- Author:
- Hanne Nielsen <hnie010@aucklanduni.ac.nz>
- Date:
- 2011-09-26 13:51:05+13:00
- Desc:
- Added cellML models for 2a, 2b, 3a, 3b, 4a and 4b and clickable sessions.
- Permanent Source URI:
- https://models.physiomeproject.org/w/hnielsen/grubelnik_2001/rawfile/f78690e2f46454aa4ef277c8a5e8eabda2b8759c/grubelnik_2001_4a.cellml
<?xml version="1.0"?>
<!--
This CellML file was generated on 9/23/2011 at 1:44:51 at PM using:
COR (0.9.31.1409)
Copyright 2002-2011 Dr Alan Garny
http://cor.physiol.ox.ac.uk/ - cor@physiol.ox.ac.uk
CellML 1.0 was used to generate this model
http://www.cellml.org/
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" cmeta:id="grubelnik_2001_4a" name="grubelnik_2001_4a">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="">
<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<vCard:Family>Nielsen</vCard:Family>
<vCard:Given>Hanne</vCard:Given>
</vCard:N>
<vCard:EMAIL xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<rdf:value>hnie010@aucklanduni.ac.nz</rdf:value>
<rdf:type 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">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>Auckland Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</dc:creator>
<dcterms:created xmlns:dcterms="http://purl.org/dc/terms/" rdf:parseType="Resource">
<dcterms:W3CDTF>2011-09-26</dcterms:W3CDTF>
</dcterms:created>
</rdf:Description>
<rdf:Description rdf:about="#grubelnik_2001_4a">
<cmeta:species>Human</cmeta:species>
<cmeta:bio_entity>Liver</cmeta:bio_entity>
<cmeta:bio_entity>hepatocyte</cmeta:bio_entity>
<bqs:reference xmlns:bqs="http://www.cellml.org/bqs/1.0#" rdf:parseType="Resource">
<dc:subject xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource">
<bqs:subject_type>keyword</bqs:subject_type>
<rdf:value>
<rdf:Bag>
<rdf:li>hepatology</rdf:li>
<rdf:li>liver</rdf:li>
<rdf:li>hepatocyte</rdf:li>
</rdf:Bag>
</rdf:value>
</dc:subject>
</bqs:reference>
<bqs:reference xmlns:bqs="http://www.cellml.org/bqs/1.0#" rdf:parseType="Resource">
<bqs:Pubmed_id>11744191</bqs:Pubmed_id>
<bqs:JournalArticle rdf:parseType="Resource">
<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">
<rdf:Seq>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<vCard:Family>Grubelnik</vCard:Family>
<vCard:Given>V</vCard:Given>
</vCard:N>
</bqs:Person>
</rdf:li>
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<bqs:Person rdf:parseType="Resource">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<vCard:Family>Larsen</vCard:Family>
<vCard:Given>A</vCard:Given>
<vCard:Other>Z</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<vCard:Family>Kummer</vCard:Family>
<vCard:Given>U</vCard:Given>
</vCard:N>
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<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<vCard:Family>Olsen</vCard:Family>
<vCard:Given>L</vCard:Given>
<vCard:Other>F</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<vCard:Family>Marhl</vCard:Family>
<vCard:Given>M</vCard:Given>
</vCard:N>
</bqs:Person>
</rdf:li>
</rdf:Seq>
</dc:creator>
<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">
Mitochondria regulate the amplitude of simple and complex calcium oscillations
</dc:title>
<dcterms:issued xmlns:dcterms="http://purl.org/dc/terms/" rdf:parseType="Resource">
<dcterms:W3CDTF>2011-09-26</dcterms:W3CDTF>
</dcterms:issued>
<bqs:Journal rdf:parseType="Resource">
<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">Biophysical Chemistry</dc:title>
</bqs:Journal>
<bqs:volume>94</bqs:volume>
<bqs:first_page>59</bqs:first_page>
<bqs:last_page>74</bqs:last_page>
</bqs:JournalArticle>
</bqs:reference>
</rdf:Description>
</rdf:RDF>
<units name="micromole">
<unit prefix="micro" units="mole"/>
</units>
<units name="micromolar">
<unit units="micromole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="micromolar_per_minute">
<unit units="micromolar"/>
<unit exponent="-1" units="second"/>
</units>
<units name="per_micromolar_per_second">
<unit exponent="-1" units="micromolar"/>
<unit exponent="-1" units="second"/>
</units>
<units name="minute">
<unit multiplier="60" units="second"/>
</units>
<units name="per_minute">
<unit exponent="-1" units="minute"/>
</units>
<units name="per_second">
<unit exponent="-1" units="second"/>
</units>
<component name="environment">
