{
 "about": {
  "method": "inhibition-global-fit",
  "recordedOn": "2026-10-12",
  "script": "pipeline/assay-analyser/oracles/inhibition_global_v2.py",
  "scriptSha256": "371e47cbd8c03189af6a413a7cd34dba75c93604d0034cef0c43e31eca2c6cd7",
  "origin": "Self-constructed rates from known parameters, with one recorded noise vector (NumPy seed 20261010); no published dataset",
  "tolerances": {
   "rss": "within 1e-6 relative, or both at the rates' numeric resolution",
   "vmax, km, ki and kiPrime": "within 1e-5 relative; hand values within 1e-9 relative",
   "correlations": "within 1e-4 absolute",
   "statuses, refusals, the named level and the parameters at the box": "exact",
   "flags": "exact"
  },
  "crossCheck": {
   "tool": "R stats::nls",
   "version": "R version 4.4.3 (2025-02-28)",
   "script": "pipeline/assay-analyser/oracles/r/inhibition_nls.R",
   "scriptSha256": "0bef47676ab0dc0477973d4f5058c06c2552eedd5cb2a79965bec676f092c700",
   "ran": true,
   "settings": "nls.control(maxiter = 1000, tol = 1e-8, then 1e-6 as reference.R's NLS_TOLERANCES, minFactor = 1e-12, scaleOffset = 1), started from the SciPy estimates; each case records the tolerance that held; scaleOffset 1 because R's convergence test divides by the residual size, which is zero on noiseless data",
   "tolerances": {
    "constants": "1e-5 relative",
    "rss": "1e-6 relative, or both at the rates' numeric resolution"
   },
   "cases": 11,
   "agreeing": 11,
   "scipyOnly": [
    {
     "case": "adverse-competitive-as-mixed",
     "status": "bound"
    },
    {
     "case": "adverse-uncompetitive-as-mixed",
     "status": "bound"
    },
    {
     "case": "noisy-as-mixed",
     "status": "bound"
    },
    {
     "case": "refused-no-control",
     "status": "refused"
    },
    {
     "case": "refused-one-level",
     "status": "refused"
    },
    {
     "case": "refused-three-substrates",
     "status": "refused"
    },
    {
     "case": "refused-negative-inhibitor",
     "status": "refused"
    }
   ],
   "result": [
    {
     "case": "competitive-noiseless",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "vmax": 10,
      "km": 2,
      "ki": 5
     },
     "rss": 2.26458546580829e-29,
     "maxRelativeDifference": 3.552713678800502e-16,
     "rssScaledDifference": 3.716515517772626e-27,
     "agrees": true
    },
    {
     "case": "uncompetitive-noiseless",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "vmax": 10,
      "km": 2,
      "kiPrime": 5
     },
     "rss": 9.82378346033041e-30,
     "maxRelativeDifference": 3.552713678800502e-16,
     "rssScaledDifference": 5.756811620339443e-28,
     "agrees": true
    },
    {
     "case": "mixed-equal-noiseless",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "vmax": 10,
      "km": 2,
      "ki": 5.00000000000001,
      "kiPrime": 5
     },
     "rss": 7.49726008751063e-30,
     "maxRelativeDifference": 8.881784197001242e-16,
     "rssScaledDifference": 3.272826595659664e-28,
     "agrees": true
    },
    {
     "case": "mixed-equal-as-noncompetitive",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "vmax": 10,
      "km": 2,
      "ki": 5
     },
     "rss": 1.1811343162938e-29,
     "maxRelativeDifference": 1.7763568394002508e-16,
     "rssScaledDifference": 9.491197127413026e-27,
     "agrees": true
    },
    {
     "case": "mixed-distinct",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "vmax": 10,
      "km": 2,
      "ki": 5,
      "kiPrime": 50
     },
     "rss": 1.43350817620631e-29,
     "maxRelativeDifference": 8.526512829121195e-16,
     "rssScaledDifference": 4.010655778719118e-27,
     "agrees": true
    },
    {
     "case": "mixed-distinct-as-noncompetitive",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "vmax": 10.9552248017865,
      "km": 2.79995528826824,
      "ki": 16.2665235387339
     },
     "rss": 1.96915544965829,
     "maxRelativeDifference": 2.1079110041117113e-15,
     "rssScaledDifference": 2.0297040994626026e-15,
     "agrees": true
    },
    {
     "case": "noisy-competitive",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "vmax": 10.0477529590137,
      "km": 2.05088681667829,
      "ki": 5.24377994633643
     },
     "rss": 0.545105816144007,
     "maxRelativeDifference": 1.732281689027893e-15,
     "rssScaledDifference": 6.110133070008495e-16,
     "agrees": true
    },
    {
     "case": "noisy-as-uncompetitive",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "vmax": 11.4968514511484,
      "km": 3.60283625655236,
      "kiPrime": 19.296981893236
     },
     "rss": 13.3086626215366,
     "maxRelativeDifference": 1.656964974424947e-15,
