{
 "about": {
  "method": "thermal-shift-apparent-tm",
  "recordedOn": "2026-10-12",
  "script": "pipeline/assay-analyser/oracles/thermal_shift_v2.py",
  "scriptSha256": "377c1ae84ec990c89bd3de090385d041ce22d9c34f22421b3018315fdd26e9a5",
  "origin": "Self-constructed synthetic melts from known Boltzmann parameters, with one recorded noise vector (NumPy seed 20261010); no published dataset",
  "tolerances": {
   "sigmoid Tm": "within 1e-3 C absolute",
   "ln k": "within 1e-4 absolute",
   "F_lo and F_hi": "within 1e-4 of the span",
   "RSS": "within 1e-6 relative",
   "derivative values": "within 1e-9 relative",
   "derivative Tm (the argmax temperature)": "exact",
   "statuses, reasons and the disagreement flag": "exact"
  },
  "crossCheck": {
   "tool": "R stats::nls with SSfpl",
   "version": "R version 4.4.3 (2025-02-28)",
   "script": "pipeline/assay-analyser/oracles/r/thermal_ssfpl.R",
   "scriptSha256": "c4c22a63a73804a336d37b35cd58a9fed7d0ca0fdf531703b6c08afabf7c7d8b",
   "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": {
    "tm": "1e-3 C absolute",
    "lnK": "1e-4 absolute",
    "fLo and fHi": "1e-4 of the span",
    "rss": "1e-6 relative"
   },
   "cases": 7,
   "agreeing": 7,
   "scipyOnly": [
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     "case": "adverse-flat",
     "status": "refused",
     "reason": "no-transition"
    },
    {
     "case": "adverse-two-transitions",
     "status": "refused",
     "reason": "two-transitions"
    },
    {
     "case": "adverse-window-at-53",
     "status": "refused",
     "reason": "unbracketed"
    },
    {
     "case": "adverse-duplicate-temperatures",
     "status": "refused",
     "reason": "temperatures"
    },
    {
     "case": "adverse-sign",
     "status": "refused",
     "reason": "sign"
    },
    {
     "case": "adverse-few-points",
     "status": "refused",
     "reason": "points"
    }
   ],
   "result": [
    {
     "case": "noiseless",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "A": 1000,
      "B": 9000,
      "xmid": 52,
      "scal": 1.8
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     "points": 141,
     "differences": {
      "tm": 0.0,
      "lnK": 0.0,
      "fLo": 0.0,
      "fHi": 0.0,
      "rss": 0
     },
     "agrees": true
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    {
     "case": "noisy",
     "converged": true,
     "nlsTol": 1e-06,
     "parameters": {
      "A": 999.562486640446,
      "B": 9000.51735860134,
      "xmid": 51.9696974932214,
      "scal": 1.8110983929305
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     "points": 141,
     "differences": {
      "tm": 4.263256414560601e-14,
      "lnK": 2.220446049250313e-15,
      "fLo": 4.262747617288589e-17,
      "fHi": 6.820396187661742e-16,
      "rss": 1.6264134875795153e-15
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     "agrees": true
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    {
     "case": "ligand-shifted",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "A": 1004.09099475132,
      "B": 9002.41309158389,
      "xmid": 56.2962690479675,
      "scal": 1.8202778314018
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     "points": 141,
     "differences": {
      "tm": 2.1316282072803006e-14,
      "lnK": 1.4432899320127035e-15,
      "fLo": 4.832704204380154e-16,
      "fHi": 4.548427486475438e-16,
      "rss": 1.7234584084196632e-15
     },
     "agrees": true
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    {
     "case": "falls",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "A": 9000,
      "B": 1000,
      "xmid": 52,
      "scal": 1.8
     },
     "points": 141,
     "differences": {
      "tm": 0.0,
      "lnK": 0.0,
      "fLo": 0.0,
      "fHi": 4.263256414560601e-17,
      "rss": 0
     },
     "agrees": true
    },
    {
     "case": "nonuniform-steps",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "A": 1000,
      "B": 9000,
      "xmid": 52,
      "scal": 1.8
     },
     "points": 127,
     "differences": {
      "tm": 0.0,
      "lnK": 1.1102230246251565e-16,
      "fLo": 0.0,
      "fHi": 0.0,
      "rss": 2.991758887410948e-16
     },
     "agrees": true
    },
    {
     "case": "metamorphic-plus-one",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "A": 999.562487761032,
      "B": 9000.51735856612,
      "xmid": 52.9696974939536,
      "scal": 1.8110983915397
     },
     "points": 141,
     "differences": {
      "tm": 4.263256414560601e-14,
      "lnK": 2.55351295663786e-15,
      "fLo": 2.841831745269584e-17,
      "fHi": 2.2734653962156673e-16,
      "rss": 1.8766309472071394e-15
     },
     "agrees": true
    },
    {
     "case": "adverse-post-decline",
     "converged": true,
     "nlsTol": 1e-08,
     "parameters": {
      "A": 1054.08434844907,
      "B": 6944.10954861059,
      "xmid": 50.8657162779827,
      "scal": 1.11189959902365
     },
     "points": 141,
     "differences": {
      "tm": 6.72217126407304e-08,
