- 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.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="INaCa_modified_ischemic"
cmeta:id="INaCa_modified_ischemic"
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">
<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 ischemic 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 conditions.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="H_i" initial_value="3.98e-3" 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="3.0" 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>