Location: Some test SED-ML to play with the nested proposal @ cbb19e3cc4cc / nestedTask-cellType-ORd.xml

Author:

David Nickerson <nickerso@users.sourceforge.net>

Date:

2012-05-25 14:11:05+02:00

Desc:

adding initial SED-ML describing the nested tasks from nestedTask-cellType-ORd.xml as three separate tasks with three different CellML models. Runs in SED-ML Web Tools to produce the expected action potentials.

Permanent Source URI:

https://models.fieldml.org/w/andre/testing-Sed-ML-nesting/rawfile/cbb19e3cc4ccd3e9ee72b4d7f51b13f77f8e8f61/nestedTask-cellType-ORd.xml

<?xml version="1.0" encoding="utf-8"?>
<sedML  xmlns="http://sed-ml.org/" 
       xmlns:math="http://www.w3.org/1998/Math/MathML" level="1" version="1">
 <listOfSimulations>
   <uniformTimeCourse id="simulation1" 
    initialTime="0" outputStartTime="0" outputEndTime="1000" 
    numberOfPoints="2000" >
     <algorithm kisaoID="KISAO:0000019"/>
    </uniformTimeCourse>
 </listOfSimulations>
 <listOfModels>
  <model id="model1" name="ORd" language="urn:sedml:language:cellml" source="http://models.cellml.org/w/andre/SAN-ORd/@@rawfile/3f84a54207ab2f29b4a29639f17a34a29353e002/Ohara_Rudy_2011.cellml"/>
 </listOfModels>
 
    <listOfTasks>
        <repeatedTask id="scanTask" master="true"
            modelReference="model1" simulationReference="simulation1"
            resetModel="true">
            <ranges>
                <vectorRange id="current">
                    <value>0</value> <!-- endocardial cell type -->
                    <value>1</value> <!-- mid-myocardial cell type -->
                    <value>2</value> <!-- epicardial cell type -->
                </vectorRange>
            </ranges>
            <changes>
                <setValue target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='celltype']/@initial_value">
                    <listOfVariables>
                        <variable id="loopValue" name="current loop value"
                        target="#current"/>
                    </listOfVariables>
                    <math xmlns="http://www.w3.org/1998/Math/MathML">
                        <ci>loopValue</ci>
                    </math>
                </setValue>
            </changes>
        </repeatedTask>
  </listOfTasks>
  <listOfDataGenerators>
    <dataGenerator id="time" name="time">
      <listOfVariables>
        <variable id="t" taskReference="task1" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" />
      </listOfVariables>
      <math:math>
        <math:ci>t</math:ci>
      </math:math>
    </dataGenerator>
    
    <dataGenerator id="Vm" name="Membrane Potential">
      <listOfVariables>
        <variable id="v" taskReference="task1" target="/cellml:model/cellml:component[@name='membrane']/cellml:variable[@name='v']" />
      </listOfVariables>
      <math:math>
        <math:ci>v</math:ci>
      </math:math>
    </dataGenerator>
  </listOfDataGenerators>
  
  <listOfOutputs>
    <plot2D id="plot1" name="Action Potential">
      <listOfCurves>
        <curve id="c1" logX="false" logY="false" xDataReference="time" yDataReference="Vm" />
      </listOfCurves>
    </plot2D>
  </listOfOutputs>
</sedML>