<meta name="qrichtext" content="1"/> </head> <body style="font-size:12pt;font-family:Arial"> <p style="margin-top:18px" dir="ltr"> <span style="font-size:23pt;font-weight:600">Two-gene model of the Ostreococcus circadian clock</span> </p> <p dir="ltr">This is a model of the circadian clock of Ostreococcus tauri, with a negative feedback loop between TOC1 and CCA1 (a.k.a. LHY) and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011).</p> <p dir="ltr">This version of the model has eliminated one light input by setting the CCA1 degradation rate to its light value, corresponding to Figure 2B of Dixon et al., New Phytologist (2014). The model has been entrained in LD 12:12 and will be given one LD cycle before going into constant light. The length of the day before LL is defined in the function called light.</p> <p dir="ltr">The model incorporates luciferase reporters, and in this SBML model the four different versions of the model for transcriptional and translational reporter lines (pTOC1::LUC, pCCA1::LUC, TOC1-LUC and CCA1-LUC) are all accessible by setting one of the rep_X parameters to 1 and the others to 0. You can also set all four to 0 to only simulate the non-reporter core of the system.</p> <p dir="ltr">Input to the system should be provided by modifying the "light" function. Implementations of an LD cycles and transition to LL are provided as examples, but the model was also used with more complicated light regimes that vary between data sets and are not convenient to express directly in SBML.</p> <p dir="ltr">The functions "ox_cca1" and "ox_toc1" can be altered to add overexpression of CCA1 and TOC1. Setting either to <span style="font-style:italic">x</span> gives additional, constitutive transcription at <span style="font-style:italic">x</span> times the maximal (and typically not realizable) transcription rate of the native gene. The overexpression mutant fits in Figure 7 of Troein et al. (2011) used ox_cca1 = 0.115 and oc_toc1 = 0.0584, respectively. </p> <p dir="ltr">The functions "copies_toc1" and "copies_cca1" are normally 1 but can be lowered to simulate knockdown experiments. The functions "transcription", "translation" and "proteasome" can be modified to simulate the effects of altering the overall rate of transcription, translation and protein degradation.</p> <p dir="ltr">The parameters were fitted specifically to data from transgenic reporter lines TOC8, pTOC3, LHY7 and pLHY7 (Corellou et al., Plant Cell 2009). Parameters that begin with "effcopies" describe the effective number of copies of CCA1 or TOC1 in the respective translational fusion lines, with anything above 1 due to the fusion proteins.</p> <p dir="ltr">For the model fitting, the initial values were fitted to the data in the various time courses. The initial values given here correspond to the limit cycle of the system in LD 12:12. The system converges to the limit cycle in just a few days under most light conditions, so these initial values are biologically meaningful.</p> <p dir="ltr">The species cca1luc_c and cca1luc_n have been merged into cca1luc (which corresponds to the observable luminescence signal), because Copasi refused to run the system otherwise. For TOC1-LUC, the predicted output signal is the sum of toc1luc_1 and toc1luc_2.</p> </body> </html> </notes> <listOfFunctionDefinitions> <functionDefinition metaid="COPASI53" id="function_2" name="Light accumulator decrease"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI53"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2014-04-17T12:37:07Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <math xmlns="http://www.w3.org/1998/Math/MathML"> <lambda> <bvar> <ci> acc_rate </ci> </bvar> <bvar> <ci> acc </ci> </bvar> <apply> <times/> <ci> acc_rate </ci> <ci> acc </ci> </apply> </lambda> </math> </functionDefinition> <functionDefinition id="transcription" name="transcription"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <lambda> <bvar> <ci> t </ci> </bvar> 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<ci> t </ci> </bvar> <bvar> <ci> D_l </ci> </bvar> <bvar> <ci> D_d </ci> </bvar> <bvar> <ci> level </ci> </bvar> <apply> <times/> <apply> <ci> proteasome </ci> <ci> t </ci> </apply> <apply> <plus/> <apply> <times/> <apply> <ci> light </ci> <ci> t </ci> </apply> <ci> D_l </ci> </apply> <apply> <times/> <apply> <minus/> <cn> 1 </cn> <apply> <ci> light </ci> <ci> t </ci> </apply> </apply> <ci> D_d </ci> </apply> </apply> <ci> level </ci> </apply> </lambda> </math> </functionDefinition> <functionDefinition id="function_5" name="Light-dependent transport"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <lambda> <bvar> <ci> t </ci> </bvar> <bvar> <ci> Di_l </ci> </bvar> <bvar> <ci> Di_d </ci> </bvar> <bvar> <ci> level </ci> </bvar> <apply> <times/> <apply> <plus/> <apply> <times/> <apply> <ci> light </ci> <ci> t </ci> </apply> <ci> Di_l </ci> </apply> <apply> <times/> <apply> <minus/> <cn> 1 </cn> <apply> <ci> light </ci> <ci> t </ci> </apply> </apply> <ci> Di_d </ci> </apply> </apply> <ci> level </ci> </apply> </lambda> </math> </functionDefinition> <functionDefinition metaid="COPASI67" id="function_6" name="CCA1 transcription"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI67"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:30:23Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <math