- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2021-09-15 16:32:46+12:00
- Desc:
- Updates to Aliev and Panfilov model:
* Make sure model is valid OpenCOR CellML Text format;
* Make sure model is valid CellML;
* Add SED-ML for single stimulus experiment.
Using OpenCOR snapshot 2021-09-14
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/a1/rawfile/077833f63bee089a0bb0061d4c295ab133ebab35/models/1998_fenton/experiments/periodic-stimulus-generic.xml
<?xml version="1.0"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" name="fenton_karma_model_1998_experiment_model" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" cmeta:id="fenton_karma_model_1998_experiment_model">
<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>2009-06-17</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Bioengineering Institute, The University of Auckland
</dc:publisher>
</rdf:Description>
</rdf:RDF>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="../fenton_karma_model_1998_interface_model.xml">
<component component_ref="fenton_karma_model_1998_interface_component" name="fenton_karma_model_1998_interface_component"/>
</import>
<component name="interface" cmeta:id="interface">
<variable name="g_fi_max" private_interface="out" public_interface="in" units="mS_per_mm2"/>
<variable name="tau_0" private_interface="out" public_interface="in" units="ms"/>
<variable name="tau_r" private_interface="out" public_interface="in" units="ms"/>
<variable name="tau_si" private_interface="out" public_interface="in" units="ms"/>
<variable name="tau_v1_minus" private_interface="out" public_interface="in" units="ms"/>
<variable name="tau_v2_minus" private_interface="out" public_interface="in" units="ms"/>
<variable name="tau_v_plus" private_interface="out" public_interface="in" units="ms"/>
<variable name="tau_w_minus" private_interface="out" public_interface="in" units="ms"/>
<variable name="tau_w_plus" private_interface="out" public_interface="in" units="ms"/>
<variable name="u_v" private_interface="out" public_interface="in" units="dimensionless"/>
</component>
<connection>
<map_components component_1="fenton_karma_model_1998_interface_component" component_2="interface"/>
<map_variables variable_1="u_v" variable_2="u_v"/>
<map_variables variable_1="g_fi_max" variable_2="g_fi_max"/>
<map_variables variable_1="tau_v1_minus" variable_2="tau_v1_minus"/>
<map_variables variable_1="tau_v2_minus" variable_2="tau_v2_minus"/>
<map_variables variable_1="tau_v_plus" variable_2="tau_v_plus"/>
<map_variables variable_1="tau_0" variable_2="tau_0"/>
<map_variables variable_1="tau_r" variable_2="tau_r"/>
<map_variables variable_1="tau_si" variable_2="tau_si"/>
<map_variables variable_1="tau_w_minus" variable_2="tau_w_minus"/>
<map_variables variable_1="tau_w_plus" variable_2="tau_w_plus"/>
</connection>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="../fenton_karma_model_1998_variable_values_model.xml">
<component component_ref="parameters" name="generic_parameters"/>
<component component_ref="initial_values" name="initial_values"/>
</import>
<connection>
<map_components component_1="fenton_karma_model_1998_interface_component" component_2="generic_parameters"/>
<map_variables variable_1="Cm" variable_2="Cm"/>
<map_variables variable_1="V_o" variable_2="V_o"/>
<map_variables variable_1="V_fi" variable_2="V_fi"/>
<map_variables variable_1="u_c" variable_2="u_c"/>
<map_variables variable_1="u_csi" variable_2="u_csi"/>
<map_variables variable_1="k" variable_2="k"/>
</connection>
<connection>
<map_components component_1="fenton_karma_model_1998_interface_component" component_2="initial_values"/>
<map_variables variable_1="Vm_initial" variable_2="Vm_initial"/>
<map_variables variable_1="v_initial" variable_2="v_initial"/>
<map_variables variable_1="w_initial" variable_2="w_initial"/>
</connection>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="../../protocols/periodic-IStim.xml">
<component name="stimulus_protocol" component_ref="stimulus_protocol"/>
</import>
<component name="stimulus_parameters" cmeta:id="stimulus_parameters">
<variable name="stimPeriod" public_interface="out" private_interface="out" initial_value="500.0" units="ms"/>
<variable name="stimDuration" public_interface="out" private_interface="out" initial_value="1.0" units="ms"/>
<variable name="stimCurrent" public_interface="out" private_interface="out" initial_value="80" units="uA_per_mmcu"/>
<variable name="Am" public_interface="out" private_interface="out" initial_value="200" units="per_mm"/>
</component>
<connection>
<map_components component_1="stimulus_protocol" component_2="stimulus_parameters"/>
<map_variables variable_1="stimPeriod" variable_2="stimPeriod"/>
<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>
<connection>
<map_components component_1="stimulus_protocol" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="fenton_karma_model_1998_interface_component" component_2="stimulus_protocol"/>
<map_variables variable_1="I_stim" variable_2="IStim"/>
</connection>
<component name="time" cmeta:id="time_component">
<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_component">
<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="fenton_karma_model_1998_interface_component" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="../fenton_karma_model_1998_units_model.xml">
<units name="ms" units_ref="ms"/>
<units name="per_ms" units_ref="per_ms"/>
<units name="mV" units_ref="mV"/>
<units name="per_mV" units_ref="per_mV"/>
<units name="per_mV_ms" units_ref="per_mV_ms"/>
<units name="mS_per_mm2" units_ref="mS_per_mm2"/>
<units name="uF_per_mm2" units_ref="uF_per_mm2"/>
<units name="uA_per_mm2" units_ref="uA_per_mm2"/>
<units name="concentration_units" units_ref="concentration_units"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="../../common/units.xml">
<units name="per_mm" units_ref="per_mm"/>
<units name="uA_per_mmcu" units_ref="uA_per_mmcu"/>
</import>
<group>
<relationship_ref relationship="encapsulation"/>
<component_ref component="interface">
<component_ref component="fenton_karma_model_1998_interface_component"/>
<component_ref component="time"/>
<component_ref component="generic_parameters"/>
<component_ref component="stimulus_protocol"/>
<component_ref component="stimulus_parameters"/>
<component_ref component="generic_parameters"/>
<component_ref component="initial_values"/>
</component_ref>
</group>
</model>
