/
GDP-Fucose_v7XGSK_with_PE9XGSK_setup.cps
2387 lines (2379 loc) · 141 KB
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GDP-Fucose_v7XGSK_with_PE9XGSK_setup.cps
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<?xml version="1.0" encoding="UTF-8"?>
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E_PPA*kcat_F*(1/(1+(Km_PP/PP)))
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E_PPK3*(((kcat_F*(ADP/Km_ADP))-(kcat_F*(1/K_eq_PPK3_A)*(ATP/(Km_ADP))))/((1+(ADP/Km_ADP))+(1+(ATP/Km_ATP))-1))
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<ParameterDescription key="FunctionParameter_265" name="ADP" order="2" role="substrate"/>
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E_FKP*(((kcat_F*(Fuc/Km_Fuc)*(ATP/Km_ATP))-(kcat_F*(1/K_eq_FKP_fk)*((Fuc1P*ADP)/(Km_Fuc*Km_ATP))))/(((1+(Fuc/Km_Fuc))*(1+(ATP/Km_ATP)))+(((1+(Fuc1P/Km_Fuc1P))*(1+(ADP/Km_ADP)))-1)))
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<ParameterDescription key="FunctionParameter_275" name="Fuc" order="2" role="substrate"/>
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((ki_PP)/(ki_PP+PP))*(E_FKP*(((kcat_F*(Fuc1P/Km_Fuc1P)*(GTP/Km_GTP))-(kcat_F*(1/K_eq_FKP_gt)*((GDP_Fuc*PP)/(Km_Fuc1P*Km_GTP))))/(((1+(Fuc1P/Km_Fuc1P))*(1+(GTP/Km_GTP)))+((1+(GDP_Fuc/Km_GDP_Fuc))*(1+(PP/Km_PP)))-1)))
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<ParameterDescription key="FunctionParameter_290" name="Fuc1P" order="2" role="substrate"/>
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<ParameterDescription key="FunctionParameter_288" name="GTP" order="4" role="substrate"/>
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<ParameterDescription key="FunctionParameter_286" name="GDP_Fuc" order="6" role="product"/>
<ParameterDescription key="FunctionParameter_285" name="Km_GDP_Fuc" order="7" role="constant"/>
<ParameterDescription key="FunctionParameter_284" name="PP" order="8" role="product"/>
<ParameterDescription key="FunctionParameter_283" name="Km_PP" order="9" role="constant"/>
<ParameterDescription key="FunctionParameter_282" name="K_eq_FKP_gt" order="10" role="constant"/>
<ParameterDescription key="FunctionParameter_293" name="ki_PP" order="11" role="constant"/>
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<Function key="Function_44" name="Rate Law for PPK3_G" type="UserDefined" reversible="unspecified">
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E_PPK3*(((kcat_F*(GDP/Km_GDP))-(kcat_F*(1/K_eq_PPK3_G)*(GTP/Km_GDP)))/((1+(GDP/Km_GDP))+(1+(GTP/Km_GTP))-1))
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<ParameterDescription key="FunctionParameter_304" name="kcat_F" order="1" role="constant"/>
<ParameterDescription key="FunctionParameter_303" name="GDP" order="2" role="substrate"/>
<ParameterDescription key="FunctionParameter_302" name="Km_GDP" order="3" role="constant"/>
<ParameterDescription key="FunctionParameter_301" name="GTP" order="4" role="product"/>
<ParameterDescription key="FunctionParameter_300" name="Km_GTP" order="5" role="constant"/>
<ParameterDescription key="FunctionParameter_299" name="K_eq_PPK3_G" order="6" role="constant"/>
</ListOfParameterDescriptions>
</Function>
<Function key="Function_45" name="Rate Law for GMPK" type="UserDefined" reversible="unspecified">
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<Expression>
E_GMPK*(((kcat_F*(GMP/Km_GMP)*(ATP/Km_ATP))-(kcat_F*(1/K_eq_GMPK)*((GDP*ADP)/(Km_GMP*Km_ATP))))/(((1+(GMP/Km_GMP))*(1+(ATP/Km_ATP)))+((1+(GDP/Km_GDP))*(1+(ADP/Km_ADP)))-1))
</Expression>
<ListOfParameterDescriptions>
<ParameterDescription key="FunctionParameter_307" name="E_GMPK" order="0" role="modifier"/>
<ParameterDescription key="FunctionParameter_306" name="kcat_F" order="1" role="constant"/>
<ParameterDescription key="FunctionParameter_294" name="GMP" order="2" role="substrate"/>
<ParameterDescription key="FunctionParameter_295" name="Km_GMP" order="3" role="constant"/>
<ParameterDescription key="FunctionParameter_296" name="ATP" order="4" role="substrate"/>
<ParameterDescription key="FunctionParameter_297" name="Km_ATP" order="5" role="constant"/>
<ParameterDescription key="FunctionParameter_298" name="GDP" order="6" role="product"/>
<ParameterDescription key="FunctionParameter_308" name="Km_GDP" order="7" role="constant"/>
<ParameterDescription key="FunctionParameter_309" name="ADP" order="8" role="product"/>
<ParameterDescription key="FunctionParameter_310" name="Km_ADP" order="9" role="constant"/>
<ParameterDescription key="FunctionParameter_311" name="K_eq_GMPK" order="10" role="constant"/>
</ListOfParameterDescriptions>
</Function>
</ListOfFunctions>
<Model key="Model_1" name="GDP-Fucose_v7XGSK" simulationType="time" timeUnit="h" volumeUnit="l" areaUnit="m²" lengthUnit="m" quantityUnit="mmol" type="deterministic" avogadroConstant="6.0221408570000002e+23">
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<Comment>
GDP-Fucose Model
Cell-free production of GDP-Fucose from Fucose, Guanosine, ATP and PolyP (created by Reza Mahour and Dr. Thomas Rexer)
