Location: Models for the OpenCOR and PMR tutorial by Peter Hunter @ e3ef4cf57b9b / sodium_ion_channel.sedml

Author:
David Nickerson <nickerso@users.sourceforge.net>
Date:
2017-09-13 14:24:42+12:00
Desc:
update Noble 62 SED-ML to match changes in the CellML
Permanent Source URI:
https://models.physiomeproject.org/workspace/25d/rawfile/e3ef4cf57b9be0b9f5ccb72e98dac46f2381add5/sodium_ion_channel.sedml

<?xml version='1.0' encoding='UTF-8'?>
<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
    <listOfSimulations>
        <uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="400" outputEndTime="40" outputStartTime="0">
            <algorithm kisaoID="KISAO:0000019">
                <listOfAlgorithmParameters>
                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
                    <algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
                    <algorithmParameter kisaoID="KISAO:0000481" value="true"/>
                    <algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
                    <algorithmParameter kisaoID="KISAO:0000477" value="Dense"/>
                    <algorithmParameter kisaoID="KISAO:0000480" value="0"/>
                    <algorithmParameter kisaoID="KISAO:0000415" value="500"/>
                    <algorithmParameter kisaoID="KISAO:0000467" value="0.01"/>
                    <algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
                    <algorithmParameter kisaoID="KISAO:0000479" value="0"/>
                </listOfAlgorithmParameters>
            </algorithm>
        </uniformTimeCourse>
    </listOfSimulations>
    <listOfModels>
        <model id="model" language="urn:sedml:language:cellml.1_0" source="sodium_ion_channel.cellml"/>
    </listOfModels>
    <listOfTasks>
        <repeatedTask id="repeatedTask" range="once" resetModel="true">
            <listOfRanges>
                <vectorRange id="once">
                    <value> 1 </value>
                </vectorRange>
            </listOfRanges>
            <listOfSubTasks>
                <subTask order="1" task="task1"/>
            </listOfSubTasks>
        </repeatedTask>
        <task id="task1" modelReference="model" simulationReference="simulation1"/>
    </listOfTasks>
    <listOfDataGenerators>
        <dataGenerator id="xDataGenerator1_1">
            <listOfVariables>
                <variable id="xVariable1_1" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='t']" taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci> xVariable1_1 </ci>
            </math>
        </dataGenerator>
        <dataGenerator id="yDataGenerator1_1">
            <listOfVariables>
                <variable id="yVariable1_1" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='V']" taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci> yVariable1_1 </ci>
            </math>
        </dataGenerator>
        <dataGenerator id="xDataGenerator2_1">
            <listOfVariables>
                <variable id="xVariable2_1" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='t']" taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci> xVariable2_1 </ci>
            </math>
        </dataGenerator>
        <dataGenerator id="yDataGenerator2_1">
            <listOfVariables>
                <variable id="yVariable2_1" target="/cellml:model/cellml:component[@name='sodium_channel_m_gate']/cellml:variable[@name='m']" taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci> yVariable2_1 </ci>
            </math>
        </dataGenerator>
        <dataGenerator id="xDataGenerator3_1">
            <listOfVariables>
                <variable id="xVariable3_1" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='t']" taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci> xVariable3_1 </ci>
            </math>
        </dataGenerator>
        <dataGenerator id="yDataGenerator3_1">
            <listOfVariables>
                <variable id="yVariable3_1" target="/cellml:model/cellml:component[@name='sodium_channel_h_gate']/cellml:variable[@name='h']" taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci> yVariable3_1 </ci>
            </math>
        </dataGenerator>
        <dataGenerator id="xDataGenerator4_1">
            <listOfVariables>
                <variable id="xVariable4_1" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='t']" taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci> xVariable4_1 </ci>
            </math>
        </dataGenerator>
        <dataGenerator id="yDataGenerator4_1">
            <listOfVariables>
                <variable id="yVariable4_1" target="/cellml:model/cellml:component[@name='sodium_channel']/cellml:variable[@name='Na_conductance']" taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci> yVariable4_1 </ci>
            </math>
        </dataGenerator>
        <dataGenerator id="xDataGenerator5_1">
            <listOfVariables>
                <variable id="xVariable5_1" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='t']" taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci> xVariable5_1 </ci>
            </math>
        </dataGenerator>
        <dataGenerator id="yDataGenerator5_1">
            <listOfVariables>
                <variable id="yVariable5_1" target="/cellml:model/cellml:component[@name='sodium_channel']/cellml:variable[@name='i_Na']" taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci> yVariable5_1 </ci>
            </math>
        </dataGenerator>
    </listOfDataGenerators>
    <listOfOutputs>
        <plot2D id="plot1">
            <listOfCurves>
                <curve id="curve1_1" logX="false" logY="false" xDataReference="xDataGenerator1_1" yDataReference="yDataGenerator1_1"/>
            </listOfCurves>
        </plot2D>
        <plot2D id="plot2">
            <listOfCurves>
                <curve id="curve2_1" logX="false" logY="false" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1"/>
            </listOfCurves>
        </plot2D>
        <plot2D id="plot3">
            <listOfCurves>
                <curve id="curve3_1" logX="false" logY="false" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1"/>
            </listOfCurves>
        </plot2D>
        <plot2D id="plot4">
            <listOfCurves>
                <curve id="curve4_1" logX="false" logY="false" xDataReference="xDataGenerator4_1" yDataReference="yDataGenerator4_1"/>
            </listOfCurves>
        </plot2D>
        <plot2D id="plot5">
            <listOfCurves>
                <curve id="curve5_1" logX="false" logY="false" xDataReference="xDataGenerator5_1" yDataReference="yDataGenerator5_1"/>
            </listOfCurves>
        </plot2D>
    </listOfOutputs>
</sedML>