- Author:
- AnandR <a.rampadarath@auckland.ac.nz>
- Date:
- 2019-04-05 14:25:01+13:00
- Desc:
- Added some semgen annotated models (AnandR)
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/584/rawfile/ade7933153a72bb89e0b02d75db92d6e4be285f5/Nima/mc_sodium_channel.cellml
<?xml version='1.0'?>
<model name="mc_sodium_channel" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
<import xlink:href="chang_fujita_b_1999_units_model.xml">
<units name="millivolt" units_ref="millivolt"/>
<units name="cm_per_s" units_ref="cm_per_s"/>
<units name="mmol_per_cm3" units_ref="mmol_per_cm3"/>
<units name="flux" units_ref="flux"/>
<units name="C_per_mmol" units_ref="C_per_mmol"/>
<units name="J_per_mmol" units_ref="J_per_mmol"/>
<units name="mmHg" units_ref="mmHg"/>
<units name="cm_per_s_mmHg" units_ref="cm_per_s_mmHg"/>
<units name="cm" units_ref="cm"/>
</import>
<import xlink:href="chang_fujita_b_1999.cellml">
<component component_ref="solute_concentrations" name="solute_concentrations"/>
<component component_ref="mc_sodium_flux" name="mc_sodium_flux"/>
<component component_ref="ms_sodium_flux" name="ms_sodium_flux"/>
<component component_ref="sc_sodium_flux" name="sc_sodium_flux"/>
<component component_ref="mc_potassium_flux" name="mc_potassium_flux"/>
<component component_ref="ms_potassium_flux" name="ms_potassium_flux"/>
<component component_ref="sc_potassium_flux" name="sc_potassium_flux"/>
<component component_ref="mc_chloride_flux" name="mc_chloride_flux"/>
<component component_ref="ms_chloride_flux" name="ms_chloride_flux"/>
<component component_ref="sc_chloride_flux" name="sc_chloride_flux"/>
<component component_ref="environment" name="environment"/>
<component component_ref="constants" name="constants"/>
<component component_ref="imported_variables" name="imported_variables"/>
</import>
<component name="mc_sodium">
<variable name="G_mc_Na" public_interface="out" units="flux"/>
<variable initial_value="3.27E-6" name="P_mc_Na" units="cm_per_s"/>
<variable name="RT" public_interface="in" units="J_per_mmol"/>
<!-- constants-->
<variable name="F" public_interface="in" units="C_per_mmol"/>
<variable name="psi_m" public_interface="in" units="millivolt"/>
<!-- imported_variables -->
<variable name="psi_c" public_interface="in" units="millivolt"/>
<variable name="C_m_Na" public_interface="in" units="mmol_per_cm3"/>
<!-- solute_concentrations-->
<variable name="C_c_Na" public_interface="in" units="mmol_per_cm3"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="G_mc_Na_calculation">
<eq/>
<ci>G_mc_Na</ci>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>P_mc_Na</ci>
<ci>F</ci>
<apply>
<minus/>
<ci>psi_m</ci>
<ci>psi_c</ci>
</apply>
</apply>
<ci>RT</ci>
</apply>
<apply>
<minus/>
<ci>C_m_Na</ci>
<apply>
<times/>
<ci>C_c_Na</ci>
<apply>
<exp/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<minus/>
<ci>F</ci>
</apply>
<ci>RT</ci>
</apply>
<apply>
<minus/>
<ci>psi_m</ci>
<ci>psi_c</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<minus/>
<cn cellml:units="dimensionless">1.0</cn>
<apply>
<exp/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<minus/>
<ci>F</ci>
</apply>
<ci>RT</ci>
</apply>
<apply>
<minus/>
<ci>psi_m</ci>
<ci>psi_c</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="imported_variables" component_2="mc_sodium"/>
<map_variables variable_1="psi_m" variable_2="psi_m"/>
<map_variables variable_1="psi_c" variable_2="psi_c"/>
</connection>
<connection>
<map_components component_1="solute_concentrations" component_2="mc_sodium"/>
<map_variables variable_1="C_m_Na" variable_2="C_m_Na"/>
<map_variables variable_1="C_c_Na" variable_2="C_c_Na"/>
</connection>
<connection>
<map_components component_1="constants" component_2="mc_sodium"/>
<map_variables variable_1="RT" variable_2="RT"/>
<map_variables variable_1="F" variable_2="F"/>
</connection>
<connection>
<map_components component_1="solute_concentrations" component_2="mc_sodium_flux"/>
<map_variables variable_1="J_mc_Na" variable_2="J_mc_Na"/>
</connection>
<connection>
<map_components component_1="solute_concentrations" component_2="ms_sodium_flux"/>
<map_variables variable_1="J_ms_Na" variable_2="J_ms_Na"/>
</connection>
<connection>
<map_components component_1="solute_concentrations" component_2="sc_sodium_flux"/>
<map_variables variable_1="J_sc_Na" variable_2="J_sc_Na"/>
</connection>
<connection>
<map_components component_1="solute_concentrations" component_2="mc_potassium_flux"/>
<map_variables variable_1="J_mc_K" variable_2="J_mc_K"/>
</connection>
