- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2021-09-16 00:41:19+12:00
- Desc:
- Updating Noble 1962 model:
* Exposing the membrane potential to the top-level model;
* adding SED-ML for the paced and pacemaker variants of the model.
Using OpenCOR Snapshot release 2021-09-14.
- Permanent Source URI:
- https://models.fieldml.org/workspace/a1/rawfile/f954e59183314cd37f86c8832dc81317d01c8ec5/models/1961_fitzhugh/experiments/single-stimulus.xml
<?xml version='1.0' encoding='UTF-8'?>
<model cmeta:id="single_stimulus" name="single_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">
<import xlink:href="../../common/units.xml">
<units name="ms" units_ref="ms"/>
<units name="mV" units_ref="mV"/>
<units name="per_mm" units_ref="per_mm"/>
<units name="uA_per_mmcu" units_ref="uA_per_mmcu"/>
</import>
<import xlink:href="../model.xml">
<component component_ref="interface" name="math_model"/>
<units name="uApmmsq" units_ref="uApmmsq"/>
</import>
<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="t" variable_2="time"/>
</connection>
<import xlink:href="../../protocols/single-pulse-IStim.xml">
<component component_ref="stimulus_protocol" name="stimulus_protocol"/>
</import>
<component cmeta:id="stimulus_parameters" name="stimulus_parameters">
<variable initial_value="100" name="stimTime" public_interface="out" units="ms"/>
<variable initial_value="0.5" name="stimDuration" public_interface="out" units="ms"/>
<variable initial_value="400" name="stimCurrent" public_interface="out" units="uA_per_mmcu"/>
<variable initial_value="200" name="Am" public_interface="out" units="per_mm"/>
</component>
<connection>
<map_components component_1="math_model" component_2="stimulus_protocol"/>
<map_variables variable_1="Istim" variable_2="IStim"/>
</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="stimulus_parameters" component_2="stimulus_protocol"/>
<map_variables variable_1="stimTime" variable_2="stimTime"/>
<map_variables variable_1="stimDuration" variable_2="stimDuration"/>
<map_variables variable_1="stimCurrent" variable_2="stimCurrent"/>
<map_variables variable_1="Am" variable_2="Am"/>
</connection>
<component cmeta:id="output_variables" name="output_variables">
<variable name="Vm" public_interface="in" units="mV"/>
<variable name="v" public_interface="in" units="dimensionless"/>
<variable name="Iion" public_interface="in" units="uApmmsq"/>
</component>
<connection>
<map_components component_1="math_model" component_2="output_variables"/>
<map_variables variable_1="Vm" variable_2="Vm"/>
<map_variables variable_1="v" variable_2="v"/>
<map_variables variable_1="Iion" variable_2="Iion"/>
</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/">2009-06-16</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="#single_stimulus">
<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">
Action potential simulation with single stimulus.
</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 is the CellML description of a action potential simulation
with a single stimulus current applied to the default FHN 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#">
0.1
</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#">
800
</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_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 parameters for the standard stimulus protocol we import for this experiment.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
</model>
