- 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/INaCa-modified-ischemic-pHi.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="INaCa_modified_ischemic_pHi"
cmeta:id="INaCa_modified_ischemic_pHi"
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>2007-06-20</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#INaCa_modified_ischemic_pHi">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
This model imports the pre-configured base TNNP model extended with the INaCa
modifications. Here we are only defining the parameters
for the modifications and defining the simulation metadata. The parameters
are for the ischemic pHi conditions.
</rdf:value>
<dc:creator rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</dc:creator>
</cmeta:comment>
<cs:simulation>
<rdf:Description rdf:ID="simulation">
<cs:simulationName>Simulation</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="INaCa-modified.xml#time"/>
</cs:boundVariable>
<cs:maximumStepSize
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
0.1
</cs:maximumStepSize>
<cs:tabulationStepSize
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
0.1
</cs:tabulationStepSize>
<cs:startingValue
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
0
</cs:startingValue>
<cs:endingValue
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
2000
</cs:endingValue>
</rdf:Description>
</cs:boundIntervals>
</rdf:Description>
</cs:simulation>
</rdf:Description>
</rdf:RDF>
<import xlink:href="../../../cellml/models/common/units.xml">
<units name="mM" units_ref="mM"/>
</import>
<import xlink:href="INaCa-modified.xml">
<component name="model" component_ref="interface"/>
</import>
<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 extra parameters for the modified INaCa, under ischemic pHi conditions.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="H_i" initial_value="3.98e-4" public_interface="out" units="mM"/>
<variable name="k_half_pHi" initial_value="3.343e-5" public_interface="out" units="mM"/>
<variable name="H_pHi" initial_value="0.813" public_interface="out" units="dimensionless"/>
<variable name="ATP_i" initial_value="6.8" public_interface="out" units="mM"/>
<variable name="k_ATPi" initial_value="23.0588" public_interface="out" units="dimensionless"/>
</component>
<connection>
<map_components component_1="parameters" component_2="model"/>
<map_variables variable_1="H_i" variable_2="H_i"/>
<map_variables variable_1="k_half_pHi" variable_2="k_half_pHi"/>
<map_variables variable_1="H_pHi" variable_2="H_pHi"/>
<map_variables variable_1="ATP_i" variable_2="ATP_i"/>
<map_variables variable_1="k_ATPi" variable_2="k_ATPi"/>
</connection>
</model>
