- Author:
- mtcooling <mtcooling.development@gmail.com>
- Date:
- 2015-08-24 10:57:56+12:00
- Desc:
- Split the annotation for the protocols into separate files in line with the metadata spec 2.0
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/cooling_hunter_crampin_2009/rawfile/e4e4bc1366292fd3387f8391e774271f5a4e9c14/NFATCycling_DualProtocol.cellml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="NFATCycling"
cmeta:id="NFATCycling"
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#">
<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="#NFATCycling">
<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 NFAT Cycling module for the Dual calcium protocol</dc:title>
</rdf:Description>
</rdf:RDF>
<!--
*******************************************************
*** U N I T S ***
*******************************************************
-->
<units name="s">
<unit units="second"/>
</units>
<units name="nM">
<unit units="mole" prefix="nano"/>
<unit units="liter" exponent="-1"/>
</units>
<units name="per_s">
<unit units="s" exponent="-1"/>
</units>
<units name="nM_per_s">
<unit units="nM"/>
<unit units="s" exponent="-1"/>
</units>
<units name="per_nM_s">
<unit units="nM" exponent="-1"/>
<unit units="s" exponent="-1"/>
</units>
<!--
*********************************************************
*** C O M P O N E N T S ***
*********************************************************
-->
<component name="NFAT_Cycling">
<variable cmeta:id="v17" name="t" units="s" public_interface="in"/>
<variable cmeta:id="v13" name="NFATN_c" units="nM" initial_value="0.0017047398"/>
<variable cmeta:id="v12" name="NFATN_n" units="nM" initial_value="0.50910553" public_interface="out"/>
<variable cmeta:id="v11" name="NFATp_c" units="nM" initial_value="0.9825855442"/>
<variable cmeta:id="v10" name="NFATp_n" units="nM" initial_value="0.27638027" public_interface="out"/>
<variable cmeta:id="v16" name="Ccn" units="dimensionless" public_interface="in"/>
<variable cmeta:id="v15" name="Ntot" units="nM" public_interface="in"/>
<variable cmeta:id="v14" name="act_N" units="dimensionless" public_interface="in"/>
<variable cmeta:id="v4" name="k_f1" units="per_nM_s" initial_value="7.68934e-6"/>
<variable cmeta:id="v8" name="k_r1" units="per_s" initial_value="0.019256"/>
<variable cmeta:id="v5" name="k_f2" units="per_s" initial_value="0.00144192"/>
<variable cmeta:id="v6" name="k_f3" units="per_s" initial_value="0.000361944"/>
<variable cmeta:id="v9" name="k_r3" units="per_nM_s" initial_value="4.70813e-5"/>
<variable cmeta:id="v7" name="k_f4" units="per_s" initial_value="0.000444695"/>
<variable cmeta:id="v0" name="J1" units="nM_per_s"/>
<variable cmeta:id="v1" name="J2" units="nM_per_s"/>
<variable cmeta:id="v2" name="J3" units="nM_per_s"/>
<variable cmeta:id="v3" name="J4" units="nM_per_s"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J1</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>k_f1</ci>
<ci>NFATp_c</ci>
<ci>Ntot</ci>
<ci>act_N</ci>
</apply>
<apply>
<times/>
<ci>k_r1</ci>
<ci>NFATN_c</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>act_N</ci>
</apply>
</apply>
</apply>
</apply>
<apply id="eq_0">
<eq/>
<ci>J2</ci>
<apply>
<times/>
<ci>k_f2</ci>
<ci>NFATN_c</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>J3</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>k_f3</ci>
<ci>NFATN_n</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>act_N</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_r3</ci>
<ci>NFATp_n</ci>
<ci>Ntot</ci>
<ci>act_N</ci>
</apply>
</apply>
</apply>
<apply id="eq_1">
<eq/>
<ci>J4</ci>
<apply>
<times/>
<ci>k_f4</ci>
<ci>NFATp_n</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>NFATp_c</ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<ci>J4</ci>
<ci>Ccn</ci>
</apply>
<ci>J1</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>NFATN_c</ci>
</apply>
<apply>
<minus/>
<ci>J1</ci>
<ci>J2</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>NFATN_n</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>J2</ci>
<ci>Ccn</ci>
</apply>
<ci>J3</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>NFATp_n</ci>
</apply>
<apply>
<minus/>
<ci>J3</ci>
<ci>J4</ci>
</apply>
</apply>
</math>
</component>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:ro="http://www.obofoundry.org/ro/ro.owl#"
