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<b>Mass action rate law for first order irreversible reactions</b>
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Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant.
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<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 the light accumulator (acc), replacing it with the light value, corresponding to Figure 2F 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>
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<Constant key="Parameter_3954" name="Di_l" value="0.136491"/>
<Constant key="Parameter_3953" name="Di_d" value="0.326619"/>
</ListOfConstants>
<KineticLaw function="Function_45">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_283">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_269">
<SourceParameter reference="ModelValue_9"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_284">
<SourceParameter reference="ModelValue_10"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_286">
<SourceParameter reference="Metabolite_2"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_6" name="TOC1 mRNA degradation" reversible="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_6">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T18:15:26Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_1" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3952" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="ModelValue_7"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_1"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_7" name="CCA1 transcription" reversible="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_7">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:31:29Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_4" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_3951" name="R_cca1_toc1_2_l" value="3.2752"/>
<Constant key="Parameter_3950" name="R_cca1_toc1_2_d" value="1.38564"/>
<Constant key="Parameter_3949" name="H_cca1_toc1" value="2.50071"/>
<Constant key="Parameter_3948" name="rep_TOC1" value="0"/>
<Constant key="Parameter_3947" name="effcopies_toc1_TOC8" value="1"/>
</ListOfConstants>
<KineticLaw function="Function_46">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_287">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_290">
<SourceParameter reference="Metabolite_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_292">
<SourceParameter reference="ModelValue_14"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_294">
<SourceParameter reference="ModelValue_15"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_296">
<SourceParameter reference="ModelValue_13"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_275">
<SourceParameter reference="ModelValue_24"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_288">
<SourceParameter reference="ModelValue_22"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_8" name="CCA1 mRNA degradation" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_8">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:30:10Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_4" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3946" name="k1" value="1.33082"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="ModelValue_16"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_4"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_9" name="CCA1 translation" reversible="false">
<ListOfProducts>
<Product metabolite="Metabolite_5" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_4" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_3945" name="T" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_43">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_281">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_277">
<SourceParameter reference="ModelValue_17"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_273">
<SourceParameter reference="Metabolite_4"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_10" name="CCA1 nuclear transport" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_10">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T18:27:53Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_5" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_6" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_3944" name="k1" value="10"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="ModelValue_18"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_5"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_11" name="CCA1 degradation, cytosol" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_11">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T14:28:08Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_5" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3943" name="D_l" value="0.424178"/>
<Constant key="Parameter_3942" name="D_d" value="0.26938"/>
</ListOfConstants>
<KineticLaw function="Function_44">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_271">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_279">
<SourceParameter reference="ModelValue_19"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_267">
<SourceParameter reference="ModelValue_20"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_282">
<SourceParameter reference="Metabolite_5"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_12" name="CCA1 degradation, nucleus" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_12">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T18:15:53Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_6" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3941" name="D_l" value="0.424178"/>
<Constant key="Parameter_3940" name="D_d" value="0.26938"/>
</ListOfConstants>
