{
 "about": {
  "date": "2026-10-24",
  "python": "3.12.14",
  "generator": "pipeline/bioreactor-simulator/wave8/batch-fit-flags.py",
  "generatorSha256": "1550cf5ba65d24385a9a3e280fc435637eab3ee9dde99a2778e1a02df68a467d",
  "derivedFrom": {
   "file": "pipeline/bioreactor-simulator/fixtures/batch-fit-0.9.0.json",
   "sha256": "64572644292639aa07c5591f8b49da0fff2b77dc364863470d77d78f24d263ba",
   "version": "0.9.0"
  },
  "ruling": "docs/board/memos/2026-10-24-cso-bioreactor-b2-fixture-read.md, \u00a72; docs/board/memos/2026-10-24-cso-bioreactor-b2-engine-acceptance.md, ruling 3; D-0131",
  "meaning": "resolved means numerically resolved: 0.9.0's verdict says the optimum is numerically determined, not that the data constrain muMax or that the model fits them; an estimate is applicable only when resolved and carrying no withholding flag",
  "computation": "adds no new oracle computation: every value below is read from, or computed by arithmetic on, values stored in 0.9.0",
  "supersedes": {
   "version": "0.10.0",
   "file": "pipeline/bioreactor-simulator/fixtures/batch-fit-flags-0.10.0.json",
   "sha256": "251b962ccfc02e22d5ab7537adbc05a4d5816ae43fe6d02fa1fffc5f7481b44c",
   "why": "the same flags by the same rule; its manifest lacked the values, statements and applicability marking ruling 3 asks for"
  },
  "thresholds": {
   "deltaJ": 4.0,
   "misfitRms": 2.0,
   "withholding": [
    "weak-profile",
    "near-competing-minimum"
   ],
   "shownOnly": [
    "second-minimum",
    "misfit"
   ],
   "otherBasin": "a basin of 0.9.0's result.basins whose u lies more than 2 x tolerance.achievedResolutionU from the estimate's",
   "rules": {
    "weak-profile": "min(tolerance.profileRiseLeft, tolerance.profileRiseRight) < deltaJ",
    "near-competing-minimum": "some other basin has J - estimate.J < deltaJ",
    "second-minimum": "some other basin has J - estimate.J >= deltaJ",
    "misfit": "sqrt(estimate.J / n) > misfitRms, n the number of result.residuals"
   },
   "source": "docs/board/memos/2026-10-24-cso-bioreactor-b2-fixture-read.md, \u00a72 (judgements frozen before engine code; deltaJ 4 sits just above chi-squared(1) 0.95 = 3.84 with correct known SDs and has no probability meaning with balancing scales; never drawn or reported as an interval)"
  }
 },
 "cases": [
  {
   "id": "noiseless-glucose",
   "requiredCase": 1,
   "verdict": "resolved",
   "practical": {
    "flags": [],
    "application": "applicable",
    "values": {
     "estimateJ": 1.0016421516492251e-13,
     "profileRiseLeft": 54126.58044416323,
     "profileRiseRight": 29852.80803188035,
     "weakerProfileRise": 29852.80803188035,
     "otherBasins": [],
     "residualCount": 20,
     "sumOfSquaredScaledResiduals": 1.0016421516492252e-13,
     "rmsScaledResidual": 7.076871313120033e-08
    }
   }
  },
  {
   "id": "noiseless-slow-product",
   "requiredCase": 1,
   "verdict": "resolved",
   "practical": {
    "flags": [],
    "application": "applicable",
    "values": {
     "estimateJ": 3.610997153989733e-14,
     "profileRiseLeft": 263157.88220355083,
     "profileRiseRight": 100567.5186113494,
     "weakerProfileRise": 100567.5186113494,
     "otherBasins": [],
     "residualCount": 20,
     "sumOfSquaredScaledResiduals": 3.610997153989733e-14,
     "rmsScaledResidual": 4.249115880974378e-08
    }
   }
  },
  {
   "id": "noiseless-methanol-haldane",
   "requiredCase": 1,
   "verdict": "resolved",
   "practical": {
    "flags": [],
    "application": "applicable",
    "values": {
     "estimateJ": 1.142360740238272e-18,
     "profileRiseLeft": 25332.947840146695,
     "profileRiseRight": 3949.7138683346407,
     "weakerProfileRise": 3949.7138683346407,
