- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2012-09-26 15:20:08+12:00
- Desc:
- adding a bit more to the tutorial regarding instantiation in a simulation experiment. Adding a basic SED-ML for the action potential simulation and images of the results calculated using the SED-ML web tools.
- Permanent Source URI:
- https://models.fieldml.org/w/andre/VPH-MIP/rawfile/8ab1ec7d863da476b8ab55a47eac203ade558a60/sed-ml/periodic-stimulus.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="20"
numberOfPoints="250">
<algorithm kisaoID="KISAO:0000019" />
</uniformTimeCourse>
</listOfSimulations>
<listOfModels>
<model id="model1" name="periodic_stimulus" language="urn:sedml:language:cellml"
source="http://models.cellml.org/w/andre/HH/rawfile/954c3ffaada1883360c21e49fe10878db10cad81/experiments/periodic-stimulus.xml" />
</listOfModels>
<listOfTasks>
<task id="task1" name="ActionPotentials" modelReference="model1"
simulationReference="simulation1" />
</listOfTasks>
<listOfDataGenerators>
<dataGenerator id="dgTime" name="Time">
<listOfVariables>
<variable id="time" taskReference="task1"
target="/cellml:model/cellml:component[@name='time']/cellml:variable[@name='time']" />
</listOfVariables>
<math:math>
<math:ci>time</math:ci>
</math:math>
</dataGenerator>
<dataGenerator id="dgVm" name="Membrane potential">
<listOfVariables>
<variable id="Vm" taskReference="task1"
target="/cellml:model/cellml:component[@name='outputs']/cellml:variable[@name='minus_V']" />
</listOfVariables>
<math:math>
<math:ci>Vm</math:ci>
</math:math>
</dataGenerator>
<dataGenerator id="dgINa" name="Sodium current">
<listOfVariables>
<variable id="INa" taskReference="task1"
target="/cellml:model/cellml:component[@name='outputs']/cellml:variable[@name='INa']" />
</listOfVariables>
<math:math>
<math:ci>INa</math:ci>
</math:math>
</dataGenerator>
<dataGenerator id="dgIK" name="Potassium current">
<listOfVariables>
<variable id="IK" taskReference="task1"
target="/cellml:model/cellml:component[@name='outputs']/cellml:variable[@name='IK']" />
</listOfVariables>
<math:math>
<math:ci>IK</math:ci>
</math:math>
</dataGenerator>
<dataGenerator id="dgIleak" name="Leakage current">
<listOfVariables>
<variable id="Ileak" taskReference="task1"
target="/cellml:model/cellml:component[@name='outputs']/cellml:variable[@name='Ileak']" />
</listOfVariables>
<math:math>
<math:ci>Ileak</math:ci>
</math:math>
</dataGenerator>
</listOfDataGenerators>
<listOfOutputs>
<plot2D id="plot1" name="Action Potentials">
<listOfCurves>
<curve id="c1" logX="false" logY="false" xDataReference="dgTime"
yDataReference="dgVm" />
</listOfCurves>
</plot2D>
<plot2D id="plot2" name="Membrane currents">
<listOfCurves>
<curve id="c2" logX="false" logY="false" xDataReference="dgTime"
yDataReference="dgINa" />
<curve id="c3" logX="false" logY="false" xDataReference="dgTime"
yDataReference="dgIK" />
<curve id="c4" logX="false" logY="false" xDataReference="dgTime"
yDataReference="dgIleak" />
</listOfCurves>
</plot2D>
</listOfOutputs>
</sedML>