<KineticLaw function="Function_44">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_271">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_279">
<SourceParameter reference="ModelValue_19"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_267">
<SourceParameter reference="ModelValue_20"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_282">
<SourceParameter reference="Metabolite_6"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_14" name="LUC mRNA degradation" reversible="false">
<ListOfSubstrates>
<Substrate metabolite="Metabolite_12" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3934" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="ModelValue_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_12"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_15" name="LUC translation" reversible="false">
<ListOfProducts>
<Product metabolite="Metabolite_13" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_12" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_3933" name="T" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_43">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_281">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_277">
<SourceParameter reference="ModelValue_23"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_273">
<SourceParameter reference="Metabolite_12"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_16" name="LUC decay" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_16">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:30:12Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_13" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3932" name="k1" value="0.182881"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="ModelValue_0"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_13"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_18" name="TOC1-LUC mRNA degradation" reversible="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_18">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:30:52Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_7" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3926" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="ModelValue_7"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_7"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_19" name="TOC1-LUC translation" reversible="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_19">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:29:17Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_8" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_7" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_3925" name="T" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_43">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_281">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_277">
<SourceParameter reference="ModelValue_8"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_273">
<SourceParameter reference="Metabolite_7"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_20" name="TOC1-LUC conversion" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_20">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:30:36Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_8" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_9" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_3924" name="Di_l" value="0.136491"/>
<Constant key="Parameter_3923" name="Di_d" value="0.326619"/>
</ListOfConstants>
<KineticLaw function="Function_45">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_283">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_269">
<SourceParameter reference="ModelValue_9"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_284">
<SourceParameter reference="ModelValue_10"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_286">
<SourceParameter reference="Metabolite_8"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_21" name="TOC1-LUC degradation" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_21">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:30:42Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_9" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3922" name="D_l" value="0.461551"/>
<Constant key="Parameter_3921" name="D_d" value="0.356614"/>
</ListOfConstants>
<KineticLaw function="Function_44">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_271">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_279">
<SourceParameter reference="ModelValue_11"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_267">
<SourceParameter reference="ModelValue_12"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_282">
<SourceParameter reference="Metabolite_9"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_22" name="TOC1-LUC(1) deactivation" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_22">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:29:21Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_8" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3920" name="k1" value="0.182881"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="ModelValue_0"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_8"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_23" name="TOC1-LUC(2) deactivation" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_23">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:30:31Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_9" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3919" name="k1" value="0.182881"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="ModelValue_0"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_9"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_24" name="LUC transcription, pCCA1" reversible="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_24">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:30:15Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_12" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_3918" name="R_cca1_toc1_2_l" value="0.1"/>
