Location: VPH-MIP case study on CellML @ a29bfba242e7 / components / default-variable-values.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/default-variable-values.xml
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<?xml version="1.0" encoding="iso-8859-1"?>

<model
      name="variable_values_model"
      cmeta:id="variable_values_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="#variable_values_model">
      <dc:title>
        Default parameter values and initial conditions.
      </dc:title>
      <cmeta:comment rdf:parseType="Resource">
        <rdf:value>
          Default parameter values and initial conditions for the Hodgkin &amp; Huxley (1952) squid axon 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="units.xml">
    <units name="K" units_ref="K"/>
    <units name="ms" units_ref="ms"/>
    <units name="mV" units_ref="mV"/>
    <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>
  <component name="parameters" cmeta:id="parameters_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="#parameters_component">
        <dc:title>
          Hodgkin &amp; Huxley default parameters.
        </dc:title>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Here we define the complete set of default parameter values.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
    </rdf:RDF>
    <variable cmeta:id="Tref_rates" name="Tref_rates" public_interface="out"
              private_interface="out" units="K" initial_value="279.45"/>
    <variable cmeta:id="T" name="T" public_interface="out"
              private_interface="out" units="K" initial_value="279.45"/>
    <variable cmeta:id="Q10_rates" name="Q10_rates" public_interface="out"
              private_interface="out" units="dimensionless" initial_value="3.0"/>
    <variable cmeta:id="VK" name="VK" public_interface="out"
              private_interface="out" units="mV" initial_value="12.0"/>
    <variable cmeta:id="VNa" name="VNa" public_interface="out"
              private_interface="out" units="mV" initial_value="-115.0"/>
    <variable cmeta:id="Vleak" name="Vleak" public_interface="out"
              private_interface="out" units="mV" initial_value="-10.613"/>
    <variable cmeta:id="gK_max" name="gK_max" public_interface="out"
              private_interface="out" units="mS_per_cmsq" initial_value="36.0"/>
    <variable cmeta:id="gNa_max" name="gNa_max" public_interface="out"
              private_interface="out" units="mS_per_cmsq" initial_value="120.0"/>
    <variable cmeta:id="gleak_max" name="gleak_max" public_interface="out"
              private_interface="out" units="mS_per_cmsq" initial_value="0.3"/>
    <variable cmeta:id="Cm" name="Cm" public_interface="out" 
              private_interface="out" units="uF_per_cmsq" initial_value="1.0"/>
  </component>
  <component name="initial_conditions" cmeta:id="initial_conditions_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="#initial_conditions_component">
        <dc:title>
          Hodgkin &amp; Huxley default initial conditions.
        </dc:title>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Here we define the complete set set of default initial conditions for the model's differental variables.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
    </rdf:RDF>
    <variable cmeta:id="V_initial" name="V_initial" public_interface="out"
              private_interface="out" units="mV" initial_value="0.0"/>
    <variable cmeta:id="n_initial" name="n_initial" public_interface="out"
              private_interface="out" units="dimensionless"
              initial_value="0.315"/>
    <variable cmeta:id="m_initial" name="m_initial" public_interface="out"
              private_interface="out" units="dimensionless"
              initial_value="0.042"/>
    <variable cmeta:id="h_initial" name="h_initial" public_interface="out"
              private_interface="out" units="dimensionless"
              initial_value="0.608"/>
  </component>
</model>