- Author:
- Tommy Yu <tommy.yu@auckland.ac.nz>
- Date:
- 2010-08-25 17:02:03+12:00
- Desc:
- e-notation fix
- Permanent Source URI:
- http://models.cellml.org/workspace/cooling_hunter_crampin_CellML_2008/rawfile/990b7b2b938c15874ac605e07b65f7c0d924ae67/IP3Submodel_Main.cellml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="IP3Submodel"
cmeta:id="IP3Submodel"
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"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bqs="http://www.cellml.org/bqs/1.0#"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"
>
<rdf:RDF>
<rdf:Description rdf:about="">
<!--
The Model Builder Metadata. The Dublin Core "creator" element is used
to indicate the person who translated the model into CellML.
The rdf:about of the Description has to remain blank for PMR2 to pick this up properly....
-->
<dc:creator rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Cooling</vCard:Family>
<vCard:Given>Mike</vCard:Given>
</vCard:N>
<vCard:EMAIL rdf:parseType="Resource">
<rdf:value>m.cooling@auckland.ac.nz</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet" />
</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>Auckland Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</dc:creator>
</rdf:Description>
<rdf:Description rdf:about="#IP3Submodel">
<bqs:reference rdf:parseType="Resource">
<bqs:JournalArticle rdf:parseType="Resource">
<dc:creator>
<rdf:Seq>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Cooling</vCard:Family>
<vCard:Given>Mike</vCard:Given>
</vCard:N>
<vCard:EMAIL rdf:parseType="Resource">
<rdf:value>m.cooling@auckland.ac.nz</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>Auckland Bioengineering Institute</vCard:Orgname>
<vCard:Orgunit>University of Auckland</vCard:Orgunit>
</vCard:ORG>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Hunter</vCard:Family>
<vCard:Given>Peter</vCard:Given>
</vCard:N>
<vCard:EMAIL rdf:parseType="Resource">
<rdf:value>p.hunter@auckland.ac.nz</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>Auckland Bioengineering Institute</vCard:Orgname>
<vCard:Orgunit>University of Auckland</vCard:Orgunit>
</vCard:ORG>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Crampin</vCard:Family>
<vCard:Given>Edmund</vCard:Given>
</vCard:N>
<vCard:EMAIL rdf:parseType="Resource">
<rdf:value>e.crampin@auckland.ac.nz</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>Auckland Bioengineering Institute</vCard:Orgname>
<vCard:Orgunit>University of Auckland</vCard:Orgunit>
</vCard:ORG>
</rdf:li>
</rdf:Seq>
</dc:creator>
<dc:title>Modeling Biological Modularity with CellML</dc:title>
<bqs:volume>2</bqs:volume>
<bqs:first_page>73</bqs:first_page>
<bqs:last_page>79</bqs:last_page>
<bqs:Journal rdf:parseType="Resource">
<dc:title>IET Systems Biology</dc:title>
</bqs:Journal>
<dcterms:issued rdf:parseType="Resource">
<dcterms:W3CDTF>2008-00-00 00:00</dcterms:W3CDTF>
</dcterms:issued>
</bqs:JournalArticle>
</bqs:reference>
<bqs:reference rdf:parseType="Resource">
<dc:subject rdf:parseType="Resource">
<bqs:subject_type>keyword</bqs:subject_type>
<rdf:value>
<rdf:Bag>
<rdf:li>Signal Transduction</rdf:li>
<rdf:li>Modularity</rdf:li>
</rdf:Bag>
</rdf:value>
</dc:subject>
</bqs:reference>
</rdf:Description>
</rdf:RDF>
<import xlink:href="extracellular_ligand.cellml">
<component name="ligand" component_ref="ligand" />
</import>
<import xlink:href="GPCR_Cycle.cellml">
<component name="GPCR_Cycle" component_ref="GPCR_Cycle" />