xmlns="http://www.w3.org/1998/Math/MathML"> <lambda> <bvar> <ci> t </ci> </bvar> <bvar> <ci> toc1_2 </ci> </bvar> <bvar> <ci> R_cca1_toc1_2_l </ci> </bvar> <bvar> <ci> R_cca1_toc1_2_d </ci> </bvar> <bvar> <ci> H_cca1_toc1 </ci> </bvar> <bvar> <ci> rep_TOC1 </ci> </bvar> <bvar> <ci> effcopies_toc1_TOC8 </ci> </bvar> <apply> <times/> <apply> <ci> transcription </ci> <ci> t </ci> </apply> <apply> <plus/> <apply> <ci> ox_cca1 </ci> <ci> t </ci> </apply> <apply> <divide/> <apply> <times/> <apply> <ci> copies_cca1 </ci> <ci> t </ci> </apply> <apply> <power/> <apply> <times/> <apply> <ci> tf_output </ci> <ci> rep_TOC1 </ci> <ci> effcopies_toc1_TOC8 </ci> <ci> toc1_2 </ci> </apply> <apply> <plus/> <apply> <times/> <apply> <ci> light </ci> <ci> t </ci> </apply> <ci> R_cca1_toc1_2_l </ci> </apply> <apply> <times/> <apply> <minus/> <cn> 1 </cn> <apply> <ci> light </ci> <ci> t </ci> </apply> </apply> <ci> R_cca1_toc1_2_d </ci> </apply> </apply> </apply> <ci> H_cca1_toc1 </ci> </apply> </apply> <apply> <plus/> <apply> <power/> <apply> <times/> <apply> <ci> tf_output </ci> <ci> rep_TOC1 </ci> <ci> effcopies_toc1_TOC8 </ci> <ci> toc1_2 </ci> </apply> <apply> <plus/> <apply> <times/> <apply> <ci> light </ci> <ci> t </ci> </apply> <ci> R_cca1_toc1_2_l </ci> </apply> <apply> <times/> <apply> <minus/> <cn> 1 </cn> <apply> <ci> light </ci> <ci> t </ci> </apply> </apply> <ci> R_cca1_toc1_2_d </ci> </apply> </apply> </apply> <ci> H_cca1_toc1 </ci> </apply> <cn> 1 </cn> </apply> </apply> </apply> </apply> </lambda> </math> </functionDefinition> <functionDefinition metaid="COPASI68" id="function_9" name="LUC transcription for pCCA1"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI68"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T18:04:25Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <math xmlns="http://www.w3.org/1998/Math/MathML"> <lambda> <bvar> <ci> t </ci> </bvar> <bvar> <ci> toc1_2 </ci> </bvar> <bvar> <ci> R_cca1_toc1_2_l </ci> </bvar> <bvar> <ci> R_cca1_toc1_2_d </ci> </bvar> <bvar> <ci> H_cca1_toc1 </ci> </bvar> <bvar> <ci> rep_pCCA1 </ci> </bvar> <apply> <divide/> <apply> <times/> <ci> rep_pCCA1 </ci> <apply> <ci> transcription </ci> <ci> t </ci> </apply> <apply> <power/> <apply> <times/> <ci> toc1_2 </ci> <apply> <plus/> <apply> <times/> <apply> <ci> light </ci> <ci> t </ci> </apply> <ci> R_cca1_toc1_2_l </ci> </apply> <apply> <times/> <apply> <minus/> <cn> 1 </cn> <apply> <ci> light </ci> <ci> t </ci> </apply> </apply> <ci> R_cca1_toc1_2_d </ci> </apply> </apply> </apply> <ci> H_cca1_toc1 </ci> </apply> </apply> <apply> <plus/> <apply> <power/> <apply> <times/> <ci> toc1_2 </ci> <apply> <plus/> <apply> <times/> <apply> <ci> light </ci> <ci> t </ci> </apply> <ci> R_cca1_toc1_2_l </ci> </apply> <apply> <times/> <apply> <minus/> <cn> 1 </cn> <apply> <ci> light </ci> <ci> t </ci> </apply> </apply> <ci> R_cca1_toc1_2_d </ci> </apply> </apply> </apply> <ci> H_cca1_toc1 </ci> </apply> <cn> 1 </cn> </apply> </apply> </lambda> </math> </functionDefinition> </listOfFunctionDefinitions> <listOfUnitDefinitions> <unitDefinition id="time" name="time"> <listOfUnits> <unit kind="second" exponent="1" scale="0" multiplier="3600"/> </listOfUnits> </unitDefinition> <unitDefinition id="substance" name="substance"> <listOfUnits> <unit kind="mole" exponent="1" scale="-9" multiplier="1"/> </listOfUnits> </unitDefinition> </listOfUnitDefinitions> <listOfCompartments> <compartment metaid="COPASI2" id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI2"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:19:06Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> <CopasiMT:is rdf:resource="urn:miriam:obo.go:GO%3A0005623"/> </rdf:Description> </rdf:RDF> </COPASI> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" 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#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#COPASI2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:go:GO:0005623"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment> </listOfCompartments> <listOfSpecies> <species metaid="COPASI3" id="acc" name="acc" compartment="compartment" initialConcentration="0.272067483201623" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI3"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2000-01-01T00:00:00Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI4" id="toc1_mrna" name="toc1_mrna" compartment="compartment" initialConcentration="0.0547616549903228" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI4"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:53:26Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> <CopasiMT:isHomologTo rdf:resource="urn:miriam:uniprot:O81713"/> </rdf:Description> </rdf:RDF> </COPASI> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" 