- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2012-08-28 16:59:24+12:00
- Desc:
- replacing CellML simulation metadata with CSim summary description; bubbling up membrane currents and potential to allow output/referencing via SED-ML.
- Permanent Source URI:
- http://models.cellml.org/w/andre/VPH-MIP/rawfile/a29bfba242e747b82657c6d2d782937d0a01be79/experiments/INa-gating-kinetics.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="INa_gating_kinetics"
cmeta:id="INa_gating_kinetics_model"
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>david.nickerson@nus.edu.sg</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>National University of Singapore</vCard:Orgname>
<vCard:Orgunit>Division of Bioengineering</vCard:Orgunit>
</vCard:ORG>
</dc:creator>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-03-14</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#INa_gating_kinetics_model">
<dc:title>
The gating kinetics of the Hodgkin & Huxley (1952) sodium current.
</dc:title>
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
Here we investigate the gating kinetics of the Hodgkin & Huxley sodium current by applying a linear potential ramp.
</rdf:value>
<dc:creator rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</dc:creator>
</cmeta:comment>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Update to use the new INa gating rates model in order to work around a possible bug in the API implementation (or my understanding of the CellML specification) which doesn't like importing encapsulated children directly.
</rdf:value>
<cmeta:modifier rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</cmeta:modifier>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2008-08-11</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<cs:simulation>
<rdf:Description rdf:ID="simulation">
<cs:simulationName>INa gating kinetics</cs:simulationName>
<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">
0.1
</cs:maximumStepSize>
<cs:tabulationStepSize
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
0.1
</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">
200
</cs:endingValue>
</rdf:Description>
</cs:boundIntervals>
</rdf:Description>
</cs:simulation>
</rdf:Description>
</rdf:RDF>
<import xlink:href="../components/units.xml">
<units name="ms" units_ref="ms"/>
<units name="mV_per_ms" units_ref="mV_per_ms"/>
<units name="mV" units_ref="mV"/>
</import>
<import xlink:href="../components/INa-gating-rates.xml">
<component name="alpha_m" component_ref="alpha_m"/>
<component name="beta_m" component_ref="beta_m"/>
<component name="alpha_h" component_ref="alpha_h"/>
<component name="beta_h" component_ref="beta_h"/>
</import>
<import xlink:href="../components/gating-variable.xml">
<component name="m_gate" component_ref="hh_gating_variable_steady_state"/>
</import>
<connection>
<map_components component_1="m_gate" component_2="alpha_m"/>
<map_variables variable_1="alpha" variable_2="alpha"/>
</connection>
<connection>
<map_components component_1="m_gate" component_2="beta_m"/>
<map_variables variable_1="beta" variable_2="beta"/>
</connection>
<import xlink:href="../components/gating-variable.xml">
<component name="h_gate" component_ref="hh_gating_variable_steady_state"/>
</import>
<connection>
<map_components component_1="h_gate" component_2="alpha_h"/>
<map_variables variable_1="alpha" variable_2="alpha"/>
</connection>
<connection>
<map_components component_1="h_gate" component_2="beta_h"/>
<map_variables variable_1="beta" variable_2="beta"/>
</connection>
<import xlink:href="potential-ramp.xml">
<component name="V" component_ref="ramp"/>
</import>
<import xlink:href="../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="m_gate" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="h_gate" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="time" component_2="V"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<component name="V_parameters" cmeta:id="V_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="#V_parameters">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
Here we define the parameters for the applied voltage ramp.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="k" initial_value="1.0" public_interface="out"
units="mV_per_ms"/>
<variable cmeta:id="V" name="V" public_interface="in" units="mV"/>
<variable cmeta:id="m_inf" name="m_inf" public_interface="in"
units="dimensionless"/>
<variable cmeta:id="h_inf" name="h_inf" public_interface="in"
units="dimensionless"/>
</component>
<connection>
<map_components component_1="V_parameters"
component_2="V"/>
<map_variables variable_1="k" variable_2="k"/>
<map_variables variable_1="V" variable_2="y"/>
</connection>
<connection>
<map_components component_1="alpha_m" component_2="V"/>
<map_variables variable_1="V" variable_2="y"/>
</connection>
<connection>
<map_components component_1="beta_m" component_2="V"/>
<map_variables variable_1="V" variable_2="y"/>
</connection>
<connection>
<map_components component_1="alpha_h" component_2="V"/>
<map_variables variable_1="V" variable_2="y"/>
</connection>
<connection>
<map_components component_1="beta_h" component_2="V"/>
<map_variables variable_1="V" variable_2="y"/>
</connection>
<connection>
<map_components component_1="m_gate" component_2="V_parameters"/>
<map_variables variable_1="gate_inf" variable_2="m_inf"/>
</connection>
<connection>
<map_components component_1="h_gate" component_2="V_parameters"/>
<map_variables variable_1="gate_inf" variable_2="h_inf"/>
</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 - in this case we use all default values.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
</component>
<connection>
<map_components component_1="alpha_m" component_2="default_parameters"/>
<map_variables variable_1="Tref" variable_2="Tref_rates"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="Q10" variable_2="Q10_rates"/>
</connection>
<connection>
<map_components component_1="beta_m" component_2="default_parameters"/>
<map_variables variable_1="Tref" variable_2="Tref_rates"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="Q10" variable_2="Q10_rates"/>
</connection>
<connection>
<map_components component_1="alpha_h" component_2="default_parameters"/>
<map_variables variable_1="Tref" variable_2="Tref_rates"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="Q10" variable_2="Q10_rates"/>
</connection>
<connection>
<map_components component_1="beta_h" component_2="default_parameters"/>
<map_variables variable_1="Tref" variable_2="Tref_rates"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="Q10" 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>
<variable cmeta:id="V_initial" name="V_initial" public_interface="out"
units="mV" initial_value="-120.0"/>
</component>
<connection>
<map_components component_1="m_gate"
component_2="default_initial_conditions"/>
<map_variables variable_1="gate_initial" variable_2="m_initial"/>
</connection>
<connection>
<map_components component_1="h_gate"
component_2="default_initial_conditions"/>
<map_variables variable_1="gate_initial" variable_2="h_initial"/>
</connection>
<connection>
<map_components component_1="V" component_2="initial_conditions"/>
<map_variables variable_1="y_initial" variable_2="V_initial"/>
</connection>
</model>