</import>
<import xlink:href="Galpha.cellml">
<component name="Galpha" component_ref="Galpha" />
</import>
<import xlink:href="calcium.cellml">
<component name="calcium" component_ref="calcium" />
</import>
<import xlink:href="PLC_Cycle.cellml">
<component name="PLC_Cycle" component_ref="PLC_Cycle" />
</import>
<import xlink:href="PIP2.cellml">
<component name="PIP2" component_ref="PIP2" />
</import>
<import xlink:href="IP3.cellml">
<component name="IP3" component_ref="IP3" />
</import>
<import xlink:href="IP3_degradation.cellml">
<component name="IP3_degradation" component_ref="IP3_degradation" />
</import>
<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#">
<rdf:Description rdf:about="#IP3Submodel">
<dc:creator rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Cooling</vCard:Family>
<vCard:Given>Michael</vCard:Given>
</vCard:N>
<vCard:EMAIL rdf:parseType="Resource">
<rdf:value>m.cooling@auckland.ac.nz</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet" />
</vCard:EMAIL>
</dc:creator>
<dc:title>Cooling's IP3 Pathway Submodel</dc:title>
</rdf:Description>
</rdf:RDF>
<!--
*******************************************************
*** U N I T S ***
*******************************************************
-->
<units name="s">
<unit units="second" />
</units>
<units name="um2">
<unit units="um" exponent="2" />
</units>
<units name="um">
<unit prefix="micro" units="meter" />
</units>
<units name="per_um">
<unit units="um" exponent="-1" />
</units>
<units name="uM_um2">
<unit units="um2"/>
<unit units="uM"/>
</units>
<units name="uM">
<unit prefix="micro" units="mole" />
<unit units="liter" exponent="-1" />
</units>
<units name="per_um2">
<unit units="um2" exponent="-1" />
</units>
<units name="um3">
<unit units="um" exponent="3" />
</units>
<units name="per_um2">
<unit units="um2" exponent="-1" />
</units>
<units name="per_um2_per_s">
<unit units="um2" exponent="-1" />
<unit units="s" exponent="-1" />
</units>
<units name="uM_per_s">
<unit units="uM" exponent="1"/>
<unit units="s" exponent="-1" />
</units>
<units name="per_uM_per_um3">
<unit units="uM" exponent="-1" />
<unit units="um3" exponent="-1" />
</units>
<!--
*******************************************************
*** C O M P O N E N T S ***
*******************************************************
-->
<component name="environment">
<variable name="t" private_interface="out" units="s" />
</component>
<component name="geometry">
<variable name="Cpc" units="uM_um2" private_interface="out" />
<variable name="Cc" units="uM" />
<variable name="Cp" units="per_um2" />
<variable name="Vc" initial_value="2550" units="um3" />
<variable name="Rpc" initial_value="4.61" units="per_um"/>
<math xmlns="http://www.w3.org/1998/Math/MathML"
cmeta:id="Cc_eq">
<apply id="Cc_eq">
<eq/> />
<ci>Cc</ci>
<apply>
<divide />
<cn cellml:units="dimensionless">1</cn>
<apply>
<times />
<ci>Vc</ci>
<cn type="e-notation" cellml:units="per_uM_per_um3">6.022<sep/>2</cn>
</apply>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML"
cmeta:id="Cp_eq">
<apply id="Cp_eq">
<eq/> />
<ci>Cp</ci>
<apply>
<divide />
<cn cellml:units="dimensionless">1</cn>
<apply>
<times />
<ci>Vc</ci>
<ci>Rpc</ci>
</apply>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML"
cmeta:id="Cpc_eq">
<apply id="Cpc_eq">
<eq/> />
<ci>Cpc</ci>
<apply>
<divide />
<ci>Cc</ci>
<ci>Cp</ci>
</apply>
</apply>
</math>
</component>
<component name="Galpha_interface">
