{
 "about": {
  "what": "Runs of the hosts model's equations (the module docstring of reference.py states them) solved by an independent solver, for src/lib/hosts and src/lib/fit/ode.ts to agree with.",
  "oracle": "scipy.integrate.solve_ivp, method Radau (implicit Runge-Kutta, order 5) with a central-difference Jacobian, piecewise between time events and the state events where growth switches or the feed reaches its volume limit (located by solve_ivp's event finder), dense output sampled at the output times",
  "rtol": 1e-09,
  "atol": "per run, in each scenario's atol: a hundredth (1e-9 ÷ 1e-7) of the engine's rule, min(fixed, ceiling), with the CSO's ceilings (Q2) computed here from the run's own parameters; the rule is restated in reference.py, no code is shared",
  "dissolvedOxygen": "each scenario names its model: dynamic (dissolved oxygen as its own differential equation; the app's only model, the CSO's Q1 as amended) or quasi-steady (Brent's method on the oxygen balance with the exhaust gas coupled; the cross-check). The oxygen-limited runs are solved both ways",
  "outputTimes": "every half hour, and 1, 2, 3 and 5 time constants (1/kLa) after each time event (the run's start, the feed starting, reaching the pump's limit, the cap and stopping, aeration steps, chemostat steps)",
  "units": {
   "t": "h",
   "X": "g/L",
   "S": "g/L",
   "P": "g/L",
   "V": "L",
   "DO": "mg/L",
   "Cstar": "mg/L",
   "mu": "1/h",
   "F": "L/h",
   "OUR": "mmol/L/h",
   "OTR": "mmol/L/h",
   "CER": "mmol/L/h",
   "yO2out": "mole fraction, dry",
   "kLa": "1/h"
  },
  "triggers": "where each trigger is on, found on a 0.01 h scan of the dense output and refined by Brent's method, with jumps where the aeration steps counted at the step (the CSO's third addendum): oxygen (oxygen-supply@1), while the O2 the culture would take up at its substrate with oxygen in excess exceeds kLa·C* at C = 0 (C* from the exhaust gas at the culture's CO2 production); respiratory (respiratory-limit@1), while qS/qS,max is at or above 0.95; overflow (overflow@1), while qS is at or above the scenario's qSCrit (none without one)",
  "slopes": "d/dt of each series at each output point, for the time-shift allowance at fronts (the CSO's third addendum): the states from the right-hand side, the rest by differences of the dense output inside the point's piece",
  "events": "oxygenOut: the start of the first oxygen interval (0 when it holds from the start; the headline 'oxygen runs out'); doBelowOnePercent: the first time dissolved oxygen falls below 1 percent of air saturation; switches: the times growth switched off or on (regimes: G growing, P product only, M maintenance only)",
  "resolvedFeed": "F0 and Fcap as resolved (designed from the state at the feed's start and the cap's time where the scenario leaves them out: [((1 + α)·μ + β)/Y + ms]·X·V/(Sf − S)); stoppedAt where the volume reached Vmax",
  "balances": "at the horizon: |in − (in the broth + out)| / in for carbon (CO2 and washout counted, the product counted as biomass) and for electrons (4 per O2 taken up)",
  "excursions": "for every trigger, excursions separated by gaps shorter than 0.05 h are merged, then excursions shorter than 0.05 h are dropped (the CSO's second addendum), as in the engine",
  "tolerances": "the engine's state variables within 0.5 percent of each series' peak at every output time (brief §4.3); quasi-steady against dynamic within 2 percent of peak where OUR is below the transfer capacity, oxygen-out times within 0.01 h; switch, trigger and event times within 1e-3 h at the engine's shipped rtol; balances within 0.5 percent (the engine reaches far less)",
  "testSets": "FAST_GLUCOSE, FAST_GLUCOSE_TINY_KS, SLOW_GLUCOSE_PRODUCT and METHANOL_HALDANE in reference.py are stated solver test inputs, named by what they test; they are not the app's presets and describe no organism. Some runs lie outside every preset's valid range on purpose (for example batch growth on 20 g/L glucose)",
  "publishedRuns": "the scenarios whose ids start with preset- are the app's published runs, their inputs read from preset-specs.json (written by export-presets.mts from the presets; inputs only, including the rescue's steps as the engine chose them), solved here the same way as the test scenarios",
  "model": "hosts-model-2",
  "versions": {
   "python": "3.12.14",
   "scipy": "1.17.0",
   "numpy": "2.3.5"
  },
  "recordedOn": "2026-10-07",
  "script": "pipeline/bioreactor-simulator/reference.py"
 },
 "scenarios": [
  {
   "id": "batch-monod",
   "description": "Batch Monod growth on glucose at 37 °C, oxygen not limiting; an overflow onset of 0.8 g/g/h watched",
   "mode": "batch",
   "kinetics": {
    "muMax": 0.61,
    "Ks": 0.05,
    "Ki": null,
    "Yxs": 0.42,
    "ms": 0.067,
    "Ko": 0.1,
    "substrate": "glucose",
    "biomassCarbon": 0.4738,
    "biomassGamma": 4.169999999999999,
    "alpha": 0.0,
    "beta": 0.0
   },
   "initial": {
    "X": 0.1,
    "S": 10.0,
    "V": 6.0
   },
   "oxygen": {
    "model": "dynamic",
    "kLa": 2500.0,
    "temperature": 37.0,
    "pressure": 1.01325,
    "yO2": 0.2095,
    "vvm": 1.0
   },
   "horizon": 12.0,
   "biology": {
    "qSCrit": 0.8
   },
   "atol": [
    1e-10,
    1e-11,
    1e-10,
    6e-11,
    1e-09,
    1e-12,
    1e-12,
    1e-10,
    1e-12,
    1e-12
   ],
   "rtol": 1e-09,
   "outputs": {
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