- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2021-09-16 22:13:11+12:00
- Desc:
- adding SED-ML for LRd, JRW, and N98 models and adding them to the jupyter notebook
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/a1/rawfile/ab0ecb950e3419f414b804ff0022c328f36fc046/models/1975_hunter/experiments/stimulus.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="cubic_with_stimulus"
cmeta:id="cubic_with_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>d.nickerson@auckland.ac.nz</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</dc:creator>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2005-01-06</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Bioengineering Institute, The University of Auckland
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#cubic_with_stimulus">
<dc:title>
The cubic polynomial model of Hunter et al. (1975) stimulated.
</dc:title>
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
This is the CellML description of an action potential simulation
with the cubic polynomial model (Hunter et al. 1975)
</rdf:value>
<dc:creator rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</dc:creator>
</cmeta:comment>
<bqs:reference>
<bqs:Pubmed_id>792954</bqs:Pubmed_id>
</bqs:reference>
<cs:simulation>
<rdf:Description rdf:ID="simulation">
<cs:multistepMethod>adams</cs:multistepMethod>
<cs:iterationMethod>functional</cs:iterationMethod>
<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">
0.05
</cs:maximumStepSize>
<cs:tabulationStepSize rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
0.5
</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">
40
</cs:endingValue>
</rdf:Description>
</cs:boundIntervals>
</rdf:Description>
</cs:simulation>
</rdf:Description>
</rdf:RDF>
<import xlink:href="../../common/units.xml">
<units name="ms" units_ref="ms"/>
<units name="mV" units_ref="mV"/>
<units name="mV_per_ms" units_ref="mV_per_ms"/>
<units name="uF_per_mmsq" units_ref="uF_per_mmsq"/>
<units name="mS_per_mmsq" units_ref="mS_per_mmsq"/>
<units name="uA_per_mmsq" units_ref="uA_per_mmsq"/>
<units name="uA_per_mmcu" units_ref="uA_per_mmcu"/>
<units name="per_mm" units_ref="per_mm"/>
</import>
<import xlink:href="../1975_cubic_polynomial.xml">
<component name="model" component_ref="interface"/>
</import>
<component name="time" cmeta:id="timeComponent">
<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="#timeComponent">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The actual definition of the time variable.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="time" cmeta:id="time" initial_value="0.0" public_interface="out" units="ms"/>
</component>
<connection>
<map_components component_1="model" component_2="time"/>
<map_variables variable_1="t" variable_2="time"/>
</connection>
<component name="stimulus_protocol" cmeta:id="stimulus_protocol">
<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">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
Here we define the stimulus protocol for the simulation.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="IStim" public_interface="out" units="uA_per_mmsq"/>
<variable name="time" public_interface="in" units="ms"/>
<variable name="stimTime" initial_value="20" units="ms"/>
<variable name="stimDuration" initial_value="1" units="ms"/>
<variable name="stimCurrent" initial_value="100" units="uA_per_mmcu"/>
<variable name="Am" initial_value="200" 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><and/>
<apply><geq/>
<ci>time</ci>
<ci>stimTime</ci>
</apply>
<apply><leq/>
<ci>time</ci>
<apply><plus/>
<ci>stimTime</ci>
<ci>stimDuration</ci>
</apply>
</apply>
</apply>
</piece>
<otherwise>
<cn cellml:units="uA_per_mmsq">0.0</cn>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<connection>
<map_components component_1="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>
<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>
Model parameters.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="Cm" initial_value="0.01" public_interface="out" units="uF_per_mmsq"/>
<variable name="Vm_rest" initial_value="-85.0" public_interface="out" units="mV"/>
<variable name="Vm_plateau" initial_value="15.0" public_interface="out" units="mV"/>
<variable name="Vm_threshold" initial_value="-75.0" public_interface="out" units="mV"/>
<variable name="Vm_initial" initial_value="-85.0" public_interface="out" units="mV"/>
<variable name="membrane_conductance" initial_value="0.004" public_interface="out" units="mS_per_mmsq"/>
</component>
<connection>
<map_components component_1="model" component_2="parameters"/>
<map_variables variable_1="Cm" variable_2="Cm"/>
<map_variables variable_1="Vm_rest" variable_2="Vm_rest"/>
<map_variables variable_1="Vm_plateau" variable_2="Vm_plateau"/>
<map_variables variable_1="Vm_threshold" variable_2="Vm_threshold"/>
<map_variables variable_1="Vm_initial" variable_2="Vm_initial"/>
<map_variables variable_1="membrane_conductance" variable_2="membrane_conductance"/>
</connection>
</model>
