Location: Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model @ d6328d18c94e / experiments / IKATP-Matsuoka-control.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://models.physiomeproject.org/w/andre/nickerson-2008/rawfile/d6328d18c94e9dad70f4d0e4b250e89429773b62/experiments/IKATP-Matsuoka-control.xml

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

<model
    name="IKATP_Matsuoka_control"
    cmeta:id="IKATP_Matsuoka_control"
    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#"
      xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">
    <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>2007-05-25</dcterms:W3CDTF>
      </dcterms:created>
      <dc:publisher>
        Division of Bioengineering, National University of Singapore
      </dc:publisher>
    </rdf:Description>
    <rdf:Description rdf:about="#IKATP_Shaw_control">
      <cmeta:comment rdf:parseType="Resource">
        <rdf:value>
          This model imports the pre-configured base TNNP model extended with the 
          Matsuoka et al (2004) IKatp formulation. Here we are only defining the parameters
          for the IKatp channel and defining the simulation metadata. The parameters
          are the control conditions for this channel
        </rdf:value>
        <dc:creator rdf:parseType="Resource">
          <vCard:FN>David Nickerson</vCard:FN>
        </dc:creator>
      </cmeta:comment>
      <cs:simulation>
        <rdf:Description rdf:ID="simulation">
          <cs:simulationName>Simulation</cs:simulationName>
          <cs:multistepMethod>bdf</cs:multistepMethod>
          <cs:iterationMethod>newton</cs:iterationMethod>
          <cs:linearSolver>dense</cs:linearSolver>
          <cs:boundIntervals rdf:parseType="Collection">
            <rdf:Description>
              <cs:boundVariable>
                <rdf:Description rdf:about="IKATP-Shaw.xml#time"/>
              </cs:boundVariable>
              <cs:maximumStepSize 
                                  rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
                0.1
              </cs:maximumStepSize>
              <cs:tabulationStepSize
                                    rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
                0.1
              </cs:tabulationStepSize>
              <cs:startingValue
                               rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
                0
              </cs:startingValue>
              <cs:endingValue
                             rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
                2000
              </cs:endingValue>
            </rdf:Description>
          </cs:boundIntervals>
        </rdf:Description>
      </cs:simulation>
    </rdf:Description>
  </rdf:RDF>
  
  <import xlink:href="../../../cellml/models/common/units.xml">
    <units name="mS_per_mmsq" units_ref="mS_per_mmsq"/>
    <units name="mM" units_ref="mM"/>
  </import>
  <import xlink:href="IKATP-Matsuoka.xml">
    <component name="model" component_ref="interface"/>
  </import>
  
  <component name="parameters" cmeta:id="parameters">
    <rdf:RDF
            xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
            xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
      <rdf:Description rdf:about="#parameters">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The IKatp channel parameters.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
    </rdf:RDF>
    <variable name="N_K_ATP" initial_value="0.17674" public_interface="out" units="mS_per_mmsq"/>
    <variable name="ATP_i" initial_value="6.8" public_interface="out" units="mM"/>
  </component>
  <connection>
    <map_components component_1="parameters" component_2="model"/>
    <map_variables variable_1="N_K_ATP" variable_2="N_K_ATP"/>
    <map_variables variable_1="ATP_i" variable_2="ATP_i"/>
  </connection>

</model>