Location: Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model @ 240f8797a5aa / TNNP-extended / components / INaCa-modifications.xml

Author:
David Nickerson <nickerso@users.sourceforge.net>
Date:
2013-05-04 07:38:15+12:00
Desc:
adding initial raw import of all the models from my 2008 practical application of CellML 1.1 paper.
Permanent Source URI:
https://staging.physiomeproject.org/w/andre/nickerson-2008/rawfile/240f8797a5aa86cc265df8c04d65514de45bfda6/TNNP-extended/components/INaCa-modifications.xml
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<?xml version="1.0" encoding="iso-8859-1"?>

<model
    name="TNNP_extended_INaCa_modifications"
    cmeta:id="TNNP_extended_INaCa_modifications"
    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>2007-06-20</dcterms:W3CDTF>
      </dcterms:created>
      <dc:publisher>
        Division of Bioengineering, National University of Singapore
      </dc:publisher>
    </rdf:Description>
    <rdf:Description rdf:about="#TNNP_extended_INaCa_modifications">
      <dc:title>
        Various modifications for INaCa due to ischemic effects.
      </dc:title>
    </rdf:Description>
  </rdf:RDF>
  
  <import xlink:href="../../../../cellml/models/common/units.xml">
    <units name="mV" units_ref="mV"/>
    <units name="mM" units_ref="mM"/>
    <units name="uA_per_mmsq" units_ref="uA_per_mmsq"/>
  </import>
  
  <component name="pHi" cmeta:id="pHi">
    <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="#pHi">
        <dc:title>
          Doering and Lederer (1993) based formulation of pHi dependence of INaCa.
        </dc:title>
        <cmeta:species>guinea pig</cmeta:species>
        <cmeta:bio_entity>Ventricular Myocyte</cmeta:bio_entity>
        <bqs:reference rdf:parseType="Resource">
          <bqs:Pubmed_id>8410703</bqs:Pubmed_id>
          <bqs:JournalArticle rdf:parseType="Resource">
            <dc:creator>
              <rdf:Seq>
                <rdf:li rdf:parseType="Resource">
                  <bqs:Person rdf:parseType="Resource">
                    <vCard:N rdf:parseType="Resource">
                      <vCard:Family>Doering</vCard:Family>
                      <vCard:Given>A</vCard:Given>
                      <vCard:Other>E</vCard:Other>
                    </vCard:N>
                  </bqs:Person>
                </rdf:li>
                <rdf:li rdf:parseType="Resource">
                  <bqs:Person rdf:parseType="Resource">
                    <vCard:N rdf:parseType="Resource">
                      <vCard:Family>Lederer</vCard:Family>
                      <vCard:Given>W</vCard:Given>
                      <vCard:Other>J</vCard:Other>
                    </vCard:N>
                  </bqs:Person>
                </rdf:li>
              </rdf:Seq>
            </dc:creator> 
            <dc:title>
              The mechanism by which cytoplasmic protons inhibit the sodium&#45;calcium exchanger in guinea&#45;pig heart cells.
            </dc:title>
            <dcterms:issued rdf:parseType="Resource">
              <dcterms:W3CDTF>1993</dcterms:W3CDTF>
            </dcterms:issued>
            <bqs:Journal rdf:parseType="Resource">
              <dc:title>J Physiol</dc:title>
            </bqs:Journal>
            <bqs:volume>466</bqs:volume>
            <bqs:first_page>481</bqs:first_page>
            <bqs:last_page>499</bqs:last_page>
          </bqs:JournalArticle>
        </bqs:reference>
      </rdf:Description>
    </rdf:RDF>
    
    <variable name="relative_conductance" public_interface="out" private_interface="out" units="dimensionless"/>
    <variable name="H_i" public_interface="in" private_interface="out" units="mM"/>
    <variable name="k_half" public_interface="in" private_interface="out" units="mM"/>
    <variable name="H" public_interface="in" private_interface="out" units="dimensionless"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply><eq/>
        <ci>relative_conductance</ci>
        <apply><divide/>
          <cn cellml:units="dimensionless">2.273</cn>
          <apply><plus/>
            <cn cellml:units="dimensionless">1.0</cn>
            <apply><power/>
              <apply><divide/>
                <ci>H_i</ci>
                <ci>k_half</ci>
              </apply>
              <ci>H</ci>
            </apply>
          </apply>
        </apply>
      </apply>
    </math>
  </component>