includes PPA reaction to convert diphosphate to 2 inorganic phosphates
XGSK = GSK reaction (Guanosine -> GMP) removed; start directly with initial GMP
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<ListOfCompartments>
<Compartment key="Compartment_0" name="compartment" simulationType="fixed" dimensionality="3" addNoise="false">
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<ListOfMetabolites>
<Metabolite key="Metabolite_0" name="PP" simulationType="reactions" compartment="Compartment_0" addNoise="false">
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<Metabolite key="Metabolite_1" name="P" simulationType="reactions" compartment="Compartment_0" addNoise="false">
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<Metabolite key="Metabolite_2" name="ATP" simulationType="reactions" compartment="Compartment_0" addNoise="false">
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<Metabolite key="Metabolite_3" name="ADP" simulationType="reactions" compartment="Compartment_0" addNoise="false">
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</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_4" name="E_PPA" simulationType="reactions" compartment="Compartment_0" addNoise="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="#Metabolite_4">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-04-23T10:13:23Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_5" name="E_PPK3" simulationType="reactions" compartment="Compartment_0" addNoise="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="#Metabolite_5">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-04-23T10:19:14Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_6" name="E_FKP" simulationType="reactions" compartment="Compartment_0" addNoise="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="#Metabolite_6">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-07-16T11:37:19Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_7" name="Fuc" simulationType="reactions" compartment="Compartment_0" addNoise="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="#Metabolite_20">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-07-16T11:37:19Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_8" name="Fuc1P" simulationType="reactions" compartment="Compartment_0" addNoise="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="#Metabolite_20">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-07-16T11:37:19Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_9" name="GDP_Fucose" simulationType="reactions" compartment="Compartment_0" addNoise="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="#Metabolite_9">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-07-16T11:41:01Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_10" name="GTP" simulationType="reactions" compartment="Compartment_0" addNoise="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="#Metabolite_23">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-07-16T11:41:01Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_11" name="GDP" simulationType="reactions" compartment="Compartment_0" addNoise="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="#Metabolite_11">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-07-16T11:48:11Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_12" name="GMP" simulationType="reactions" compartment="Compartment_0" addNoise="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="#Metabolite_26">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-07-16T11:50:04Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_13" name="E_GMPK" simulationType="reactions" compartment="Compartment_0" addNoise="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="#Metabolite_13">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-07-16T11:52:22Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
</ListOfMetabolites>
<ListOfModelValues>
<ModelValue key="ModelValue_0" name="GDP-Fucose at 40h" simulationType="fixed" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
</ModelValue>
<ModelValue key="ModelValue_1" name="E_tot" simulationType="assignment" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<Expression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_FKP],Reference=InitialConcentration>+<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_GMPK],Reference=InitialConcentration>+<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_PPA],Reference=InitialConcentration>+<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_PPK3],Reference=InitialConcentration>
</Expression>
</ModelValue>
<ModelValue key="ModelValue_2" name="GDP-Fucose at 24h" simulationType="fixed" addNoise="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="#ModelValue_2">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</ModelValue>
<ModelValue key="ModelValue_3" name="Yield_Fucose" simulationType="assignment" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<Expression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[GDP-Fucose at 24h],Reference=Value>/<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Dyn. Updated Initial Fucose Conc],Reference=Value>
