Location: Andre's Hodgkin Huxley model @ 957c2190e1ee / sed-ml / periodic-stimulus.xml

Author:

David Nickerson <nickerso@users.sourceforge.net>

Date:

2015-05-25 08:31:46+12:00

Desc:

adding a SED-ML document which does nested repeated tasks to iterate over clamp potential and temperature; doesn't work with get-sed-ml-client

Permanent Source URI:

https://models.cellml.org/w/andre/HH/rawfile/957c2190e1eed47d7634613250bc274dc836b826/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"
	xmlns:cellml="http://www.cellml.org/cellml/1.1#">
	<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="../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>
		<report id="report" name="timecourse data">
			<listOfDataSets>
				<dataSet id="col_1" dataReference="dgTime" label="time" />
				<dataSet id="col_2" dataReference="dgVm" label="membrane potential"/>
				<dataSet id="col_3" dataReference="dgINa" label="INa"/>
				<dataSet id="col_4" dataReference="dgIK" label="IK"/>
				<dataSet id="col_5" dataReference="dgIleak" label="Ileak"/>
			</listOfDataSets>
		</report>
		<!-- 
		<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>