Location: Some test SED-ML to play with the nested proposal @ 0b3ce74c3413 / nest-scan.xml

Author:

David Nickerson <nickerso@users.sourceforge.net>

Date:

2012-05-24 17:22:03+02:00

Desc:

adding a second example using the ORd electrophysiology model with nested repeat tasks which now iterate over each of the three supported cell types and apply the stimulus current at multiple times.

Permanent Source URI:

http://models.cellml.org/w/andre/testing-Sed-ML-nesting/rawfile/0b3ce74c3413037b50b32f6ce8a80d9ba9472662/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>