{
 "about": {
  "fixture": "MTT worked example (brief section 4.3 (2)), generated from known parameters with a seeded noise model, as brief section 5.4 allows unless the CSO supplies a licensed dataset",
  "generatedBy": "pipeline/assay-analyser/generate_curves.py",
  "scriptSha256": "721b80f5d3355bda4ee92e2b8b1cb003ce6b7074ff8e817096cf255941ec5c2f",
  "numpy": "2.4.6",
  "python": "3.11.15",
  "model": "y = Bottom + (Top - Bottom) / (1 + 10^((logIC50 - x) * Hill)), x = log10(concentration in M); Hill < 0 for a falling curve",
  "drcMapping": "drc LL.4: b = -Hill, c = Bottom, d = Top, e = IC50 = 10^logIC50",
  "rule": "Synthetic data from known parameters; no value comes from the Drybench engine under test.",
  "licence": "MIT (generated data; no third-party data)"
 },
 "description": "Worked MTT cell-viability example: absorbance at 570 nm on one 96-well plate, three compounds in a 3-fold series from 100 uM, vehicle and kill controls and blanks",
 "readout": "absorbance at 570 nm (A570), blank wells read but not subtracted for the fit",
 "layout": {
  "columns 2-11": "compound, 3-fold series: column 2 = 100 uM down to column 11 = 5.08 nM",
  "rows A-C": "Compound A (triplicate)",
  "rows D-F": "Compound B (triplicate)",
  "rows G-H": "Compound C (duplicate)",
  "column 1": "vehicle (0.5% DMSO), 8 wells: the 100% viability control",
  "column 12, rows A-D": "kill control, 4 wells: the 0% viability control",
  "column 12, rows E-H": "blank (medium and MTT, no cells), 4 wells: read but not used in the normalisation"
 },
 "normalisation": "percent viability = 100 x (A570 - mean(kill)) / (mean(vehicle) - mean(kill)); brief section 4.1's percent = 100 (y - mu_neg) / (mu_pos - mu_neg) with mu_pos the vehicle mean and mu_neg the kill-control mean",
 "zPrime": "Z' from the vehicle wells (8) against the kill-control wells (4)",
 "generativeModel": {
  "viability": "4PL in percent viability with each compound's true parameters (below)",
  "a570": "true A570 = 0.06 + (1.25 - 0.06) x viability / 100; vehicle 1.25, kill 0.06, blank 0.045",
  "noise": "A570 = true + N(0, sd^2), sd = sqrt((0.05 x true)^2 + 0.008^2); rounded to 3 decimals, as plate readers print",
  "seed": 20261106,
  "generator": "numpy.random.RandomState(seed).standard_normal(size=(8, 12)): row A..H, column 1..12"
 },
 "concentrations_M": [
  0.0001,
  3.3333333333333335e-05,
  1.1111111111111112e-05,
  3.7037037037037037e-06,
  1.234567901234568e-06,
  4.11522633744856e-07,
  1.3717421124828532e-07,
  4.5724737082761776e-08,
  1.5241579027587257e-08,
  5.080526342529086e-09
 ],
 "compounds": {
  "Compound A": {
   "rows": [
    "A",
    "B",
    "C"
   ],
   "truth": {
    "top": 100.0,
    "bottom": 3.0,
    "logIC50": -5.698970004336019,
    "hill": -1.2,
    "ic50_M": 2.0000000000000003e-06,
    "drcLL4": {
     "b": 1.2,
     "c": 3.0,
     "d": 100.0,
     "e": 2.0000000000000003e-06
    }
   }
  },
  "Compound B": {
   "rows": [
    "D",
    "E",
    "F"
   ],
   "truth": {
    "top": 100.0,
    "bottom": 15.0,
    "logIC50": -6.823908740944319,
    "hill": -0.9,
    "ic50_M": 1.5000000000000005e-07,
    "drcLL4": {
     "b": 0.9,
     "c": 15.0,
     "d": 100.0,
     "e": 1.5000000000000005e-07
    }
   }
  },
  "Compound C": {
   "rows": [
    "G",
    "H"
   ],
   "truth": {
    "top": 100.0,
    "bottom": 0.0,
    "logIC50": -4.221848749616356,
    "hill": -1.0,
    "ic50_M": 6.000000000000003e-05,
    "drcLL4": {
     "b": 1.0,
     "c": 0.0,
     "d": 100.0,
     "e": 6.000000000000003e-05
    }
   }
  }
 },
 "wells": [
  {
   "well": "A1",
   "row": "A",
   "column": 1,
   "role": "vehicle",
   "description": "0.5% DMSO vehicle: 100% viability control",
   "trueA570": 1.25,
   "A570": 1.19
  },
  {
   "well": "A2",
   "row": "A",
   "column": 2,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 0.0001,
   "trueViability": 3.879131178157449,
   "trueA570": 0.10616166102007364,
   "A570": 0.109
  },
  {
   "well": "A3",
   "row": "A",
   "column": 3,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 3.3333333333333335e-05,
