Location: Andre's Hodgkin Huxley model @ 957c2190e1ee / experiments / periodic-stimulus-graphs.xml

Author:

David Nickerson <nickerso@users.sourceforge.net>

Date:

2015-05-25 08:31:46+12:00

Desc:

adding a SED-ML document which does nested repeated tasks to iterate over clamp potential and temperature; doesn't work with get-sed-ml-client

Permanent Source URI:

https://models.physiomeproject.org/w/andre/HH/rawfile/957c2190e1eed47d7634613250bc274dc836b826/experiments/periodic-stimulus-graphs.xml

<?xml version="1.0" encoding="iso-8859-1"?>
<rdf:RDF
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        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#"
        xmlns:cg="http://www.cellml.org/metadata/graphs/1.0#">
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      <rdf:value>david.nickerson@nus.edu.sg</rdf:value>
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    <vCard:ORG rdf:parseType="Resource">
      <vCard:Orgname>National University of Singapore</vCard:Orgname>
      <vCard:Orgunit>Division of Bioengineering</vCard:Orgunit>
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    <dc:publisher>
      Division of Bioengineering, National University of Singapore
    </dc:publisher>
  </rdf:Description>
  <rdf:Description>
    <cg:graph>
      <rdf:Description rdf:ID="potential">
        <cg:title>Action Potentials</cg:title>
        <cmeta:modification rdf:parseType="Resource">
          <rdf:value>
            Adding more comprehensive metadata to the graph.
          </rdf:value>
          <cmeta:modifier rdf:parseType="Resource">
            <vCard:FN>David Nickerson</vCard:FN>
          </cmeta:modifier>
          <dcterms:modified rdf:parseType="Resource">
            <dcterms:W3CDTF>2008-03-17</dcterms:W3CDTF>
          </dcterms:modified>
        </cmeta:modification>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            This graph illustrates the action potentials simulated using the Hodgkin &amp; Huxley (1952) squid axon model with a periodic electrical stimulus current applied.
          </rdf:value>
        </cmeta:comment>
        <bqs:reference rdf:parseType="Resource">
          <bqs:Pubmed_id>12991237</bqs:Pubmed_id>
        </bqs:reference>
        <cmeta:species>loligo</cmeta:species>
        <cmeta:bio_entity>giant nerve fibre</cmeta:bio_entity>
        <cg:x-label>Time (ms)</cg:x-label>
        <cg:y-label>Potential (mV)</cg:y-label>
        <cg:background-colour>#ffffff</cg:background-colour>
        <cg:traces rdf:parseType="Collection">
          <rdf:Description>
            <cg:label>-V</cg:label>
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            <cg:x-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="periodic-stimulus.xml#time"/>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/stimulated.xml#minus_V"/>
            </cg:y-variable>
          </rdf:Description>
        </cg:traces>
      </rdf:Description>
    </cg:graph>
    <cg:graph>
      <rdf:Description rdf:ID="currents">
        <cg:title>Membrane Currents</cg:title>
        <cmeta:modification rdf:parseType="Resource">
          <rdf:value>
            Adding more comprehensive metadata to the graph.
          </rdf:value>
          <cmeta:modifier rdf:parseType="Resource">
            <vCard:FN>David Nickerson</vCard:FN>
          </cmeta:modifier>
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            <dcterms:W3CDTF>2008-03-17</dcterms:W3CDTF>
          </dcterms:modified>
        </cmeta:modification>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            This graph illustrates the membrane currents simulated using the Hodgkin &amp; Huxley (1952) squid axon model with a periodic electrical stimulus current applied.
          </rdf:value>
        </cmeta:comment>
        <bqs:reference rdf:parseType="Resource">
          <bqs:Pubmed_id>12991237</bqs:Pubmed_id>
        </bqs:reference>
        <cmeta:species>loligo</cmeta:species>
        <cmeta:bio_entity>giant nerve fibre</cmeta:bio_entity>
        <cg:x-label>Time (ms)</cg:x-label>
        <cg:y-label>Current (uA.cm^-2)</cg:y-label>
        <cg:background-colour>#ffffff</cg:background-colour>
        <cg:traces rdf:parseType="Collection">
          <rdf:Description>
            <cg:label>INa</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#ff0000</cg:colour>
            <cg:line-type rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</cg:line-type>
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              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="periodic-stimulus.xml#time"/>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/INa.xml#INa"/>
            </cg:y-variable>
          </rdf:Description>
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            <cg:label>IK</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
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              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="periodic-stimulus.xml#time"/>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/IK.xml#IK"/>
            </cg:y-variable>
          </rdf:Description>
          <rdf:Description>
            <cg:label>Ileak</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#008000</cg:colour>
            <cg:line-type rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</cg:line-type>
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              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="periodic-stimulus.xml#time"/>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/Ileak.xml#Ileak"/>