</Expression>
</ModelValue>
<ModelValue key="ModelValue_4" name="Yield_GMP" simulationType="assignment" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<Expression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[GDP-Fucose at 24h],Reference=Value>/<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Dyn. Updated Initial GMP Conc],Reference=Value>
</Expression>
</ModelValue>
<ModelValue key="ModelValue_5" name="Substrate Weighted Cost" simulationType="assignment" addNoise="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="#ModelValue_5">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
Extra factors are used to convert mmol/l concentrations to g/l concentrations since prices are given as Euros/g:
sructure of the terms: price * mmol/l concentration * MW in g/mmol
-> unit of the toal weighted sum will be: (Euros/g)*(mmol/l)*(g/mmol) = Euros/l
</Comment>
<Expression>
0.25*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[GMP],Reference=InitialConcentration>*0.36322+5.66*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[Fuc],Reference=InitialConcentration>*0.16416+0.51*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[ATP],Reference=InitialConcentration>*0.50718
</Expression>
</ModelValue>
<ModelValue key="ModelValue_6" name="Productivity" simulationType="assignment" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<Expression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[GDP-Fucose at 24h],Reference=Value>/<CN=Root,Model=GDP-Fucose_v7XGSK,Reference=Time>
</Expression>
</ModelValue>
<ModelValue key="ModelValue_7" name="S_tot" simulationType="assignment" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<Expression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[Fuc],Reference=InitialConcentration>+<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[GMP],Reference=InitialConcentration>+<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[ATP],Reference=InitialConcentration>
</Expression>
</ModelValue>
<ModelValue key="ModelValue_8" name="Dyn. Updated Initial Fucose Conc" simulationType="fixed" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
</ModelValue>
<ModelValue key="ModelValue_9" name="Dyn. Updated Initial GMP Conc" simulationType="fixed" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
</ModelValue>
<ModelValue key="ModelValue_10" name="Enzyme Weighted Cost" simulationType="assignment" addNoise="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="#ModelValue_10">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
Extra factors are used to convert mmol/l concentrations to g/l concentrations since prices are given as Euros/g:
sructure of the terms: price * mmol/l concentration * MW in g/mmol
-> unit of the toal weighted sum will be: (Euros/g)*(mmol/l)*(g/mmol) = Euros/l
</Comment>
<Expression>
200.449*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_FKP],Reference=InitialConcentration>*105.66+58.64511*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_GMPK],Reference=InitialConcentration>*23.592+162.4384*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_PPA],Reference=InitialConcentration>*19.313+541.7541*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_PPK3],Reference=InitialConcentration>*34.74
</Expression>
</ModelValue>
<ModelValue key="ModelValue_11" name="Fixed Cost" simulationType="fixed" addNoise="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="#ModelValue_11">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
(10h * 50 Euros/h) / 1 litre
Unit: Euros/l
</Comment>
</ModelValue>
<ModelValue key="ModelValue_12" name="Cost_per_Product" simulationType="assignment" addNoise="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="#ModelValue_12">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
Unit: (Euros/litre) / (mmol/litre) -> Euros/mmol
</Comment>
<Expression>
(<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Enzyme Weighted Cost],Reference=InitialValue>+<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Substrate Weighted Cost],Reference=InitialValue>+<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Fixed Cost],Reference=InitialValue>)/<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[GDP-Fucose at 24h],Reference=Value>
</Expression>
</ModelValue>
<ModelValue key="ModelValue_13" name="E_tot_MW" simulationType="assignment" addNoise="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="#ModelValue_13">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
105.66*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_FKP],Reference=InitialConcentration>+23.592*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_GMPK],Reference=InitialConcentration>+19.313*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_PPA],Reference=InitialConcentration>+34.74*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[E_PPK3],Reference=InitialConcentration>
