- 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/Jrel-modified.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="Jrel_modified"
cmeta:id="Jrel_modified"
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>2007-06-22</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#Jrel_modified">
<dc:title>
Base TNNP epicardial model with periodic stimulus and Jrel modification for pHi.
</dc:title>
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
This model imports the base TNNP epicardial model with default parameter
values and boundary conditions specified. This model defines a periodic
potassium stimulus current and also adds intacellular pH dependence of Jrel.
It is expected that this model will be imported into a
model which defines the parameters for the extra Jrel dependence models.
</rdf:value>
<dc:creator rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</dc:creator>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<import xlink:href="../../../cellml/models/common/units.xml">
<units name="ms" units_ref="ms"/>
<units name="uA_per_mmcu" units_ref="uA_per_mmcu"/>
<units name="uA_per_mmsq" units_ref="uA_per_mmsq"/>
<units name="mM" units_ref="mM"/>
<units name="mM_per_ms" units_ref="mM_per_ms"/>
</import>
<import xlink:href="TNNP.xml">
<component name="base_model" component_ref="interface"/>
</import>
<import xlink:href="../../../cellml/protocols/periodic-IStim.xml">
<component name="stimulus_protocol" component_ref="stimulus_protocol"/>
</import>
<import xlink:href="../TNNP-extended/components/Jrel-modifications.xml">
<component name="Jrel_modified" component_ref="Jrel"/>
</import>
<component name="interface" cmeta:id="interface">
<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="#interface">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The interface by which this model can be accessed.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="H_i" public_interface="in" private_interface="out" units="mM"/>
<variable name="k_half_pHi" public_interface="in" private_interface="out" units="mM"/>
<variable name="H_pHi" public_interface="in" private_interface="out" units="dimensionless"/>
<variable name="k_pHi" public_interface="in" private_interface="out" units="dimensionless"/>
</component>
<connection>
<map_components component_1="Jrel_modified" component_2="interface"/>
<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="k_pHi" variable_2="k_pHi"/>
</connection>
<component name="time" cmeta:id="time">
<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="#time">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The actual definition of the time variable.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable cmeta:id="time" name="time" initial_value="0.0" public_interface="out" units="ms"/>
</component>
<connection>
<map_components component_1="base_model" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="time" component_2="stimulus_protocol"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<component name="stimulus_protocol_params" cmeta:id="stimulus_protocol_params">
<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="#stimulus_protocol_params">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
Here we define the parameters for the applied periodic stimulus.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="stimPeriod" initial_value="1000" public_interface="out" units="ms"/>
<variable name="stimDuration" initial_value="1" public_interface="out" units="ms"/>
<variable name="stimCurrent" initial_value="100" public_interface="out" units="uA_per_mmcu"/>
</component>
<connection>
<map_components component_1="stimulus_protocol_params" component_2="stimulus_protocol"/>
<map_variables variable_1="stimPeriod" variable_2="stimPeriod"/>
<map_variables variable_1="stimDuration" variable_2="stimDuration"/>
<map_variables variable_1="stimCurrent" variable_2="stimCurrent"/>
</connection>
<connection>
<map_components component_1="base_model" component_2="stimulus_protocol"/>
<map_variables variable_1="Am" variable_2="Am"/>
</connection>
<connection>
<map_components component_1="additional_currents" component_2="stimulus_protocol"/>
<map_variables variable_1="Istim" variable_2="IStim"/>
</connection>
<component name="additional_currents" cmeta:id="additional_currents">
<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="#additional_currents">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
Here we define any additional currents for use in the model.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable cmeta:id="IK_additional" name="IK_additional" public_interface="out" private_interface="out" units="uA_per_mmsq"/>
<variable cmeta:id="ICa_additional" name="ICa_additional" initial_value="0.0" public_interface="out" private_interface="out" units="uA_per_mmsq"/>
<variable cmeta:id="INa_additional" name="INa_additional" initial_value="0.0" public_interface="out" private_interface="out" units="uA_per_mmsq"/>
<variable cmeta:id="JCaSR_additional" name="JCaSR_additional" public_interface="out" private_interface="out" units="mM_per_ms"/>
<variable name="Istim" public_interface="in" units="uA_per_mmsq"/>
<variable cmeta:id="Jrel_modified" name="Jrel_modified" public_interface="in" units="mM_per_ms"/>
<variable cmeta:id="Jrel_original" name="Jrel_original" public_interface="in" units="mM_per_ms"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="IK_additional_eq"><eq/>
<ci>IK_additional</ci>
<apply><minus/>
<ci>Istim</ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="JCaSR_additional_eq"><eq/>
<ci>JCaSR_additional</ci>
<apply><minus/>
<ci>Jrel_modified</ci>
<ci>Jrel_original</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="base_model" component_2="additional_currents"/>
<map_variables variable_1="IK_additional" variable_2="IK_additional"/>
<map_variables variable_1="Jrel" variable_2="Jrel_original"/>
<map_variables variable_1="ICa_additional" variable_2="ICa_additional"/>
<map_variables variable_1="INa_additional" variable_2="INa_additional"/>
<map_variables variable_1="JCaSR_additional" variable_2="JCaSR_additional"/>
</connection>
<connection>
<map_components component_1="base_model" component_2="Jrel_modified"/>
<map_variables variable_1="Jrel" variable_2="Jrel_original"/>
</connection>
<connection>
<map_components component_1="additional_currents" component_2="Jrel_modified"/>
<map_variables variable_1="Jrel_modified" variable_2="Jrel"/>
</connection>
<group>
<relationship_ref relationship="encapsulation"/>
<component_ref component="interface">
<component_ref component="base_model"/>
<component_ref component="additional_currents"/>
<component_ref component="stimulus_protocol"/>
<component_ref component="stimulus_protocol_params"/>
<component_ref component="time"/>
<component_ref component="Jrel_modified"/>
</component_ref>
</group>
</model>
