- 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/experiments/TNNP.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="tnnp_base"
cmeta:id="tnnp_base"
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>2007-04-19</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
</rdf:Description>
<rdf:Description rdf:about="#tnnp_base">
<dc:title>
The default base TNNP epicardial model.
</dc:title>
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
This is the base TNNP epicardial model with default parameters and intial
conditions defined and connected. Designed to be re-used with various
stimulus protocols and other additional currents.
</rdf:value>
<dc:creator rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</dc:creator>
</cmeta:comment>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Moving to using ion-specific additional currents which incorporate
the stimulus current.
</rdf:value>
<cmeta:modifier rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</cmeta:modifier>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2007-05-23</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Similar to additional membrane currents now adding in addtional
SR calcium flux.
</rdf:value>
<cmeta:modifier rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</cmeta:modifier>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2007-06-22</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Exposing the SR calcium fluxes through the model interface.
</rdf:value>
<cmeta:modifier rdf:parseType="Resource">
<vCard:FN>David Nickerson</vCard:FN>
</cmeta:modifier>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2007-06-22</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
</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="uA_per_mmsq" units_ref="uA_per_mmsq"/>
<units name="per_mm" units_ref="per_mm"/>
<units name="mM_per_ms" units_ref="mM_per_ms"/>
</import>
<import xlink:href="../../../cellml/models/2004_tenTusscher-version-2/2004_tenTusscher_noble_noble_panfilov-epi.xml">
<component name="model" component_ref="interface"/>
</import>
<import xlink:href="../../../cellml/models/2004_tenTusscher-version-2/variable_values.xml">
<component name="default_parameters" component_ref="parameters"/>
<component name="default_initial_conditions" component_ref="initial_conditions"/>
</import>
<component name="interface" cmeta:id="interface">
<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="#interface">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The interface by which this model can be accessed.
</rdf:value>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:about="#time">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The model importing this model is expected to define the time variable.
</rdf:value>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:about="#IK_additional">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The model importing this one is expected to set the total additional
K sarcolemmal membrane current (this would usually include the stimulus
current).
</rdf:value>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:about="#ICa_additional">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The model importing this one is expected to set the total additional
Ca sarcolemmal membrane current.
</rdf:value>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:about="#INa_additional">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The model importing this one is expected to set the total additional
Na sarcolemmal membrane current.
</rdf:value>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:about="#JCaSR_additional">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The model importing this one is expected to set the total additional
SR calcium flux.
</rdf:value>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:about="#Am">
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
The surface to volume ratio (Am) is provided to the importing model
as it may be useful in calculating the stimulus current.
</rdf:value>
</cmeta:comment>
</rdf:Description>
</rdf:RDF>
<variable cmeta:id="time" name="time" public_interface="in" private_interface="out" units="ms"/>
<variable cmeta:id="IK_additional" name="IK_additional" public_interface="in" private_interface="out" units="uA_per_mmsq"/>
<variable cmeta:id="ICa_additional" name="ICa_additional" public_interface="in" private_interface="out" units="uA_per_mmsq"/>
<variable cmeta:id="INa_additional" name="INa_additional" public_interface="in" private_interface="out" units="uA_per_mmsq"/>
<variable cmeta:id="JCaSR_additional" name="JCaSR_additional" public_interface="in" private_interface="out" units="mM_per_ms"/>
<variable cmeta:id="Am" name="Am" public_interface="out" private_interface="in" units="per_mm"/>
<variable cmeta:id="V" name="V" public_interface="out" private_interface="in" units="mV"/>
<variable cmeta:id="E_K" name="E_K" public_interface="out" private_interface="in" units="mV"/>
<variable cmeta:id="E_Ks" name="E_Ks" public_interface="out" private_interface="in" units="mV"/>
<variable cmeta:id="E_Ca" name="E_Ca" public_interface="out" private_interface="in" units="mV"/>
<variable cmeta:id="E_Na" name="E_Na" public_interface="out" private_interface="in" units="mV"/>
<variable cmeta:id="Ko" name="Ko" public_interface="out" private_interface="in" units="mM"/>
<variable name="INa" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="IK1" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="Ito" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="IKr" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="IKs" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="INaK" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="IpK" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="IbNa" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="ICaL" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="IpCa" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="INaCa" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="IbCa" public_interface="out" private_interface="in" units="uA_per_mmsq"/>
<variable name="Jrel" public_interface="out" private_interface="in" units="mM_per_ms"/>
<variable name="Jleak" public_interface="out" private_interface="in" units="mM_per_ms"/>
<variable name="Jup" public_interface="out" private_interface="in" units="mM_per_ms"/>
</component>
<connection>
<map_components component_1="model" component_2="interface"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="V" variable_2="V"/>
<map_variables variable_1="E_K" variable_2="E_K"/>
<map_variables variable_1="E_Ks" variable_2="E_Ks"/>
<map_variables variable_1="E_Ca" variable_2="E_Ca"/>
<map_variables variable_1="E_Na" variable_2="E_Na"/>
<map_variables variable_1="IK_additional" variable_2="IK_additional"/>
<map_variables variable_1="ICa_additional" variable_2="ICa_additional"/>
<map_variables variable_1="INa_additional" variable_2="INa_additional"/>
<map_variables variable_1="JCaSR_additional" variable_2="JCaSR_additional"/>
<map_variables variable_1="INa" variable_2="INa"/>
<map_variables variable_1="IK1" variable_2="IK1"/>
<map_variables variable_1="Ito" variable_2="Ito"/>
<map_variables variable_1="IKr" variable_2="IKr"/>
<map_variables variable_1="IKs" variable_2="IKs"/>
<map_variables variable_1="INaK" variable_2="INaK"/>
<map_variables variable_1="IpK" variable_2="IpK"/>
<map_variables variable_1="IbNa" variable_2="IbNa"/>
<map_variables variable_1="ICaL" variable_2="ICaL"/>
<map_variables variable_1="IpCa" variable_2="IpCa"/>
<map_variables variable_1="INaCa" variable_2="INaCa"/>
<map_variables variable_1="IbCa" variable_2="IbCa"/>
<map_variables variable_1="Jrel" variable_2="Jrel"/>
<map_variables variable_1="Jleak" variable_2="Jleak"/>
<map_variables variable_1="Jup" variable_2="Jup"/>
</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="interface" component_2="default_parameters"/>
<map_variables variable_1="Am" variable_2="Am"/>
<map_variables variable_1="Ko" variable_2="Ko"/>
</connection>
<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>
<group>
<relationship_ref relationship="encapsulation"/>
<component_ref component="interface">
<component_ref component="model"/>
<component_ref component="default_initial_conditions"/>
<component_ref component="default_parameters"/>
</component_ref>
</group>
</model>
