Location: VPH-MIP case study on CellML @ bd1651a373bb / sed-ml / periodic-stimulus.xml

Author:

David Nickerson <david.nickerson@gmail.com>

Date:

2019-11-04 22:25:48+09:00

Desc:

adding CellML 2.0 version of this model generated using the CellML1to2 XSL

Permanent Source URI:

https://models.fieldml.org/w/andre/VPH-MIP/rawfile/bd1651a373bbed124d4bd763a86c32c2bf2f3ff0/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/VPH-MIP/rawfile/a631d4cb2c449e107dc53444c9c9c605002d383d/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>
		<dataGenerator id="dgHgate" name="H gate">
			<listOfVariables>
				<variable id="h" taskReference="task1"
					target="/cellml:model/cellml:component[@name='outputs']/cellml:variable[@name='h']" />
			</listOfVariables>
			<math:math>
				<math:ci>h</math:ci>
			</math:math>
		</dataGenerator>
		<dataGenerator id="dgMgate" name="M gate">
			<listOfVariables>
				<variable id="m" taskReference="task1"
					target="/cellml:model/cellml:component[@name='outputs']/cellml:variable[@name='m']" />
			</listOfVariables>
			<math:math>
				<math:ci>m</math:ci>
			</math:math>
		</dataGenerator>
		<dataGenerator id="dgNgate" name="N gate">
			<listOfVariables>
				<variable id="n" taskReference="task1"
					target="/cellml:model/cellml:component[@name='outputs']/cellml:variable[@name='n']" />
			</listOfVariables>
			<math:math>
				<math:ci>n</math:ci>
			</math:math>
		</dataGenerator>
	</listOfDataGenerators>

	<listOfOutputs>
		<plot2D id="plot1" name="Action Potentials">
			<listOfCurves>
				<curve id="c11" logX="false" logY="false" xDataReference="dgTime"
					yDataReference="dgVm" />
			</listOfCurves>
		</plot2D>
		<plot2D id="plot2" name="Membrane currents">
			<listOfCurves>
				<curve id="c21" logX="false" logY="false" xDataReference="dgTime"
					yDataReference="dgINa" />
				<curve id="c22" logX="false" logY="false" xDataReference="dgTime"
					yDataReference="dgIK" />
				<curve id="c23" logX="false" logY="false" xDataReference="dgTime"
					yDataReference="dgIleak" />
			</listOfCurves>
		</plot2D>
		<plot2D id="plot3" name="Gating kinetics">
			<listOfCurves>
				<curve id="c31" logX="false" logY="false" xDataReference="dgTime"
					yDataReference="dgHgate" />
				<curve id="c32" logX="false" logY="false" xDataReference="dgTime"
					yDataReference="dgMgate" />
				<curve id="c33" logX="false" logY="false" xDataReference="dgTime"
					yDataReference="dgNgate" />
			</listOfCurves>
		</plot2D>
	</listOfOutputs>
</sedML>