<Constant key="Parameter_3917" name="R_cca1_toc1_2_d" value="0.1"/>
<Constant key="Parameter_3916" name="H_cca1_toc1" value="0.1"/>
<Constant key="Parameter_3915" name="rep_pCCA1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_49">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_310">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_295">
<SourceParameter reference="Metabolite_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_300">
<SourceParameter reference="ModelValue_14"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_315">
<SourceParameter reference="ModelValue_15"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_317">
<SourceParameter reference="ModelValue_13"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_314">
<SourceParameter reference="ModelValue_27"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_25" name="CCA1-LUC transcription" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_25">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T14:28:14Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_10" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_3914" name="R_cca1_toc1_2_l" value="3.2752"/>
<Constant key="Parameter_3913" name="R_cca1_toc1_2_d" value="1.38564"/>
<Constant key="Parameter_3912" name="H_cca1_toc1" value="2.50071"/>
<Constant key="Parameter_3911" name="rep_CCA1" value="1"/>
<Constant key="Parameter_3910" name="rep_TOC1" value="0"/>
<Constant key="Parameter_3909" name="effcopies_toc1_TOC8" value="1"/>
</ListOfConstants>
<KineticLaw function="Function_63">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_457">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_433">
<SourceParameter reference="ModelValue_24"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_430">
<SourceParameter reference="ModelValue_22"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_448">
<SourceParameter reference="Metabolite_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_426">
<SourceParameter reference="ModelValue_14"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_424">
<SourceParameter reference="ModelValue_15"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_422">
<SourceParameter reference="ModelValue_13"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_419">
<SourceParameter reference="ModelValue_26"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_26" name="CCA1-LUC mRNA degradation" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_26">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:29:50Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_10" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3908" name="k1" value="1.33082"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="ModelValue_16"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_10"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_27" name="CCA1-LUC translation" reversible="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_27">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:30:04Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_11" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_10" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_3907" name="T" value="0"/>
</ListOfConstants>
<KineticLaw function="Function_43">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_281">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_277">
<SourceParameter reference="ModelValue_17"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_273">
<SourceParameter reference="Metabolite_10"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_28" name="CCA1-LUC degradation" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_28">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:29:39Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_11" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3906" name="D_l" value="0.424178"/>
<Constant key="Parameter_3905" name="D_d" value="0.424178"/>
</ListOfConstants>
<KineticLaw function="Function_44">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_271">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_279">
<SourceParameter reference="ModelValue_19"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_267">
<SourceParameter reference="ModelValue_20"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_282">
<SourceParameter reference="Metabolite_11"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_29" name="CCA1-LUC deactivation" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_29">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2011-01-07T17:29:26Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_11" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_3904" name="k1" value="0.182881"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="ModelValue_0"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_11"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_17" name="TOC1 transcription" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_17">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-04-17T13:20:26Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_1" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_6" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_3927" name="R_toc1_acc" value="0.231107"/>
<Constant key="Parameter_3928" name="R_toc1_cca1" value="1.08706"/>
<Constant key="Parameter_3929" name="H_toc1_cca1" value="2.07808"/>
<Constant key="Parameter_3930" name="L_toc1" value="0.0001"/>
<Constant key="Parameter_3931" name="rep_CCA1" value="1"/>
<Constant key="Parameter_3935" name="effcopies_cca1_LHY7" value="1.13966"/>
</ListOfConstants>