<connection>
<map_components component_1="solute_concentrations" component_2="ms_potassium_flux"/>
<map_variables variable_1="J_ms_K" variable_2="J_ms_K"/>
</connection>
<connection>
<map_components component_1="solute_concentrations" component_2="sc_potassium_flux"/>
<map_variables variable_1="J_sc_K" variable_2="J_sc_K"/>
</connection>
<connection>
<map_components component_1="solute_concentrations" component_2="mc_chloride_flux"/>
<map_variables variable_1="J_mc_Cl" variable_2="J_mc_Cl"/>
</connection>
<connection>
<map_components component_1="solute_concentrations" component_2="ms_chloride_flux"/>
<map_variables variable_1="J_ms_Cl" variable_2="J_ms_Cl"/>
</connection>
<connection>
<map_components component_1="solute_concentrations" component_2="sc_chloride_flux"/>
<map_variables variable_1="J_sc_Cl" variable_2="J_sc_Cl"/>
</connection>
<connection>
<map_components component_1="solute_concentrations" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="mc_sodium_flux" component_2="constants"/>
<map_variables variable_1="RT" variable_2="RT"/>
<map_variables variable_1="F" variable_2="F"/>
</connection>
<connection>
<map_components component_1="imported_variables" component_2="mc_sodium_flux"/>
<map_variables variable_1="psi_m" variable_2="psi_m"/>
<map_variables variable_1="psi_c" variable_2="psi_c"/>
</connection>
<connection>
<map_components component_1="ms_sodium_flux" component_2="constants"/>
<map_variables variable_1="RT" variable_2="RT"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="psi_s" variable_2="psi_s"/>
</connection>
<connection>
<map_components component_1="imported_variables" component_2="ms_sodium_flux"/>
<map_variables variable_1="psi_m" variable_2="psi_m"/>
</connection>
<connection>
<map_components component_1="mc_potassium_flux" component_2="constants"/>
<map_variables variable_1="RT" variable_2="RT"/>
<map_variables variable_1="F" variable_2="F"/>
</connection>
<connection>
<map_components component_1="imported_variables" component_2="mc_potassium_flux"/>
<map_variables variable_1="psi_m" variable_2="psi_m"/>
<map_variables variable_1="psi_c" variable_2="psi_c"/>
</connection>
<connection>
<map_components component_1="ms_potassium_flux" component_2="constants"/>
<map_variables variable_1="RT" variable_2="RT"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="psi_s" variable_2="psi_s"/>
</connection>
<connection>
<map_components component_1="imported_variables" component_2="ms_potassium_flux"/>
<map_variables variable_1="psi_m" variable_2="psi_m"/>
</connection>
<connection>
<map_components component_1="sc_potassium_flux" component_2="constants"/>
<map_variables variable_1="RT" variable_2="RT"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="psi_s" variable_2="psi_s"/>
</connection>
<connection>
<map_components component_1="imported_variables" component_2="mc_potassium_flux"/>
<map_variables variable_1="psi_m" variable_2="psi_m"/>
<map_variables variable_1="psi_c" variable_2="psi_c"/>
</connection>
<connection>
<map_components component_1="imported_variables" component_2="sc_potassium_flux"/>
<map_variables variable_1="psi_c" variable_2="psi_c"/>
</connection>
<connection>
<map_components component_1="mc_chloride_flux" component_2="constants"/>
<map_variables variable_1="RT" variable_2="RT"/>
<map_variables variable_1="F" variable_2="F"/>
</connection>
<connection>
<map_components component_1="imported_variables" component_2="mc_chloride_flux"/>
<map_variables variable_1="psi_m" variable_2="psi_m"/>
<map_variables variable_1="psi_c" variable_2="psi_c"/>
</connection>
<connection>
<map_components component_1="ms_chloride_flux" component_2="constants"/>
<map_variables variable_1="RT" variable_2="RT"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="psi_s" variable_2="psi_s"/>
</connection>
<connection>
<map_components component_1="imported_variables" component_2="ms_chloride_flux"/>
<map_variables variable_1="psi_m" variable_2="psi_m"/>
</connection>
<connection>
<map_components component_1="sc_chloride_flux" component_2="constants"/>
<map_variables variable_1="RT" variable_2="RT"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="psi_s" variable_2="psi_s"/>
</connection>
<connection>
<map_components component_1="imported_variables" component_2="sc_chloride_flux"/>
<map_variables variable_1="psi_c" variable_2="psi_c"/>
</connection>
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A CellML description of Chang and Fujita's 1999 numerical model of the 
renal distal tubule. 