<variable name="gpcrJ2" units="per_um2_per_s" public_interface="in"/>
<variable name="gpcrJ3" units="per_um2_per_s" public_interface="in"/>
<variable name="plcJ5" units="per_um2_per_s" public_interface="in"/>
<variable name="plcJ6" units="per_um2_per_s" public_interface="in"/>
<variable name="J_gain_Gd" units="per_um2_per_s" public_interface="out"/>
<variable name="gpcrJ6" units="per_um2_per_s" public_interface="in"/>
<variable name="plcJ2" units="per_um2_per_s" public_interface="in"/>
<variable name="plcJ3" units="per_um2_per_s" public_interface="in" />
<variable name="J_gain_Gt" units="per_um2_per_s" public_interface="out"/>
<math xmlns="http://www.w3.org/1998/Math/MathML"
cmeta:id="J_gain_Gd_eq">
<apply id="J_gain_Gd_eq">
<eq/>
<ci>J_gain_Gd</ci>
<apply>
<minus />
<apply>
<plus />
<ci>plcJ5</ci>
<ci>plcJ6</ci>
</apply>
<apply>
<plus />
<ci>gpcrJ2</ci>
<ci>gpcrJ3</ci>
</apply>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML"
cmeta:id="J_gain_Gt_eq">
<apply id="J_gain_Gt_eq">
<eq/>
<ci>J_gain_Gt</ci>
<apply>
<minus />
<ci>gpcrJ6</ci>
<apply>
<plus />
<ci>plcJ2</ci>
<ci>plcJ3</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="calcium_interface">
<variable name="J_gain_Ca" units="uM_per_s" public_interface="out" />
<variable name="Cpc" units="uM_um2" private_interface="in" />
<variable name="plcJ1" units="per_um2_per_s" public_interface="in"/>
<variable name="plcJ4" units="per_um2_per_s" public_interface="in" />
<math xmlns="http://www.w3.org/1998/Math/MathML"
cmeta:id="J_gain_Ca_eq">
<apply id="J_gain_Ca_eq">
<eq/>
<ci>J_gain_Ca</ci>
<apply>
<times />
<ci>Cpc</ci>
<apply>
<times />
<cn cellml:units="dimensionless">-1</cn>
<apply>
<plus />
<ci>plcJ1</ci>
<ci>plcJ4</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="IP3_interface" >
<variable name="Cpc" units="uM_um2" private_interface="in" />
<variable name="J_gain_IP3" units="uM_per_s" public_interface="out" />
<variable name="pip2J1" units="per_um2_per_s" public_interface="in"/>
<variable name="pip2J2" units="per_um2_per_s" public_interface="in"/>
<variable name="IP3degJ" units="uM_per_s" public_interface="in"/>
<math xmlns="http://www.w3.org/1998/Math/MathML"
cmeta:id="J_gain_IP3">
<apply id="J_gain_IP3">
<eq/>
<ci>J_gain_IP3</ci>
<apply>
<minus />
<apply>
<times />
<ci>Cpc</ci>
<apply>
<plus />
<ci>pip2J1</ci>
<ci>pip2J2</ci>
</apply>
</apply>
<ci>IP3degJ</ci>
</apply>
</apply>
</math>
</component>
<group>
<relationship_ref relationship="encapsulation" />
<component_ref component="environment">
<component_ref component="geometry">
<component_ref component="ligand"/>
<component_ref component="GPCR_Cycle"/>
<component_ref component="Galpha_interface"/>
<component_ref component="Galpha"/>
<component_ref component="PLC_Cycle"/>
<component_ref component="calcium"/>
<component_ref component="calcium_interface"/>
<component_ref component="PIP2"/>
<component_ref component="IP3"/>
<component_ref component="IP3_interface" />
</component_ref>
</component_ref>
</group>
<connection>
<map_components
component_1="environment" component_2="ligand" />
<map_variables variable_1="t" variable_2="t" />
</connection>
<connection>
<map_components
component_1="environment" component_2="GPCR_Cycle" />
<map_variables variable_1="t" variable_2="t" />
</connection>
<connection>
<map_components
component_1="environment" component_2="Galpha" />
<map_variables variable_1="t" variable_2="t" />
</connection>
<connection>
<map_components
