Location: A review of cardiac cellular electrophysiology models @ 1e62f9a11a1b / tutorial / modified-hh.xml

Author:
David Nickerson <nickerso@users.sourceforge.net>
Date:
2011-06-21 15:56:12+12:00
Desc:
adding a standalone version of the SED-ML document for this example, updating to pass validation using Frank's new web tools
Permanent Source URI:
https://models.physiomeproject.org/workspace/a1/rawfile/1e62f9a11a1b467aff7bc1ddd0b4fc8ac3f052c0/tutorial/modified-hh.xml
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<?xml version="1.0" encoding="iso-8859-1"?>

<model
      name="modified_hh"
      cmeta:id="modified_hh_model"
      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">
  <rdf:RDF
          xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
          xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
          xmlns:bqs="http://www.cellml.org/bqs/1.0#"
          xmlns:dc="http://purl.org/dc/elements/1.1/"
          xmlns:dcterms="http://purl.org/dc/terms/"
          xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
    <rdf:Description rdf:about="">
      <dc:creator rdf:parseType="Resource">
        <vCard:N rdf:parseType="Resource">
          <vCard:Family>Nickerson</vCard:Family>
          <vCard:Given>David</vCard:Given>
        </vCard:N>
        <vCard:EMAIL rdf:parseType="Resource">
          <rdf:value>d.nickerson@auckland.ac.nz</rdf:value>
          <rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
        </vCard:EMAIL>
        <vCard:ORG rdf:parseType="Resource">
          <vCard:Orgname>The University of Auckland</vCard:Orgname>
          <vCard:Orgunit>Auckland Bioengineering Institute</vCard:Orgunit>
        </vCard:ORG>
      </dc:creator>
      <dcterms:created rdf:parseType="Resource">
        <dcterms:W3CDTF>2009-07-07</dcterms:W3CDTF>
      </dcterms:created>
      <dc:publisher>
        Auckland Bioengineering Institute, The University of Auckland.
      </dc:publisher>
    </rdf:Description>
    <rdf:Description rdf:about="#modified_HH_model">
      <dc:title>
        Modified version of HH model with an applied period stimulus current.
      </dc:title>
      <cmeta:comment rdf:parseType="Resource">
        <rdf:value>
          This is a modified version of the HH model from http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/components/stimulated.xml. The modification is to replace the potassium current model with a description based on the Noble 1962 model.
        </rdf:value>
        <dc:creator rdf:parseType="Resource">
          <vCard:FN>David Nickerson</vCard:FN>
        </dc:creator>
      </cmeta:comment>
    </rdf:Description>
  </rdf:RDF>
  <import xlink:href="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/components/units.xml">
    <units name="mV" units_ref="mV"/>
    <units name="ms" units_ref="ms"/>
    <units name="K" units_ref="K"/>
    <units name="uA_per_cmsq" units_ref="uA_per_cmsq"/>
    <units name="mS_per_cmsq" units_ref="mS_per_cmsq"/>
    <units name="uF_per_cmsq" units_ref="uF_per_cmsq"/>
  </import>
  <import xlink:href="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/components/INa.xml">
    <component name="INa" component_ref="INa"/>
  </import>
  <import xlink:href="IK.xml">
    <component name="IK" component_ref="IK"/>
  </import>
  <import xlink:href="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/components/Ileak.xml">
    <component name="Ileak" component_ref="Ileak"/>
  </import>
  <component name="action_potential" cmeta:id="action_potential">
    <rdf:RDF
            xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
            xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
            xmlns:dc="http://purl.org/dc/elements/1.1/">
      <rdf:Description rdf:about="#action_potential">
        <dc:title>
          Hodgkin &amp; Huxley with applied electrical stimulus.