  <component name="ATPi" cmeta:id="ATPi">
    <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="#ATPi">
        <dc:title>
          Haworth and Goknur (1992) based formulation of [ATP]i dependence of INaCa.
        </dc:title>
        <cmeta:species>rat</cmeta:species>
        <bqs:reference rdf:parseType="Resource">
          <bqs:Pubmed_id>1606663</bqs:Pubmed_id>
          <bqs:JournalArticle rdf:parseType="Resource">
            <dc:creator>
              <rdf:Seq>
                <rdf:li rdf:parseType="Resource">
                  <bqs:Person rdf:parseType="Resource">
                    <vCard:N rdf:parseType="Resource">
                      <vCard:Family>Haworth</vCard:Family>
                      <vCard:Given>R</vCard:Given>
                      <vCard:Other>A</vCard:Other>
                    </vCard:N>
                  </bqs:Person>
                </rdf:li>
                <rdf:li rdf:parseType="Resource">
                  <bqs:Person rdf:parseType="Resource">
                    <vCard:N rdf:parseType="Resource">
                      <vCard:Family>Goknur</vCard:Family>
                      <vCard:Given>A</vCard:Given>
                      <vCard:Other>B</vCard:Other>
                    </vCard:N>
                  </bqs:Person>
                </rdf:li>
              </rdf:Seq>
            </dc:creator> 
            <dc:title>
              ATP dependence of calcium uptake by the Na&#45;Ca exchanger of adult heart cells.
            </dc:title>
            <dcterms:issued rdf:parseType="Resource">
              <dcterms:W3CDTF>1992</dcterms:W3CDTF>
            </dcterms:issued>
            <bqs:Journal rdf:parseType="Resource">
              <dc:title>Circ. Res.</dc:title>
            </bqs:Journal>
            <bqs:volume>71</bqs:volume>
            <bqs:issue>1</bqs:issue>
            <bqs:first_page>210</bqs:first_page>
            <bqs:last_page>217</bqs:last_page>
          </bqs:JournalArticle>
        </bqs:reference>
      </rdf:Description>
    </rdf:RDF>
    
    <variable name="relative_conductance" public_interface="out" private_interface="out" units="dimensionless"/>
    <variable name="ATP_i" public_interface="in" private_interface="out" units="mM"/>
    <variable name="k" public_interface="in" private_interface="out" units="dimensionless"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply><eq/>
        <ci>relative_conductance</ci>
        <apply><divide/>
          <apply><times/>
            <ci>k</ci>
            <ci>ATP_i</ci>
          </apply>
          <apply><plus/>
            <cn cellml:units="mM">150.0</cn>
            <ci>ATP_i</ci>
          </apply>
        </apply>
      </apply>
    </math>
  </component>
  
  <component name="INaCa" cmeta:id="INaCa">
    <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="#INaCa">
        <dc:title>
          Modified INaCa current taking intracellular pH and [ATP]i into account.
        </dc:title>
      </rdf:Description>
    </rdf:RDF>
    
    <variable cmeta:id="conductance_pHi" name="pHi" public_interface="out" private_interface="in" units="dimensionless"/>
    <variable cmeta:id="conductance_ATPi" name="ATPi" public_interface="out" private_interface="in" units="dimensionless"/>
    
    <variable cmeta:id="INaCa" name="INaCa" public_interface="out" units="uA_per_mmsq"/>
    <variable cmeta:id="INaCa_original" name="INaCa_original" public_interface="in" units="uA_per_mmsq"/>
    
    <variable name="H_i" public_interface="in" private_interface="out" units="mM"/>
    <variable name="k_half_pHi" public_interface="in" private_interface="out" units="mM"/>
    <variable name="H_pHi" public_interface="in" private_interface="out" units="dimensionless"/>
    <variable name="ATP_i" public_interface="in" private_interface="out" units="mM"/>
    <variable name="k_ATPi" public_interface="in" private_interface="out" units="dimensionless"/>
    
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="INaCa_eq"><eq/>
        <ci>INaCa</ci>
        <apply><times/>
          <ci>pHi</ci>
          <ci>ATPi</ci>
          <ci>INaCa_original</ci>
        </apply>
      </apply>
    </math>
  </component>
  
  <group>
    <relationship_ref relationship="encapsulation"/>
    <component_ref component="INaCa">
      <component_ref component="pHi"/>
      <component_ref component="ATPi"/>
    </component_ref>
  </group>
  <connection>
    <map_components component_1="INaCa" component_2="pHi"/>
    <map_variables variable_1="pHi" variable_2="relative_conductance"/>
    <map_variables variable_1="H_i" variable_2="H_i"/>
    <map_variables variable_1="k_half_pHi" variable_2="k_half"/>
    <map_variables variable_1="H_pHi" variable_2="H"/>
  </connection>
  <connection>
    <map_components component_1="INaCa" component_2="ATPi"/>
    <map_variables variable_1="ATPi" variable_2="relative_conductance"/>
    <map_variables variable_1="ATP_i" variable_2="ATP_i"/>
    <map_variables variable_1="k_ATPi" variable_2="k"/>
  </connection>
</model>