- 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/TNNP-extended/experiments/single-stimulus-epicardial-Xu_Ito-ischemic.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="single_stimulus_epi_Xu_Ito_ischemic"
cmeta:id="single_stimulus_epi_Xu_Ito_ischemic"
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>2007-03-19</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#single_stimulus_epi_Xu_Ito_ischemic">
<dc:title>
Action potential simulation with single stimulus.
</dc:title>
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
This is the CellML description of a action potential simulation
with a single stimulus current applied to the extended TNNP (2004)
model.
</rdf:value>
<dc:creator rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</dc:creator>
</cmeta:comment>
<cs:simulation>
<rdf:Description rdf:ID="SingleStimulus">
<cs:simulationName>Single Stimulus</cs:simulationName>
<cs:multistepMethod>bdf</cs:multistepMethod>
<cs:iterationMethod>newton</cs:iterationMethod>
<cs:linearSolver>dense</cs:linearSolver>
<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">
1000
</cs:endingValue>
</rdf:Description>
</cs:boundIntervals>
</rdf:Description>
</cs:simulation>
</rdf:Description>
</rdf:RDF>
<import xlink:href="../../../../cellml/models/common/units.xml">
<units name="ms" units_ref="ms"/>
<units name="mV" units_ref="mV"/>
<units name="mM" units_ref="mM"/>
<units name="uA_per_mmsq" units_ref="uA_per_mmsq"/>
<units name="uA_per_mmcu" units_ref="uA_per_mmcu"/>
<units name="mM_per_ms" units_ref="mM_per_ms"/>
<units name="per_mm" units_ref="per_mm"/>
<units name="uF_per_mmsq" units_ref="uF_per_mmsq"/>
<units name="mmcu" units_ref="mmcu"/>
<units name="mS_per_mmsq" units_ref="mS_per_mmsq"/>
<units name="K" units_ref="K"/>
<units name="mm_per_ms" units_ref="mm_per_ms"/>
<units name="per_ms" units_ref="per_ms"/>
</import>
<import xlink:href="../epicardial-Xu_Ito.xml">
<component name="model" component_ref="interface"/>
</import>
<import xlink:href="../../../../cellml/models/2004_tenTusscher-version2/variable_values.xml">
<component name="default_parameters" component_ref="parameters"/>
<component name="default_initial_conditions" component_ref="initial_conditions"/>
</import>
<import xlink:href="../../../../cellml/protocols/single-pulse-IStim.xml">
<component name="stimulus_protocol" component_ref="stimulus_protocol"/>
</import>
<component name="time" cmeta:id="time">
<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">
<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>
<component name="stimulus_protocol_params" cmeta:id="stimulus_protocol_params">
<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="#stimulus_protocol_params">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
Here we define the parameters for the applied stimulus.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="stimTime" initial_value="500" public_interface="out" units="ms"/>
<variable name="stimDuration" initial_value="1" public_interface="out" units="ms"/>
<variable name="stimCurrent" initial_value="100" public_interface="out" units="uA_per_mmcu"/>
</component>
<connection>
<map_components component_1="stimulus_protocol_params" component_2="stimulus_protocol"/>
<map_variables variable_1="stimTime" variable_2="stimTime"/>
<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="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 which differ from the default.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable name="V_half_act" initial_value="-5.3" public_interface="out" private_interface="out" units="mV"/>
<variable name="V_half_inact" initial_value="-47.0" public_interface="out" private_interface="out" units="mV"/>
<variable name="k_act" initial_value="11.0" public_interface="out" private_interface="out" units="mV"/>
<variable name="k_inact" initial_value="-8.6" public_interface="out" private_interface="out" units="mV"/>
