- 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/TNNP-periodic-increasing-frequency.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="tnnp_periodic_stimulus_increasing_stimulus"
cmeta:id="tnnp_periodic_stimulus_increasing_stimulus"
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>2007-04-30</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#tnnp_periodic_stimulus_increasing_stimulus">
<dc:title>
Base TNNP epicardial model with periodic stimulus applied with
increasing frequency.
</dc:title>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Moving to using ion-specific additional currents which incorporate
the stimulus current.
</rdf:value>
<cmeta:modifier rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</cmeta:modifier>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2007-05-24</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Adding in additional SR Ca flux term.
</rdf:value>
<cmeta:modifier rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</cmeta:modifier>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2007-6-22</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<cs:simulation>
<rdf:Description rdf:ID="simulation">
<cs:simulationName>PeriodicStimulus</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">
0.1
</cs:maximumStepSize>
<cs:tabulationStepSize
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
1.0
</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">
4200e3
</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="uA_per_mmcu" units_ref="uA_per_mmcu"/>
<units name="uA_per_mmsq" units_ref="uA_per_mmsq"/>
<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>
<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>
<connection>
<map_components component_1="time" component_2="stimulus_protocol_params"/>
<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="time" public_interface="in" units="ms"/>
<variable name="stimPeriod" 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"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply><eq/>
<ci>stimPeriod</ci>
<piecewise>
<piece>
<!-- 0.25 Hz -->
<cn cellml:units="ms">4e3</cn>
<apply><lt/>
<ci>time</ci>
<cn cellml:units="ms">600e3</cn>
</apply>
</piece>
<piece>
<!-- 0.5 Hz -->
<cn cellml:units="ms">2e3</cn>
<apply><and/>
<apply><geq/>
<ci>time</ci>
<cn cellml:units="ms">600e3</cn>
</apply>
<apply><lt/>
<ci>time</ci>
<cn cellml:units="ms">1200e3</cn>
</apply>
</apply>
</piece>
<piece>
<!-- 1 Hz -->
<cn cellml:units="ms">1e3</cn>
<apply><and/>
<apply><geq/>
<ci>time</ci>
<cn cellml:units="ms">1200e3</cn>
</apply>
<apply><lt/>
<ci>time</ci>
<cn cellml:units="ms">1800e3</cn>
</apply>
</apply>
</piece>
<piece>
<!-- 1.5 Hz -->
<cn cellml:units="ms">666.66</cn>
<apply><and/>
<apply><geq/>
<ci>time</ci>
<cn cellml:units="ms">1800e3</cn>
</apply>
<apply><lt/>
<ci>time</ci>
<cn cellml:units="ms">2400e3</cn>
</apply>
</apply>
</piece>
<piece>
<!-- 2 Hz -->
<cn cellml:units="ms">500</cn>
<apply><and/>
<apply><geq/>
<ci>time</ci>
<cn cellml:units="ms">2400e3</cn>
</apply>
<apply><lt/>
<ci>time</ci>
<cn cellml:units="ms">3000e3</cn>
</apply>
</apply>
</piece>
<piece>
<!-- 2.5 Hz -->
<cn cellml:units="ms">400</cn>
<apply><and/>
<apply><geq/>
<ci>time</ci>
<cn cellml:units="ms">3000e3</cn>
</apply>
<apply><lt/>
<ci>time</ci>
<cn cellml:units="ms">3600e3</cn>
</apply>
</apply>
</piece>
<piece>
<!-- 3 Hz -->
<cn cellml:units="ms">333.33</cn>
<apply><and/>
<apply><geq/>
<ci>time</ci>
<cn cellml:units="ms">3600e3</cn>
</apply>
<apply><lt/>
<ci>time</ci>
<cn cellml:units="ms">4200e3</cn>
</apply>
</apply>
</piece>
<otherwise>
<cn cellml:units="ms">1e3</cn>
</otherwise>
</piecewise>
</apply>
</math>
</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, in this case
just the stimulus current as an additional potassium current.
</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" initial_value="0.0" public_interface="out" private_interface="out" units="mM_per_ms"/>
<variable name="Istim" public_interface="in" units="uA_per_mmsq"/>
<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>
</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="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>
</model>