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#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#COPASI4"> <bqbiol:isHomologTo> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:uniprot:O81713"/> </rdf:Bag> </bqbiol:isHomologTo> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="COPASI5" id="toc1_1" name="toc1_1" compartment="compartment" initialConcentration="0.244447718691095" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI5"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:53:13Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI6" id="toc1_2" name="toc1_2" compartment="compartment" initialConcentration="0.336814802373972" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI6"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:53:15Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI7" id="cca1_mrna" name="cca1_mrna" compartment="compartment" initialConcentration="0.117711771853057" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI7"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:27:49Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI8" id="cca1_c" name="cca1_c" compartment="compartment" initialConcentration="0.0566237882923905" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI8"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:19:16Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI9" id="cca1_n" name="cca1_n" compartment="compartment" initialConcentration="1.8629532083789" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI9"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:53:05Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI10" id="toc1luc_mrna" name="toc1luc_mrna" compartment="compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI10"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:52:33Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI11" id="toc1luc_1" name="toc1luc_1" compartment="compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI11"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:53:15Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI12" id="toc1luc_2" name="toc1luc_2" compartment="compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI12"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:53:19Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI13" id="cca1luc_mrna" name="cca1luc_mrna" compartment="compartment" initialConcentration="0.117711771853057" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI13"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:52:52Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI14" id="cca1luc" name="cca1luc" compartment="compartment" initialConcentration="1.27695487280015" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI14"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:19:25Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI15" id="luc_mrna" name="luc_mrna" compartment="compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI15"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:53:12Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> <species metaid="COPASI16" id="luc" name="luc" compartment="compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI16"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:53:08Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </species> </listOfSpecies> <listOfParameters> <parameter id="D_luc" name="D_luc" value="0.182881217463259" constant="true"/> <parameter id="D_mrna_luc" name="D_mrna_luc" value="1" constant="true"/> <parameter metaid="COPASI17" id="acc_rate" name="acc_rate" value="0.0820132250303287" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI17"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:20:14Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> <parameter id="R_toc1_cca1" name="R_toc1_cca1" value="1.08706126858966" constant="true"/> <parameter metaid="COPASI18" id="H_toc1_cca1" name="H_toc1_cca1" value="2.07807738692343" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI18"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T18:18:41Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> <parameter id="L_toc1" name="L_toc1" value="0.0001" constant="true"/> <parameter id="R_toc1_acc" name="R_toc1_acc" value="0.231107032949407" constant="true"/> <parameter id="D_mrna_toc1" name="D_mrna_toc1" value="0.29213049778373" constant="true"/> <parameter metaid="COPASI19" id="T_toc1" name="T_toc1" value="0.769970172977886" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI19"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:20:31Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> <parameter id="Di_toc1_12_l" name="Di_toc1_12_l" value="0.136490583368648" constant="true"/> <parameter id="Di_toc1_12_d" name="Di_toc1_12_d" value="0.326619492089715" constant="true"/> <parameter id="D_toc1_2_l" name="D_toc1_2_l" value="0.461550559180802" constant="true"/> <parameter id="D_toc1_2_d" name="D_toc1_2_d" value="0.356613920551118" constant="true"/> <parameter id="H_cca1_toc1" name="H_cca1_toc1" value="2.5007062880634" constant="true"/> <parameter metaid="COPASI20" id="R_cca1_toc1_2_l" name="R_cca1_toc1_2_l" value="3.27520292103832" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI20"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T15:03:45Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> <parameter id="R_cca1_toc1_2_d" name="R_cca1_toc1_2_d" value="1.38563901682266" constant="true"/> <parameter metaid="COPASI21" id="D_mrna_cca1" name="D_mrna_cca1" value="1.33082080954527" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI21"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:38:01Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> <parameter id="T_cca1" name="T_cca1" value="4.90486610428652" constant="true"/> <parameter