</Expression>
</ModelValue>
<ModelValue key="ModelValue_14" name="Cost" simulationType="assignment" addNoise="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="#ModelValue_14">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Enzyme Weighted Cost],Reference=InitialValue>+<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Substrate Weighted Cost],Reference=InitialValue>+<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Fixed Cost],Reference=InitialValue>
</Expression>
</ModelValue>
<ModelValue key="ModelValue_15" name="Income" simulationType="assignment" addNoise="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="#ModelValue_15">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
48190*<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[GDP-Fucose at 24h],Reference=Value>*0.5893
</Expression>
</ModelValue>
<ModelValue key="ModelValue_16" name="Profit" simulationType="assignment" addNoise="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="#ModelValue_16">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
(<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Income],Reference=Value>-<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Cost],Reference=InitialValue>)*0.0002
</Expression>
</ModelValue>
</ListOfModelValues>
<ListOfReactions>
<Reaction key="Reaction_0" name="FKP (fucokinase)" reversible="true" fast="false" addNoise="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_0">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-03-12T13:47:22Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_7" stoichiometry="1"/>
<Substrate metabolite="Metabolite_2" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_8" stoichiometry="1"/>
<Product metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_6" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_6913" name="kcat_F" value="1404"/>
<Constant key="Parameter_6912" name="Km_Fuc" value="0.045"/>
<Constant key="Parameter_6910" name="Km_ATP" value="1.08"/>
<Constant key="Parameter_6909" name="Km_Fuc1P" value="0.1"/>
<Constant key="Parameter_6911" name="Km_ADP" value="0.1"/>
<Constant key="Parameter_6908" name="K_eq_FKP_fk" value="4"/>
</ListOfConstants>
<KineticLaw function="Function_42" unitType="Default" scalingCompartment="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_277">
<SourceParameter reference="Metabolite_6"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_276">
<SourceParameter reference="Parameter_6913"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_275">
<SourceParameter reference="Metabolite_7"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_274">
<SourceParameter reference="Parameter_6912"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_273">
<SourceParameter reference="Metabolite_2"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_272">
<SourceParameter reference="Parameter_6910"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_271">
<SourceParameter reference="Metabolite_8"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_278">
<SourceParameter reference="Parameter_6909"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_279">
<SourceParameter reference="Metabolite_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_280">
<SourceParameter reference="Parameter_6911"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_281">
<SourceParameter reference="Parameter_6908"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_1" name="FKP (guanylyltransferase)" reversible="true" fast="false" addNoise="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_1">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-03-12T13:48:03Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_8" stoichiometry="1"/>
<Substrate metabolite="Metabolite_10" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_9" stoichiometry="1"/>
<Product metabolite="Metabolite_0" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_6" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_6907" name="kcat_F" value="36252"/>
<Constant key="Parameter_6905" name="Km_Fuc1P" value="0.03295"/>
<Constant key="Parameter_6904" name="Km_GTP" value="0.012"/>
<Constant key="Parameter_6906" name="Km_GDP_Fuc" value="0.12"/>
<Constant key="Parameter_6903" name="Km_PP" value="0.135"/>
<Constant key="Parameter_6902" name="K_eq_FKP_gt" value="20"/>
<Constant key="Parameter_6900" name="ki_PP" value="1e-08"/>
</ListOfConstants>
<KineticLaw function="Function_43" unitType="Default" scalingCompartment="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_292">
<SourceParameter reference="Metabolite_6"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_291">
<SourceParameter reference="Parameter_6907"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_290">
<SourceParameter reference="Metabolite_8"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_289">
<SourceParameter reference="Parameter_6905"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_288">
<SourceParameter reference="Metabolite_10"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_287">
