Location: VPH-MIP case study on CellML @ a29bfba242e7 / components / IK-gating-rates.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/IK-gating-rates.xml

<?xml version="1.0" encoding="iso-8859-1"?>

<model
      name="IK_gating_rates"
      cmeta:id="IK_gating_rates_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>2008-08-11</dcterms:W3CDTF>
      </dcterms:created>
      <dc:publisher>
        Division of Bioengineering, National University of Singapore
      </dc:publisher>
    </rdf:Description>
    <rdf:Description rdf:about="#IK_gating_rates_model">
      <dc:title>
        Hodgkin-Huxley potassium current gating rates.
      </dc:title>
      <cmeta:comment rdf:parseType="Resource">
        <rdf:value>
          A CellML description of the gating rates for the Hodgkin &amp; Huxley potassium current, IK.
        </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="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>
  <component name="alpha_n" cmeta:id="alpha_n_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="#alpha_n_component">
        <dc:title>
          Description of the activation rate constant for the n gate.
        </dc:title>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            A description of the voltage-dependent activation rate constant for the n gate of the Hodgkin &amp; Huxley (1952) potassium current.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#alpha_n">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The temperature corrected activation rate constant of the n gate for the potassium current.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#alpha_n_base">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The base (non-temperature corrected) value of the activation rate constant for the n gate of the potassium current.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#alpha_n_Q10">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The Q10 for the temperature dependence of the activation rate constant of the n gate of the potassium current.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#alpha_n_T">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The actual temperature at which the activation rate constant for the n gate of the potassium current is desired.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#alpha_n_Tref">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The reference temperature to use for the Q10 temperature correction of the activation rate constant for the n gate of the potassium current.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#alpha_n_V">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The membrane potential value at which the activation rate constant for the n gate of the potassium current is desired.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#alpha_n_base_calculation">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Represents equation 12 of the Hodgkin &amp; Huxley (1952) model. Calculates the non-temperature corrected value of the activation rate constant for the n gate of the potassium current for a specified value of membrane potential.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#alpha_n_calculation">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Represents the temperature correction of equation 12 of the Hodgkin &amp; Huxley (1952) model used to calculate the activation rate constant for the n gate of the potassium current for a specified value of membrane potential at a given temperature.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
    </rdf:RDF>
    <variable cmeta:id="alpha_n" name="alpha" public_interface="out"
              private_interface="out" units="per_ms"/>
    <variable cmeta:id="alpha_n_base" name="alpha_base" public_interface="out"
              private_interface="out" units="per_ms"/>
    <variable cmeta:id="alpha_n_Q10" name="Q10" public_interface="in"
              private_interface="out" units="dimensionless"/>
    <variable cmeta:id="alpha_n_T" name="T" public_interface="in"
              private_interface="out" units="K"/>
    <variable cmeta:id="alpha_n_Tref" name="Tref" public_interface="in"
              private_interface="out" units="K"/>
    <variable cmeta:id="alpha_n_V" name="V" public_interface="in"
              private_interface="out" units="mV"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="alpha_n_base_calculation"><eq/>
        <ci>alpha_base</ci>
        <apply><divide/>
          <apply><times/>
            <cn cellml:units="per_ms_mV">0.01</cn>
            <apply><plus/>
              <ci>V</ci>
              <cn cellml:units="mV">10.0</cn>
            </apply>
          </apply>
          <apply><minus/>
            <apply><exp/>
              <apply><divide/>
                <apply><plus/>
                  <ci>V</ci>
                  <cn cellml:units="mV">10.0</cn>
                </apply>
                <cn cellml:units="mV">10.0</cn>
              </apply>
            </apply>
            <cn cellml:units="dimensionless">1.0</cn>
          </apply>
        </apply>
      </apply>
    </math>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="alpha_n_calculation"><eq/>
        <ci>alpha</ci>
        <apply><times/>
          <apply><power/>
            <ci>Q10</ci>
            <apply><divide/>
              <apply><minus/>
                <ci>T</ci>
                <ci>Tref</ci>
              </apply>
              <cn cellml:units="K">10.0</cn>
            </apply>
          </apply>
          <ci>alpha_base</ci>
        </apply>
      </apply>
    </math>
  </component>
  <component name="beta_n" cmeta:id="beta_n_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="#beta_n_component">
        <dc:title>
          Description of the inactivation rate constant for the n gate.
        </dc:title>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            A description of the voltage-dependent inactivation rate constant for the n gate of the Hodgkin &amp; Huxley (1952) potassium current.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#beta_n">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The temperature corrected inactivation rate constant of the n gate for the potassium current.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#beta_n_base">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The base (non-temperature corrected) value of the inactivation rate constant for the n gate of the potassium current.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#beta_n_Q10">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The Q10 for the temperature dependence of the inactivation rate constant of the n gate for the potassium current.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#beta_n_T">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The actual temperature at which the inactivation rate constant for the n gate of the potassium current is desired.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#beta_n_Tref">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The reference temperature to use for the Q10 temperature correction of the inactivation rate constant for the n gate of the potassium current.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#beta_n_V">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The membrane potential value at which the inactivation rate constant for the n gate of the potassium current is desired.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#beta_n_base_calculation">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Represents equation 13 of the Hodgkin &amp; Huxley (1952) model. Calculates the non-temperature corrected value of the inactivation rate constant for the n gate of the potassium current for a specified value of membrane potential.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#beta_n_calculation">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Represents the temperature correction of equation 13 of the Hodgkin &amp; Huxley (1952) model used to calculate the inactivation rate constant for the n gate of the potassium current for a specified value of membrane potential at a given temperature.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
    </rdf:RDF>
    <variable cmeta:id="beta_n" name="beta" public_interface="out"
              private_interface="out" units="per_ms"/>
    <variable cmeta:id="beta_n_base" name="beta_base" public_interface="out"
              private_interface="out" units="per_ms"/>
    <variable cmeta:id="beta_n_Q10" name="Q10" public_interface="in"
              private_interface="out" units="dimensionless"/>
    <variable cmeta:id="beta_n_T" name="T" public_interface="in"
              private_interface="out" units="K"/>
    <variable cmeta:id="beta_n_Tref" name="Tref" public_interface="in"
              private_interface="out" units="K"/>
    <variable cmeta:id="beta_n_V" name="V" public_interface="in"
              private_interface="out" units="mV"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="beta_n_base_calculation"><eq/>
        <ci>beta_base</ci>
        <apply><times/>
          <cn cellml:units="per_ms">0.125</cn>
          <apply><exp/>
            <apply><divide/>
              <ci>V</ci>
              <cn cellml:units="mV">80.0</cn>
            </apply>
          </apply>
        </apply>
      </apply>
    </math>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="beta_n_calculation"><eq/>
        <ci>beta</ci>
        <apply><times/>
          <apply><power/>
            <ci>Q10</ci>
            <apply><divide/>
              <apply><minus/>
                <ci>T</ci>
                <ci>Tref</ci>
              </apply>
              <cn cellml:units="K">10.0</cn>
            </apply>
          </apply>
          <ci>beta_base</ci>
        </apply>
      </apply>
    </math>
  </component>
</model>