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<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">A numerical model of the renal distal tubule</dc:title>
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<bqs:first_page xmlns:bqs="http://www.cellml.org/bqs/1.0#">F931</bqs:first_page>
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<dcterms:issued xmlns:dcterms="http://purl.org/dc/terms/" rdf:resource="rdf:#7b8eacdf-c2d6-42ea-b7f9-cb663bbf73b8" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
<bqs:last_page xmlns:bqs="http://www.cellml.org/bqs/1.0#">F951</bqs:last_page>
</rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#cbbd8328-cc4b-44ec-b53d-ec4caedd48b1">
<vCard:Given xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Toshiro</vCard:Given>
<vCard:Family xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Fujita</vCard:Family>
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<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#697dc2eb-2e74-46d0-8a2d-f226062e9021">
<dcterms:W3CDTF xmlns:dcterms="http://purl.org/dc/terms/">2007-06-05T09:18:35+12:00</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#a907b383-1dcf-427b-a3cf-f75cada2346e">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:resource="rdf:#675a277e-e91c-4dfb-a6e5-fa3133847503" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
</rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#7b8eacdf-c2d6-42ea-b7f9-cb663bbf73b8">
<dcterms:W3CDTF xmlns:dcterms="http://purl.org/dc/terms/">1999-01-01</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#20d1b786-7957-4457-bda5-1d4df2f79cf6">
<vCard:FN xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Catherine Lloyd</vCard:FN>
</rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#b28db5be-4a73-4d50-9675-5137f4a8235f">
<dcterms:modified xmlns:dcterms="http://purl.org/dc/terms/" rdf:resource="rdf:#697dc2eb-2e74-46d0-8a2d-f226062e9021" 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 new version of this model has been re-coded to remove the reaction element and replace it with a simple MathML description of the model reaction kinetics. This is thought to be truer to the original publication, and information regarding the enzyme kinetics etc will later be added to the metadata through use of an ontology. The model runs in the PCEnv simulator but gives a flat output.</rdf:value>
<cmeta:modifier xmlns:cmeta="http://www.cellml.org/metadata/1.0#" rdf:resource="rdf:#a907b383-1dcf-427b-a3cf-f75cada2346e" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
</rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#9413f374-026c-4147-b850-de6e1c16827a">
<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:resource="rdf:#1dc4bf73-201d-4503-b8fc-2eeb36898c2c" 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 Chang and Fujita's 1999 numerical model of the renal distal tubule. It should be noted that the initial conditions used in this description represent those in the early distal tubule. For model representations of the late distal tublule, these initial values should be replaced with those listed in the orginal paper for the late distal tubule. The model from the original paper has been modified slightly to include differential equations defining the change in solute concentrations over time. These equations were added to facilitate the use of the CellML code in CMISS.</rdf:value>
</rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#1dc4bf73-201d-4503-b8fc-2eeb36898c2c">
<vCard:FN xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Catherine Lloyd</vCard:FN>
</rdf:Description>
</rdf:RDF>
</model>