metaid="COPASI22" id="Di_cca1_cn" name="Di_cca1_cn" value="10" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI22"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:20:18Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> <parameter id="D_cca1_l" name="D_cca1_l" value="0.424177877449438" constant="true"/> <parameter id="D_cca1_d" name="D_cca1_d" value="0.269380178154091" constant="true"/> <parameter metaid="COPASI23" id="effcopies_cca1_LHY7" name="effcopies_cca1_LHY7" value="1.13965755508623" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI23"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:37:50Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> <parameter metaid="COPASI24" id="effcopies_toc1_TOC8" name="effcopies_toc1_TOC8" value="1" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI24"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:37:55Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> <parameter id="parameter_1" name="T_luc" value="1" constant="true"/> <parameter metaid="COPASI25" id="parameter_2" name="rep_TOC1" value="0" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI25"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T15:03:35Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> <parameter metaid="COPASI26" id="parameter_3" name="rep_pTOC1" value="0" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI26"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:53:48Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> <parameter metaid="COPASI27" id="parameter_4" name="rep_CCA1" value="1" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI27"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:37:48Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> <parameter metaid="COPASI28" id="parameter_5" name="rep_pCCA1" value="0" constant="true"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI28"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:53:49Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> </parameter> </listOfParameters> <listOfReactions> <reaction id="reaction_1" name="Light accumulator increase" reversible="false"> <listOfProducts> <speciesReference species="acc" stoichiometry="1"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> function_1 </ci> <ci> acc_rate </ci> <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="reaction_2" name="Light accumulator decrease" reversible="false"> <listOfReactants> <speciesReference species="acc" stoichiometry="1"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> function_2 </ci> <ci> acc_rate </ci> <ci> acc </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI29" id="reaction_3" name="TOC1 transcription" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI29"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T17:31:40Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <listOfProducts> <speciesReference species="toc1_mrna" stoichiometry="1"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="acc"/> <modifierSpeciesReference species="cca1_n"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> function_3 </ci> <ci> R_toc1_acc </ci> <ci> acc </ci> <ci> R_toc1_cca1 </ci> <ci> H_toc1_cca1 </ci> <ci> cca1_n </ci> <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol> <ci> L_toc1 </ci> <ci> parameter_4 </ci> <ci> effcopies_cca1_LHY7 </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI30" id="reaction_4" name="TOC1 degradation" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI30"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T17:30:20Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <listOfReactants> <speciesReference species="toc1_2" stoichiometry="1"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> function_4 </ci> <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol> <ci> D_toc1_2_l </ci> <ci> D_toc1_2_d </ci> <ci> toc1_2 </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="reaction_5" name="TOC1 translation" reversible="false"> <listOfProducts> <speciesReference species="toc1_1" stoichiometry="1"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="toc1_mrna"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> Translation </ci> <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol> <ci> T_toc1 </ci> <ci> toc1_mrna </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI31" id="reaction_6" name="TOC1 conversion" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI31"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T17:30:19Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <listOfReactants> <speciesReference species="toc1_1" stoichiometry="1"/> </listOfReactants> <listOfProducts> <speciesReference species="toc1_2" stoichiometry="1"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> function_5 </ci> <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol> <ci> Di_toc1_12_l </ci> <ci> Di_toc1_12_d </ci> <ci> toc1_1 </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI32" id="reaction_7" name="TOC1 mRNA degradation" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI32"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T18:15:26Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <listOfReactants> <speciesReference species="toc1_mrna" stoichiometry="1"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> D_mrna_toc1 </ci> <ci> toc1_mrna </ci> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI33" id="reaction_8" name="CCA1 