-few-wells",
     "nPositive": 1,
     "nNegative": 1
    },
    "signalWindow": {
     "status": "withheld",
     "reason": "too-few-wells",
     "nPositive": 1,
     "nNegative": 1
    },
    "ssmd": {
     "status": "withheld",
     "reason": "too-few-wells",
     "nPositive": 1,
     "nNegative": 1
    },
    "controlSpan": null,
    "z": {
     "status": "withheld",
     "reason": "too-few-wells",
     "nSamples": 20,
     "nNegative": 1,
     "concentration": 1e-05
    },
    "pattern": [
     {
      "group": "positive",
      "n": 1,
      "edge": {
       "status": "withheld",
       "reason": "too-few-wells",
       "nEdge": 1,
       "nInterior": 0
      },
      "rows": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 1,
       "rows": 1,
       "columns": 1
      },
      "columns": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 1,
       "rows": 1,
       "columns": 1
      }
     },
     {
      "group": "negative",
      "n": 1,
      "edge": {
       "status": "withheld",
       "reason": "too-few-wells",
       "nEdge": 1,
       "nInterior": 0
      },
      "rows": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 1,
       "rows": 1,
       "columns": 1
      },
      "columns": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 1,
       "rows": 1,
       "columns": 1
      }
     },
     {
      "group": "samples",
      "n": 20,
      "edge": {
       "status": "withheld",
       "reason": "too-few-wells",
       "nEdge": 0,
       "nInterior": 20
      },
      "rows": {
       "status": "computed",
       "n": 20,
       "rows": 4,
       "columns": 5,
       "residualDf": 12,
       "F": 0.5138383253360146,
       "df1": 3,
       "df2": 12,
       "p": 0.6804137773705817,
       "levelMeans": [
        96.6614,
        96.2654,
        93.2652,
        95.5172
       ],
       "spread": 3.3962000000000074,
       "spreadPercentOfSpan": null
      },
      "columns": {
       "status": "computed",
       "n": 20,
       "rows": 4,
       "columns": 5,
       "residualDf": 12,
       "F": 0.4441638048030393,
       "df1": 4,
       "df2": 12,
       "p": 0.7746784752474669,
       "levelMeans": [
        96.1695,
        97.075,
        93.75025,
        93.7255,
        96.41625
       ],
       "spread": 3.349500000000006,
       "spreadPercentOfSpan": null
      }
     }
    ]
   }
  },
  {
   "id": "P03",
   "about": "Vehicle wells identical: SW withheld (no scale); SSMD and Z' computed",
   "format": 96,
   "wells": [
    {
     "well": "A1",
     "role": "positive",
     "concentration": null,
     "value": 100,
     "excluded": false
    },
    {
     "well": "B1",
     "role": "positive",
     "concentration": null,
     "value": 100,
     "excluded": false
    },
    {
     "well": "C1",
     "role": "positive",
     "concentration": null,
     "value": 100,
     "excluded": false
    },
    {
     "well": "D1",
     "role": "positive",
     "concentration": null,
     "value": 100,
     "excluded": false
    },
    {
     "well": "A12",
     "role": "negative",
     "concentration": null,
     "value": 4.0,
     "excluded": false
    },
    {
     "well": "B12",
     "role": "negative",
     "concentration": null,
     "value": 6.0,
     "excluded": false
    },
    {
     "well": "C12",
     "role": "negative",
     "concentration": null,
     "value": 5.0,
     "excluded": false
    },
    {
     "well": "D12",
     "role": "negative",
     "concentration": null,
     "value": 5.5,
     "excluded": false
    }
   ],
   "expected": {
    "zPrime": {
     "status": "computed",
     "value": 0.9729988122109101,
     "nPositive": 4,
     "nNegative": 4
    },
    "signalWindow": {
     "status": "withheld",
     "reason": "no-vehicle-spread",
     "nPositive": 4,
     "nNegative": 4
    },
    "ssmd": {
     "status": "computed",
     "value": 111.1062233051905,
     "nPositive": 4,
     "nNegative": 4
    },
    "controlSpan": 94.875,
    "z": null,
    "pattern": [
     {
      "group": "positive",
      "n": 4,
      "edge": {
       "status": "withheld",
