Location: Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model @ d6328d18c94e / TNNP-extended / components / ICaL-modifications.xml

Author:
David Nickerson <nickerso@users.sourceforge.net>
Date:
2013-05-04 07:40:04+12:00
Desc:
adding initial TODO list to keep track of what I need to do to get things working with more recent tools than my original CellMLSimulator that I used in this paper
Permanent Source URI:
https://staging.physiomeproject.org/w/andre/nickerson-2008/rawfile/d6328d18c94e9dad70f4d0e4b250e89429773b62/TNNP-extended/components/ICaL-modifications.xml
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<?xml version="1.0" encoding="iso-8859-1"?>

<model
    name="TNNP_extended_ICaL_modifications"
    cmeta:id="TNNP_extended_ICaL_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>2007-06-13</dcterms:W3CDTF>
      </dcterms:created>
      <dc:publisher>
        Division of Bioengineering, National University of Singapore
      </dc:publisher>
    </rdf:Description>
    <rdf:Description rdf:about="#TNNP_extended_ICaL_modifications">
      <dc:title>
        Various modifications for ICaL 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="pHo" cmeta:id="pHo">
    <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="#pHo">
        <dc:title>
          Irisawa and Sato (1986) formulation of pHo dependence of ICaL.
        </dc:title>
        <cmeta:species>guinea pig</cmeta:species>
        <cmeta:bio_entity>Ventricular Myocyte</cmeta:bio_entity>
        <bqs:reference rdf:parseType="Resource">
          <bqs:Pubmed_id>2429781</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>Irisawa</vCard:Family>
                      <vCard:Given>H</vCard:Given>
                    </vCard:N>
                  </bqs:Person>
                </rdf:li>
                <rdf:li rdf:parseType="Resource">
                  <bqs:Person rdf:parseType="Resource">
                    <vCard:N rdf:parseType="Resource">
                      <vCard:Family>Sato</vCard:Family>
                      <vCard:Given>R</vCard:Given>
                    </vCard:N>
                  </bqs:Person>
                </rdf:li>
              </rdf:Seq>
            </dc:creator>
            <dc:title>
              Intra- and extracellular actions of proton on the calcium current of isolated guinea pig ventricular cells.
            </dc:title>
            <dcterms:issued rdf:parseType="Resource">
              <dcterms:W3CDTF>1986</dcterms:W3CDTF>
            </dcterms:issued>
            <bqs:Journal rdf:parseType="Resource">
              <dc:title>Circ Res</dc:title>
            </bqs:Journal>
            <bqs:volume>59</bqs:volume>
            <bqs:first_page>348</bqs:first_page>
            <bqs:last_page>355</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_o" public_interface="in" private_interface="out" units="mM"/>
    <variable name="k_half" public_interface="in" private_interface="out" units="mM"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply><eq/>
        <ci>relative_conductance</ci>
        <apply><divide/>
          <cn cellml:units="dimensionless">1.0</cn>
          <apply><plus/>
            <cn cellml:units="dimensionless">1.0</cn>
            <apply><divide/>
              <ci>H_o</ci>
              <ci>k_half</ci>
            </apply>
          </apply>
        </apply>
      </apply>
    </math>
  </component>

