Location: Cooling, Hunter, Crampin, 2009 @ e4e4bc136629 / NFATCycling_DualProtocol.cellml

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>