<variable cmeta:id="environment_time" name="time" public_interface="out" units="second"/>
</component>
<component name="Ca_cyt">
<variable cmeta:id="Ca_cyt_Ca_cyt" initial_value="0.01" name="Ca_cyt" public_interface="out" units="micromolar"/>
<variable name="J_ERch" public_interface="in" units="micromolar"/>
<variable name="J_ERpump" public_interface="in" units="micromolar"/>
<variable name="J_ERleak" public_interface="in" units="micromolar"/>
<variable name="J_CaPr" public_interface="in" units="micromolar"/>
<variable name="J_Pr" public_interface="in" units="micromolar"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>Ca_cyt</ci>
</apply>
<apply>
<times/>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<ci>J_ERch</ci>
<ci>J_ERpump</ci>
</apply>
<ci>J_ERleak</ci>
<ci>J_CaPr</ci>
</apply>
<ci>J_Pr</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_minute">1</cn>
</apply>
</apply>
</math>
</component>
<component name="Ca_ER">
<variable cmeta:id="Ca_ER_Ca_ER" initial_value="20" name="Ca_ER" public_interface="out" units="micromolar"/>
<variable initial_value="0.0025" name="beta_ER" public_interface="out" units="dimensionless"/>
<variable initial_value="0.01" name="rho_ER" public_interface="out" units="dimensionless"/>
<variable name="J_ERpump" public_interface="in" units="micromolar"/>
<variable name="J_ERleak" public_interface="in" units="micromolar"/>
<variable name="J_ERch" public_interface="in" units="micromolar"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>Ca_ER</ci>
</apply>
<apply>
<times/>
<apply>
<divide/>
<ci>beta_ER</ci>
<ci>rho_ER</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>J_ERpump</ci>
<ci>J_ERleak</ci>
</apply>
<ci>J_ERch</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_minute">1</cn>
</apply>
</apply>
</math>
</component>
<component name="J_ERch">
<variable cmeta:id="J_ERch_J_ERch" name="J_ERch" public_interface="out" units="micromolar"/>
<variable initial_value="0.001" name="k_ERch" units="micromolar"/>
<variable initial_value="5" name="K_ch" units="micromolar"/>
<variable name="Ca_cyt" public_interface="in" units="micromolar"/>
<variable name="Ca_ER" public_interface="in" units="micromolar"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_ERch</ci>
<apply>
<times/>
<ci>k_ERch</ci>
<apply>
<divide/>
<apply>
<power/>
<ci>Ca_cyt</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>K_ch</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn>
</apply>
<apply>
<power/>
<ci>Ca_cyt</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
</apply>
<apply>
<minus/>
<ci>Ca_ER</ci>
<ci>Ca_cyt</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="J_ERpump">
<variable cmeta:id="J_ERpump_J_ERpump" name="J_ERpump" public_interface="out" units="micromolar"/>
<variable name="Ca_cyt" public_interface="in" units="micromolar"/>
<variable initial_value="20" name="k_ERpump" units="per_second"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_ERpump</ci>
<apply>
<times/>
<ci>k_ERpump</ci>
<ci>Ca_cyt</ci>
</apply>
</apply>
</math>
</component>
<component name="J_ERleak">
<variable cmeta:id="J_ERleak_J_ERleak" name="J_ERleak" public_interface="out" units="micromolar"/>
<variable initial_value="0.05" name="k_ERleak" units="per_second"/>
<variable name="Ca_ER" public_interface="in" units="micromolar"/>
<variable name="Ca_cyt" public_interface="in" units="micromolar"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_ERleak</ci>
<apply>
<times/>
<ci>k_ERleak</ci>
<apply>
<minus/>
<ci>Ca_ER</ci>
<ci>Ca_cyt</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="J_CaPr">
<variable cmeta:id="J_CaPr_J_CaPr" name="J_CaPr" public_interface="out" units="micromolar"/>
<variable initial_value="0.01" name="k_min" units="per_second"/>
<variable name="CaPr" public_interface="in" units="micromolar"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_CaPr</ci>
<apply>
<times/>
<ci>k_min</ci>
<ci>CaPr</ci>
</apply>
</apply>
</math>
</component>
<component name="J_Pr">
<variable cmeta:id="J_Pr_J_Pr" name="J_Pr" public_interface="out" units="micromolar"/>
<variable initial_value="0.1" name="k_plus" units="per_micromolar_per_second"/>
<variable name="Ca_cyt" public_interface="in" units="micromolar"/>
<variable name="Pr" public_interface="in" units="micromolar"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_Pr</ci>
