Location: Cooling, Hunter, Crampin, 2009 @ e4e4bc136629 / NFATCycling_TomidaProtocol.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_TomidaProtocol.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#"
	>
    
<!--
*******************************************************
***         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="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"/>
		  
		  <variable cmeta:id="v4" name="k_f1" units="per_nM_s" initial_value="7.68934e-6"/>
		  <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="v7" name="k_f4" units="per_s" initial_value="0.000444695"/>
		  
		  <variable cmeta:id="v8" name="k_r1" units="per_s" initial_value="0.019256"/>
		  <variable cmeta:id="v9" name="k_r3" units="per_nM_s" initial_value="4.70813e-5"/>
		  
		  <variable cmeta:id="v10" name="NFATp_n" units="nM" initial_value="0.077917275" public_interface="out"/>
		  <variable cmeta:id="v11" name="NFATp_c" units="nM" initial_value="0.9957805651"/>
		  <variable cmeta:id="v12" name="NFATN_n" units="nM" initial_value="0.10902441" public_interface="out"/>
          <variable cmeta:id="v13" name="NFATN_c" units="nM" initial_value="0.0004806012"/>
          
          <variable cmeta:id="v14" name="act_N" units="dimensionless" public_interface="in"/>
          <variable cmeta:id="v15" name="Ntot" units="nM" public_interface="in"/>
          <variable cmeta:id="v16" name="Ccn" units="dimensionless" public_interface="in"/> 
		  
		  <variable cmeta:id="v17" name="t"   units="s" public_interface="in"/>
    

     <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>
	
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    <rdf:Description rdf:about="http://www.cellml.org/cellml/1.1#NFATCycling">
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            <rdf:value>m.cooling@auckland.ac.nz</rdf:value>
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      </dc:creator>
      <dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">Cooling's NFAT Cycling module for the Dual calcium protocol</dc:title>
    </rdf:Description>
	
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            <semsim:refersTo rdf:resource="file:///C:/Users/rlyn081/Documents/local_ontologies/gene_ontology_edit.obo#GO:2001318"/> <!-- no GO term exists for NFAT export -->
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		<cito:usesDataFrom>doi:10.1093/emboj/cdg381</cito:usesDataFrom>
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	<rdf:Description
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		<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:10.1093/emboj/cdg381</cito:usesDataFrom>
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	<rdf:Description
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		<cito:usesDataFrom>doi:10.1093/emboj/cdg381</cito:usesDataFrom>
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	<rdf:Description
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		<cito:usesDataFrom>doi:10.1093/emboj/cdg381</cito:usesDataFrom>
	</rdf:Description>
	
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