- 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/voltage-clamp.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="voltage_clamp"
cmeta:id="voltage_clamp_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>2008-03-14</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#voltage_clamp_model">
<dc:title>
Hodgkin-Huxley with applied voltage clamp.
</dc:title>
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
A CellML description of the Hodgkin & Huxley model assembled to calculate total membrane current for a specified voltage clamp step.
</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="mV" units_ref="mV"/>
<units name="ms" units_ref="ms"/>
<units name="K" units_ref="K"/>
<units name="uA_per_cmsq" units_ref="uA_per_cmsq"/>
<units name="mS_per_cmsq" units_ref="mS_per_cmsq"/>
<units name="uF_per_cmsq" units_ref="uF_per_cmsq"/>
</import>
<import xlink:href="INa.xml">
<component name="INa" component_ref="INa"/>
</import>
<import xlink:href="IK.xml">
<component name="IK" component_ref="IK"/>
</import>
<import xlink:href="Ileak.xml">
<component name="Ileak" component_ref="Ileak"/>
</import>
<component name="voltage_clamp" cmeta:id="voltage_clamp_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:dc="http://purl.org/dc/elements/1.1/">
<rdf:Description rdf:about="#voltage_clamp_component">
<dc:title>
Hodgkin & Huxley with applied voltage clamp.
</dc:title>
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The Hodgkin & Huxley (1952) model assembled such that the total membrane current is calculated for a given step in holding potential.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable cmeta:id="V_initial" name="V_initial" public_interface="in"
private_interface="out" units="mV"/>
<variable cmeta:id="n_initial" name="n_initial" public_interface="in"
private_interface="out" units="dimensionless"/>
<variable cmeta:id="m_initial" name="m_initial" public_interface="in"
private_interface="out" units="dimensionless"/>
<variable cmeta:id="h_initial" name="h_initial" public_interface="in"
private_interface="out" units="dimensionless"/>
<variable cmeta:id="INa" name="INa" public_interface="out"
private_interface="in" units="uA_per_cmsq"/>
<variable cmeta:id="IK" name="IK" public_interface="out"
private_interface="in" units="uA_per_cmsq"/>
<variable cmeta:id="Ileak" name="Ileak" public_interface="out"
private_interface="in" units="uA_per_cmsq"/>
<variable cmeta:id="VNa" name="VNa" public_interface="in"
private_interface="out" units="mV"/>
<variable cmeta:id="VK" name="VK" public_interface="in"
private_interface="out" units="mV"/>
<variable cmeta:id="Vleak" name="Vleak" public_interface="in"
private_interface="out" units="mV"/>
<variable cmeta:id="gNa_max" name="gNa_max" public_interface="in"
private_interface="out" units="mS_per_cmsq"/>
<variable cmeta:id="gK_max" name="gK_max" public_interface="in"
private_interface="out" units="mS_per_cmsq"/>
<variable cmeta:id="gleak_max" name="gleak_max" public_interface="in"
private_interface="out" units="mS_per_cmsq"/>
<variable cmeta:id="Tref_rates" name="Tref_rates" public_interface="in"
private_interface="out" units="K"/>
<variable cmeta:id="T" name="T" public_interface="in"
private_interface="out" units="K"/>
<variable cmeta:id="Q10_rates" name="Q10_rates" public_interface="in"
private_interface="out" units="dimensionless" />
<variable cmeta:id="time" name="time" public_interface="in"
private_interface="out" units="ms" />
<variable cmeta:id="V" name="V" public_interface="out"
private_interface="out" units="mV"/>
<variable cmeta:id="Vnew" name="Vnew" public_interface="in"
private_interface="out" units="mV"/>
<variable cmeta:id="I" name="I" public_interface="out"
private_interface="out" units="uA_per_cmsq"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="I_calculation"><eq/>
<ci>I</ci>
<apply><plus/>
<ci>INa</ci>
<ci>IK</ci>
<ci>Ileak</ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_calculation"><eq/>
<ci>V</ci>
<piecewise>
<piece>
<ci>Vnew</ci>
<apply><gt/>
<ci>time</ci>
<cn cellml:units="ms">0.0</cn>
</apply>
</piece>
<otherwise>
<ci>V_initial</ci>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<group>
<relationship_ref relationship="encapsulation"/>
<component_ref component="voltage_clamp">
<component_ref component="INa"/>
<component_ref component="IK"/>
<component_ref component="Ileak"/>
</component_ref>
</group>
<connection>
<map_components component_1="voltage_clamp" component_2="INa"/>
<map_variables variable_1="INa" variable_2="INa"/>
<map_variables variable_1="m_initial" variable_2="m_initial"/>
<map_variables variable_1="h_initial" variable_2="h_initial"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="Tref_rates" variable_2="Tref"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="Q10_rates" variable_2="Q10"/>
<map_variables variable_1="V" variable_2="V"/>
<map_variables variable_1="VNa" variable_2="VNa"/>
<map_variables variable_1="gNa_max" variable_2="gNa_max"/>
</connection>
<connection>
<map_components component_1="voltage_clamp" component_2="IK"/>
<map_variables variable_1="IK" variable_2="IK"/>
<map_variables variable_1="n_initial" variable_2="n_initial"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="Tref_rates" variable_2="Tref"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="Q10_rates" variable_2="Q10"/>
<map_variables variable_1="V" variable_2="V"/>
<map_variables variable_1="VK" variable_2="VK"/>
<map_variables variable_1="gK_max" variable_2="gK_max"/>
</connection>
<connection>
<map_components component_1="voltage_clamp" component_2="Ileak"/>
<map_variables variable_1="Ileak" variable_2="Ileak"/>
<map_variables variable_1="V" variable_2="V"/>
<map_variables variable_1="Vleak" variable_2="Vleak"/>
<map_variables variable_1="gleak_max" variable_2="gleak_max"/>
</connection>
</model>