- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2013-05-04 07:40:04+12:00
- Desc:
- adding initial TODO list to keep track of what I need to do to get things working with more recent tools than my original CellMLSimulator that I used in this paper
- Permanent Source URI:
- https://staging.physiomeproject.org/w/andre/nickerson-2008/rawfile/d6328d18c94e9dad70f4d0e4b250e89429773b62/TNNP-extended/components/Ito-pH-dependence.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="Ito_pH_dependence"
cmeta:id="Ito_pH_dependence"
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>2007-02-16</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#Ito_pH_dependence">
<dc:title>
Various formulations for the pH dependence of the Ito current.
</dc:title>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Moving to new formulation of base TNNP model.
</rdf:value>
<cmeta:modifier rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</cmeta:modifier>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2007-06-06</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
</rdf:Description>
</rdf:RDF>
<import xlink:href="../../../../cellml/models/common/units.xml">
<units name="mV" units_ref="mV"/>
<units name="mM" units_ref="mM"/>
<units name="ms" units_ref="ms"/>
<units name="uA_per_mmsq" units_ref="uA_per_mmsq"/>
<units name="mS_per_mmsq" units_ref="mS_per_mmsq"/>
</import>
<component name="Ito_Xu" cmeta:id="Ito_Xu">
<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="#Ito_Xu">
<dc:title>
Formulation of pH dependence of Ito based on work of Xu et al. (1997).
</dc:title>
<cmeta:species>rat</cmeta:species>
<cmeta:bio_entity>Ventricular Myocyte</cmeta:bio_entity>
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>9140808</bqs:Pubmed_id>
<bqs:JournalArticle rdf:parseType="Resource">
<dc:creator>
<rdf:Seq>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Xu</vCard:Family>
<vCard:Given>Zhi</vCard:Given>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Rozanski</vCard:Family>
<vCard:Given>George</vCard:Given>
<vCard:Other>J</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
</rdf:Seq>
</dc:creator>
<dc:title>
Proton inhibition of transient outward potassium current in rat ventricular myocytes.
</dc:title>
<dcterms:issued rdf:parseType="Resource">
<dcterms:W3CDTF>1997</dcterms:W3CDTF>
</dcterms:issued>
<bqs:Journal rdf:parseType="Resource">
<dc:title>J Mol Cell Cardiol</dc:title>
</bqs:Journal>
<bqs:volume>29</bqs:volume>
<bqs:first_page>481</bqs:first_page>
<bqs:last_page>490</bqs:last_page>
</bqs:JournalArticle>
</bqs:reference>
</rdf:Description>
</rdf:RDF>
<variable cmeta:id="Ito" name="Ito" public_interface="out" units="uA_per_mmsq"/>
<!-- variables used and defined by the original Ito formulation -->
<variable cmeta:id="Ito_original" name="Ito_original" public_interface="in" private_interface="out" units="uA_per_mmsq"/>
<variable name="V" public_interface="in" private_interface="out" units="mV"/>
<variable name="time" public_interface="in" units="ms"/>
<!-- variables for the pH dependence -->
<variable name="V_half_act" public_interface="in" private_interface="out" units="mV"/>
<variable name="V_half_inact" public_interface="in" private_interface="out" units="mV"/>
<variable name="k_act" public_interface="in" private_interface="out" units="mV"/>
<variable name="k_inact" public_interface="in" private_interface="out" units="mV"/>
<!-- steady state activation -->
<variable cmeta:id="act" name="act" public_interface="out" private_interface="out" units="dimensionless"/>
<!-- steady state inactivation -->
<variable cmeta:id="inact" name="inact" public_interface="out" private_interface="out" units="dimensionless"/>
<variable cmeta:id="ph_gate" name="gate" initial_value="1.0" public_interface="out" private_interface="out" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply><eq/>
<ci>act</ci>
<apply><times/>
<apply><divide/>
<cn cellml:units="dimensionless">1.0</cn>
<apply><plus/>
<cn cellml:units="dimensionless">1.0</cn>
<apply><exp/>
<apply><divide/>
<apply><minus/>
<ci>V_half_act</ci>
<ci>V</ci>
</apply>
<ci>k_act</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply><eq/>
<ci>inact</ci>
<apply><times/>
<apply><divide/>
<cn cellml:units="dimensionless">1.0</cn>
<apply><plus/>
<cn cellml:units="dimensionless">1.0</cn>
<apply><exp/>
<apply><divide/>
<apply><minus/>
<ci>V_half_inact</ci>
<ci>V</ci>
</apply>
<ci>k_inact</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<!--
<apply><eq/>
<apply><diff/>
<ci>gate</ci>
<bvar><ci>time</ci></bvar>
</apply>
<apply><minus/>
<apply><times/>
<ci>act</ci>
<apply><minus/>
<cn cellml:units="dimensionless">1.0</cn>
<ci>gate</ci>
</apply>
</apply>
<apply><times/>
<ci>inact</ci>
<ci>gate</ci>
</apply>
</apply>
</apply>
-->
<apply><eq/>
<ci>Ito</ci>
<apply><times/>
<ci>act</ci>
<ci>inact</ci>
<ci>Ito_original</ci>
</apply>
</apply>
</math>
</component>
</model>