<KineticLaw function="Function_42">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_268">
<SourceParameter reference="ModelValue_6"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_272">
<SourceParameter reference="ModelValue_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_280">
<SourceParameter reference="ModelValue_4"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_278">
<SourceParameter reference="Metabolite_6"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_265">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_266">
<SourceParameter reference="ModelValue_5"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_274">
<SourceParameter reference="ModelValue_26"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_276">
<SourceParameter reference="ModelValue_21"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_13" name="TOC1-LUC transcription" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_13">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-04-17T13:22:10Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_7" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_6" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_3936" name="R_toc1_acc" value="0.231107"/>
<Constant key="Parameter_3937" name="R_toc1_cca1" value="1.08706"/>
<Constant key="Parameter_3938" name="H_toc1_cca1" value="2.07808"/>
<Constant key="Parameter_3939" name="rep_TOC1" value="0"/>
<Constant key="Parameter_4125" name="L_toc1" value="0.0001"/>
</ListOfConstants>
<KineticLaw function="Function_48">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_302">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_291">
<SourceParameter reference="ModelValue_6"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_309">
<SourceParameter reference="ModelValue_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_311">
<SourceParameter reference="Metabolite_6"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_313">
<SourceParameter reference="ModelValue_4"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_306">
<SourceParameter reference="ModelValue_24"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_298">
<SourceParameter reference="ModelValue_5"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_2" name="LUC transcription, pTOC1" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_2">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-04-17T13:23:24Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_0" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_6" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_4124" name="R_toc1_acc" value="0.231107"/>
<Constant key="Parameter_4123" name="R_toc1_cca1" value="1.08706"/>
<Constant key="Parameter_4122" name="H_toc1_cca1" value="2.07808"/>
<Constant key="Parameter_4121" name="rep_pTOC1" value="0"/>
<Constant key="Parameter_4120" name="L_toc1" value="0.0001"/>
</ListOfConstants>
<KineticLaw function="Function_47">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_293">
<SourceParameter reference="Model_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_285">
<SourceParameter reference="ModelValue_6"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_301">
<SourceParameter reference="ModelValue_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_303">
<SourceParameter reference="Metabolite_6"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_305">
<SourceParameter reference="ModelValue_4"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_297">
<SourceParameter reference="ModelValue_25"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_289">
<SourceParameter reference="ModelValue_5"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
</ListOfReactions>
<StateTemplate>
<StateTemplateVariable objectReference="Model_1"/>
<StateTemplateVariable objectReference="Metabolite_5"/>
<StateTemplateVariable objectReference="Metabolite_8"/>
<StateTemplateVariable objectReference="Metabolite_11"/>
<StateTemplateVariable objectReference="Metabolite_9"/>
<StateTemplateVariable objectReference="Metabolite_1"/>
<StateTemplateVariable objectReference="Metabolite_7"/>
<StateTemplateVariable objectReference="Metabolite_2"/>
<StateTemplateVariable objectReference="Metabolite_4"/>
<StateTemplateVariable objectReference="Metabolite_10"/>
<StateTemplateVariable objectReference="Metabolite_12"/>
<StateTemplateVariable objectReference="Metabolite_13"/>
<StateTemplateVariable objectReference="Metabolite_6"/>
<StateTemplateVariable objectReference="Metabolite_3"/>
<StateTemplateVariable objectReference="Metabolite_0"/>
<StateTemplateVariable objectReference="Compartment_0"/>
<StateTemplateVariable objectReference="ModelValue_0"/>
<StateTemplateVariable objectReference="ModelValue_1"/>
<StateTemplateVariable objectReference="ModelValue_2"/>
<StateTemplateVariable objectReference="ModelValue_3"/>
<StateTemplateVariable objectReference="ModelValue_4"/>
<StateTemplateVariable objectReference="ModelValue_5"/>
<StateTemplateVariable objectReference="ModelValue_6"/>
<StateTemplateVariable objectReference="ModelValue_7"/>
<StateTemplateVariable objectReference="ModelValue_8"/>
<StateTemplateVariable objectReference="ModelValue_9"/>
<StateTemplateVariable objectReference="ModelValue_10"/>
<StateTemplateVariable objectReference="ModelValue_11"/>
<StateTemplateVariable objectReference="ModelValue_12"/>
<StateTemplateVariable objectReference="ModelValue_13"/>
<StateTemplateVariable objectReference="ModelValue_14"/>
<StateTemplateVariable objectReference="ModelValue_15"/>
<StateTemplateVariable objectReference="ModelValue_16"/>
<StateTemplateVariable objectReference="ModelValue_17"/>
<StateTemplateVariable objectReference="ModelValue_18"/>
<StateTemplateVariable objectReference="ModelValue_19"/>
<StateTemplateVariable objectReference="ModelValue_20"/>