        </dc:title>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The Hodgkin &amp; Huxley (1952) model assembled such that given an electrical stimulus current it will simulate action potential transients.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
    </rdf:RDF>
    <variable cmeta:id="V_initial" name="V_initial" public_interface="in"
              private_interface="out" units="mV"/>
    <variable cmeta:id="n_initial" name="n_initial" public_interface="in"
              private_interface="out" units="dimensionless"/>
    <variable cmeta:id="m_initial" name="m_initial" public_interface="in"
              private_interface="out" units="dimensionless"/>
    <variable cmeta:id="h_initial" name="h_initial" public_interface="in"
              private_interface="out" units="dimensionless"/>
    <variable cmeta:id="Istim" name="Istim" public_interface="in"
              private_interface="out" units="uA_per_cmsq"/>
    <variable cmeta:id="INa" name="INa" public_interface="out"
              private_interface="in" units="uA_per_cmsq"/>
    <variable cmeta:id="IK" name="IK" public_interface="out"
              private_interface="in" units="uA_per_cmsq"/>
    <variable cmeta:id="Ileak" name="Ileak" public_interface="out"
              private_interface="in" units="uA_per_cmsq"/>
    <variable cmeta:id="V" name="V" public_interface="out"
              private_interface="out" units="mV" initial_value="V_initial"/>
    <variable cmeta:id="minus_V" name="minus_V" public_interface="out"
              private_interface="out" units="mV"/>
    <variable cmeta:id="VNa" name="VNa" public_interface="in"
              private_interface="out" units="mV"/>
    <variable cmeta:id="VK" name="VK" public_interface="in"
              private_interface="out" units="mV"/>
    <variable cmeta:id="Vleak" name="Vleak" public_interface="in"
              private_interface="out" units="mV"/>
    <variable cmeta:id="gNa_max" name="gNa_max" public_interface="in"
              private_interface="out" units="mS_per_cmsq"/>
    <variable cmeta:id="gK_max" name="gK_max" public_interface="in"
              private_interface="out" units="mS_per_cmsq"/>
    <variable cmeta:id="gleak_max" name="gleak_max" public_interface="in"
              private_interface="out" units="mS_per_cmsq"/>
    <variable cmeta:id="Cm" name="Cm" public_interface="in"
              private_interface="out" units="uF_per_cmsq"/>
    <variable cmeta:id="Tref_rates" name="Tref_rates" public_interface="in"
              private_interface="out" units="K"/>
    <variable cmeta:id="T" name="T" public_interface="in"
              private_interface="out" units="K"/>
    <variable cmeta:id="Q10_rates" name="Q10_rates" public_interface="in"
              private_interface="out" units="dimensionless" />
    <variable cmeta:id="time" name="time" public_interface="in"
              private_interface="out" units="ms" />
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="V_calculation"><eq/>
        <apply><diff/>
          <bvar><ci>time</ci></bvar>
          <ci>V</ci>
        </apply>
        <apply><divide/>
          <apply><minus/>
            <ci>Istim</ci>
            <apply><plus />
              <ci>INa</ci>
              <ci>IK</ci>
              <ci>Ileak</ci>
            </apply>
          </apply>
          <ci>Cm</ci>
        </apply>
      </apply>
    </math>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="minus_V_calculation"><eq/>
        <ci>minus_V</ci>
        <apply><minus/>
          <ci>V</ci>
        </apply>
      </apply>
    </math>
  </component>
  <group>
    <relationship_ref relationship="encapsulation"/>
    <component_ref component="action_potential">
      <component_ref component="INa"/>
      <component_ref component="IK"/>
      <component_ref component="Ileak"/>
    </component_ref>
  </group>
  <connection>
    <map_components component_1="action_potential" component_2="INa"/>
    <map_variables variable_1="INa" variable_2="INa"/>
    <map_variables variable_1="m_initial" variable_2="m_initial"/>
    <map_variables variable_1="h_initial" variable_2="h_initial"/>
    <map_variables variable_1="time" variable_2="time"/>
    <map_variables variable_1="Tref_rates" variable_2="Tref"/>
    <map_variables variable_1="T" variable_2="T"/>
    <map_variables variable_1="Q10_rates" variable_2="Q10"/>
    <map_variables variable_1="V" variable_2="V"/>
    <map_variables variable_1="VNa" variable_2="VNa"/>
    <map_variables variable_1="gNa_max" variable_2="gNa_max"/>
  </connection>
  <connection>
    <map_components component_1="action_potential" component_2="IK"/>
    <map_variables variable_1="IK" variable_2="IK"/>
    <map_variables variable_1="n_initial" variable_2="n_initial"/>
    <map_variables variable_1="time" variable_2="time"/>
    <map_variables variable_1="Tref_rates" variable_2="Tref"/>
    <map_variables variable_1="T" variable_2="T"/>
    <map_variables variable_1="Q10_rates" variable_2="Q10"/>
    <map_variables variable_1="V" variable_2="V"/>
    <map_variables variable_1="VK" variable_2="VK"/>
    <map_variables variable_1="gK_max" variable_2="gK_max"/>
  </connection>
  <connection>
    <map_components component_1="action_potential" component_2="Ileak"/>
    <map_variables variable_1="Ileak" variable_2="Ileak"/>
    <map_variables variable_1="V" variable_2="V"/>
    <map_variables variable_1="Vleak" variable_2="Vleak"/>
    <map_variables variable_1="gleak_max" variable_2="gleak_max"/>
  </connection>
</model>