- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2021-09-16 01:07:43+12:00
- Desc:
- adding BR variant comparison to jupyter notebook
- Permanent Source URI:
- https://models.fieldml.org/workspace/a1/rawfile/faebb18f1db53a7d1f8f4e7fc588d660d45744c0/models/1962_noble/experiments/periodic-stimulus.xml
<?xml version='1.0' encoding='UTF-8'?>
<model cmeta:id="noble_paced" name="noble_1962_paced" 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">
<import xlink:href="../../common/units.xml">
<units name="ms" units_ref="ms"/>
<units name="uA_per_mmsq" units_ref="uA_per_mmsq"/>
<units name="uA_per_mmcu" units_ref="uA_per_mmcu"/>
<units name="mV" units_ref="mV"/>
<units name="mS_per_mmsq" units_ref="mS_per_mmsq"/>
<units name="per_mm" units_ref="per_mm"/>
</import>
<import xlink:href="../1962_noble.xml">
<component component_ref="interface" name="math_model"/>
</import>
<component name="output_variables">
<variable name="V" public_interface="in" units="mV"/>
</component>
<connection>
<map_components component_1="math_model" component_2="output_variables"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<component cmeta:id="time_component" name="time">
<variable cmeta:id="time" initial_value="0.0" name="time" public_interface="out" units="ms"/>
</component>
<connection>
<map_components component_1="math_model" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<component cmeta:id="stimulus_protocol" name="stimulus_protocol">
<variable name="IStim" public_interface="out" units="uA_per_mmsq"/>
<variable name="time" public_interface="in" units="ms"/>
<variable initial_value="750" name="stimPeriod" units="ms"/>
<variable initial_value="1" name="stimDuration" units="ms"/>
<variable initial_value="400" name="stimCurrent" units="uA_per_mmcu"/>
<variable initial_value="200" name="Am" units="per_mm"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="stimulus_calculation">
<eq/>
<ci>IStim</ci>
<piecewise>
<piece>
<apply>
<divide/>
<ci>stimCurrent</ci>
<ci>Am</ci>
</apply>
<apply>
<lt/>
<apply>
<rem/>
<ci>time</ci>
<ci>stimPeriod</ci>
</apply>
<ci>stimDuration</ci>
</apply>
</piece>
<otherwise>
<cn cellml:units="uA_per_mmsq">0.0</cn>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<connection>
<map_components component_1="math_model" component_2="stimulus_protocol"/>
<map_variables variable_1="I_stim" variable_2="IStim"/>
</connection>
<connection>
<map_components component_1="time" component_2="stimulus_protocol"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<component cmeta:id="parameters" name="parameters">
<variable initial_value="0.001" name="g_K_add" public_interface="out" units="mS_per_mmsq"/>
</component>
<connection>
<map_components component_1="math_model" component_2="parameters"/>
<map_variables variable_1="g_K_add" variable_2="g_K_add"/>
</connection>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="">
<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<vCard:Family xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Nickerson</vCard:Family>
<vCard:Given xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">David</vCard:Given>
</vCard:N>
<vCard:EMAIL xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">d.nickerson@auckland.ac.nz</rdf:value>
<rdf:type xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:resource="http://imc.org/vCard/3.0#internet"/>
</vCard:EMAIL>
<vCard:ORG xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<vCard:Orgname xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">The University of Auckland</vCard:Orgname>
<vCard:Orgunit xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</dc:creator>
<dcterms:created xmlns:dcterms="http://purl.org/dc/terms/" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<dcterms:W3CDTF xmlns:dcterms="http://purl.org/dc/terms/">2004-12-21</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher xmlns:dc="http://purl.org/dc/elements/1.1/">
Bioengineering Institute, The University of Auckland.
</dc:publisher>
</rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#1962_noble_paced">
<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">
Paced version of Noble (1962) Purkinje fibre model
</dc:title>
<cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
This CellML file describes the boundary conditions used with the
Noble (1962) cardiac Purkinje fibre electrophysiology model to
produce a free running (pacemaker) version of the model.
</rdf:value>
<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<vCard:FN xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">David Nickerson</vCard:FN>
</dc:creator>
</cmeta:comment>
<cs:simulation xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:ID="simulation">
<cs:multistepMethod xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">bdf</cs:multistepMethod>
<cs:iterationMethod xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">functional</cs:iterationMethod>
<cs:boundIntervals xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:parseType="Collection" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<cs:boundVariable xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#time"/>
</cs:boundVariable>
<cs:maximumStepSize xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
0.01
</cs:maximumStepSize>
<cs:tabulationStepSize xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
1.0
</cs:tabulationStepSize>
<cs:startingValue xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
0
</cs:startingValue>
<cs:endingValue xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
3000
</cs:endingValue>
</rdf:Description>
</cs:boundIntervals>
</rdf:Description>
</cs:simulation>
</rdf:Description>
</rdf:RDF>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#time_component">
<cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
The actual definition of the time variable.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#stimulus_protocol">
<cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
Here we define the stimulus protocol for the simulation.
In this case there is no stimulus applied.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#parameters">
<cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
Here we define the parameter values for this simulation. g_K_add
is used to cancel out the self-activating nature of the model.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
</model>