     "rssScaledDifference": 3.4703169760774855e-15,
     "agrees": true
    },
    {
     "case": "noisy-as-noncompetitive",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "vmax": 11.2351276605835,
      "km": 3.10452806400119,
      "ki": 23.6530156281319
     },
     "rss": 7.02914454453511,
     "maxRelativeDifference": 4.2688998392134036e-15,
     "rssScaledDifference": 3.7906963531884523e-16,
     "agrees": true
    },
    {
     "case": "metamorphic-inhibitor-mM",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "vmax": 10.0477529625519,
      "km": 2.05088681986631,
      "ki": 0.00524377995365048
     },
     "rss": 0.545105816144008,
     "maxRelativeDifference": 3.3590375952110107e-15,
     "rssScaledDifference": 6.110133070008491e-16,
     "agrees": true
    },
    {
     "case": "metamorphic-row-order",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "vmax": 10.0477529580138,
      "km": 2.05088681514046,
      "ki": 5.24377993863243
     },
     "rss": 0.545105816144008,
     "maxRelativeDifference": 3.1822461442687562e-15,
     "rssScaledDifference": 2.0367110233361628e-16,
     "agrees": true
    }
   ]
  },
  "builderRules": "The medians of the starts are the lower middle of the sorted distinct values; 'failed' is every start ending at the evaluation limit; an all-zero inhibitor-free series is 'invalid'. No Ki interval is recorded: the A3 increment reports none.",
  "computedBy": {
   "script": "pipeline/assay-analyser/oracles/inhibition_global_v2_base.py",
   "sha256": "4a57ddbd3798ab54bb2e95322fb779ac25a4833e935c2bf600957598c96c2ec9",
   "lineage": "pipeline/assay-analyser/oracles/lineage.py",
   "lineageSha256": "e122fc0c22e32c739645d7866e9a4c723c5d4279f7c08f4f7e548ad194005d27",
   "note": "the base script run by the wrapper in a temporary copy of its directory, never in place"
  },
  "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",
    "MASS": "7.3-64"
   },
   "python": "3.11.15",
   "numpy": "2.0.2",
   "scipy": "1.13.1",
   "recordedOn": "2026-10-12",
   "cpu": "AMD EPYC 7763 64-Core Processor",
   "cpuClass": "x86-64-v3",
   "simd": [
    "SSSE3",
    "SSE41",
    "POPCNT",
    "SSE42",
    "AVX",
    "F16C",
    "FMA3",
    "AVX2"
   ],
   "openblasCore": "Haswell",
   "threads": 1
  },
  "basedOn": {
   "file": "pipeline/assay-analyser/oracles/fixtures/inhibition-global.json",
   "version": "0.4.0",
   "sha256": "e6549c82df06bf17de6f69d9aaaac07493b0b9869fee4f54ef7ede09f0059b59",
   "script": "pipeline/assay-analyser/oracles/inhibition_global.py",
   "scriptSha256": "eb0227378ce06da850b85bc13d495f9421c243ad9ed6932b0ed19814c58efd80",
   "environment": "not recorded",
   "classes": {
    "rules": [
     {
      "pattern": "^cases\\[\\d+\\]\\.expected\\.parameters\\.vmax$",
      "class": "span"
     },
     {
      "pattern": "^cases\\[\\d+\\]\\.expected\\.parameters\\.(km|ki|kiPrime)$",
      "class": "conc"
     },
     {
      "pattern": "^cases\\[\\d+\\]\\.expected\\.correlation\\.matrix\\[\\d+\\]\\[\\d+\\]$",
      "class": "one"
     },
     {
      "pattern": "^cases\\[\\d+\\]\\.expected\\.residuals\\[\\d+\\]$",
      "class": "span"
     },
     {
      "pattern": "^cases\\[\\d+\\]\\.expected\\.rss$",
      "class": "rss"
     },
     {
      "pattern": "^cases\\[\\d+\\]\\.expected\\.alpha$",
      "class": "one"
     }
    ],
    "default": "exact",
    "spanFrom": "rate",
    "scales": "span: max - min of the case's spanFrom values; rss: 1e-20 x their sum of squares; one: 1; conc: 1e-6",
    "tolerance": 1e-08,
    "thresholdTolerance": 1e-10,
    "illConditioned": [],
    "illTolerance": 1e-06,
    "illRssTolerance": 1e-12,
    "ruling": "docs/board/memos/2026-10-12-cso-lineage-tolerance-under-the-cpu-pin.md"
   },
   "agreement": {
    "exact": {
     "largestScaledDifference": 0.0,
     "where": "reductions.zeroInhibitor.competitive",
     "tolerance": 0.0
    },
    "span": {
     "largestScaledDifference": 2.014775407323698e-09,
     "where": "cases[9].expected.residuals[54]",
     "tolerance": 1e-08
    },
    "conc": {
     "largestScaledDifference": 7.200932999307465e-09,
     "where": "cases[9].expected.parameters.km",
     "tolerance": 1e-08
    },
    "rss": {
     "largestScaledDifference": 7.535281819621184e-13,
     "where": "cases[2].expected.rss",
     "tolerance": 1e-08
    },
    "one": {
     "largestScaledDifference": 6.939399055383433e-10,
     "where": "cases[9].expected.correlation.matrix[1][0]",
     "tolerance": 1e-08
    }
   }
  }
 },
 "oracle": {
  "engine": "scipy.optimize.least_squares",