<StateTemplateVariable objectReference="ModelValue_21"/>
<StateTemplateVariable objectReference="ModelValue_22"/>
<StateTemplateVariable objectReference="ModelValue_23"/>
<StateTemplateVariable objectReference="ModelValue_24"/>
<StateTemplateVariable objectReference="ModelValue_25"/>
<StateTemplateVariable objectReference="ModelValue_26"/>
<StateTemplateVariable objectReference="ModelValue_27"/>
</StateTemplate>
<InitialState type="initialState">
0 13482678329538.12 0 756585410751038 0 5534385198399.876 0 57218367400153.34 27005247606810.84 27005247606810.84 0 0 1631755628827254 121387591859123.2 602214179000000 1 0.1828812174632586 1 0.08201322503032867 1.087061268589661 2.078077386923434 0.0001 0.2311070329494072 0.2921304977837297 0.7699701729778862 0.1364905833686477 0.3266194920897148 0.4615505591808016 0.3566139205511183 2.500706288063396 3.275202921038323 1.385639016822662 1.330820809545275 4.904866104286524 10 0.4241778774494377 0.2693801781540909 1.139657555086233 1 1 0 0 1 0
</InitialState>
</Model>
<ListOfTasks>
<Task key="Task_27" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
<Report reference="Report_9" target="" append="1" confirmOverwrite="0"/>
<Problem>
<Parameter name="JacobianRequested" type="bool" value="1"/>
<Parameter name="StabilityAnalysisRequested" type="bool" value="1"/>
</Problem>
<Method name="Enhanced Newton" type="EnhancedNewton">
<Parameter name="Resolution" type="unsignedFloat" value="1e-09"/>
<Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/>
<Parameter name="Use Newton" type="bool" value="1"/>
<Parameter name="Use Integration" type="bool" value="1"/>
<Parameter name="Use Back Integration" type="bool" value="1"/>
<Parameter name="Accept Negative Concentrations" type="bool" value="0"/>
<Parameter name="Iteration Limit" type="unsignedInteger" value="50"/>
<Parameter name="Maximum duration for forward integration" type="unsignedFloat" value="1000000000"/>
<Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1000000"/>
</Method>
</Task>
<Task key="Task_15" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
<Report reference="Report_9" target="" append="0" confirmOverwrite="0"/>
<Problem>
<Parameter name="StepNumber" type="unsignedInteger" value="12000"/>
<Parameter name="StepSize" type="float" value="0.01"/>
<Parameter name="Duration" type="float" value="120"/>
<Parameter name="TimeSeriesRequested" type="bool" value="1"/>
<Parameter name="OutputStartTime" type="float" value="0"/>
<Parameter name="Output Event" type="bool" value="0"/>
</Problem>
<Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
<Parameter name="Integrate Reduced Model" type="bool" value="0"/>
<Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-06"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-09"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
</Method>
</Task>
<Task key="Task_16" name="Scan" type="scan" scheduled="false" updateModel="false">
<Problem>
<Parameter name="Subtask" type="unsignedInteger" value="1"/>
<ParameterGroup name="ScanItems">
</ParameterGroup>
<Parameter name="Output in subtask" type="bool" value="1"/>
<Parameter name="Adjust initial conditions" type="bool" value="0"/>
</Problem>
<Method name="Scan Framework" type="ScanFramework">
</Method>
</Task>
<Task key="Task_17" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
<Report reference="Report_10" target="" append="1" confirmOverwrite="0"/>
<Problem>
</Problem>
<Method name="EFM Algorithm" type="EFMAlgorithm">
</Method>
</Task>
<Task key="Task_18" name="Optimization" type="optimization" scheduled="false" updateModel="false">
<Report reference="Report_11" target="" append="1" confirmOverwrite="0"/>
<Problem>
<Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
<ParameterText name="ObjectiveExpression" type="expression">
</ParameterText>
<Parameter name="Maximize" type="bool" value="0"/>
<Parameter name="Randomize Start Values" type="bool" value="0"/>
<Parameter name="Calculate Statistics" type="bool" value="1"/>
<ParameterGroup name="OptimizationItemList">
</ParameterGroup>
<ParameterGroup name="OptimizationConstraintList">
</ParameterGroup>
<Parameter name="ObjectiveFunction" type="key" value=""/>
</Problem>
<Method name="Random Search" type="RandomSearch">
<Parameter name="Number of Iterations" type="unsignedInteger" value="100000"/>
<Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
<Parameter name="Seed" type="unsignedInteger" value="0"/>
</Method>
</Task>
<Task key="Task_19" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
<Report reference="Report_12" target="" append="1" confirmOverwrite="0"/>
<Problem>
<Parameter name="Maximize" type="bool" value="0"/>
<Parameter name="Randomize Start Values" type="bool" value="0"/>
<Parameter name="Calculate Statistics" type="bool" value="1"/>
<ParameterGroup name="OptimizationItemList">
</ParameterGroup>
<ParameterGroup name="OptimizationConstraintList">
</ParameterGroup>
<Parameter name="Steady-State" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
<Parameter name="Time-Course" type="cn" value="CN=Root,Vector=TaskList[Time-Course]"/>
<ParameterGroup name="Experiment Set">
</ParameterGroup>
<ParameterGroup name="Validation Set">
<Parameter name="Threshold" type="unsignedInteger" value="5"/>
<Parameter name="Weight" type="unsignedFloat" value="1"/>
</ParameterGroup>
</Problem>
<Method name="Evolutionary Programming" type="EvolutionaryProgram">
<Parameter name="Number of Generations" type="unsignedInteger" value="200"/>
<Parameter name="Population Size" type="unsignedInteger" value="20"/>
<Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
<Parameter name="Seed" type="unsignedInteger" value="0"/>
</Method>
</Task>
<Task key="Task_20" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
<Report reference="Report_13" target="" append="1" confirmOverwrite="0"/>
