- Author:
- Jonathan Cooper <jonathan.cooper@cs.ox.ac.uk>
- Date:
- 2012-09-05 09:18:42+01:00
- Desc:
- Add some unit test style simulations of a very simple single ODE model, in
order to check that implementations are processing the proposed extension
elements as expected.
- Permanent Source URI:
- https://models.fieldml.org/w/andre/testing-Sed-ML-nesting/rawfile/0382d975a69edd8a34c13bbb8b57e47d6856f285/nestedTask-cellType-stimulusTime.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="cellTypeTask" master="true"
modelReference="model1" simulationReference="simulation1"
resetModel="true">
<ranges>
<vectorRange id="cellTypeRange">
<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="cellTypeValue" name="current loop value"
target="#cellTypeRange"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci>cellTypeValue</ci>
</math>
</setValue>
</changes>
<listOfSubTasks>
<subTask order="1" task="stimulusTimeTask"/>
</listOfSubTasks>
</repeatedTask>
<repeatedTask id="stimulusTimeTask" master="true"
modelReference="model1" simulationReference="simulation1"
resetModel="true">
<ranges>
<uniformRange id="stimulusStartRange" start="10" end="400" numberOfPoints="10" />
</ranges>
<changes>
<setValue target="/cellml:model/cellml:component[@name='membrane']/cellml:variable[@name='stimStart']/@initial_value">
<listOfVariables>
<variable id="stimulusStartValue" name="current loop value"
target="#stimulusStartRange"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci>stimulusStartValue</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>
