Location: Some test SED-ML to play with the nested proposal @ 9def2d7f03b8 / ORd-cell-types-timecourse.xml

Author:
David Nickerson <nickerso@users.sourceforge.net>
Date:
2015-05-25 08:28:39+12:00
Desc:
also need to update the CellML namespace
Permanent Source URI:
https://models.physiomeproject.org/w/andre/testing-Sed-ML-nesting/rawfile/9def2d7f03b8cd9a7b2471dba578106687bf5faf/ORd-cell-types-timecourse.xml

<?xml version="1.0" encoding="utf-8"?>
<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:math="http://www.w3.org/1998/Math/MathML"
	level="1" version="2"
	xmlns:cellml="http://www.cellml.org/cellml/1.1#">
	<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="Ohara_Rudy_2011.cellml" />
	</listOfModels>

	<listOfTasks>
		<task id="task0" modelReference="model1" simulationReference="simulation1" />
		<repeatedTask id="task1" resetModel="true" range="current">
			<listOfRanges>
				<vectorRange id="current">
					<value>0</value> <!-- endocardial cell type -->
					<value>1</value> <!-- mid-myocardial cell type -->
					<value>2</value> <!-- epicardial cell type -->
				</vectorRange>
				<uniformRange id="testUniform" start="0" end="10" numberOfPoints="100" type="linear"/>
			</listOfRanges>
			<listOfChanges>
				<setValue
					target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='celltype']"
					range="current" modelReference="model1">
					<math xmlns="http://www.w3.org/1998/Math/MathML">
						<ci>current</ci>
					</math>
				</setValue>
			</listOfChanges>
			<listOfSubTasks>
				<subTask order="1" task="task0" />
			</listOfSubTasks>
		</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>
		
		<dataGenerator id="CellType" name="Cell Type">
			<listOfVariables>
				<variable id="ct" taskReference="task1"
					target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='celltype']" />
			</listOfVariables>
			<math:math>
				<math:ci>v</math:ci>
			</math:math>
		</dataGenerator>
	</listOfDataGenerators>

	<listOfOutputs>
		<report id="report" name="timecourse data">
			<listOfDataSets>
				<dataSet id="col_1" dataReference="time" label="time" />
				<dataSet id="col_2" dataReference="Vm" label="membrane potential"/>
				<dataSet id="col_3" dataReference="CellType" label="cell type"/>
			</listOfDataSets>
		</report>
		<!--
		<plot2D id="plot1" name="Action Potential">
			<listOfCurves>
				<curve id="c1" logX="false" logY="false" xDataReference="time"
					yDataReference="Vm" />
			</listOfCurves>
		</plot2D>
		-->
	</listOfOutputs>
</sedML>