xmlns:service="http://www.cenitmio.es/ontologies/Service.owl#"
xmlns:opb="http://bhi.washington.edu/OPB#"
xmlns:semsim="http://www.bhi.washington.edu/SemSim#"
xmlns:cito="http://purl.org/spar/cito"
xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
>
<rdf:Description rdf:ID="v4">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_4">
<service:isAParameterOf>
<rdf:Description rdf:about="#entity_0">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#entity_1">
<ro:contained_in>
<rdf:Description rdf:about="#entity_2">
<ro:contained_in>
<rdf:Description rdf:about="#entity_3">
<semsim:refersTo rdf:resource="http://identifiers.org/fma/FMA:14067" />
</rdf:Description>
</ro:contained_in>
<semsim:refersTo rdf:resource="http://identifiers.org/fma/FMA:66835" />
</rdf:Description>
</ro:contained_in>
<semsim:refersTo rdf:resource="http://identifiers.org/go/GO:0033173" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000101" />
</rdf:Description>
</service:isAParameterOf>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000614" />
</rdf:Description>
</semsim:isComputationalComponentFor>
</rdf:Description>
<rdf:Description rdf:ID="v5">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_5">
<service:isAParameterOf>
<rdf:Description rdf:about="#entity_5">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#entity_4">
<ro:contained_in>
<rdf:Description rdf:about="#entity_3">
<semsim:refersTo rdf:resource="http://identifiers.org/fma/FMA:14067" />
</rdf:Description>
</ro:contained_in>
<semsim:refersTo rdf:resource="http://identifiers.org/go/GO:0051531" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000044" />
</rdf:Description>
</service:isAParameterOf>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000614" />
</rdf:Description>
</semsim:isComputationalComponentFor>
</rdf:Description>
<rdf:Description rdf:ID="v6">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_6">
<service:isAParameterOf>
<rdf:Description rdf:about="#entity_0">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#entity_1">
<ro:contained_in>
<rdf:Description rdf:about="#entity_2">
<ro:contained_in>
<rdf:Description rdf:about="#entity_3">
<semsim:refersTo rdf:resource="http://identifiers.org/fma/FMA:14067" />
</rdf:Description>
</ro:contained_in>
<semsim:refersTo rdf:resource="http://identifiers.org/fma/FMA:63840" />
</rdf:Description>
</ro:contained_in>
<semsim:refersTo rdf:resource="http://identifiers.org/go/GO:0033173" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000101" />
</rdf:Description>
</service:isAParameterOf>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000614" />
</rdf:Description>
</semsim:isComputationalComponentFor>
</rdf:Description>
<rdf:Description rdf:ID="v7">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_7">
<bqmodel:identity>
<rdf:Description rdf:about="#entity_6">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#entity_7">
<ro:contained_in>
<rdf:Description rdf:about="#entity_8">
<semsim:refersTo rdf:resource="http://identifiers.org/fma/FMA:14067" />
</rdf:Description>
</ro:contained_in>
<semsim:refersTo rdf:resource="file:///C:/Users/rlyn081/Documents/local_ontologies/gene_ontology_edit.obo#GO:2001318" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000044" />
</rdf:Description>
</bqmodel:identity>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000614" />
</rdf:Description>
</semsim:isComputationalComponentFor>
</rdf:Description>
<rdf:Description rdf:ID="v8">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_8">
<bqmodel:identity>
<rdf:Description rdf:about="#entity_0">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#entity_1">
<ro:contained_in>
<rdf:Description rdf:about="#entity_2">
<ro:contained_in>
<rdf:Description rdf:about="#entity_3">
<semsim:refersTo rdf:resource="http://identifiers.org/fma/FMA:14067" />
</rdf:Description>
</ro:contained_in>
<semsim:refersTo rdf:resource="http://identifiers.org/fma/FMA:66835" />
</rdf:Description>
</ro:contained_in>
<semsim:refersTo rdf:resource="http://identifiers.org/go/GO:0033173" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000104" />
</rdf:Description>
</bqmodel:identity>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000033" />
</rdf:Description>
</semsim:isComputationalComponentFor>
</rdf:Description>
<rdf:Description rdf:ID="v9">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_9">
