- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2021-09-17 15:50:49+12:00
- Desc:
- tweak html formatting
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/a1/rawfile/1b3862589abf79ae9119ee0b5e99a8b785d762e1/models/2004_tenTusscher/experiments/periodic-stimulus-endocardial.xml
<?xml version='1.0' encoding='UTF-8'?>
<model cmeta:id="periodic_stimulus_endo" name="periodic_stimulus_endo" 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">
<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="pA_per_pF" units_ref="pA_per_pF"/>
<units name="mM_per_ms" units_ref="mM_per_ms"/>
<units name="per_mm" units_ref="per_mm"/>
<units name="uF_per_cmsq" units_ref="uF_per_cmsq"/>
<units name="umcu" units_ref="umcu"/>
<units name="nS_per_pF" units_ref="nS_per_pF"/>
<units name="K" units_ref="K"/>
<units name="cmcu_per_uF_per_s" units_ref="cmcu_per_uF_per_s"/>
<units name="per_ms" units_ref="per_ms"/>
<units name="mM_per_s" units_ref="mM_per_s"/>
</import>
<import xlink:href="../2004_tenTusscher_noble_noble_panfilov-endo.xml">
<component component_ref="interface" name="math_model"/>
</import>
<component cmeta:id="timeComponent" name="time">
<variable cmeta:id="time" initial_value="0.0" name="time" public_interface="out" units="ms"/>
</component>
<connection>
<map_components component_1="math_model" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<component name="output_variables">
<variable name="V" public_interface="in" units="mV"/>
</component>
<connection>
<map_components component_1="math_model" component_2="output_variables"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<component cmeta:id="stimulus_protocol" name="stimulus_protocol">
<variable name="IStim" public_interface="out" units="pA_per_pF"/>
<variable name="time" public_interface="in" units="ms"/>
<variable initial_value="1000" name="stimPeriod" units="ms"/>
<variable initial_value="1" name="stimDuration" units="ms"/>
<variable initial_value="52" name="stimCurrent" units="pA_per_pF"/>
<variable name="Am" public_interface="in" units="per_mm"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="stimulus_calculation">
<eq/>
<ci>IStim</ci>
<piecewise>
<piece>
<ci>stimCurrent</ci>
<apply>
<lt/>
<apply>
<rem/>
<ci>time</ci>
<ci>stimPeriod</ci>
</apply>
<ci>stimDuration</ci>
</apply>
</piece>
<otherwise>
<cn cellml:units="pA_per_pF">0.0</cn>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<connection>
<map_components component_1="math_model" component_2="stimulus_protocol"/>
<map_variables variable_1="Istim" variable_2="IStim"/>
</connection>
<connection>
<map_components component_1="time" component_2="stimulus_protocol"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<component cmeta:id="parameters" name="parameters">
<variable initial_value="200" name="Am" public_interface="out" units="per_mm"/>
<variable initial_value="1.0" name="Cm" public_interface="out" units="uF_per_cmsq"/>
<variable initial_value="0.185" name="Capacitance" public_interface="out" units="uF_per_cmsq"/>
<variable initial_value="310" name="temperature" public_interface="out" units="K"/>
<variable initial_value="0.016404" name="vC" public_interface="out" units="umcu"/>
<variable initial_value="0.001094" name="vSR" public_interface="out" units="umcu"/>
<variable initial_value="14.838" name="g_Na" public_interface="out" units="nS_per_pF"/>
<variable initial_value="5.405" name="g_K1" public_interface="out" units="nS_per_pF"/>
<variable initial_value="0.073" name="g_to" public_interface="out" units="nS_per_pF"/>
<variable initial_value="0.096" name="g_Kr" public_interface="out" units="nS_per_pF"/>
<variable initial_value="0.245" name="g_Ks" public_interface="out" units="nS_per_pF"/>
<variable initial_value="0.0146" name="g_pK" public_interface="out" units="nS_per_pF"/>
<variable initial_value="0.29e-3" name="g_bNa" public_interface="out" units="nS_per_pF"/>
<variable initial_value="0.592e-3" name="g_bCa" public_interface="out" units="nS_per_pF"/>
<variable initial_value="0.03" name="p_KNa" public_interface="out" units="dimensionless"/>
<variable initial_value="1.362" name="P_NaK" public_interface="out" units="pA_per_pF"/>
<variable initial_value="40.0" name="K_mNa" public_interface="out" units="mM"/>
<variable initial_value="1.0" name="K_mK" public_interface="out" units="mM"/>
<variable initial_value="1.75e-4" name="g_CaL" public_interface="out" units="cmcu_per_uF_per_s"/>
<variable initial_value="0.15" name="Bufc" public_interface="out" units="mM"/>
<variable initial_value="0.001" name="Kbufc" public_interface="out" units="mM"/>
<variable initial_value="10.0" name="Bufsr" public_interface="out" units="mM"/>
<variable initial_value="0.3" name="Kbufsr" public_interface="out" units="mM"/>
<variable initial_value="140" name="Nao" public_interface="out" units="mM"/>
<variable initial_value="5.4" name="Ko" public_interface="out" units="mM"/>
<variable initial_value="2.0" name="Cao" public_interface="out" units="mM"/>
<variable initial_value="0.08e-3" name="V_leak" public_interface="out" units="per_ms"/>
<variable initial_value="0.25e-3" name="K_up" public_interface="out" units="mM"/>
<variable initial_value="0.425e-3" name="Vmax_up" public_interface="out" units="mM_per_ms"/>
<variable initial_value="0.016464" name="a_rel" public_interface="out" units="mM_per_s"/>
<variable initial_value="0.25" name="b_rel" public_interface="out" units="mM"/>
<variable initial_value="0.008232" name="c_rel" public_interface="out" units="mM_per_s"/>
<variable initial_value="2" name="tau_g" public_interface="out" units="ms"/>
<variable initial_value="0.825" name="g_pCa" public_interface="out" units="pA_per_pF"/>
<variable initial_value="0.5e-3" name="K_pCa" public_interface="out" units="mM"/>
<variable initial_value="1.0e3" name="k_NaCa" public_interface="out" units="pA_per_pF"/>
<variable initial_value="87.5" name="K_mNai" public_interface="out" units="mM"/>
<variable initial_value="1.38" name="K_mCa" public_interface="out" units="mM"/>
