Location: Hodgkin & Huxley (1952) model @ c56e1d025518 / sed-ml / periodic-stimulus.xml

Author:

WeiweiAi <wai484@aucklanduni.ac.nz>

Date:

2021-04-28 18:15:33+12:00

Desc:

Change the unit of T from celsius to kelvin to in line with CellML2.0 spec (but the real temperature unit is still celsius, no need to do conversion when setting the temperature parameter for simulation)

Permanent Source URI:

https://staging.physiomeproject.org/workspace/64f/rawfile/c56e1d0255183a1d725eec025cbe79eeee2c8087/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>