Location: VPH-MIP case study on CellML @ a29bfba242e7 / components / INa.xml

Author:
David Nickerson <nickerso@users.sourceforge.net>
Date:
2012-08-28 16:59:24+12:00
Desc:
replacing CellML simulation metadata with CSim summary description; bubbling up membrane currents and potential to allow output/referencing via SED-ML.
Permanent Source URI:
http://models.cellml.org/w/andre/VPH-MIP/rawfile/a29bfba242e747b82657c6d2d782937d0a01be79/components/INa.xml
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<?xml version="1.0" encoding="iso-8859-1"?>

<model
      name="INa"
      cmeta:id="INa_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>david.nickerson@nus.edu.sg</rdf:value>
          <rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
        </vCard:EMAIL>
        <vCard:ORG rdf:parseType="Resource">
          <vCard:Orgname>National University of Singapore</vCard:Orgname>
          <vCard:Orgunit>Division of Bioengineering</vCard:Orgunit>
        </vCard:ORG>
      </dc:creator>
      <dcterms:created rdf:parseType="Resource">
        <dcterms:W3CDTF>2008-03-12</dcterms:W3CDTF>
      </dcterms:created>
      <dc:publisher>
        Division of Bioengineering, National University of Singapore
      </dc:publisher>
    </rdf:Description>
    <rdf:Description rdf:about="#INa_model">
      <dc:title>
        Hodgkin-Huxley sodium current.
      </dc:title>
      <cmeta:comment rdf:parseType="Resource">
        <rdf:value>
          A CellML description of the Hodgkin &amp; Huxley sodium current, INa.
        </rdf:value>
        <dc:creator rdf:parseType="Resource">
          <vCard:FN>David Nickerson</vCard:FN>
        </dc:creator>
      </cmeta:comment>
    </rdf:Description>
    <rdf:Description rdf:about="#m_gate">
      <dc:title>
        Hodgkin-Huxley sodium current's activation gate.
      </dc:title>
      <dcterms:abstract rdf:parseType="Resource">
        <rdf:value>
          We import the standard HH voltage-dependent gating variable description to use as the sodium channel's activation gating variable - 'm'.
        </rdf:value>
      </dcterms:abstract>
    </rdf:Description>
    <rdf:Description rdf:about="#h_gate">
      <dc:title>
        Hodgkin-Huxley sodium current's inactivation gate.
      </dc:title>
      <dcterms:abstract rdf:parseType="Resource">
        <rdf:value>
        We import the standard HH voltage-dependent gating variable description to use as the sodium channel's inactivation gating variable - 'h'.
        </rdf:value>
      </dcterms:abstract>
      <cmeta:modification rdf:parseType="Resource">
        <rdf:value>
          Splitting out the gating rate equation components to their own model to test out a possible bug in the API implementation which arises when importing encapsulated children directly into other models.
        </rdf:value>
        <cmeta:modifier rdf:parseType="Resource">
          <vCard:FN>David Nickerson</vCard:FN>
        </cmeta:modifier>
        <dcterms:modified rdf:parseType="Resource">
          <dcterms:W3CDTF>2008-08-11</dcterms:W3CDTF>
        </dcterms:modified>
      </cmeta:modification>
    </rdf:Description>
  </rdf:RDF>
  <import xlink:href="units.xml">
    <units name="K" units_ref="K"/>
    <units name="ms" units_ref="ms"/>
    <units name="mV" units_ref="mV"/>
    <units name="per_ms" units_ref="per_ms"/>
    <units name="per_ms_mV" units_ref="per_ms_mV"/>
    <units name="uA_per_cmsq" units_ref="uA_per_cmsq"/>
    <units name="mS_per_cmsq" units_ref="mS_per_cmsq"/>
  </import>
  <import xlink:href="gating-variable.xml">
    <component cmeta:id="m_gate" name="m_gate" component_ref="hh_gating_variable_dynamic"/>
  </import>
  <import xlink:href="gating-variable.xml">
    <component cmeta:id="h_gate" name="h_gate" component_ref="hh_gating_variable_dynamic"/>
  </import>
  <import xlink:href="INa-gating-rates.xml">
    <component cmeta:id="alpha_m" name="alpha_m" component_ref="alpha_m"/>
    <component cmeta:id="beta_m" name="beta_m" component_ref="beta_m"/>
    <component cmeta:id="alpha_h" name="alpha_h" component_ref="alpha_h"/>
    <component cmeta:id="beta_h" name="beta_h" component_ref="beta_h"/>
  </import>
  <component name="INa" cmeta:id="INa_component">
    <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="#INa_component">
        <dc:title>
          Hodgkin &amp; Huxley sodium current.