   "trueViability": 6.205950318507178,
   "trueA570": 0.13385080879023542,
   "A570": 0.123
  },
  {
   "well": "A4",
   "row": "A",
   "column": 4,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 1.1111111111111112e-05,
   "trueViability": 13.987268684056161,
   "trueA570": 0.2264484973402683,
   "A570": 0.212
  },
  {
   "well": "A5",
   "row": "A",
   "column": 5,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 3.7037037037037037e-06,
   "trueViability": 34.34363428120807,
   "trueA570": 0.468689247946376,
   "A570": 0.48
  },
  {
   "well": "A6",
   "row": "A",
   "column": 6,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 1.234567901234568e-06,
   "trueViability": 65.15923699426604,
   "trueA570": 0.8353949202317659,
   "A570": 0.942
  },
  {
   "well": "A7",
   "row": "A",
   "column": 7,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 4.11522633744856e-07,
   "trueViability": 87.34921380741314,
   "trueA570": 1.0994556443082164,
   "A570": 1.026
  },
  {
   "well": "A8",
   "row": "A",
   "column": 8,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 1.3717421124828532e-07,
   "trueViability": 96.25739286482005,
   "trueA570": 1.2054629750913586,
   "A570": 1.312
  },
  {
   "well": "A9",
   "row": "A",
   "column": 9,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 4.5724737082761776e-08,
   "trueViability": 98.96942792229022,
   "trueA570": 1.2377361922752537,
   "A570": 1.082
  },
  {
   "well": "A10",
   "row": "A",
   "column": 10,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 1.5241579027587257e-08,
   "trueViability": 99.72207630778951,
   "trueA570": 1.246692708062695,
   "A570": 1.333
  },
  {
   "well": "A11",
   "row": "A",
   "column": 11,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 5.080526342529086e-09,
   "trueViability": 99.92547664478384,
   "trueA570": 1.2491131720729278,
   "A570": 1.245
  },
  {
   "well": "A12",
   "row": "A",
   "column": 12,
   "role": "kill",
   "description": "kill control (all cells dead): 0% viability",
   "trueA570": 0.06,
   "A570": 0.06
  },
  {
   "well": "B1",
   "row": "B",
   "column": 1,
   "role": "vehicle",
   "description": "0.5% DMSO vehicle: 100% viability control",
   "trueA570": 1.25,
   "A570": 1.183
  },
  {
   "well": "B2",
   "row": "B",
   "column": 2,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 0.0001,
   "trueViability": 3.879131178157449,
   "trueA570": 0.10616166102007364,
   "A570": 0.099
  },
  {
   "well": "B3",
   "row": "B",
   "column": 3,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 3.3333333333333335e-05,
   "trueViability": 6.205950318507178,
   "trueA570": 0.13385080879023542,
   "A570": 0.135
  },
  {
   "well": "B4",
   "row": "B",
   "column": 4,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 1.1111111111111112e-05,
   "trueViability": 13.987268684056161,
   "trueA570": 0.2264484973402683,
   "A570": 0.208
  },
  {
   "well": "B5",
   "row": "B",
   "column": 5,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 3.7037037037037037e-06,
   "trueViability": 34.34363428120807,
   "trueA570": 0.468689247946376,
   "A570": 0.451
  },
  {
   "well": "B6",
   "row": "B",
   "column": 6,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 1.234567901234568e-06,
   "trueViability": 65.15923699426604,
   "trueA570": 0.8353949202317659,
   "A570": 0.874
  },
  {
   "well": "B7",
   "row": "B",
   "column": 7,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 4.11522633744856e-07,
   "trueViability": 87.34921380741314,
   "trueA570": 1.0994556443082164,
   "A570": 1.05
  },
  {
   "well": "B8",
   "row": "B",
   "column": 8,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 1.3717421124828532e-07,
   "trueViability": 96.25739286482005,
   "trueA570": 1.2054629750913586,
   "A570": 1.24
  },
  {
   "well": "B9",
   "row": "B",
   "column": 9,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 4.5724737082761776e-08,
   "trueViability": 98.96942792229022,
   "trueA570": 1.2377361922752537,
   "A570": 1.209
  },
  {
   "well": "B10",