       "reason": "too-few-wells",
       "nEdge": 4,
       "nInterior": 0
      },
      "rows": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      },
      "columns": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      }
     },
     {
      "group": "negative",
      "n": 4,
      "edge": {
       "status": "withheld",
       "reason": "too-few-wells",
       "nEdge": 4,
       "nInterior": 0
      },
      "rows": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      },
      "columns": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      }
     }
    ]
   }
  },
  {
   "id": "P04",
   "about": "Both controls without spread: SSMD withheld, Z' exactly 1",
   "format": 96,
   "wells": [
    {
     "well": "A1",
     "role": "positive",
     "concentration": null,
     "value": 100,
     "excluded": false
    },
    {
     "well": "B1",
     "role": "positive",
     "concentration": null,
     "value": 100,
     "excluded": false
    },
    {
     "well": "C1",
     "role": "positive",
     "concentration": null,
     "value": 100,
     "excluded": false
    },
    {
     "well": "D1",
     "role": "positive",
     "concentration": null,
     "value": 100,
     "excluded": false
    },
    {
     "well": "A12",
     "role": "negative",
     "concentration": null,
     "value": 5,
     "excluded": false
    },
    {
     "well": "B12",
     "role": "negative",
     "concentration": null,
     "value": 5,
     "excluded": false
    },
    {
     "well": "C12",
     "role": "negative",
     "concentration": null,
     "value": 5,
     "excluded": false
    },
    {
     "well": "D12",
     "role": "negative",
     "concentration": null,
     "value": 5,
     "excluded": false
    }
   ],
   "expected": {
    "zPrime": {
     "status": "computed",
     "value": 1.0,
     "nPositive": 4,
     "nNegative": 4
    },
    "signalWindow": {
     "status": "withheld",
     "reason": "no-vehicle-spread",
     "nPositive": 4,
     "nNegative": 4
    },
    "ssmd": {
     "status": "withheld",
     "reason": "no-spread",
     "nPositive": 4,
     "nNegative": 4
    },
    "controlSpan": 95.0,
    "z": null,
    "pattern": [
     {
      "group": "positive",
      "n": 4,
      "edge": {
       "status": "withheld",
       "reason": "too-few-wells",
       "nEdge": 4,
       "nInterior": 0
      },
      "rows": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      },
      "columns": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      }
     },
     {
      "group": "negative",
      "n": 4,
      "edge": {
       "status": "withheld",
       "reason": "too-few-wells",
       "nEdge": 4,
       "nInterior": 0
      },
      "rows": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      },
      "columns": {
       "status": "withheld",
       "reason": "too-few-levels",
       "n": 4,
       "rows": 4,
       "columns": 1
      }
     }
    ]
   }
  },
  {
   "id": "P05",
   "about": "Coinciding control means: SW, Z' and Z withheld; SSMD 0",
   "format": 96,
   "wells": [
    {
     "well": "A1",
     "role": "positive",
     "concentration": null,
     "value": 1,
     "excluded": false
    },
    {
     "well": "B1",
     "role": "positive",
     "concentration": null,
     "value": 2,
     "excluded": false
    },
    {
     "well": "C1",
     "role": "positive",
     "concentration": null,
     "value": 3,
     "excluded": false
    },
    {
     "well": "A12",
     "role": "negative",
     "concentration": null,
     "value": 3,
     "excluded": false
    },
    {
     "well": "B12",
     "role": "negative",
     "concentration": null,
     "value": 2,
     "excluded": false
    },
    {
     "well": "C12",
     "role": "negative",
     "concentration": null,
     "value": 1,
     "excluded": false
    },
    {
     "well": "B3",
     "role": "sample",
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   "id": "P09",
   "about": "Screen: vehicle column 1, kill column 12, 80 samples at 10 uM with an edge loss: control edge tests withheld",
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