        </dc:title>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            A description of the membrane sodium current of the Hodgkin &amp; Huxley (1952) model.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#INa_calculation">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Represents equation 3 of the Hodgkin &amp; Huxley (1952) model used to calculate the sodium current for a specified value of membrane potential at a given temperature.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
    </rdf:RDF>
    <variable cmeta:id="INa" name="INa" public_interface="out"
              private_interface="out" units="uA_per_cmsq"/>
    <variable cmeta:id="m_initial" name="m_initial" public_interface="in"
              private_interface="out" units="dimensionless"/>
    <variable cmeta:id="m" name="m" public_interface="out" private_interface="in"
              units="dimensionless"/>
    <variable cmeta:id="h_initial" name="h_initial" public_interface="in"
              private_interface="out" units="dimensionless"/>
    <variable cmeta:id="h" name="h" public_interface="out" private_interface="in"
              units="dimensionless"/>
    <variable cmeta:id="time" name="time" public_interface="in" 
              private_interface="out" units="ms"/>
    <variable cmeta:id="Tref" name="Tref" 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" name="Q10" public_interface="in"
              private_interface="out" units="dimensionless"/>
    <variable cmeta:id="V" name="V" public_interface="in"
              private_interface="out" units="mV"/>
    <variable cmeta:id="VNa" name="VNa" public_interface="in"
              private_interface="out" units="mV"/>
    <variable cmeta:id="gNa" name="gNa" public_interface="out"
              private_interface="out" units="mS_per_cmsq"/>
    <variable cmeta:id="gNa_max" name="gNa_max" public_interface="in"
              private_interface="out" units="mS_per_cmsq"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="INa_calculation"><eq/>
        <ci>INa</ci>
        <apply><times/>
          <ci>gNa</ci>
          <apply><minus/>
            <ci>V</ci>
            <ci>VNa</ci>
          </apply>
        </apply>
      </apply>
    </math>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="gNa_calculation"><eq/>
        <ci>gNa</ci>
        <apply><times/>
          <ci>gNa_max</ci>
          <apply><power/>
            <ci>m</ci>
            <cn cellml:units="dimensionless">3.0</cn>
          </apply>
          <ci>h</ci>
        </apply>
      </apply>
    </math>
  </component>
  <group>
    <relationship_ref relationship="encapsulation"/>
    <component_ref component="INa">
      <component_ref component="alpha_m"/>
      <component_ref component="beta_m"/>
      <component_ref component="alpha_h"/>
      <component_ref component="beta_h"/>
      <component_ref component="m_gate"/>
      <component_ref component="h_gate"/>
    </component_ref>
  </group>
  <connection>
    <map_components component_1="INa" component_2="m_gate"/>
    <map_variables variable_1="time" variable_2="time"/>
    <map_variables variable_1="m_initial" variable_2="gate_initial"/>
    <map_variables variable_1="m" variable_2="gate"/>
  </connection>
  <connection>
    <map_components component_1="INa" component_2="h_gate"/>
    <map_variables variable_1="time" variable_2="time"/>
    <map_variables variable_1="h_initial" variable_2="gate_initial"/>
    <map_variables variable_1="h" variable_2="gate"/>
  </connection>
  <connection>
    <map_components component_1="INa" component_2="alpha_m"/>
    <map_variables variable_1="Q10" variable_2="Q10"/>
    <map_variables variable_1="T" variable_2="T"/>
    <map_variables variable_1="Tref" variable_2="Tref"/>
    <map_variables variable_1="V" variable_2="V"/>
  </connection>
  <connection>
    <map_components component_1="INa" component_2="beta_m"/>
    <map_variables variable_1="Q10" variable_2="Q10"/>
    <map_variables variable_1="T" variable_2="T"/>
    <map_variables variable_1="Tref" variable_2="Tref"/>
    <map_variables variable_1="V" variable_2="V"/>
  </connection>
  <connection>
    <map_components component_1="INa" component_2="alpha_h"/>
    <map_variables variable_1="Q10" variable_2="Q10"/>
    <map_variables variable_1="T" variable_2="T"/>
    <map_variables variable_1="Tref" variable_2="Tref"/>
    <map_variables variable_1="V" variable_2="V"/>
  </connection>
  <connection>
    <map_components component_1="INa" component_2="beta_h"/>
    <map_variables variable_1="Q10" variable_2="Q10"/>
    <map_variables variable_1="T" variable_2="T"/>
    <map_variables variable_1="Tref" variable_2="Tref"/>
    <map_variables variable_1="V" variable_2="V"/>
  </connection>
  <connection>
    <map_components component_1="m_gate" component_2="alpha_m"/>
    <map_variables variable_1="alpha" variable_2="alpha"/>
  </connection>
  <connection>
    <map_components component_1="m_gate" component_2="beta_m"/>
    <map_variables variable_1="beta" variable_2="beta"/>
  </connection>
  <connection>
    <map_components component_1="h_gate" component_2="alpha_h"/>
    <map_variables variable_1="alpha" variable_2="alpha"/>
  </connection>
  <connection>
    <map_components component_1="h_gate" component_2="beta_h"/>
    <map_variables variable_1="beta" variable_2="beta"/>
  </connection>
</model>