  <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>
          Kaibara and Kameyama (1988) formulation of pHi dependence of ICaL.
        </dc:title>
        <cmeta:species>guinea pig</cmeta:species>
        <cmeta:bio_entity>Ventricular Myocyte</cmeta:bio_entity>
        <bqs:reference rdf:parseType="Resource">
          <bqs:Pubmed_id>2855346</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>Kaibara</vCard:Family>
                      <vCard:Given>M</vCard:Given>
                    </vCard:N>
                  </bqs:Person>
                </rdf:li>
                <rdf:li rdf:parseType="Resource">
                  <bqs:Person rdf:parseType="Resource">
                    <vCard:N rdf:parseType="Resource">
                      <vCard:Family>Kameyama</vCard:Family>
                      <vCard:Given>M</vCard:Given>
                    </vCard:N>
                  </bqs:Person>
                </rdf:li>
              </rdf:Seq>
            </dc:creator> 
            <dc:title>
              Inhibition of the calcium channel by intracellular protons in single ventricular myocytes of the guinea&#45;pig.
            </dc:title>
            <dcterms:issued rdf:parseType="Resource">
              <dcterms:W3CDTF>1988</dcterms:W3CDTF>
            </dcterms:issued>
            <bqs:Journal rdf:parseType="Resource">
              <dc:title>J Physiol</dc:title>
            </bqs:Journal>
            <bqs:volume>403</bqs:volume>
            <bqs:first_page>621</bqs:first_page>
            <bqs:last_page>640</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"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply><eq/>
        <ci>relative_conductance</ci>
        <apply><divide/>
          <cn cellml:units="dimensionless">1.2381</cn>
          <apply><plus/>
            <cn cellml:units="dimensionless">1.0</cn>
            <apply><divide/>
              <ci>H_i</ci>
              <ci>k_half</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>
          Shaw and Rudy (1997) formulation of [ATP]i dependence of ICaL.
        </dc:title>
        <cmeta:species>guinea pig</cmeta:species>
        <cmeta:bio_entity>Ventricular Myocyte</cmeta:bio_entity>
        <bqs:reference rdf:parseType="Resource">
          <bqs:Pubmed_id>9349389</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>Shaw</vCard:Family>
                      <vCard:Given>Robin</vCard:Given>
                      <vCard:Other>M</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>Rudy</vCard:Family>
                      <vCard:Given>Yoram</vCard:Given>
                    </vCard:N>
                  </bqs:Person>
                </rdf:li>
              </rdf:Seq>
            </dc:creator>
            <dc:title>
              Electrophysiologic effects of acute myocardial ischemia: a
              theoretical study of altered cell excitability and action potential
              duration.
            </dc:title>
            <dcterms:issued rdf:parseType="Resource">
              <dcterms:W3CDTF>1997</dcterms:W3CDTF>
            </dcterms:issued>
            <bqs:Journal rdf:parseType="Resource">
              <dc:title>Cardiovascular Research</dc:title>
            </bqs:Journal>
            <bqs:volume>35</bqs:volume>
            <bqs:first_page>256</bqs:first_page>
            <bqs:last_page>272</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_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">1.0</cn>
          <apply><plus/>
            <cn cellml:units="dimensionless">1.0</cn>
            <apply><power/>
              <apply><divide/>
                <ci>k_half</ci>
                <ci>ATP_i</ci>
              </apply>
              <ci>H</ci>
            </apply>
          </apply>
        </apply>
      </apply>
    </math>
  </component>
  
  <component name="ICaL" cmeta:id="ICaL">
    <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="#ICaL">
        <dc:title>
          Modified ICaL current taking intra- and extracellular pH and [ATP]i into account.
        </dc:title>
      </rdf:Description>
    </rdf:RDF>
    
    <variable cmeta:id="conductance_pHo" name="pHo" public_interface="out" private_interface="in" units="dimensionless"/>
    <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="ICaL" name="ICaL" public_interface="out" units="uA_per_mmsq"/>
    <variable cmeta:id="ICaL_original" name="ICaL_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_o" public_interface="in" private_interface="out" units="mM"/>
    <variable name="k_half_pHo" public_interface="in" private_interface="out" units="mM"/>
    <variable name="ATP_i" public_interface="in" private_interface="out" units="mM"/>
    <variable name="k_half_ATPi" public_interface="in" private_interface="out" units="mM"/>
    <variable name="H_ATPi" public_interface="in" private_interface="out" units="dimensionless"/>
    
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="ICaL_eq"><eq/>
        <ci>ICaL</ci>
        <apply><times/>
          <ci>pHo</ci>
          <ci>pHi</ci>
          <ci>ATPi</ci>
          <ci>ICaL_original</ci>
        </apply>
      </apply>
    </math>
  </component>
  
  <group>
    <relationship_ref relationship="encapsulation"/>
    <component_ref component="ICaL">
      <component_ref component="pHo"/>
      <component_ref component="pHi"/>
      <component_ref component="ATPi"/>
    </component_ref>
  </group>
  <connection>
    <map_components component_1="ICaL" component_2="pHo"/>
    <map_variables variable_1="pHo" variable_2="relative_conductance"/>
    <map_variables variable_1="H_o" variable_2="H_o"/>
    <map_variables variable_1="k_half_pHo" variable_2="k_half"/>
  </connection>
  <connection>
    <map_components component_1="ICaL" 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"/>
  </connection>
  <connection>
    <map_components component_1="ICaL" 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_half_ATPi" variable_2="k_half"/>
    <map_variables variable_1="H_ATPi" variable_2="H"/>
  </connection>
</model>