Location: VPH-MIP case study on CellML @ a29bfba242e7 / experiments / voltage-clamp-010.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/voltage-clamp-010.xml

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

<model
    name="voltage_clamp"
    cmeta:id="voltage_clamp"
    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>2008-03-14</dcterms:W3CDTF>
      </dcterms:created>
      <dc:publisher>
        Division of Bioengineering, National University of Singapore
      </dc:publisher>
    </rdf:Description>
    <rdf:Description rdf:about="#voltage_clamp">
      <dc:title>
        Hodgkin &amp; Huxley (1952) with voltage clamp of -10 mV applied.
      </dc:title>
      <cmeta:comment rdf:parseType="Resource">
        <rdf:value>
          Import the base voltage clamp model and set the clamp potential to -10 mV.
        </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>Voltage clamp</cs:simulationName>
          <cs:multistepMethod>bdf</cs:multistepMethod>
          <cs:iterationMethod>functional</cs:iterationMethod>
          <cs:boundIntervals rdf:parseType="Collection">
            <rdf:Description>
              <cs:boundVariable>
                <rdf:Description rdf:about="voltage-clamp.xml#time"/>
              </cs:boundVariable>
              <cs:maximumStepSize 
                                  rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
                0.01
              </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">
                -10
              </cs:startingValue>
              <cs:endingValue
                             rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
                100
              </cs:endingValue>
            </rdf:Description>
          </cs:boundIntervals>
        </rdf:Description>
      </cs:simulation>
    </rdf:Description>
  </rdf:RDF>

  <import xlink:href="../components/units.xml">
    <units name="mV" units_ref="mV"/>
  </import>
  <import xlink:href="voltage-clamp.xml">
    <component name="model" component_ref="interface"/>
  </import>

  <component cmeta:id="clamp_potential_component" name="clamp_potential">
    <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="#clamp_potential_component">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Simply defining the clamp potential variable to connect to the voltage clamp model.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
    </rdf:RDF>
    <variable cmeta:id="clamp_potential" name="clamp_potential"
              public_interface="out" private_interface="out"
              units="mV" initial_value="-10.0001"/>
  </component>
  <connection>
    <map_components component_1="clamp_potential" component_2="model"/>
    <map_variables variable_1="clamp_potential" variable_2="Vnew"/>
  </connection>
</model>