   "row": "B",
   "column": 10,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 1.5241579027587257e-08,
   "trueViability": 99.72207630778951,
   "trueA570": 1.246692708062695,
   "A570": 1.184
  },
  {
   "well": "B11",
   "row": "B",
   "column": 11,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 5.080526342529086e-09,
   "trueViability": 99.92547664478384,
   "trueA570": 1.2491131720729278,
   "A570": 1.206
  },
  {
   "well": "B12",
   "row": "B",
   "column": 12,
   "role": "kill",
   "description": "kill control (all cells dead): 0% viability",
   "trueA570": 0.06,
   "A570": 0.048
  },
  {
   "well": "C1",
   "row": "C",
   "column": 1,
   "role": "vehicle",
   "description": "0.5% DMSO vehicle: 100% viability control",
   "trueA570": 1.25,
   "A570": 1.277
  },
  {
   "well": "C2",
   "row": "C",
   "column": 2,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 0.0001,
   "trueViability": 3.879131178157449,
   "trueA570": 0.10616166102007364,
   "A570": 0.099
  },
  {
   "well": "C3",
   "row": "C",
   "column": 3,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 3.3333333333333335e-05,
   "trueViability": 6.205950318507178,
   "trueA570": 0.13385080879023542,
   "A570": 0.156
  },
  {
   "well": "C4",
   "row": "C",
   "column": 4,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 1.1111111111111112e-05,
   "trueViability": 13.987268684056161,
   "trueA570": 0.2264484973402683,
   "A570": 0.219
  },
  {
   "well": "C5",
   "row": "C",
   "column": 5,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 3.7037037037037037e-06,
   "trueViability": 34.34363428120807,
   "trueA570": 0.468689247946376,
   "A570": 0.445
  },
  {
   "well": "C6",
   "row": "C",
   "column": 6,
   "role": "sample",
   "compound": "Compound A",
   "concentration_M": 1.234567901234568e-06,
   "trueViability": 65.15923699426604,
   "trueA570": 0.8353949202317659,
   "A570": 0.833
  },
  {
   "well": "C7",
   "row": "C",
   "column": 7,
   "role": "sample",
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   "concentration_M": 4.11522633744856e-07,
   "trueViability": 87.34921380741314,
   "trueA570": 1.0994556443082164,
   "A570": 1.086
  },
  {
   "well": "C8",
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   "role": "sample",
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   "trueViability": 96.25739286482005,
   "trueA570": 1.2054629750913586,
   "A570": 1.111
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  {
   "well": "C9",
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   "role": "sample",
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   "trueViability": 98.96942792229022,
   "trueA570": 1.2377361922752537,
   "A570": 1.268
  },
  {
   "well": "C10",
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   "trueViability": 99.72207630778951,
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   "A570": 1.209
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  {
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   "role": "sample",
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   "trueViability": 99.92547664478384,
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   "A570": 1.206
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  {
   "well": "C12",
   "row": "C",
   "column": 12,
   "role": "kill",
   "description": "kill control (all cells dead): 0% viability",
   "trueA570": 0.06,
   "A570": 0.053
  },
  {
   "well": "D1",
   "row": "D",
   "column": 1,
   "role": "vehicle",
   "description": "0.5% DMSO vehicle: 100% viability control",
   "trueA570": 1.25,
   "A570": 1.298
  },
  {
   "well": "D2",
   "row": "D",
   "column": 2,
   "role": "sample",
   "compound": "Compound B",
   "concentration_M": 0.0001,
   "trueViability": 15.243587332751325,
   "trueA570": 0.24139868925974073,
   "A570": 0.254
  },
  {
   "well": "D3",
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   "role": "sample",
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   "A570": 0.273
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  {