component_1="environment" component_2="PLC_Cycle" />
<map_variables variable_1="t" variable_2="t" />
</connection>
<connection>
<map_components
component_1="environment" component_2="calcium" />
<map_variables variable_1="t" variable_2="t" />
</connection>
<connection>
<map_components
component_1="geometry" component_2="calcium_interface" />
<map_variables variable_1="Cpc" variable_2="Cpc" />
</connection>
<connection>
<map_components
component_1="geometry" component_2="PIP2" />
<map_variables variable_1="Cpc" variable_2="Cpc" />
</connection>
<connection>
<map_components
component_1="geometry" component_2="IP3_interface" />
<map_variables variable_1="Cpc" variable_2="Cpc" />
</connection>
<connection>
<map_components
component_1="environment" component_2="IP3" />
<map_variables variable_1="t" variable_2="t" />
</connection>
<connection>
<map_components
component_1="ligand" component_2="GPCR_Cycle" />
<map_variables variable_1="L" variable_2="L" />
</connection>
<connection>
<map_components
component_1="GPCR_Cycle" component_2="Galpha_interface" />
<map_variables variable_1="J2" variable_2="gpcrJ2" />
<map_variables variable_1="J3" variable_2="gpcrJ3" />
<map_variables variable_1="J6" variable_2="gpcrJ6" />
</connection>
<connection>
<map_components
component_1="PLC_Cycle" component_2="Galpha_interface" />
<map_variables variable_1="J2" variable_2="plcJ2" />
<map_variables variable_1="J3" variable_2="plcJ3" />
<map_variables variable_1="J5" variable_2="plcJ5" />
<map_variables variable_1="J6" variable_2="plcJ6" />
</connection>
<connection>
<map_components
component_1="Galpha" component_2="Galpha_interface" />
<map_variables variable_1="J_gain_Gd" variable_2="J_gain_Gd" />
<map_variables variable_1="J_gain_Gt" variable_2="J_gain_Gt" />
</connection>
<connection>
<map_components
component_1="Galpha" component_2="PLC_Cycle" />
<map_variables variable_1="Gt" variable_2="Gt" />
</connection>
<connection>
<map_components
component_1="Galpha" component_2="GPCR_Cycle" />
<map_variables variable_1="Gd" variable_2="Gd" />
</connection>
<connection>
<map_components
component_1="PLC_Cycle" component_2="calcium_interface" />
<map_variables variable_1="J1" variable_2="plcJ1" />
<map_variables variable_1="J4" variable_2="plcJ4" />
</connection>
<connection>
<map_components
component_1="calcium" component_2="calcium_interface" />
<map_variables variable_1="J_gain_Ca" variable_2="J_gain_Ca" />
</connection>
<connection>
<map_components
component_1="PLC_Cycle" component_2="calcium" />
<map_variables variable_1="Ca" variable_2="Ca" />
</connection>
<connection>
<map_components
component_1="PLC_Cycle" component_2="PIP2" />
<map_variables variable_1="Pc" variable_2="Eb" />
<map_variables variable_1="Pcg" variable_2="Es" />
</connection>
<connection>
<map_components
component_1="IP3_interface" component_2="PIP2" />
<map_variables variable_1="pip2J1" variable_2="J1" />
<map_variables variable_1="pip2J2" variable_2="J2" />
</connection>
<connection>
<map_components
component_1="IP3_interface" component_2="IP3" />
<map_variables variable_1="J_gain_IP3" variable_2="J_gain_IP3" />
</connection>
<connection>
<map_components
component_1="IP3_interface" component_2="IP3_degradation" />
<map_variables variable_1="IP3degJ" variable_2="J1" />
</connection>
<connection>
<map_components
component_1="IP3" component_2="IP3_degradation" />
<map_variables variable_1="IP3" variable_2="IP3" />
</connection>
</model>