<SourceParameter reference="Parameter_6904"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_286">
<SourceParameter reference="Metabolite_9"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_285">
<SourceParameter reference="Parameter_6906"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_284">
<SourceParameter reference="Metabolite_0"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_283">
<SourceParameter reference="Parameter_6903"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_282">
<SourceParameter reference="Parameter_6902"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_293">
<SourceParameter reference="Parameter_6900"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_2" name="PPA" reversible="false" fast="false" addNoise="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>2021-03-12T13:48:33Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_0" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_1" stoichiometry="2"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_4" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_6899" name="kcat_F" value="558000"/>
<Constant key="Parameter_6901" name="Km_PP" value="0.003"/>
</ListOfConstants>
<KineticLaw function="Function_40" unitType="Default" scalingCompartment="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_264">
<SourceParameter reference="Metabolite_4"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_263">
<SourceParameter reference="Parameter_6899"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_262">
<SourceParameter reference="Metabolite_0"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_261">
<SourceParameter reference="Parameter_6901"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_3" name="GMPK" reversible="true" fast="false" addNoise="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_3">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-03-12T13:49:15Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_12" stoichiometry="1"/>
<Substrate metabolite="Metabolite_2" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_11" stoichiometry="1"/>
<Product metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_13" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_6898" name="kcat_F" value="752400"/>
<Constant key="Parameter_6897" name="Km_GMP" value="0.156"/>
<Constant key="Parameter_6895" name="Km_ATP" value="0.5"/>
<Constant key="Parameter_6894" name="Km_GDP" value="0.097"/>
<Constant key="Parameter_6896" name="Km_ADP" value="0.017"/>
<Constant key="Parameter_6893" name="K_eq_GMPK" value="1"/>
</ListOfConstants>
<KineticLaw function="Function_45" unitType="Default" scalingCompartment="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_307">
<SourceParameter reference="Metabolite_13"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_306">
<SourceParameter reference="Parameter_6898"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_294">
<SourceParameter reference="Metabolite_12"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_295">
<SourceParameter reference="Parameter_6897"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_296">
<SourceParameter reference="Metabolite_2"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_297">
<SourceParameter reference="Parameter_6895"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_298">
<SourceParameter reference="Metabolite_11"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_308">
<SourceParameter reference="Parameter_6894"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_309">
<SourceParameter reference="Metabolite_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_310">
<SourceParameter reference="Parameter_6896"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_311">
<SourceParameter reference="Parameter_6893"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_4" name="PPK3_G" reversible="true" fast="false" addNoise="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_4">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-03-12T13:50:05Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_11" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_10" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_5" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_6892" name="kcat_F" value="15048"/>
<Constant key="Parameter_7530" name="Km_GDP" value="1.2"/>
<Constant key="Parameter_7531" name="Km_GTP" value="0.1"/>
<Constant key="Parameter_7533" name="K_eq_PPK3_G" value="1"/>
</ListOfConstants>
<KineticLaw function="Function_44" unitType="Default" scalingCompartment="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_305">
<SourceParameter reference="Metabolite_5"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_304">
<SourceParameter reference="Parameter_6892"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_303">
<SourceParameter reference="Metabolite_11"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_302">
<SourceParameter reference="Parameter_7530"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_301">
