- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2013-05-04 07:40:04+12:00
- Desc:
- adding initial TODO list to keep track of what I need to do to get things working with more recent tools than my original CellMLSimulator that I used in this paper
- Permanent Source URI:
- https://models.physiomeproject.org/w/andre/nickerson-2008/rawfile/d6328d18c94e9dad70f4d0e4b250e89429773b62/cellml/models/2004_tenTusscher-version-2/experiments/Ito_gates-voltage_clamp-epi.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="Ito_gates_voltage_clamp_epi"
cmeta:id="Ito_gates_voltage_clamp_epi"
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#">
<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>2004-12-28</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#Ito_gates_voltage_clamp_epi">
<dc:title>
Voltage clamp experiment using ten Tusscher et al. (2004) epicardial
transient outward current gates.
</dc:title>
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
This is the CellML description of a voltage clamp experiment examining
the epicardial transient outward current's gating variables from the
ten Tusscher et al. (2004) human AP model. This produces data for
comparison to Fig. 3 of the AJP paper.
</rdf:value>
<dc:creator rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</dc:creator>
</cmeta:comment>
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>14656705</bqs:Pubmed_id>
<bqs:JournalArticle rdf:parseType="Resource">
<dc:creator>
<rdf:Seq>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>ten Tusscher</vCard:Family>
<vCard:Given>K</vCard:Given>
<vCard:Other>H</vCard:Other>
<vCard:Other>W</vCard:Other>
<vCard:Other>J</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Noble</vCard:Family>
<vCard:Given>D</vCard:Given>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Noble</vCard:Family>
<vCard:Given>P</vCard:Given>
<vCard:Other>J</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Panfilov</vCard:Family>
<vCard:Given>A</vCard:Given>
<vCard:Other>V</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
</rdf:Seq>
</dc:creator>
<dc:title>
A model for human ventricular tissue
</dc:title>
<dcterms:issued rdf:parseType="Resource">
<dcterms:W3CDTF>2004-04</dcterms:W3CDTF>
</dcterms:issued>
<bqs:Journal rdf:parseType="Resource">
<dc:title>American Journal of Physiology</dc:title>
</bqs:Journal>
<bqs:volume>286</bqs:volume>
<bqs:first_page>H1573</bqs:first_page>
<bqs:last_page>H1589</bqs:last_page>
</bqs:JournalArticle>
</bqs:reference>
<sim:integration id="simulator-data"
xmlns:sim="http://www.cellml.org/simulation-data/1.0#">
<rdf:RDF>
<rdf:Description rdf:about="#simulator-data">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
Here we put information for Andre's simulator program to
use when running this experiment. It is possible that some
of this data could be useful to other simulation programs.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<!-- A suitable range for the bound variable -->
<!-- Vm from -150 -> +100 mV -->
<sim:bound-variable-range
start="0"
end="250"
tabulation-step-size="0.1"
maximum-step-size="0.01"/>
<!-- The numerical solver we want to use -->
<sim:numerical-solver
linear-multistep-method="ADAMS"
iteration-method="FUNCTIONAL"
linear-solver="NONE"/>
<!-- The numerical tolerances? -->
</sim:integration>
</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"/>
</import>
<import xlink:href="../components/Ito-components.xml">
<!-- need to import from the components model since the
import in the current model needs to resolve everything -->
<component name="r_gate" component_ref="r_gate"/>
<component name="s_gate" component_ref="epi_M_s_gate"/>
</import>
<component name="voltage_clamp" cmeta:id="voltage_clamp">
<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="#voltage_clamp">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
We define here the voltage clamp experiment, in this case
a simple linear variation of membrane potential, expressed
as a differential equation.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="time" public_interface="out" units="ms"/>
<variable name="Vm" initial_value="-150" public_interface="out" units="mV"/>
<variable name="dummy" initial_value="0" public_interface="out" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply><eq/>
<apply><diff/>
<bvar><ci>time</ci></bvar>
<ci>Vm</ci>
</apply>
<cn cellml:units="mV_per_ms">1.0</cn>
</apply>
</math>
</component>
<connection>
<map_components component_1="r_gate" component_2="voltage_clamp"/>
<map_variables variable_1="V" variable_2="Vm"/>
<map_variables variable_1="r_initial" variable_2="dummy"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="s_gate" component_2="voltage_clamp"/>
<map_variables variable_1="V" variable_2="Vm"/>
<map_variables variable_1="s_initial" variable_2="dummy"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
</model>
