Location: Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model @ d6328d18c94e / experiments / Jup-modified-ischemic-pHi.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/Jup-modified-ischemic-pHi.xml

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

<model
    name="Jup_modified_control"
    cmeta:id="Jup_modified_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>2007-06-22</dcterms:W3CDTF>
      </dcterms:created>
      <dc:publisher>
        Division of Bioengineering, National University of Singapore
      </dc:publisher>
    </rdf:Description>
    <rdf:Description rdf:about="#Jup_modified_control">
      <cmeta:comment rdf:parseType="Resource">
        <rdf:value>
          This model imports the pre-configured base TNNP model extended with the Jup
          modifications. Here we are only defining the parameters
          for the modifications and defining the simulation metadata. The parameters
          are the control conditions.
        </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="Jup-modified.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="mM" units_ref="mM"/>
  </import>
  <import xlink:href="Jup-modified.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 extra parameters for the modified Jup, under normal conditions.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
    </rdf:RDF>
    <variable name="H_i" initial_value="3.98e-4" public_interface="out" units="mM"/>
    <variable name="k_half_pHi" initial_value="3.02e-5" public_interface="out" units="mM"/>
    <variable name="H_pHi" initial_value="1.18" public_interface="out" units="dimensionless"/>
    <variable name="k_pHi" initial_value="4.1746" public_interface="out" units="dimensionless"/>
  </component>
  <connection>
    <map_components component_1="parameters" component_2="model"/>
    <map_variables variable_1="H_i" variable_2="H_i"/>
    <map_variables variable_1="k_half_pHi" variable_2="k_half_pHi"/>
    <map_variables variable_1="H_pHi" variable_2="H_pHi"/>
    <map_variables variable_1="k_pHi" variable_2="k_pHi"/>
  </connection>

</model>