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   "A570": 0.241
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  {
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   "A570": 0.293
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  {
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  {
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  {
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   "A570": 0.799
  },
  {
   "well": "D9",
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   "A570": 0.928
  },
  {
   "well": "D10",
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   "trueViability": 90.37359630970451,
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   "A570": 1.222
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  {
   "well": "D11",
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   "role": "sample",
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   "concentration_M": 5.080526342529086e-09,
   "trueViability": 96.14438063125978,
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  {
   "well": "D12",
   "row": "D",
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   "role": "kill",
   "description": "kill control (all cells dead): 0% viability",
   "trueA570": 0.06,
   "A570": 0.079
  },
  {
   "well": "E1",
   "row": "E",
   "column": 1,
   "role": "vehicle",
   "description": "0.5% DMSO vehicle: 100% viability control",
   "trueA570": 1.25,
   "A570": 1.328
  },
  {
   "well": "E2",
   "row": "E",
   "column": 2,
   "role": "sample",
   "compound": "Compound B",
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   "trueViability": 15.243587332751325,
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   "A570": 0.241
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  {
   "well": "E3",
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   "trueViability": 15.651580698155726,
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   "A570": 0.25
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  {
   "well": "E4",
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   "A570": 0.275
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  {
   "well": "E5",
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   "A570": 0.316
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  {
   "well": "E6",
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   "A570": 0.397
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  {
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   "A570": 0.795
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  {
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   "A570": 1.016
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  {
   "well": "E10",
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   "role": "sample",
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   "role": "vehicle",
   "description": "0.5% DMSO vehicle: 100% viability control",
   "trueA570": 1.25,
   "A570": 1.275
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  {
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  {
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   "role": "sample",
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  },
  {
   "well": "H11",
   "row": "H",
   "column": 11,
   "role": "sample",
   "compound": "Compound C",
   "concentration_M": 5.080526342529086e-09,
   "trueViability": 99.99153317302807,
   "trueA570": 1.249899244759034,
   "A570": 1.307
  },
  {
   "well": "H12",
   "row": "H",
   "column": 12,
   "role": "blank",
   "description": "medium and MTT, no cells",
   "trueA570": 0.045,
   "A570": 0.055
  }
 ],
 "teachingNotes": [
  "Compound A: full curve with both plateaus; relative and absolute IC50 nearly agree.",
  "Compound B: partial inhibition (bottom about 15%): the relative IC50 (parameter) and the absolute IC50 (50% of the controls) differ.",
  "Compound C: the top concentration reaches only about 60% inhibition: no lower plateau, so neither IC50 can be determined from this plate (reference.R applies the rules)."
 ]
}