Location: VPH-MIP case study on CellML @ a29bfba242e7 / components / gating-variable.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/components/gating-variable.xml

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

<model
      name="hh_gating_variable"
      cmeta:id="hh_gating_variable_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: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>2008-03-11</dcterms:W3CDTF>
      </dcterms:created>
      <dc:publisher>
        Division of Bioengineering, National University of Singapore
      </dc:publisher>
    </rdf:Description>
    <rdf:Description rdf:about="#hh_gating_variable_model">
      <dc:title>
        Standard Hodgkin-Huxley gating variable description.
      </dc:title>
      <cmeta:comment rdf:parseType="Resource">
        <rdf:value>
          Standard Hodgkin-Huxley gating variable description designed to be imported and reused for each standard gate in a model. Both the dynamic and steady state representations of a gating variable are defined in this model.
        </rdf:value>
        <dc:creator rdf:parseType="Resource">
          <vCard:FN>David Nickerson</vCard:FN>
        </dc:creator>
      </cmeta:comment>
    </rdf:Description>
  </rdf:RDF>
  <import xlink:href="units.xml">
    <units name="ms" units_ref="ms"/>
    <units name="per_ms" units_ref="per_ms"/>
  </import>
  <component name="hh_gating_variable_dynamic"
             cmeta:id="hh_gating_variable_dynamic">
    <rdf:RDF
            xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
            xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
            xmlns:dc="http://purl.org/dc/elements/1.1/">
      <rdf:Description rdf:about="#hh_gating_variable_dynamic">
        <dc:title>
          Standard Hodgkin-Huxley dynamic gating kinetics.
        </dc:title>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The standard definition of a dynamic Hodgkin &amp; Huxley gating variable.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#time">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The independent variable.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#gate_dynamic">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The standard Hodgkin &amp; Huxley dynamic gating variable.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#gate_initial_dynamic">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The initial value of the dynamic gating variable, must be defined in order to solve the dynamic expression of the gating kinetics.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#alpha_dynamic">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The rate of activation of the gating variable.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#beta_dynamic">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The rate of inactivation of the gating variable.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#dynamic_gate_calculation">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Represents equations 7, 15, &amp; 16 in the Hodgkin &amp; Huxley (1952) model.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
    </rdf:RDF>
    <variable cmeta:id="time" name="time" public_interface="in"
              private_interface="out" units="ms"/>
    <variable cmeta:id="gate_dynamic" name="gate" 
              initial_value="gate_initial" public_interface="out"
              private_interface="out" units="dimensionless"/>
    <variable cmeta:id="gate_initial_dynamic" name="gate_initial"
              public_interface="in" private_interface="out"
              units="dimensionless"/>
    <variable cmeta:id="alpha_dynamic" name="alpha" public_interface="in"
              private_interface="out" units="per_ms"/>
    <variable cmeta:id="beta_dynamic" name="beta" public_interface="in"
              private_interface="out" units="per_ms"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="dynamic_gate_calculation"><eq/>
        <apply><diff/>
          <bvar><ci>time</ci></bvar>
          <ci>gate</ci>
        </apply>
        <apply><minus/>
          <apply><times/>
            <ci>alpha</ci>
            <apply><minus/>
              <cn cellml:units="dimensionless">1.0</cn>
              <ci>gate</ci>
            </apply>
          </apply>
          <apply><times/>
            <ci>beta</ci>
            <ci>gate</ci>
          </apply>
        </apply>
      </apply>
    </math>
  </component>
  <component name="hh_gating_variable_steady_state"
             cmeta:id="hh_gating_variable_steady_state">
    <rdf:RDF
            xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
            xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
            xmlns:dc="http://purl.org/dc/elements/1.1/">
      <rdf:Description rdf:about="#hh_gating_variable_steady_state">
        <dc:title>
          Standard Hodgkin-Huxley steady state gating kinetics.
        </dc:title>
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The standard definition of a steady state Hodgkin &amp; Huxley gating variable.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#gate_steady_state">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The standard Hodgkin &amp; Huxley steady state gating variable.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#time_steady_state">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Time. Should be zero at the point of change in membrane potential.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#gate_initial_steady_state">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The value of the gating variable at time=0.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#alpha_steady_state">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The rate of activation of the gating variable.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#beta_steady_state">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            The rate of inactivation of the gating variable.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#steady_state_gate_calculation">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Represents equations 8, 17, &amp; 18 in the Hodgkin &amp; Huxley (1952) model.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#gate_inf_calculation">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Represents equation 9 and similar unlabeled equations in the Hodgkin &amp; Huxley (1952) model.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
      <rdf:Description rdf:about="#tau_calculation">
        <cmeta:comment rdf:parseType="Resource">
          <rdf:value>
            Represents equation 10 and similar unlabeled equations in the Hodgkin &amp; Huxley (1952) model.
          </rdf:value>
        </cmeta:comment>
      </rdf:Description>
    </rdf:RDF>
    <variable cmeta:id="gate_steady_state" name="gate"
              public_interface="out" private_interface="out"
              units="dimensionless"/>
    <variable cmeta:id="time_steady_state" name="time" public_interface="in"
              private_interface="out" units="ms"/>
    <variable cmeta:id="gate_initial_steady_state" name="gate_initial"
              public_interface="in" private_interface="out"
              units="dimensionless"/>
    <variable cmeta:id="alpha_steady_state" name="alpha" public_interface="in"
              private_interface="out" units="per_ms"/>
    <variable cmeta:id="beta_steady_state" name="beta" public_interface="in"
              private_interface="out" units="per_ms"/>
    <variable cmeta:id="gate_inf" name="gate_inf" public_interface="out"
              private_interface="out" units="dimensionless"/>
    <variable cmeta:id="tau" name="tau" public_interface="out"
              private_interface="out" units="ms"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="steady_state_gate_calculation"><eq/>
        <ci>gate</ci>
        <apply><minus/>
          <ci>gate_inf</ci>
          <apply><times/>
            <apply><minus/>
              <ci>gate_inf</ci>
              <ci>gate_initial</ci>
            </apply>
            <apply><minus/>
              <apply><divide/>
                <ci>time</ci>
                <ci>tau</ci>
              </apply>
            </apply>
          </apply>
        </apply>
      </apply>
    </math>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="gate_inf_calculation"><eq/>
        <ci>gate_inf</ci>
        <apply><divide/>
          <ci>alpha</ci>
          <apply><plus/>
            <ci>alpha</ci>
            <ci>beta</ci>
          </apply>
        </apply>
      </apply>
    </math>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply id="tau_calculation"><eq/>
        <ci>tau</ci>
        <apply><divide/>
          <cn cellml:units="ms">1.0</cn>
          <apply><plus/>
            <ci>alpha</ci>
            <ci>beta</ci>
          </apply>
        </apply>
      </apply>
    </math>
  </component>
</model>