- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2021-09-17 15:50:49+12:00
- Desc:
- tweak html formatting
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/a1/rawfile/1b3862589abf79ae9119ee0b5e99a8b785d762e1/tutorial/experiment.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="generic_experiment"
cmeta:id="generic_experiment"
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>Auckland Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</dc:creator>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-07</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Auckland Bioengineering Institute, The University of Auckland.
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#generic_experiment">
<dc:title>
Modified HH with periodic stimulus applied plus default parameter set.
</dc:title>
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
Applies the default set of parameters to the modified HH model and leaves some parameters free for customisation. Applies the periodic stimulus protocol from the original HH implementation from http://www.bioeng.nus.edu.sg/compbiolab/p3/.
</rdf:value>
<dc:creator rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</dc:creator>
</cmeta:comment>
<cs:simulation>
<rdf:Description rdf:ID="simulation">
<cs:multistepMethod>bdf</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">
0.5
</cs:maximumStepSize>
<cs:tabulationStepSize
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
1
</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">
3000
</cs:endingValue>
</rdf:Description>
</cs:boundIntervals>
</rdf:Description>
</cs:simulation>
</rdf:Description>
</rdf:RDF>
<import xlink:href="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/components/units.xml">
<units name="ms" units_ref="ms"/>
<units name="mV" units_ref="mV"/>
<units name="mS_per_cmsq" units_ref="mS_per_cmsq"/>
<units name="uA_per_cmsq" units_ref="uA_per_cmsq"/>
<units name="uF_per_cmsq" units_ref="uF_per_cmsq"/>
</import>
<import xlink:href="modified-hh.xml">
<component name="model" component_ref="action_potential"/>
</import>
<import xlink:href="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/periodic-IStim-protocol.xml">
<component name="stimulus_protocol" component_ref="stimulus_protocol"/>
</import>
<import xlink:href="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/components/default-variable-values.xml">
<component name="default_parameters" component_ref="parameters"/>
<component name="default_initial_conditions"
component_ref="initial_conditions"/>
</import>
<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 cmeta:id="time" name="time" initial_value="0.0"
public_interface="out" units="ms"/>
</component>
<connection>
<map_components component_1="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="model"
component_2="stimulus_protocol"/>
<map_variables variable_1="Istim" variable_2="IStim"/>
</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>
The model parameters.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="stimPeriod" initial_value="750" public_interface="out" units="ms"/>
<variable name="stimDuration" initial_value="0.5" public_interface="out" units="ms"/>
<variable name="stimCurrent" initial_value="-200.0" public_interface="out" units="uA_per_cmsq"/>
<variable cmeta:id="gK_max" name="gK_max" public_interface="out" private_interface="out" units="mS_per_cmsq" initial_value="12"/>
<variable cmeta:id="Cm" name="Cm" public_interface="out" private_interface="out" units="uF_per_cmsq" initial_value="12.0"/>
</component>
<connection>
<map_components component_1="parameters" 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="model" component_2="parameters"/>
<map_variables variable_1="gK_max" variable_2="gK_max"/>
<map_variables variable_1="Cm" variable_2="Cm"/>
</connection>
<connection>
<map_components component_1="model" component_2="default_parameters"/>
<map_variables variable_1="VNa" variable_2="VNa"/>
<map_variables variable_1="VK" variable_2="VK"/>
<map_variables variable_1="Vleak" variable_2="Vleak"/>
<map_variables variable_1="gleak_max" variable_2="gleak_max"/>
<map_variables variable_1="gNa_max" variable_2="gNa_max"/>
<map_variables variable_1="Tref_rates" variable_2="Tref_rates"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="Q10_rates" variable_2="Q10_rates"/>
</connection>
<component name="initial_conditions" cmeta:id="initial_conditions">
<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="#initial_conditions">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The initial conditions - using all default values in this case.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
</component>
<connection>
<map_components component_1="model" component_2="default_initial_conditions"/>
<map_variables variable_1="V_initial" variable_2="V_initial"/>
<map_variables variable_1="m_initial" variable_2="m_initial"/>
<map_variables variable_1="h_initial" variable_2="h_initial"/>
<map_variables variable_1="n_initial" variable_2="n_initial"/>
</connection>
</model>