            </cg:y-variable>
          </rdf:Description>
        </cg:traces>
      </rdf:Description>
    </cg:graph>
    <cg:graph>
      <rdf:Description rdf:ID="gates">
        <cg:title>Gating Variables</cg:title>
        <cmeta:modification rdf:parseType="Resource">
          <rdf:value>
            Adding more comprehensive metadata to the graph.
          </rdf:value>
          <cmeta:modifier rdf:parseType="Resource">
            <vCard:FN>David Nickerson</vCard:FN>
          </cmeta:modifier>
          <dcterms:modified rdf:parseType="Resource">
            <dcterms:W3CDTF>2008-03-17</dcterms:W3CDTF>
          </dcterms:modified>
        </cmeta:modification>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            This graph illustrates the gating variables simulated using the Hodgkin &amp; Huxley (1952) squid axon model with a periodic electrical stimulus current applied.
          </rdf:value>
        </cmeta:comment>
        <bqs:reference rdf:parseType="Resource">
          <bqs:Pubmed_id>12991237</bqs:Pubmed_id>
        </bqs:reference>
        <cmeta:species>loligo</cmeta:species>
        <cmeta:bio_entity>giant nerve fibre</cmeta:bio_entity>
        <cg:x-label>Time (ms)</cg:x-label>
        <cg:y-label>Gate value ()</cg:y-label>
        <cg:background-colour>#ffffff</cg:background-colour>
        <cg:traces rdf:parseType="Collection">
          <rdf:Description>
            <cg:label>n</cg:label>
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            <cg:colour>#ff0000</cg:colour>
            <cg:line-type rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</cg:line-type>
            <cg:x-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="periodic-stimulus.xml#time"/>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/IK.xml#n"/>
            </cg:y-variable>
          </rdf:Description>
          <rdf:Description>
            <cg:label>m</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#0000ff</cg:colour>
            <cg:line-type rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</cg:line-type>
            <cg:x-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="periodic-stimulus.xml#time"/>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/INa.xml#m"/>
            </cg:y-variable>
          </rdf:Description>
          <rdf:Description>
            <cg:label>h</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#008000</cg:colour>
            <cg:line-type rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</cg:line-type>
            <cg:x-variable rdf:parseType="Resource">
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              <cg:variable rdf:resource="periodic-stimulus.xml#time"/>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/INa.xml#h"/>
            </cg:y-variable>
          </rdf:Description>
        </cg:traces>
      </rdf:Description>
    </cg:graph>
    <cg:graph>
      <rdf:Description rdf:ID="potential-zoom">
        <cg:title>Action Potential</cg:title>
        <cmeta:modification rdf:parseType="Resource">
          <rdf:value>
            Adding more comprehensive metadata to the graph.
          </rdf:value>
          <cmeta:modifier rdf:parseType="Resource">
            <vCard:FN>David Nickerson</vCard:FN>
          </cmeta:modifier>
          <dcterms:modified rdf:parseType="Resource">
            <dcterms:W3CDTF>2008-03-17</dcterms:W3CDTF>
          </dcterms:modified>
        </cmeta:modification>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            This graph illustrates the action potentials simulated using the Hodgkin &amp; Huxley (1952) squid axon model with a periodic electrical stimulus current applied. Here we restrict the view of the time domain in order to better see an individual action potential.
          </rdf:value>
        </cmeta:comment>
        <bqs:reference rdf:parseType="Resource">
          <bqs:Pubmed_id>12991237</bqs:Pubmed_id>
        </bqs:reference>
        <cmeta:species>loligo</cmeta:species>
        <cmeta:bio_entity>giant nerve fibre</cmeta:bio_entity>
        <cg:x-label>Time (ms)</cg:x-label>
        <cg:y-label>Potential (mV)</cg:y-label>
        <cg:background-colour>#ffffff</cg:background-colour>
        <cg:traces rdf:parseType="Collection">
          <rdf:Description>
            <cg:label>-V</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#ff0000</cg:colour>
            <cg:line-type rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</cg:line-type>
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            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/stimulated.xml#minus_V"/>
            </cg:y-variable>
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        </cg:traces>
      </rdf:Description>
    </cg:graph>
    <cg:graph>
      <rdf:Description rdf:ID="currents-zoom">
        <cg:title>Membrane Currents</cg:title>
        <cmeta:modification rdf:parseType="Resource">
          <rdf:value>
            Adding more comprehensive metadata to the graph.
          </rdf:value>
          <cmeta:modifier rdf:parseType="Resource">
            <vCard:FN>David Nickerson</vCard:FN>
          </cmeta:modifier>
          <dcterms:modified rdf:parseType="Resource">
            <dcterms:W3CDTF>2008-03-17</dcterms:W3CDTF>
          </dcterms:modified>