<bqmodel:identity>
<rdf:Description rdf:about="#entity_10">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#entity_9">
<ro:contained_in>
<rdf:Description rdf:about="#entity_8">
<semsim:refersTo rdf:resource="http://identifiers.org/fma/FMA:67216" />
</rdf:Description>
</ro:contained_in>
<semsim:refersTo rdf:resource="http://identifiers.org/go/GO:0033173" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000104" />
</rdf:Description>
</bqmodel:identity>
<semsim:refersTo rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000033" />
</rdf:Description>
</semsim:isComputationalComponentFor>
</rdf:Description>
<rdf:Description rdf:ID="v16">
<bqbiol:identity rdf:resource="http://identifiers.org/opb/OPB_00375" />
</rdf:Description>
<rdf:Description rdf:ID="v17">
<bqbiol:identity rdf:resource="http://identifiers.org/opb/OPB_01361" />
</rdf:Description>
<rdf:Description rdf:ID="eq_0">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_18">
<ro:contained_in>
<rdf:Description rdf:about="#entity_3">
<semsim:refersTo rdf:resource="http://identifiers.org/fma/FMA:14067" />
</rdf:Description>
</ro:contained_in>
<semsim:refersTo rdf:resource="http://identifiers.org/go/GO:0051531" />
</rdf:Description>
</semsim:isComputationalComponentFor>
</rdf:Description>
<rdf:Description rdf:ID="eq_1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_19">
<semsim:refersTo rdf:resource="http://identifiers.org/go/GO:0051531"/>
<ro:contained_in>
<rdf:Description rdf:about="#entity_3">
<semsim:refersTo rdf:resource="http://identifiers.org/fma/FMA:14067" />
</rdf:Description>
</ro:contained_in>
<semsim:refersTo rdf:resource="file:///C:/Users/rlyn081/Documents/local_ontologies/gene_ontology_edit.obo#GO:2001318"/> <!-- There is no GO term for NFAT export-->
</rdf:Description>
</semsim:isComputationalComponentFor>
</rdf:Description>
<rdf:Description
rdf:about="#xpointernode(component[@name='NFATCycling']/variable[@name='k_f1']/@initial_value)">
<cito:usesDataFrom>doi:10.1113/jphysiol.2006.120048</cito:usesDataFrom>
<cito:usesDataFrom>doi:10.1093/emboj/cdg381</cito:usesDataFrom>
</rdf:Description>
<rdf:Description
rdf:about="#xpointernode(component[@name='NFATCycling']/variable[@name='k_f2']/@initial_value)">
<cito:usesDataFrom>doi:10.1113/jphysiol.2006.120048</cito:usesDataFrom>
<cito:usesDataFrom>doi:10.1093/emboj/cdg381</cito:usesDataFrom>
</rdf:Description>
<rdf:Description
rdf:about="#xpointernode(component[@name='NFATCycling']/variable[@name='k_f3']/@initial_value)">
<cito:usesDataFrom>doi:10.1113/jphysiol.2006.120048</cito:usesDataFrom>
<cito:usesDataFrom>doi:10.1093/emboj/cdg381</cito:usesDataFrom>
</rdf:Description>
<rdf:Description
rdf:about="#xpointernode(component[@name='NFATCycling']/variable[@name='k_f4']/@initial_value)">
<cito:usesDataFrom>doi:10.1113/jphysiol.2006.120048</cito:usesDataFrom>
<cito:usesDataFrom>doi:10.1093/emboj/cdg381</cito:usesDataFrom>
</rdf:Description>
<rdf:Description
rdf:about="#xpointernode(component[@name='NFATCycling']/variable[@name='k_r1']/@initial_value)">
<cito:usesDataFrom>doi:10.1113/jphysiol.2006.120048</cito:usesDataFrom>
<cito:usesDataFrom>doi:10.1093/emboj/cdg381</cito:usesDataFrom>
</rdf:Description>
<rdf:Description
rdf:about="#xpointernode(component[@name='NFATCycling']/variable[@name='k_r3']/@initial_value)">
<cito:usesDataFrom>doi:10.1113/jphysiol.2006.120048</cito:usesDataFrom>
<cito:usesDataFrom>doi:10.1093/emboj/cdg381</cito:usesDataFrom>
</rdf:Description>
<rdf:Description
rdf:about="#xpointernode(component[@name='NFATCycling']/variable[@name='NFATp_n']/@initial_value)">
<cito:usesDataFrom>doi:10.1113/jphysiol.2006.120048</cito:usesDataFrom>
</rdf:Description>
<rdf:Description
rdf:about="#xpointernode(component[@name='NFATCycling']/variable[@name='NFATp_c']/@initial_value)">
<cito:usesDataFrom>doi:10.1113/jphysiol.2006.120048</cito:usesDataFrom>
</rdf:Description>
<rdf:Description
rdf:about="#xpointernode(component[@name='NFATCycling']/variable[@name='NFATN_n']/@initial_value)">
<cito:usesDataFrom>doi:10.1113/jphysiol.2006.120048</cito:usesDataFrom>
</rdf:Description>
<rdf:Description
rdf:about="#xpointernode(component[@name='NFATCycling']/variable[@name='NFATN_c']/@initial_value)">
<cito:usesDataFrom>doi:10.1113/jphysiol.2006.120048</cito:usesDataFrom>
</rdf:Description>
</rdf:RDF>
</model>
