- 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://models.physiomeproject.org/w/andre/nickerson-2008/rawfile/d6328d18c94e9dad70f4d0e4b250e89429773b62/experiments/IK1-pH_clamp.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="IK1_pH_clamp"
cmeta:id="IK1_pH_clamp"
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#"
xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">
<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>2006-11-23</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#IK1_pH_clamp">
<dc:title>
pH clamp experiment using IK1 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>2007-06-04</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<cs:simulation>
<rdf:Description rdf:ID="simulation">
<cs:simulationName>pH clamp simulation on IK1</cs:simulationName>
<cs:multistepMethod>bdf</cs:multistepMethod>
<cs:iterationMethod>newton</cs:iterationMethod>
<cs:linearSolver>dense</cs:linearSolver>
<cs:boundIntervals rdf:parseType="Collection">
<rdf:Description>
<cs:boundVariable>
<rdf:Description rdf:about="#time"/>
</cs:boundVariable>
<cs:maximumStepSize
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
1.0e-5
</cs:maximumStepSize>
<cs:tabulationStepSize
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
1.0e-5
</cs:tabulationStepSize>
<cs:startingValue
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
1.0e-5
</cs:startingValue>
<cs:endingValue
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
1.0e-2
</cs:endingValue>
</rdf:Description>
</cs:boundIntervals>
</rdf:Description>
</cs:simulation>
</rdf:Description>
</rdf:RDF>
<import xlink:href="../../../cellml/models/common/units.xml">
<units name="ms" units_ref="ms"/>
<units name="mV" units_ref="mV"/>
<units name="mM" units_ref="mM"/>
<units name="mM_per_ms" units_ref="mM_per_ms"/>
<units name="uA_per_mmsq" units_ref="uA_per_mmsq"/>
<units name="mS_per_mmsq" units_ref="mS_per_mmsq"/>
</import>
<import xlink:href="../TNNP-extended/components/IK1-pH-dependence.xml">
<component name="IK1" component_ref="IK1_Ito"/>
</import>
<component name="pH_clamp" cmeta:id="pH_clamp">
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
<rdf:Description rdf:about="#pH_clamp">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
We define here the pH clamp experiment, in this case
a simple linear variation of [H], expressed as a
differential equation.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="time" public_interface="out" units="ms"/>
<variable cmeta:id="H_i" name="H_i" initial_value="1.0e-5" public_interface="out" units="mM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply><eq/>
<apply><diff/>
<bvar><ci>time</ci></bvar>
<ci>H_i</ci>
</apply>
<cn cellml:units="mM_per_ms">1.0</cn>
</apply>
</math>
</component>
<connection>
<map_components component_1="IK1" component_2="pH_clamp"/>
<map_variables variable_1="H_i" variable_2="H_i"/>
</connection>
<component name="parameters" cmeta:id="parameters">
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
<rdf:Description rdf:about="#parameters">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The model parameters which differ from the default.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="K_half_NPo" initial_value="7.7625e-4" public_interface="out" units="mM"/>
<variable name="H_NPo" initial_value="2.52" public_interface="out" units="dimensionless"/>
<variable name="K_half_IK1max" initial_value="9.61589e-3" public_interface="out" units="mM"/>
<variable name="H_IK1max" initial_value="0.633733" public_interface="out" units="dimensionless"/>
<variable name="E_K" initial_value="-85" public_interface="out" units="mV"/>
<variable name="IK1_dummy" initial_value="0" public_interface="out" units="uA_per_mmsq"/>
</component>
<connection>
<map_components component_1="IK1" component_2="parameters"/>
<map_variables variable_1="K_half_NPo" variable_2="K_half_NPo"/>
<map_variables variable_1="H_NPo" variable_2="H_NPo"/>
<map_variables variable_1="K_half_IK1max" variable_2="K_half_IK1max"/>
<map_variables variable_1="H_IK1max" variable_2="H_IK1max"/>
<map_variables variable_1="IK1_original" variable_2="IK1_dummy"/>
</connection>
</model>
