Location: VPH-MIP case study on CellML @ a29bfba242e7 / experiments / potential-ramp.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/experiments/potential-ramp.xml

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

<model
      name="ramp"
      cmeta:id="ramp_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:ID="andre">
      <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>
    </rdf:Description>
    <rdf:Description rdf:about="">
      <dc:creator rdf:resource="#andre"/>
      <dcterms:created rdf:parseType="Resource">
        <dcterms:W3CDTF>2008-03-13</dcterms:W3CDTF>
      </dcterms:created>
      <dc:publisher>
        Division of Bioengineering, National University of Singapore
      </dc:publisher>
    </rdf:Description>
    <rdf:Description rdf:about="#ramp_model">
      <dc:title>
        A potential ramp differential equation.
      </dc:title>
      <cmeta:comment rdf:parseType="Resource">
        <rdf:value>
          This is a CellML description of a generic potential ramp differential equation suitable for use as controlling boundary condition. For example, to define a linear change in voltage over some integration interval.
        </rdf:value>
        <dc:creator rdf:resource="#andre"/>
        <dcterms:created rdf:parseType="Resource">
          <dcterms:W3CDTF>2007-03-13</dcterms:W3CDTF>
        </dcterms:created>
      </cmeta:comment>
    </rdf:Description>
  </rdf:RDF>
  <import xlink:href="../components/units.xml">
    <units name="ms" units_ref="ms"/>
    <units name="mV" units_ref="mV"/>
    <units name="mV_per_ms" units_ref="mV_per_ms"/>
  </import>
  <component name="ramp" cmeta:id="ramp_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: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="#ramp_component">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Here we define a simple linear relationship dy/dt = k, specifying the change in y over time with a slope of k.
          </rdf:value>
          <dc:creator rdf:resource="#andre"/>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#y">
        <dc:title>The ramp variable.</dc:title>
      </rdf:Description>
      <rdf:Description rdf:about="#y_initial">
        <dc:title>
          The initial value of y.
        </dc:title>
      </rdf:Description>
      <rdf:Description rdf:about="#time">
        <dc:title>
          The time variable over which y is to be integrated.
        </dc:title>
      </rdf:Description>
      <rdf:Description rdf:about="#k">
        <dc:title>
          The time slope of the linear relationship.
        </dc:title>
      </rdf:Description>
    </rdf:RDF>
    <variable cmeta:id="y" name="y" public_interface="out" private_interface="out" units="mV" initial_value="y_initial"/>
    <variable cmeta:id="y_initial" name="y_initial" public_interface="in" units="mV"/>
    <variable cmeta:id="time" name="time" public_interface="in" units="ms"/>
    <variable cmeta:id="k" name="k" public_interface="in" units="mV_per_ms"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="ramp_calculation"><eq/>
        <apply><diff/>
          <bvar><ci>time</ci></bvar>
          <ci>y</ci>
        </apply>
        <ci>k</ci>
      </apply>
    </math>
  </component>
</model>