  "method": "trf with bounds, log parameters, nine starts, lowest RSS",
  "scipy": "1.13.1",
  "numpy": "2.0.2",
  "python": "3.11.15"
 },
 "reductions": {
  "zeroInhibitor": {
   "competitive": 0.0,
   "uncompetitive": 0.0,
   "noncompetitive": 0.0,
   "mixed": 0.0
  },
  "mixedEqualIsNoncompetitive": 8.881784197001252e-16,
  "against": "michaelis-menten.json case 'noiseless' (Vmax 10, Km 2); the largest absolute difference in rate"
 },
 "cases": [
  {
   "name": "competitive-noiseless",
   "about": "Competitive rates from Vmax 10, Km 2, Ki 5 at 7 S x {0, 2, 5, 10} uM I, fitted competitive: the hand values; the I = 0 series is michaelis-menten.json's noiseless case",
   "model": "competitive",
   "substrate": [
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   ],
   "inhibitor": [
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   ],
   "rate": [
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    1.1111111111111112,
    2.0,
    3.3333333333333335,
    5.0,
    6.666666666666667,
    8.0,
    0.4,
    0.7692307692307693,
    1.4285714285714286,
    2.5,
    4.0,
    5.714285714285714,
    7.2727272727272725
   ],
   "substrateUnit": "µM",
   "inhibitorUnit": "µM",
   "rateUnit": "µM/min",
   "expected": {
    "status": "estimated",
    "parameters": {
     "vmax": 10.000000000000002,
     "km": 2.0,
     "ki": 4.999999999999998
    },
    "rss": 2.2645854658082874e-29,
    "n": 28,
    "df": 25,
    "correlation": {
     "order": [
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      "km",
      "ki"
     ],
     "matrix": [
      [
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      [
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    "residuals": [
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    "flags": {
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     "kiOutsideRange": false
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   },
   "hand": {
    "vmax": 10,
    "km": 2,
    "ki": 5
   }
  },
  {
   "name": "uncompetitive-noiseless",
   "about": "Uncompetitive rates, Ki' 5, fitted uncompetitive: the hand values",
   "model": "uncompetitive",
   "substrate": [
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   ],
   "rate": [
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    4.0,
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    0.9090909090909091,
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   "substrateUnit": "µM",
   "inhibitorUnit": "µM",
   "rateUnit": "µM/min",
   "expected": {
    "status": "estimated",
    "parameters": {
     "vmax": 10.000000000000002,
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     "kiPrime": 4.999999999999998
    },
    "rss": 9.823783460330413e-30,
    "n": 28,
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    "correlation": {
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     "matrix": [
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   },
   "hand": {
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    "kiPrime": 5
   }
  },
  {
   "name": "mixed-equal-noiseless",
   "about": "Mixed rates with Ki = Ki' = 5, fitted mixed: both constants 5",
   "model": "mixed",
   "substrate": [
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   "inhibitor": [
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   "rate": [
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   "substrateUnit": "µM",
   "inhibitorUnit": "µM",
   "rateUnit": "µM/min",
   "expected": {
    "status": "estimated",
    "parameters": {
     "vmax": 10.000000000000002,
     "km": 2.000000000000001,
     "ki": 5.000000000000005,
     "kiPrime": 4.999999999999997
    },
    "rss": 7.497260087510632e-30,
    "n": 28,
    "df": 24,
    "correlation": {
     "order": [
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      "ki",
      "kiPrime"
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     "matrix": [
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   "name": "mixed-equal-as-noncompetitive",
   "about": "The same rates fitted pure noncompetitive: Ki 5, the constrained special case",
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   "name": "adverse-uncompetitive-as-mixed",
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   "name": "mixed-distinct",
   "about": "Mixed rates with Ki 5 and Ki' 50, fitted mixed: both constants recovered, alpha 10 (derived, descriptive)",
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   "name": "mixed-distinct-as-noncompetitive",
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   "name": "noisy-competitive",
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 ]
}