Location: Some test SED-ML to play with the nested proposal @ d83657a1d7c4 / nest-scan.xml

Author:

David Nickerson <nickerso@users.sourceforge.net>

Date:

2012-05-25 14:21:39+02:00

Desc:

adding the different model configurations to duplicate the nested repeated tasks in nestedTask-cellType-stimulusTime-ORd, at least for a couple of steps in the inner sub task.

Permanent Source URI:

https://models.fieldml.org/w/andre/testing-Sed-ML-nesting/rawfile/d83657a1d7c40bdd9c6a7f8c2352f17f855f2919/nest-scan.xml

<?xml version="1.0" encoding="utf-8"?>
<!-- Written by libSedML v1.1.4397.34340 see http://libsedml.sf.net -->
<sedML level="1" version="1" xmlns="http://sed-ml.org/">
  <listOfSimulations>
    <oneStep id="steady1">
      <algorithm kisaoID="KISAO:0000282" />
    </oneStep>
    <nestedSimulation id="nested1" resetModel="false" originalTask="task3" range="current">
      <ranges>
        <vectorRange id="current">
          <value>1</value>
          <value>5</value>
          <value>10</value>
          <value>50</value>
          <value>60</value>
          <value>70</value>
          <value>80</value>
          <value>90</value>
          <value>100</value>
        </vectorRange>
      </ranges>
      <changes>
        <setValue target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='J1_KK2']">
          <listOfVariables>
            <variable id="val" name="current loop value" target="//*[@id='current']" />
          </listOfVariables>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <ci> val </ci>
          </math>
        </setValue>
      </changes>
    </nestedSimulation>
    <nestedSimulation id="nested2" resetModel="false" originalTask="task2" range="current1">
      <ranges>
        <uniformRange id="current1" start="1" end="40" numberOfPoints="100" />
      </ranges>
      <changes>
        <setValue target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='J4_KK5']" range="current1">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <ci> current1 </ci>
          </math>
        </setValue>
      </changes>
    </nestedSimulation>
  </listOfSimulations>
  <listOfModels>
    <model id="model1" language="urn:sedml:language:sbml" source="model1.xml" />
  </listOfModels>
  <listOfTasks>
    <task id="task1" modelReference="model1" simulationReference="nested1" />
    <task id="task2" modelReference="model1" simulationReference="steady1" />
    <task id="task3" modelReference="model1" simulationReference="nested2" />
  </listOfTasks>
  <listOfDataGenerators>
    <dataGenerator id="J4_KK5_1" name="J4_KK5">
      <listOfVariables>
        <variable id="J4_KK5" name="J4_KK5" taskReference="task1" target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='J4_KK5']" />
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> J4_KK5 </ci>
      </math>
    </dataGenerator>
    <dataGenerator id="J1_KK2_1" name="J1_KK2">
      <listOfVariables>
        <variable id="J1_KK2" name="J1_KK2" taskReference="task1" target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='J1_KK2']" />
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> J1_KK2 </ci>
      </math>
    </dataGenerator>
    <dataGenerator id="MKK_1" name="MKK">
      <listOfVariables>
        <variable id="MKK" name="MKK" taskReference="task1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='MKK']" />
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> MKK </ci>
      </math>
    </dataGenerator>
    <dataGenerator id="MKK_P_1" name="MKK_P">
      <listOfVariables>
        <variable id="MKK_P" name="MKK_P" taskReference="task1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='MKK_P']" />
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> MKK_P </ci>
      </math>
    </dataGenerator>
  </listOfDataGenerators>
  <listOfOutputs>
    <plot2D id="plot1" name="Steady State Scan (Boris 2D)">
      <listOfCurves>
        <curve id="curve1" logX="false" logY="false" xDataReference="J4_KK5_1" yDataReference="MKK_1" />
        <curve id="curve2" logX="false" logY="false" xDataReference="J4_KK5_1" yDataReference="MKK_P_1" />
      </listOfCurves>
    </plot2D>
    <report id="report1" name="Steady State Values (Boris2D)">
      <listOfDataSets>
        <dataSet id="col0" dataReference="J4_KK5_1" label="" />
        <dataSet id="col1" dataReference="J1_KK2_1" label="" />
        <dataSet id="col2" dataReference="MKK_1" label="" />
        <dataSet id="col3" dataReference="MKK_P_1" label="" />
      </listOfDataSets>
    </report>
  </listOfOutputs>
</sedML>