</component>
<connection>
<map_components component_1="model" component_2="parameters"/>
<map_variables variable_1="V_half_act" variable_2="V_half_act"/>
<map_variables variable_1="V_half_inact" variable_2="V_half_inact"/>
<map_variables variable_1="k_act" variable_2="k_act"/>
<map_variables variable_1="k_inact" variable_2="k_inact"/>
</connection>
<connection>
<map_components component_1="model" component_2="default_parameters"/>
<map_variables variable_1="Am" variable_2="Am"/>
<map_variables variable_1="Cm" variable_2="Cm"/>
<map_variables variable_1="Capacitance" variable_2="Capacitance"/>
<map_variables variable_1="temperature" variable_2="temperature"/>
<map_variables variable_1="vC" variable_2="vC"/>
<map_variables variable_1="vSR" variable_2="vSR"/>
<map_variables variable_1="g_Na" variable_2="g_Na"/>
<map_variables variable_1="g_K1" variable_2="g_K1"/>
<map_variables variable_1="g_to" variable_2="g_to"/>
<map_variables variable_1="g_Kr" variable_2="g_Kr"/>
<map_variables variable_1="g_Ks" variable_2="g_Ks"/>
<map_variables variable_1="g_pK" variable_2="g_pK"/>
<map_variables variable_1="g_bNa" variable_2="g_bNa"/>
<map_variables variable_1="g_bCa" variable_2="g_bCa"/>
<map_variables variable_1="p_KNa" variable_2="p_KNa"/>
<map_variables variable_1="P_NaK" variable_2="P_NaK"/>
<map_variables variable_1="K_mNa" variable_2="K_mNa"/>
<map_variables variable_1="K_mK" variable_2="K_mK"/>
<map_variables variable_1="g_CaL" variable_2="g_CaL"/>
<map_variables variable_1="Bufc" variable_2="Bufc"/>
<map_variables variable_1="Kbufc" variable_2="Kbufc"/>
<map_variables variable_1="Bufsr" variable_2="Bufsr"/>
<map_variables variable_1="Kbufsr" variable_2="Kbufsr"/>
<map_variables variable_1="Nao" variable_2="Nao"/>
<map_variables variable_1="Ko" variable_2="Ko"/>
<map_variables variable_1="Cao" variable_2="Cao"/>
<map_variables variable_1="V_leak" variable_2="V_leak"/>
<map_variables variable_1="K_up" variable_2="K_up"/>
<map_variables variable_1="Vmax_up" variable_2="Vmax_up"/>
<map_variables variable_1="a_rel" variable_2="a_rel"/>
<map_variables variable_1="b_rel" variable_2="b_rel"/>
<map_variables variable_1="c_rel" variable_2="c_rel"/>
<map_variables variable_1="tau_g" variable_2="tau_g"/>
<map_variables variable_1="g_pCa" variable_2="g_pCa"/>
<map_variables variable_1="K_pCa" variable_2="K_pCa"/>
<map_variables variable_1="k_NaCa" variable_2="k_NaCa"/>
<map_variables variable_1="K_mNai" variable_2="K_mNai"/>
<map_variables variable_1="K_mCa" variable_2="K_mCa"/>
<map_variables variable_1="k_sat" variable_2="k_sat"/>
<map_variables variable_1="gamma" variable_2="gamma"/>
<map_variables variable_1="alpha" variable_2="alpha"/>
</connection>
<connection>
<map_components component_1="stimulus_protocol" component_2="default_parameters"/>
<map_variables variable_1="Am" variable_2="Am"/>
</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 - just use default values.
</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="j_initial" variable_2="j_initial"/>
<map_variables variable_1="s_initial" variable_2="s_initial"/>
<map_variables variable_1="r_initial" variable_2="r_initial"/>
<map_variables variable_1="Xr1_initial" variable_2="Xr1_initial"/>
<map_variables variable_1="Xr2_initial" variable_2="Xr2_initial"/>
<map_variables variable_1="Xs_initial" variable_2="Xs_initial"/>
<map_variables variable_1="d_initial" variable_2="d_initial"/>
<map_variables variable_1="f_initial" variable_2="f_initial"/>
<map_variables variable_1="fCa_initial" variable_2="fCa_initial"/>
<map_variables variable_1="g_initial" variable_2="g_initial"/>
<map_variables variable_1="Nai_initial" variable_2="Nai_initial"/>
<map_variables variable_1="Ki_initial" variable_2="Ki_initial"/>
<map_variables variable_1="Cai_total_initial" variable_2="Cai_total_initial"/>
<map_variables variable_1="CaSR_total_initial" variable_2="CaSR_total_initial"/>
</connection>
</model>