        </cmeta:modification>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            This graph illustrates the membrane currents simulated using the Hodgkin &amp; Huxley (1952) squid axon model with a periodic electrical stimulus current applied. Here we restrict the view of the time domain in order to better see the currents underlying an individual action potential.
          </rdf:value>
        </cmeta:comment>
        <bqs:reference rdf:parseType="Resource">
          <bqs:Pubmed_id>12991237</bqs:Pubmed_id>
        </bqs:reference>
        <cmeta:species>loligo</cmeta:species>
        <cmeta:bio_entity>giant nerve fibre</cmeta:bio_entity>
        <cg:x-label>Time (ms)</cg:x-label>
        <cg:y-label>Current (uA.cm^-2)</cg:y-label>
        <cg:background-colour>#ffffff</cg:background-colour>
        <cg:traces rdf:parseType="Collection">
          <rdf:Description>
            <cg:label>INa</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#ff0000</cg:colour>
            <cg:line-type rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</cg:line-type>
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              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
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            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/INa.xml#INa"/>
            </cg:y-variable>
          </rdf:Description>
          <rdf:Description>
            <cg:label>IK</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#0000ff</cg:colour>
            <cg:line-type rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</cg:line-type>
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              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="periodic-stimulus.xml#time"/>
              <cg:minimum rdf:datatype="http://www.w3.org/2001/XMLSchema#double">95</cg:minimum>
              <cg:maximum rdf:datatype="http://www.w3.org/2001/XMLSchema#double">120</cg:maximum>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/IK.xml#IK"/>
            </cg:y-variable>
          </rdf:Description>
          <rdf:Description>
            <cg:label>Ileak</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#008000</cg:colour>
            <cg:line-type rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</cg:line-type>
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            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/Ileak.xml#Ileak"/>
            </cg:y-variable>
          </rdf:Description>
        </cg:traces>
      </rdf:Description>
    </cg:graph>
    <cg:graph>
      <rdf:Description rdf:ID="gates-zoom">
        <cg:title>Gating Variables</cg:title>
        <cmeta:modification rdf:parseType="Resource">
          <rdf:value>
            Adding more comprehensive metadata to the graph.
          </rdf:value>
          <cmeta:modifier rdf:parseType="Resource">
            <vCard:FN>David Nickerson</vCard:FN>
          </cmeta:modifier>
          <dcterms:modified rdf:parseType="Resource">
            <dcterms:W3CDTF>2008-03-17</dcterms:W3CDTF>
          </dcterms:modified>
        </cmeta:modification>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            This graph illustrates the gating variables simulated using the Hodgkin &amp; Huxley (1952) squid axon model with a periodic electrical stimulus current applied. Here we restrict the view of the time domain in order to better see the gating transients underlying an individual action potential.
          </rdf:value>
        </cmeta:comment>
        <bqs:reference rdf:parseType="Resource">
          <bqs:Pubmed_id>12991237</bqs:Pubmed_id>
        </bqs:reference>
        <cmeta:species>loligo</cmeta:species>
        <cmeta:bio_entity>giant nerve fibre</cmeta:bio_entity>
        <cg:x-label>Time (ms)</cg:x-label>
        <cg:y-label>Gate value ()</cg:y-label>
        <cg:background-colour>#ffffff</cg:background-colour>
        <cg:traces rdf:parseType="Collection">
          <rdf:Description>
            <cg:label>n</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#ff0000</cg:colour>
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              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="periodic-stimulus.xml#time"/>
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              <cg:maximum rdf:datatype="http://www.w3.org/2001/XMLSchema#double">120</cg:maximum>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/IK.xml#n"/>
            </cg:y-variable>
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            <cg:label>m</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#0000ff</cg:colour>
            <cg:line-type rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</cg:line-type>
            <cg:x-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
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            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
              <cg:variable rdf:resource="../components/INa.xml#m"/>
            </cg:y-variable>
          </rdf:Description>
          <rdf:Description>
            <cg:label>h</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#008000</cg:colour>
            <cg:line-type rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</cg:line-type>
            <cg:x-variable rdf:parseType="Resource">
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            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="periodic-stimulus.xml#simulation"/>
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