- 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://staging.physiomeproject.org/w/andre/nickerson-2008/rawfile/d6328d18c94e9dad70f4d0e4b250e89429773b62/TNNP-extended/experiments/I_K_ATP-ATP_clamp.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="I_K_ATP_ATP_clamp"
cmeta:id="I_K_ATP_ATP_clamp"
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>2006-10-17</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#I_K_ATP_ATP_clamp">
<dc:title>
ATP clamp experiment using I_K_ATP current.
</dc:title>
<sim:integration id="simulator-data"
xmlns:sim="http://www.cellml.org/simulation-data/1.0#">
<!-- A suitable range for the bound variable -->
<!-- ATP from 0 - > 10mM -->
<sim:bound-variable-range
start="0"
end="10"
tabulation-step-size="1e-3"
maximum-step-size="1e-3"/>
<!-- 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="mM" units_ref="mM"/>
<units name="mM_per_ms" units_ref="mM_per_ms"/>
<units name="uA_per_mmsq" units_ref="uA_per_mmsq"/>
<units name="mS_per_mmsq" units_ref="mS_per_mmsq"/>
</import>
<import xlink:href="../components/I_K_ATP.xml">
<component name="I_K_ATP" component_ref="I_K_ATP_Shaw"/>
</import>
<component name="ATP_clamp" cmeta:id="ATP_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="#ATP_clamp">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
We define here the ATP clamp experiment, in this case
a simple linear variation of ATP, expressed as a
differential equation.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="time" public_interface="out" units="ms"/>
<variable name="g_K_ATP" initial_value="0.04" public_interface="out" units="mS_per_mmsq"/>
<variable name="ATP_i" initial_value="0" public_interface="out" units="mM"/>
<variable name="K_half_K_ATP" initial_value="0.25" public_interface="out" units="mM"/>
<variable name="H_K_ATP" initial_value="2" public_interface="out" units="dimensionless"/>
<variable name="n_K_ATP" initial_value="0.24" public_interface="out" units="dimensionless"/>
<variable name="Vm" initial_value="-85" public_interface="out" units="mV"/>
<variable name="E_K" initial_value="-71.3" public_interface="out" units="mV"/>
<variable name="Ko" initial_value="5.4" public_interface="out" units="mM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply><eq/>
<apply><diff/>
<bvar><ci>time</ci></bvar>
<ci>ATP_i</ci>
</apply>
<cn cellml:units="mM_per_ms">1.0</cn>
</apply>
</math>
</component>
<connection>
<map_components component_1="I_K_ATP" component_2="ATP_clamp"/>
<map_variables variable_1="V" variable_2="Vm"/>
<map_variables variable_1="g_K_ATP" variable_2="g_K_ATP"/>
<map_variables variable_1="ATP_i" variable_2="ATP_i"/>
<map_variables variable_1="K_half" variable_2="K_half_K_ATP"/>
<map_variables variable_1="H" variable_2="H_K_ATP"/>
<map_variables variable_1="n" variable_2="n_K_ATP"/>
<map_variables variable_1="E_K" variable_2="E_K"/>
<map_variables variable_1="Ko" variable_2="Ko"/>
</connection>
</model>