     "otherBasins": [],
     "residualCount": 24,
     "sumOfSquaredScaledResiduals": 1.1423607402382716e-18,
     "rmsScaledResidual": 2.181704933683624e-10
    }
   }
  },
  {
   "id": "seeded-noise-glucose",
   "requiredCase": 1,
   "verdict": "resolved",
   "practical": {
    "flags": [],
    "application": "applicable",
    "values": {
     "estimateJ": 14.993008177103336,
     "profileRiseLeft": 41729.42860586278,
     "profileRiseRight": 24019.604010202478,
     "weakerProfileRise": 24019.604010202478,
     "otherBasins": [],
     "residualCount": 20,
     "sumOfSquaredScaledResiduals": 14.993008177103336,
     "rmsScaledResidual": 0.8658235437172904
    }
   }
  },
  {
   "id": "units-g-per-l-hours",
   "requiredCase": 2,
   "verdict": "resolved",
   "practical": {
    "flags": [],
    "application": "applicable",
    "values": {
     "estimateJ": 0.00014000358554175292,
     "profileRiseLeft": 54125.60144091044,
     "profileRiseRight": 29852.111601366953,
     "weakerProfileRise": 29852.111601366953,
     "otherBasins": [],
     "residualCount": 20,
     "sumOfSquaredScaledResiduals": 0.00014000358554175292,
     "rmsScaledResidual": 0.0026457851910326445
    }
   }
  },
  {
   "id": "units-mg-per-l-minutes",
   "requiredCase": 2,
   "verdict": "resolved",
   "practical": {
    "flags": [],
    "application": "applicable",
    "values": {
     "estimateJ": 0.00014000358554175292,
     "profileRiseLeft": 54125.60144091044,
     "profileRiseRight": 29852.111601366953,
     "weakerProfileRise": 29852.111601366953,
     "otherBasins": [],
     "residualCount": 20,
     "sumOfSquaredScaledResiduals": 0.00014000358554175292,
     "rmsScaledResidual": 0.0026457851910326445
    }
   }
  },
  {
   "id": "replicates-and-exclusion",
   "requiredCase": 3,
   "verdict": "resolved",
   "practical": {
    "flags": [],
    "application": "applicable",
    "values": {
     "estimateJ": 0.569804040831716,
     "profileRiseLeft": 55308.64062601697,
     "profileRiseRight": 30878.54841008597,
     "weakerProfileRise": 30878.54841008597,
     "otherBasins": [],
     "residualCount": 22,
     "sumOfSquaredScaledResiduals": 0.5698040408317159,
     "rmsScaledResidual": 0.16093534004117588
    }
   }
  },
  {
   "id": "near-coincident-times",
   "requiredCase": 3,
   "verdict": "refused",
   "practical": null,
   "application": "not applicable (refused)"
  },
  {
   "id": "od-only",
   "requiredCase": 4,
   "verdict": "refused",
   "practical": null,
   "application": "not applicable (refused)"
  },
  {
   "id": "no-growth",
   "requiredCase": 4,
   "verdict": "not-resolved",
   "practical": null,
   "application": "not applicable (not-resolved)"
  },
  {
   "id": "poorly-excited",
   "requiredCase": 4,
   "verdict": "resolved",
   "practical": {
    "flags": [
     "weak-profile"
    ],
    "application": "withheld",
    "values": {
     "estimateJ": 2.6661044964032166e-23,
     "profileRiseLeft": 0.0005189735070024509,
     "profileRiseRight": 0.004918174599654722,
     "weakerProfileRise": 0.0005189735070024509,
     "otherBasins": [],
     "residualCount": 6,
     "sumOfSquaredScaledResiduals": 2.6661044964032166e-23,
     "rmsScaledResidual": 2.1079628777578984e-12
    }
   }
  },
  {
   "id": "misspecified-yield-detectable",
   "requiredCase": 4,
   "verdict": "resolved",
   "practical": {
    "flags": [
     "misfit"
    ],
    "application": "applicable",
    "values": {
     "estimateJ": 248.7507069969761,
     "profileRiseLeft": 53559.96761369796,
     "profileRiseRight": 32152.35659245712,
     "weakerProfileRise": 32152.35659245712,
     "otherBasins": [],
     "residualCount": 20,
     "sumOfSquaredScaledResiduals": 248.75070699697608,