<variable initial_value="0.1" name="k_sat" public_interface="out" units="dimensionless"/>
<variable initial_value="0.35" name="gamma" public_interface="out" units="dimensionless"/>
<variable initial_value="2.5" name="alpha" public_interface="out" units="dimensionless"/>
</component>
<connection>
<map_components component_1="math_model" component_2="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="parameters"/>
<map_variables variable_1="Am" variable_2="Am"/>
</connection>
<component cmeta:id="initial_conditions" name="initial_conditions">
<variable initial_value="-86.2" name="V_initial" public_interface="out" units="mV"/>
<variable initial_value="0" name="m_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="0.75" name="h_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="0.75" name="j_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="1.0" name="s_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="0.0" name="r_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="0.0" name="Xr1_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="1.0" name="Xr2_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="0.0" name="Xs_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="0.0" name="d_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="1.0" name="f_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="1.0" name="fCa_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="1.0" name="g_initial" public_interface="out" units="dimensionless"/>
<variable initial_value="11.6" name="Nai_initial" public_interface="out" units="mM"/>
<variable initial_value="138.3" name="Ki_initial" public_interface="out" units="mM"/>
<variable initial_value="0.0064" name="Cai_total_initial" public_interface="out" units="mM"/>
<variable initial_value="4.2" name="CaSR_total_initial" public_interface="out" units="mM"/>
</component>
<connection>
<map_components component_1="math_model" component_2="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>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="">
<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<vCard:Family xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Nickerson</vCard:Family>
<vCard:Given xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">David</vCard:Given>
</vCard:N>
<vCard:EMAIL xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">d.nickerson@auckland.ac.nz</rdf:value>
<rdf:type xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:resource="http://imc.org/vCard/3.0#internet"/>
</vCard:EMAIL>
<vCard:ORG xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<vCard:Orgname xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">The University of Auckland</vCard:Orgname>
<vCard:Orgunit xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</dc:creator>
<dcterms:created xmlns:dcterms="http://purl.org/dc/terms/" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<dcterms:W3CDTF xmlns:dcterms="http://purl.org/dc/terms/">2004-12-31</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher xmlns:dc="http://purl.org/dc/elements/1.1/">
Bioengineering Institute, The University of Auckland
</dc:publisher>
</rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#periodic_stimulus_endo">
<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">
Action potential simulation with periodic stimulus.
</dc:title>
<cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
This is the CellML description of a action potential simulation
with a periodic stimulus current applied. Uses the endocardial
variant of the ten Tusscher et al. (2004) human ventricular myocyte
model.
</rdf:value>
<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<vCard:FN xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">David Nickerson</vCard:FN>
</dc:creator>
</cmeta:comment>
<bqs:reference xmlns:bqs="http://www.cellml.org/bqs/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<bqs:Pubmed_id xmlns:bqs="http://www.cellml.org/bqs/1.0#">14656705</bqs:Pubmed_id>
</bqs:reference>
<cs:simulation xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:ID="simulation">
<cs:multistepMethod xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">bdf</cs:multistepMethod>
<cs:iterationMethod xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">newton</cs:iterationMethod>
<cs:linearSolver xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">dense</cs:linearSolver>
<cs:boundIntervals xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:parseType="Collection" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<cs:boundVariable xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#time"/>
</cs:boundVariable>
<cs:maximumStepSize xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
0.01
</cs:maximumStepSize>
<cs:tabulationStepSize xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
2.0
</cs:tabulationStepSize>
<cs:startingValue xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
0
</cs:startingValue>
<cs:endingValue xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#" rdf:datatype="http://www.w3.org/2001/XMLSchema#double" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
1500
</cs:endingValue>
</rdf:Description>
</cs:boundIntervals>
</rdf:Description>
</cs:simulation>
</rdf:Description>
</rdf:RDF>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#timeComponent">
<cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
The actual definition of the time variable.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#stimulus_protocol">
<cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
Here we define the stimulus protocol for the simulation.
In this case we are using a periodic stimulus.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#parameters">
<cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
The model parameters.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#initial_conditions">
<cmeta:comment xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
The initial conditions.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
</model>
