Location: A review of cardiac cellular electrophysiology models @ c47db6b2fedb / models / 1961_fitzhugh / experiments / single-stimulus.xml

Author:
David Nickerson <david.nickerson@gmail.com>
Date:
2021-09-17 15:39:51+12:00
Desc:
tweak html formatting
Permanent Source URI:
https://models.fieldml.org/workspace/a1/rawfile/c47db6b2fedb368422c7f4d5191aeb9f319ad684/models/1961_fitzhugh/experiments/single-stimulus.xml
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<?xml version='1.0' encoding='UTF-8'?>
<model cmeta:id="single_stimulus" name="single_stimulus" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink">
    <import xlink:href="../../common/units.xml">
        <units name="ms" units_ref="ms"/>
        <units name="mV" units_ref="mV"/>
        <units name="per_mm" units_ref="per_mm"/>
        <units name="uA_per_mmcu" units_ref="uA_per_mmcu"/>
    </import>
    <import xlink:href="../model.xml">
        <component component_ref="interface" name="math_model"/>
        <units name="uApmmsq" units_ref="uApmmsq"/>
    </import>
    <component cmeta:id="time_component" name="time">
        <variable cmeta:id="time" initial_value="0.0" name="time" public_interface="out" units="ms"/>
    </component>
    <connection>
        <map_components component_1="math_model" component_2="time"/>
        <map_variables variable_1="t" variable_2="time"/>
    </connection>
    <import xlink:href="../../protocols/single-pulse-IStim.xml">
        <component component_ref="stimulus_protocol" name="stimulus_protocol"/>
    </import>
    <component cmeta:id="stimulus_parameters" name="stimulus_parameters">
        <variable initial_value="100" name="stimTime" public_interface="out" units="ms"/>
        <variable initial_value="0.5" name="stimDuration" public_interface="out" units="ms"/>
        <variable initial_value="400" name="stimCurrent" public_interface="out" units="uA_per_mmcu"/>
        <variable initial_value="200" name="Am" public_interface="out" units="per_mm"/>
    </component>
    <connection>
        <map_components component_1="math_model" component_2="stimulus_protocol"/>
        <map_variables variable_1="Istim" variable_2="IStim"/>
    </connection>
    <connection>
        <map_components component_1="time" component_2="stimulus_protocol"/>
        <map_variables variable_1="time" variable_2="time"/>
    </connection>
    <connection>
        <map_components component_1="stimulus_parameters" component_2="stimulus_protocol"/>
        <map_variables variable_1="stimTime" variable_2="stimTime"/>
        <map_variables variable_1="stimDuration" variable_2="stimDuration"/>
        <map_variables variable_1="stimCurrent" variable_2="stimCurrent"/>
        <map_variables variable_1="Am" variable_2="Am"/>
    </connection>
    <component cmeta:id="output_variables" name="output_variables">
        <variable name="Vm" public_interface="in" units="mV"/>
        <variable name="v" public_interface="in" units="dimensionless"/>
        <variable name="Iion" public_interface="in" units="uApmmsq"/>
    </component>
    <connection>
        <map_components component_1="math_model" component_2="output_variables"/>
        <map_variables variable_1="Vm" variable_2="Vm"/>
        <map_variables variable_1="v" variable_2="v"/>
        <map_variables variable_1="Iion" variable_2="Iion"/>
    </connection>
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="">
            <dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                    <vCard:Family xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Nickerson</vCard:Family>
                    <vCard:Given xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">David</vCard:Given>
                </vCard:N>
                <vCard:EMAIL xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                    <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">d.nickerson@auckland.ac.nz</rdf:value>
                    <rdf:type xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:resource="http://imc.org/vCard/3.0#internet"/>
                </vCard:EMAIL>
                <vCard:ORG xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                    <vCard:Orgname xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">The University of Auckland</vCard:Orgname>
                    <vCard:Orgunit xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Bioengineering Institute</vCard:Orgunit>
                </vCard:ORG>
            </dc:creator>
            <dcterms:created xmlns:dcterms="http://purl.org/dc/terms/" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <dcterms:W3CDTF xmlns:dcterms="http://purl.org/dc/terms/">2009-06-16</dcterms:W3CDTF>
            </dcterms:created>
            <dc:publisher xmlns:dc="http://purl.org/dc/elements/1.1/">
        Bioengineering Institute, The University of Auckland
      </dc:publisher>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#single_stimulus">
            <dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">
        Action potential simulation with single stimulus.
      </dc:title>
            <cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
          This is the CellML description of a action potential simulation
          with a single stimulus current applied to the default FHN model.
        </rdf:value>
                <dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                    <vCard:FN xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">David Nickerson</vCard:FN>
                </dc:creator>
            </cmeta:comment>
            <cs:simulation xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:ID="simulation">
                    <cs:multistepMethod xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">bdf</cs:multistepMethod>
                    <cs:iterationMethod xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">functional</cs:iterationMethod>
                    <cs:boundIntervals xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:parseType="Collection" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                            <cs:boundVariable xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">
                                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#time"/>
                            </cs:boundVariable>
                            <cs:maximumStepSize xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                0.1
              </cs:maximumStepSize>
                            <cs:tabulationStepSize xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                1.0
              </cs:tabulationStepSize>
                            <cs:startingValue xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                0
              </cs:startingValue>
                            <cs:endingValue xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                800
              </cs:endingValue>
                        </rdf:Description>
                    </cs:boundIntervals>
                </rdf:Description>
            </cs:simulation>
        </rdf:Description>
    </rdf:RDF>
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#time_component">
            <cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">&#xd;
            The actual definition of the time variable.&#xd;
          </rdf:value>
            </cmeta:comment>
        </rdf:Description>
    </rdf:RDF>
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#stimulus_parameters">
            <cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">&#xd;
            Here we define the parameters for the standard stimulus protocol we import for this experiment.&#xd;
          </rdf:value>
            </cmeta:comment>
        </rdf:Description>
    </rdf:RDF>
</model>