      "lnK": 2.0599439154445065e-08,
      "fLo": 2.2265752664708358e-09,
      "fHi": 2.8887977644472726e-09,
      "rss": 2.1095336725414352e-15
     },
     "agrees": true
    }
   ],
   "mapping": "SSfpl A + (B - A) / (1 + exp((xmid - T) / scal)) against F_lo + (F_hi - F_lo) / (1 + exp((Tm - T) / k)): A = F_lo, B = F_hi, xmid = Tm, scal = k = exp(lnK); a negative scal is converted by swapping A and B (CSO ruling of 12 October 2026)"
  },
  "builderRules": "Two specifications are the builder's, to be confirmed by the CSO: the k box [median step / 100, window span / 2], and the valley condition on a second derivative maximum (below half of it between the two) so that noise in one peak's shoulder is not read as a second transition. A fitted amplitude contradicting the declared direction is refused here, as the coordinator's brief lists it; the CSO memo calls it a flag.",
  "computedBy": {
   "script": "pipeline/assay-analyser/oracles/thermal_shift.py",
   "sha256": "82fb06bb61968190a22277a86167241940a3f85f23a91ee601b4bacc886e287e",
   "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 9V45 96-Core Processor",
   "cpuClass": "x86-64-v3",
   "simd": [
    "SSSE3",
    "SSE41",
    "POPCNT",
    "SSE42",
    "AVX",
    "F16C",
    "FMA3",
    "AVX2"
   ],
   "openblasCore": "Haswell",
   "threads": 1
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  "basedOn": {
   "file": "pipeline/assay-analyser/oracles/fixtures/thermal-shift.json",
   "version": "0.4.0",
   "sha256": "f863ae673a92f8f4493477b18b4d540e61749167f4afa36b18b00d07d9a01b66",
   "script": "pipeline/assay-analyser/oracles/thermal_shift.py",
   "scriptSha256": "82fb06bb61968190a22277a86167241940a3f85f23a91ee601b4bacc886e287e",
   "environment": "not recorded",
   "classes": {
    "rules": [
     {
      "pattern": "^cases\\[\\d+\\]\\.expected\\.sigmoid\\.(fHi|fLo|span)$",
      "class": "span"
     },
     {
      "pattern": "^cases\\[\\d+\\]\\.expected\\.sigmoid\\.(tm|lnK)$",
      "class": "one"
     },
     {
      "pattern": "^cases\\[\\d+\\]\\.expected\\.sigmoid\\.rss$",
      "class": "rss"
     },
     {
      "pattern": "^deltaTm\\.sigmoid$",
      "class": "one"
     }
    ],
    "default": "exact",
    "spanFrom": "fluorescence",
    "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": [
     {
      "case": "adverse-post-decline",
      "fields": "^expected\\.sigmoid\\.(tm|lnK|fLo|fHi)$"
     }
    ],
    "illTolerance": 1e-06,
    "illRssTolerance": 1e-12,
    "ruling": "docs/board/memos/2026-10-12-cso-lineage-tolerance-under-the-cpu-pin.md"
   },
   "agreement": {
    "one": {
     "largestScaledDifference": 9.323479766010223e-10,
     "where": "cases[2].expected.sigmoid.lnK",
     "tolerance": 1e-08
    },
    "exact": {
     "largestScaledDifference": 0.0,
     "where": "deltaTm.derivative",
     "tolerance": 0.0
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    "span": {
     "largestScaledDifference": 1.014455150808984e-10,
     "where": "cases[5].expected.sigmoid.fLo",
     "tolerance": 1e-08
    },
    "rss": {
     "largestScaledDifference": 1.6280646290144578e-13,
     "where": "cases[4].expected.sigmoid.rss",
     "tolerance": 1e-08
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    "illConditioned": [
     {
      "case": "adverse-post-decline",
      "fields": [
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       "expected.sigmoid.fLo",
       "expected.sigmoid.lnK",
       "expected.sigmoid.tm"
      ],
      "reason": "a deliberately misspecified melt (a linear post-transition decline inside the window): the sigmoid's minimum is flat, its RSS agrees to about 1e-13 while lnK moves about 1e-7",
      "measured": {
       "fields": {
        "expected.sigmoid.tm": 1.3258092338724498e-09,
        "expected.sigmoid.lnK": 1.0875482901739897e-07,
        "expected.sigmoid.fLo": 1.134462804699237e-09,
        "expected.sigmoid.fHi": 1.0414705618444928e-09
       },
       "rss": {
        "expected.sigmoid.rss": 1.150654730477145e-15
       }
      },
      "tolerances": {
       "fields": "1e-06 x max(|old|, scale of the field's class)",
       "rss": "1e-12 relative"
      },
      "ruling": "docs/board/memos/2026-10-12-cso-ill-conditioned-cases-and-ssfpl.md"
     }
    ]
   }
  }
 },
 "oracle": {
  "engine": "scipy.optimize.curve_fit",
  "method": "trf with bounds, parameters (F_lo, F_hi, Tm, ln k), three starts, lowest RSS",
  "derivative": "central differences by hand in Python floats",
  "scipy": "1.13.1",
  "numpy": "2.0.2",
  "python": "3.11.15"
 },
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  "condition": "ligand-shifted",
  "reference": "noisy",
  "sigmoid": 4.326571554746032,
  "derivative": 4.0,
  "handSigmoid": 4.3
 },
 "cases": [
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   "about": "Boltzmann Tm 52.0, k 1.8, F 1000 to 9000, 25 to 95 C at 0.5 C: the hand values; the derivative extremum exactly at 52.0",
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