     "rmsScaledResidual": 3.5266890066815937
    }
   }
  },
  {
   "id": "misspecified-x0-confounded",
   "requiredCase": 4,
   "verdict": "resolved",
   "practical": {
    "flags": [],
    "application": "applicable",
    "values": {
     "estimateJ": 2.4057560407918404,
     "profileRiseLeft": 3215.4278041342895,
     "profileRiseRight": 27187.23157311565,
     "weakerProfileRise": 3215.4278041342895,
     "otherBasins": [],
     "residualCount": 10,
     "sumOfSquaredScaledResiduals": 2.4057560407918404,
     "rmsScaledResidual": 0.4904850701898928
    }
   }
  },
  {
   "id": "bounds-exclude-truth",
   "requiredCase": 5,
   "verdict": "not-resolved",
   "practical": null,
   "application": "not applicable (not-resolved)"
  },
  {
   "id": "contradictory-channels",
   "requiredCase": 5,
   "verdict": "resolved",
   "practical": {
    "flags": [
     "second-minimum",
     "misfit"
    ],
    "application": "applicable",
    "values": {
     "estimateJ": 1245.7625294149,
     "profileRiseLeft": 11755.979744183223,
     "profileRiseRight": 4215.456915685394,
     "weakerProfileRise": 4215.456915685394,
     "otherBasins": [
      {
       "muMax": 0.39217538291536547,
       "J": 10455.222557077233,
       "deltaJ": 9209.460027662333
      },
      {
       "muMax": 0.36998253525254754,
       "J": 10457.02598694228,
       "deltaJ": 9211.26345752738
      },
      {
       "muMax": 0.4443173981562262,
       "J": 10544.981427418012,
       "deltaJ": 9299.218898003111
      }
     ],
     "residualCount": 6,
     "sumOfSquaredScaledResiduals": 1245.7625294149,
     "rmsScaledResidual": 14.409270912708132
    }
   }
  },
  {
   "id": "contradictory-channels-near-tie",
   "requiredCase": 5,
   "verdict": "resolved",
   "practical": {
    "flags": [
     "near-competing-minimum",
     "misfit"
    ],
    "application": "withheld",
    "values": {
     "estimateJ": 1243.7415735278391,
     "profileRiseLeft": 1458.7301777083926,
     "profileRiseRight": 961.0830253061663,
     "weakerProfileRise": 961.0830253061663,
     "otherBasins": [
      {
       "muMax": 1.1602104091238308,
       "J": 1244.1462441021442,
       "deltaJ": 0.40467057430510067
      }
     ],
     "residualCount": 6,
     "sumOfSquaredScaledResiduals": 1243.7415735278391,
     "rmsScaledResidual": 14.397578346883195
    }
   }
  },
  {
   "id": "oxygen-limited",
   "requiredCase": 6,
   "verdict": "resolved",
   "practical": {
    "flags": [],
    "application": "applicable",
    "values": {
     "estimateJ": 1.5093052259026832e-15,
     "profileRiseLeft": 80312.56603298103,
     "profileRiseRight": 8460.92200812999,
     "weakerProfileRise": 8460.92200812999,
     "otherBasins": [],
     "residualCount": 28,
     "sumOfSquaredScaledResiduals": 1.5093052259026834e-15,
     "rmsScaledResidual": 7.341917873958614e-09
    }
   }
  },
  {
   "id": "maintenance-transition",
   "requiredCase": 6,
   "verdict": "resolved",
   "practical": {
    "flags": [],
    "application": "applicable",
    "values": {
     "estimateJ": 4.458723073550982e-15,
     "profileRiseLeft": 561.0830342632166,
     "profileRiseRight": 11.116927098176758,
     "weakerProfileRise": 11.116927098176758,
     "otherBasins": [],
     "residualCount": 24,
     "sumOfSquaredScaledResiduals": 4.458723073550983e-15,
     "rmsScaledResidual": 1.3630118417116714e-08
    }
   }
  },
  {
   "id": "evaluation-cap",
   "requiredCase": 7,
   "verdict": "refused",
   "practical": null,
   "application": "not applicable (refused)"
  },
  {
   "id": "step-cap",
   "requiredCase": 7,
   "verdict": "refused",
   "practical": null,
   "application": "not applicable (refused)"
  }
 ]
}