transcription" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI33"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T17:31:29Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <listOfProducts> <speciesReference species="cca1_mrna" stoichiometry="1"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="toc1_2"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> function_6 </ci> <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol> <ci> toc1_2 </ci> <ci> R_cca1_toc1_2_l </ci> <ci> R_cca1_toc1_2_d </ci> <ci> H_cca1_toc1 </ci> <ci> parameter_2 </ci> <ci> effcopies_toc1_TOC8 </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI34" id="reaction_9" name="CCA1 mRNA degradation" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI34"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T17:30:10Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <listOfReactants> <speciesReference species="cca1_mrna" stoichiometry="1"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> D_mrna_cca1 </ci> <ci> cca1_mrna </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="reaction_10" name="CCA1 translation" reversible="false"> <listOfProducts> <speciesReference species="cca1_c" stoichiometry="1"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cca1_mrna"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> Translation </ci> <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol> <ci> T_cca1 </ci> <ci> cca1_mrna </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI35" id="reaction_11" name="CCA1 nuclear transport" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI35"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T18:27:53Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <listOfReactants> <speciesReference species="cca1_c" stoichiometry="1"/> </listOfReactants> <listOfProducts> <speciesReference species="cca1_n" stoichiometry="1"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> Di_cca1_cn </ci> <ci> cca1_c </ci> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI36" id="reaction_12" name="CCA1 degradation, cytosol" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI36"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T14:28:08Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <listOfReactants> <speciesReference species="cca1_c" stoichiometry="1"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> function_4 </ci> <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol> <ci> D_cca1_l </ci> <ci> D_cca1_l </ci> <ci> cca1_c </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI37" id="reaction_13" name="CCA1 degradation, nucleus" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI37"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T18:15:53Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <listOfReactants> <speciesReference species="cca1_n" stoichiometry="1"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> function_4 </ci> <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol> <ci> D_cca1_l </ci> <ci> D_cca1_l </ci> <ci> cca1_n </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI38" id="reaction_14" name="LUC transcription, pTOC1" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI38"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T17:30:16Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <listOfProducts> <speciesReference species="luc_mrna" stoichiometry="1"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="acc"/> <modifierSpeciesReference species="cca1_n"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> function_7 </ci> <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol> <ci> R_toc1_acc </ci> <ci> acc </ci> <ci> R_toc1_cca1 </ci> <ci> cca1_n </ci> <ci> H_toc1_cca1 </ci> <ci> parameter_3 </ci> <ci> L_toc1 </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="reaction_15" name="LUC mRNA degradation" reversible="false"> <listOfReactants> <speciesReference species="luc_mrna" stoichiometry="1"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> D_mrna_luc </ci> <ci> luc_mrna </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="reaction_16" name="LUC translation" reversible="false"> <listOfProducts> <speciesReference species="luc" stoichiometry="1"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="luc_mrna"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> Translation </ci> <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol> <ci> parameter_1 </ci> <ci> luc_mrna </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI39" id="reaction_17" name="LUC decay" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI39"> <dcterms:created> <rdf:Description> <dcterms:W3CDTF>2011-01-07T17:30:12Z</dcterms:W3CDTF> </rdf:Description> </dcterms:created> </rdf:Description> </rdf:RDF> </COPASI> </annotation> <listOfReactants> <speciesReference species="luc" stoichiometry="1"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> D_luc </ci> <ci> luc </ci> </apply> </math> </kineticLaw> </reaction> <reaction metaid="COPASI40" id="reaction_18" name="TOC1-LUC transcription" reversible="false"> <annotation> <COPASI xmlns="http://www.copasi.org/static/sbml"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"> <rdf:Description rdf:about="#COPASI40"> <dcterms:created> <rdf:Description> 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