Location: Andre's Hodgkin Huxley model @ 957c2190e1ee / experiments / IK-gating-kinetics-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/IK-gating-kinetics-graphs.xml
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<?xml version="1.0" encoding="iso-8859-1"?>
<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#"
        xmlns:cg="http://www.cellml.org/metadata/graphs/1.0#">
  <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>2008-03-14</dcterms:W3CDTF>
    </dcterms:created>
    <dc:publisher>
      Division of Bioengineering, National University of Singapore
    </dc:publisher>
  </rdf:Description>
  <rdf:Description>
    <cg:graph>
      <rdf:Description rdf:ID="IK-gating-rates">
        <cg:title>IK Gating Rates</cg:title>
        <cmeta:modification rdf:parseType="Resource">
          <rdf:value>
            Adding cg:title property 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>2008-03-16</dcterms:W3CDTF>
          </dcterms:modified>
        </cmeta:modification>
        <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:modification rdf:parseType="Resource">
        <rdf:value>
          Updating graph for to account for the splitting out of alpha_n and beta_n components to their own model.
        </rdf:value>
        <cmeta:modifier rdf:parseType="Resource">
          <vCard:FN>David Nickerson</vCard:FN>
        </cmeta:modifier>
        <dcterms:modified rdf:parseType="Resource">
          <dcterms:W3CDTF>2008-08-13</dcterms:W3CDTF>
        </dcterms:modified>
      </cmeta:modification>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            This graph matches Figure 4 of the Hodgkin &amp; Huxley (1952) article.
          </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>V (mV)</cg:x-label>
        <cg:y-label>Rate constant (ms^-1)</cg:y-label>
        <cg:background-colour>#ffffff</cg:background-colour>
        <cg:traces rdf:parseType="Collection">
          <rdf:Description>
            <cg:label>alpha_n</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#ff0000</cg:colour>
            <cg:x-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="IK-gating-kinetics.xml#simulation"/>
              <cg:variable rdf:resource="IK-gating-kinetics.xml#V"/>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="IK-gating-kinetics.xml#simulation"/>
              <cg:variable rdf:resource="../components/IK-gating-rates.xml#alpha_n"/>
            </cg:y-variable>
          </rdf:Description>
          <rdf:Description>
            <cg:label>beta_n</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#0000ff</cg:colour>
            <cg:x-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="IK-gating-kinetics.xml#simulation"/>
              <cg:variable rdf:resource="IK-gating-kinetics.xml#V"/>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="IK-gating-kinetics.xml#simulation"/>
              <cg:variable rdf:resource="../components/IK-gating-rates.xml#beta_n"/>
            </cg:y-variable>
          </rdf:Description>
        </cg:traces>
      </rdf:Description>
    </cg:graph>
    <cg:graph>
      <rdf:Description rdf:ID="IK-gating-SS">
        <cg:title>IK Steady State Gating Kinetics</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 matches Figure 5 of the Hodgkin &amp; Huxley (1952) article.
          </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>V (mV)</cg:x-label>
        <cg:y-label>Steady state gate ()</cg:y-label>
        <cg:background-colour>#ffffff</cg:background-colour>
        <cg:traces rdf:parseType="Collection">
          <rdf:Description>
            <cg:label>n_inf</cg:label>
            <cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line"/>
            <cg:colour>#ff0000</cg:colour>
            <cg:x-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="IK-gating-kinetics.xml#simulation"/>
              <cg:variable rdf:resource="IK-gating-kinetics.xml#V"/>
            </cg:x-variable>
            <cg:y-variable rdf:parseType="Resource">
              <cs:simulation rdf:resource="IK-gating-kinetics.xml#simulation"/>
              <cg:variable rdf:resource="IK-gating-kinetics.xml#n_inf"/>
            </cg:y-variable>
          </rdf:Description>
        </cg:traces>
      </rdf:Description>
    </cg:graph>
  </rdf:Description>
</rdf:RDF>