<Problem>
<Parameter name="Steady-State" type="key" value="Task_27"/>
</Problem>
<Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
<Parameter name="Modulation Factor" type="unsignedFloat" value="1e-09"/>
</Method>
</Task>
<Task key="Task_21" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
<Report reference="Report_14" target="" append="1" confirmOverwrite="0"/>
<Problem>
<Parameter name="ExponentNumber" type="unsignedInteger" value="3"/>
<Parameter name="DivergenceRequested" type="bool" value="1"/>
<Parameter name="TransientTime" type="float" value="0"/>
</Problem>
<Method name="Wolf Method" type="WolfMethod">
<Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/>
<Parameter name="Overall time" type="unsignedFloat" value="1000"/>
<Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-06"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-12"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
</Method>
</Task>
<Task key="Task_22" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
<Report reference="Report_15" target="" append="1" confirmOverwrite="0"/>
<Problem>
<Parameter name="StepNumber" type="unsignedInteger" value="100"/>
<Parameter name="StepSize" type="float" value="0.01"/>
<Parameter name="Duration" type="float" value="1"/>
<Parameter name="TimeSeriesRequested" type="bool" value="1"/>
<Parameter name="OutputStartTime" type="float" value="0"/>
</Problem>
<Method name="ILDM (LSODA,Deuflhard)" type="TimeScaleSeparation(ILDM,Deuflhard)">
<Parameter name="Deuflhard Tolerance" type="unsignedFloat" value="1e-06"/>
</Method>
</Task>
<Task key="Task_23" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
<Report reference="Report_16" target="" append="1" confirmOverwrite="0"/>
<Problem>
<Parameter name="SubtaskType" type="unsignedInteger" value="1"/>
<ParameterGroup name="TargetFunctions">
<Parameter name="SingleObject" type="cn" value=""/>
<Parameter name="ObjectListType" type="unsignedInteger" value="7"/>
</ParameterGroup>
<ParameterGroup name="ListOfVariables">
<ParameterGroup name="Variables">
<Parameter name="SingleObject" type="cn" value=""/>
<Parameter name="ObjectListType" type="unsignedInteger" value="41"/>
</ParameterGroup>
</ParameterGroup>
</Problem>
<Method name="Sensitivities Method" type="SensitivitiesMethod">
<Parameter name="Delta factor" type="unsignedFloat" value="0.001"/>
<Parameter name="Delta minimum" type="unsignedFloat" value="1e-12"/>
</Method>
</Task>
<Task key="Task_24" name="Moieties" type="moieties" scheduled="false" updateModel="false">
<Problem>
</Problem>
<Method name="Householder Reduction" type="Householder">
</Method>
</Task>
<Task key="Task_25" name="Cross Section" type="crosssection" scheduled="false" updateModel="false">
<Problem>
<Parameter name="StepNumber" type="unsignedInteger" value="100"/>
<Parameter name="StepSize" type="float" value="0.01"/>
<Parameter name="Duration" type="float" value="1"/>
<Parameter name="TimeSeriesRequested" type="bool" value="1"/>
<Parameter name="OutputStartTime" type="float" value="0"/>
<Parameter name="Output Event" type="bool" value="0"/>
<Parameter name="LimitCrossings" type="bool" value="0"/>
<Parameter name="NumCrossingsLimit" type="unsignedInteger" value="0"/>
<Parameter name="LimitOutTime" type="bool" value="0"/>
<Parameter name="LimitOutCrossings" type="bool" value="0"/>
<Parameter name="PositiveDirection" type="bool" value="1"/>
<Parameter name="NumOutCrossingsLimit" type="unsignedInteger" value="0"/>
<Parameter name="LimitUntilConvergence" type="bool" value="0"/>
<Parameter name="ConvergenceTolerance" type="float" value="1e-06"/>
<Parameter name="Threshold" type="float" value="0"/>
<Parameter name="DelayOutputUntilConvergence" type="bool" value="0"/>
<Parameter name="OutputConvergenceTolerance" type="float" value="1e-06"/>
<ParameterText name="TriggerExpression" type="expression">
</ParameterText>
<Parameter name="SingleVariable" type="cn" value=""/>
</Problem>
<Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
<Parameter name="Integrate Reduced Model" type="bool" value="0"/>
<Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-06"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-12"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
</Method>
</Task>
<Task key="Task_14" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
<Report reference="Report_17" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Steady-State" type="key" value="Task_27"/>
</Problem>
<Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
</Method>
</Task>
</ListOfTasks>
<ListOfReports>
<Report key="Report_9" name="Steady-State" taskType="steadyState" separator="	" precision="6">
<Comment>
<body xmlns="http://www.w3.org/1999/xhtml">
Automatically generated report.
</body>
</Comment>
<Footer>
<Object cn="CN=Root,Vector=TaskList[Steady-State]"/>
</Footer>
</Report>
<Report key="Report_10" name="Elementary Flux Modes" taskType="fluxMode" separator="	" precision="6">
<Comment>
<body xmlns="http://www.w3.org/1999/xhtml">
Automatically generated report.
</body>
</Comment>
<Footer>
<Object cn="CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result"/>
</Footer>
</Report>
<Report key="Report_11" name="Optimization" taskType="optimization" separator="	" precision="6">
<Comment>
<body xmlns="http://www.w3.org/1999/xhtml">
Automatically generated report.
</body>
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Optimization],Object=Description"/>
<Object cn="String=\[Function Evaluations\]"/>
<Object cn="Separator=	"/>
<Object cn="String=\[Best Value\]"/>
<Object cn="Separator=	"/>
<Object cn="String=\[Best Parameters\]"/>
</Header>
<Body>
<Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations"/>
<Object cn="Separator=	"/>
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