<apply>
<times/>
<ci>k_plus</ci>
<ci>Ca_cyt</ci>
<ci>Pr</ci>
</apply>
</apply>
</math>
</component>
<component name="CaPr">
<variable cmeta:id="CaPr_CaPr" name="CaPr" public_interface="out" units="micromolar"/>
<variable name="Ca_cyt" public_interface="in" units="micromolar"/>
<variable name="rho_ER" public_interface="in" units="dimensionless"/>
<variable name="beta_ER" public_interface="in" units="dimensionless"/>
<variable name="Ca_ER" public_interface="in" units="micromolar"/>
<variable initial_value="90" name="Ca_tot" units="micromolar"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>CaPr</ci>
<apply>
<minus/>
<ci>Ca_tot</ci>
<apply>
<plus/>
<ci>Ca_cyt</ci>
<apply>
<times/>
<apply>
<divide/>
<ci>rho_ER</ci>
<ci>beta_ER</ci>
</apply>
<ci>Ca_ER</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="Pr">
<variable cmeta:id="Pr_Pr" name="Pr" public_interface="out" units="micromolar"/>
<variable initial_value="120" name="Pr_tot" units="micromolar"/>
<variable name="CaPr" public_interface="in" units="micromolar"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Pr</ci>
<apply>
<minus/>
<ci>Pr_tot</ci>
<ci>CaPr</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="Ca_cyt"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="environment" component_2="Ca_ER"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="environment" component_2="J_ERch"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="environment" component_2="J_ERpump"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="environment" component_2="J_ERleak"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="environment" component_2="J_CaPr"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="environment" component_2="J_Pr"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="environment" component_2="CaPr"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="environment" component_2="Pr"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="Ca_cyt" component_2="J_ERch"/>
<map_variables variable_1="J_ERch" variable_2="J_ERch"/>
<map_variables variable_1="Ca_cyt" variable_2="Ca_cyt"/>
</connection>
<connection>
<map_components component_1="Ca_cyt" component_2="J_ERpump"/>
<map_variables variable_1="J_ERpump" variable_2="J_ERpump"/>
<map_variables variable_1="Ca_cyt" variable_2="Ca_cyt"/>
</connection>
<connection>
<map_components component_1="Ca_cyt" component_2="J_ERleak"/>
<map_variables variable_1="J_ERleak" variable_2="J_ERleak"/>
<map_variables variable_1="Ca_cyt" variable_2="Ca_cyt"/>
</connection>
<connection>
<map_components component_1="Ca_cyt" component_2="J_CaPr"/>
<map_variables variable_1="J_CaPr" variable_2="J_CaPr"/>
</connection>
<connection>
<map_components component_1="Ca_cyt" component_2="J_Pr"/>
<map_variables variable_1="Ca_cyt" variable_2="Ca_cyt"/>
<map_variables variable_1="J_Pr" variable_2="J_Pr"/>
</connection>
<connection>
<map_components component_1="Ca_cyt" component_2="CaPr"/>
<map_variables variable_1="Ca_cyt" variable_2="Ca_cyt"/>
</connection>
<connection>
<map_components component_1="CaPr" component_2="Pr"/>
<map_variables variable_1="CaPr" variable_2="CaPr"/>
</connection>
<connection>
<map_components component_1="Ca_ER" component_2="J_ERpump"/>
<map_variables variable_1="J_ERpump" variable_2="J_ERpump"/>
</connection>
<connection>
<map_components component_1="Ca_ER" component_2="CaPr"/>
<map_variables variable_1="Ca_ER" variable_2="Ca_ER"/>
<map_variables variable_1="rho_ER" variable_2="rho_ER"/>
<map_variables variable_1="beta_ER" variable_2="beta_ER"/>
</connection>
<connection>
<map_components component_1="Ca_ER" component_2="J_ERch"/>
<map_variables variable_1="J_ERch" variable_2="J_ERch"/>
<map_variables variable_1="Ca_ER" variable_2="Ca_ER"/>
</connection>
<connection>
<map_components component_1="Pr" component_2="J_Pr"/>
<map_variables variable_1="Pr" variable_2="Pr"/>
</connection>
<connection>
<map_components component_1="CaPr" component_2="J_CaPr"/>
<map_variables variable_1="CaPr" variable_2="CaPr"/>
</connection>
<connection>
<map_components component_1="J_ERleak" component_2="Ca_ER"/>
<map_variables variable_1="Ca_ER" variable_2="Ca_ER"/>
<map_variables variable_1="J_ERleak" variable_2="J_ERleak"/>
</connection>
</model>