<SourceParameter reference="Metabolite_10"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_300">
<SourceParameter reference="Parameter_7531"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_299">
<SourceParameter reference="Parameter_7533"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_5" name="PPK3_A" reversible="true" fast="false" addNoise="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_5">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-03-12T14:00:05Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_2" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_5" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_7529" name="kcat_F" value="18780"/>
<Constant key="Parameter_7532" name="Km_ADP" value="2.5"/>
<Constant key="Parameter_7505" name="Km_ATP" value="2"/>
<Constant key="Parameter_7506" name="K_eq_PPK3_A" value="1"/>
</ListOfConstants>
<KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_267">
<SourceParameter reference="Metabolite_5"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_266">
<SourceParameter reference="Parameter_7529"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_265">
<SourceParameter reference="Metabolite_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_250">
<SourceParameter reference="Parameter_7532"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_268">
<SourceParameter reference="Metabolite_2"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_269">
<SourceParameter reference="Parameter_7505"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_270">
<SourceParameter reference="Parameter_7506"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
</ListOfReactions>
<ListOfEvents>
<Event key="Event_0" name="Save GDP-Fucose at 40h" fireAtInitialTime="0" persistentTrigger="0">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<TriggerExpression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Reference=Time> == 40
</TriggerExpression>
<ListOfAssignments>
<Assignment target="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[GDP-Fucose at 40h]" targetKey="ModelValue_0">
<Expression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[GDP_Fucose],Reference=Concentration>
</Expression>
</Assignment>
</ListOfAssignments>
</Event>
<Event key="Event_1" name="Save GDP-Fucose at 24h" fireAtInitialTime="0" persistentTrigger="0">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<TriggerExpression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Reference=Time> == 24
</TriggerExpression>
<ListOfAssignments>
<Assignment target="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[GDP-Fucose at 24h]" targetKey="ModelValue_2">
<Expression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[GDP_Fucose],Reference=Concentration>
</Expression>
</Assignment>
</ListOfAssignments>
</Event>
<Event key="Event_2" name="Save Initial Fucose Conc" fireAtInitialTime="0" persistentTrigger="0">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<TriggerExpression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Reference=Time> == 0.00000000001
</TriggerExpression>
<ListOfAssignments>
<Assignment target="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Dyn. Updated Initial Fucose Conc]" targetKey="ModelValue_8">
<Expression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[Fuc],Reference=Concentration>
</Expression>
</Assignment>
</ListOfAssignments>
</Event>
<Event key="Event_3" name="Save Initial GMP Conc" fireAtInitialTime="0" persistentTrigger="0">
<MiriamAnnotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
</MiriamAnnotation>
<TriggerExpression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Reference=Time> == 0.00000000001
</TriggerExpression>
<ListOfAssignments>
<Assignment target="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Values[Dyn. Updated Initial GMP Conc]" targetKey="ModelValue_9">
<Expression>
<CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[GMP],Reference=Concentration>
</Expression>
</Assignment>
</ListOfAssignments>
</Event>
</ListOfEvents>
<ListOfModelParameterSets activeSet="ModelParameterSet_1">
<ModelParameterSet key="ModelParameterSet_1" name="Initial State">
<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="#ModelParameterSet_1">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ModelParameterGroup cn="String=Initial Time" type="Group">
<ModelParameter cn="CN=Root,Model=GDP-Fucose_v7XGSK" value="0" type="Model" simulationType="time"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
<ModelParameter cn="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment]" value="1" type="Compartment" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Species Values" type="Group">
<ModelParameter cn="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[PP]" value="0" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=GDP-Fucose_v7XGSK,Vector=Compartments[compartment],Vector=Metabolites[P]" value="0" type="Species" simulationType="reactions"/>