data/pythonCopasiOpt/vcell-opt/test_data/optproblem.json

{
  "copasiOptimizationMethod": {
    "optimizationMethodType": "evolutionaryProgram",
    "optimizationParameter": [
      {
        "dataType": "int",
        "paramType": "numberOfGenerations",
        "value": 200.0
      },
      {
        "dataType": "int",
        "paramType": "populationSize",
        "value": 20.0
      },
      {
        "dataType": "int",
        "paramType": "randomNumberGenerator",
        "value": 1.0
      },
      {
        "dataType": "int",
        "paramType": "seed",
        "value": 3.0
      }
    ]
  },
  "dataSet": [
    [
      0.0,
      4.0
    ],
    [
      1.6535399245133132E-4,
      3.9995453382905546
    ],
    [
      6.276635144329321E-4,
      3.998274743619277
    ],
    [
      0.0034306276215528586,
      3.990590010029197
    ],
    [
      0.00930981017033542,
      3.9745759499569466
    ],
    [
      0.021379458033809823,
      3.942139223285978
    ],
    [
      0.041873558753016286,
      3.8883895570062883
    ],
    [
      0.07015716884832657,
      3.816872546080026
    ],
    [
      0.12746580885899947,
      3.680942136818943
    ],
    [
      0.18695226617648983,
      3.5516767175235633
    ],
    [
      0.26645702476153477,
      3.3959732254044463
    ],
    [
      0.35022514860447995,
      3.2508185754735517
    ],
    [
      0.44678336822112563,
      3.104634800348445
    ],
    [
      0.5798008594989622,
      2.9349739439153484
    ],
    [
      0.7130335067221049,
      2.7957984782266956
    ],
    [
      0.8462661539452475,
      2.681834033949502
    ],
    [
      0.9794988011683902,
      2.588513744615282
    ],
    [
      1.1127314483915325,
      2.5120980127515082
    ],
    [
      1.2459640956146747,
      2.449524652625187
    ],
    [
      1.379196742837817,
      2.398286179857271
    ],
    [
      1.5124293900609591,
      2.356329329749134
    ],
    [
      1.6456620372841013,
      2.3219727774172454
    ],
    [
      1.7788946845072435,
      2.293839762543596
    ],
    [
      1.9121273317303857,
      2.270802918851185
    ],
    [
      2.0,
      2.257942965982347
    ]
  ],
  "mathModelSbmlContents": "<?xml version='1.0' encoding='UTF-8' standalone='no'?>\n<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" level=\"2\" version=\"4\">\n  <model id=\"MathModel_NoName\">\n    <listOfCompartments>\n      <compartment id=\"compartment\"/>\n    </listOfCompartments>\n    <listOfParameters>\n      <parameter constant=\"true\" id=\"_F_\" value=\"9.64853321E4\"/>\n      <parameter constant=\"true\" id=\"_F_nmol_\" value=\"9.64853321E-5\"/>\n      <parameter constant=\"true\" id=\"_K_GHK_\" value=\"1E-9\"/>\n      <parameter constant=\"true\" id=\"_N_pmol_\" value=\"6.02214179E11\"/>\n      <parameter constant=\"true\" id=\"_PI_\" value=\"3.141592653589793\"/>\n      <parameter constant=\"true\" id=\"_R_\" value=\"8314.46261815\"/>\n      <parameter constant=\"true\" id=\"_T_\" value=\"300\"/>\n      <parameter constant=\"true\" id=\"K_millivolts_per_volt\" value=\"1000\"/>\n      <parameter constant=\"true\" id=\"Kf\" value=\"1\"/>\n      <parameter constant=\"true\" id=\"KMOLE\" value=\"0.001660538783162726\"/>\n      <parameter constant=\"true\" id=\"Kr\" value=\"2\"/>\n      <parameter constant=\"true\" id=\"s0_init_uM\" value=\"5\"/>\n      <parameter constant=\"true\" id=\"s1_init_uM\" value=\"4\"/>\n      <parameter constant=\"true\" id=\"Size_c0\" value=\"50000\"/>\n      <parameter constant=\"false\" id=\"J_r0\"/>\n      <parameter constant=\"false\" id=\"s0\"/>\n      <parameter constant=\"false\" id=\"s1\"/>\n    </listOfParameters>\n    <listOfInitialAssignments>\n      <initialAssignment id=\"ID_2\" symbol=\"s0\">\n        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">        \n          <ci> s0_init_uM </ci>\n        </math>\n            </initialAssignment>\n      <initialAssignment id=\"ID_3\" symbol=\"s1\">\n        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">        \n          <ci> s1_init_uM </ci>\n        </math>\n            </initialAssignment>\n    </listOfInitialAssignments>\n    <listOfRules>\n      <assignmentRule id=\"ID_1\" variable=\"J_r0\">\n        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">        \n          <apply>\n            <plus/>\n            <apply>\n              <times/>\n              <ci> Kf </ci>\n              <ci> s0 </ci>\n            </apply>\n            <apply>\n              <minus/>\n              <apply>\n                <times/>\n                <ci> Kr </ci>\n                <ci> s1 </ci>\n              </apply>\n            </apply>\n          </apply>\n        </math>\n            </assignmentRule>\n      <rateRule variable=\"s0\">\n        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">        \n          <apply>\n            <minus/>\n            <ci> J_r0 </ci>\n          </apply>\n        </math>\n            </rateRule>\n      <rateRule variable=\"s1\">\n        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">        \n          <ci> J_r0 </ci>\n        </math>\n            </rateRule>\n    </listOfRules>\n  </model>\n</sbml>",
  "numberOfOptimizationRuns": 1,
  "parameterDescriptionList": [
    {
      "initialValue": 0.2,
      "maxValue": 10.0,
      "minValue": 0.1,
      "name": "Kf",
      "scale": 0.2
    },
    {
      "initialValue": 0.3,
      "maxValue": 20.0,
      "minValue": 0.2,
      "name": "Kr",
      "scale": 0.3
    },
    {
      "initialValue": 2.0,
      "maxValue": 20.0,
      "minValue": 1.0E-8,
      "name": "s0_init_uM",
      "scale": 2.0
    }
  ],
  "referenceVariable": [
    {
      "referenceVariableType": "independent",
      "varName": "t"
    },
    {
      "referenceVariableType": "dependent",
      "varName": "s1"
    }
  ]
}