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Merge pull request #14 from phnmnl/feature/fluxomics_stationary
Feature/fluxomics stationary
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| Original file line number | Diff line number | Diff line change |
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| Reaction id,Lower bound,Upper bound,Objective coefficient,Reaction name | ||
| RlacEx,1,1,0,Exchange of Lactate |
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examples/fluxomics_stationary/expected_best_fit_fluxes.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| ID,Name,Stoichiometry,Minimum,Maximum | ||
| Rbottom_Glc,Glyceraldehyde phosphate dehydrogenase,Gap --> Pep,0.8681,0.8682 | ||
| RextraPyr,extra pyruvate, --> Pyr,0.1318,0.1319 | ||
| Rfba,Aldolase,Fru16bp <=> Dhap + Gap,0.422867,0.422933 | ||
| Rglc6p_pdif,Difussion between Glucose 6-phosphate pools,Glc6p_a <=> Glc6p_b,0.445217,0.445283 | ||
| RglcEx,Glucose uptake, --> Glc,0.4348,0.4349 | ||
| RglycEx,Glycogen utilization, --> Glc6p_a,0.010317,0.010483 | ||
| Rhex1,Hexokinase,Glc --> Glc6p_a,0.4348,0.4349 | ||
| RlacEx,Lactate release,Lac --> ,1.0,1.0 | ||
| Rldh_l,L-lactate dehydrogenase,Pyr <=> Lac,1.0,1.0 | ||
| RoxPPP,Glucose 6-Phosphate dehydrogenase,Glc6p_b --> Rul5p,0.067,0.0671 | ||
| Rpfk,Phosphofructokinase,Fru6p --> Fru16bp,0.422867,0.422933 | ||
| Rpgi,Glucose-6-phosphate isomerase,Glc6p_b <=> Fru6p,0.378133,0.378267 | ||
| Rpyk,Pyruvate Kinase,Pep --> Pyr,0.8681,0.8682 | ||
| Rrpe,Ribulose 5 phosphate epimerase,Rul5p <=> Xyl5p,0.044667,0.044733 | ||
| Rrpi,Ribose phosphate isomerase,Rul5p <=> Rib5p,0.022333,0.022367 | ||
| Rtala,Transaldolase,Gap + Sed7p <=> E4p + Fru6p,0.022333,0.022367 | ||
| Rtkt1,Transketolase 1,Rib5p + Xyl5p <=> Gap + Sed7p,0.022333,0.022367 | ||
| Rtkt2,Transketolase 2,E4p + Xyl5p <=> Fru6p + Gap,0.022333,0.022367 | ||
| Rtpi,Triose-phosphate isomerase,Dhap <=> Gap,0.422867,0.422933 |
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| Metabolite/s,Isotopologue,Simulated value,Experimental Mean,Experimental SD,Chi Square | ||
| Glycogen_C1-C6,m0,0.81,0.6428,0.0087,279.495 | ||
| Glycogen_C1-C6,m1,0.0,0.0006,0.0004,0.004 | ||
| Glycogen_C1-C6,m2,0.19,0.343,0.0099,233.923 | ||
| Glycogen_C1-C6,m3,0.0,0.0015,0.0003,0.022 | ||
| Glycogen_C1-C6,m4,-0.0,0.0108,0.0004,1.164 | ||
| Glycogen_C1-C6,m5,0.0,0.0003,0.0,0.001 | ||
| Glycogen_C1-C6,m6,0.0,0.0013,0.0001,0.018 | ||
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| Glycogen_C1-C6,m1/Sm,0.0,0.0017,0.001 | ||
| Glycogen_C1-C6,m2/Sm,1.0,0.9601,0.0278 | ||
| Glycogen_C1-C6,m3/Sm,0.0,0.0041,0.001 | ||
| Glycogen_C1-C6,m4/Sm,-0.0,0.0302,0.0012 | ||
| Glycogen_C1-C6,m5/Sm,0.0,0.0008,0.0001 | ||
| Glycogen_C1-C6,m6/Sm,0.0,0.0037,0.0004 | ||
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| Lactate_C1-C3,m0,0.985,0.8132,0.0048,295.103 | ||
| Lactate_C1-C3,m1,0.0094,0.0022,0.0006,0.529 | ||
| Lactate_C1-C3,m2,0.0056,0.1888,0.0018,335.813 | ||
| Lactate_C1-C3,m3,0.0,0.0001,0.0001,0.0 | ||
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| D-Ribose_C1-C5,m0,0.847,0.847,0.0127,0.0 | ||
| D-Ribose_C1-C5,m1,0.1433,0.052,0.0045,83.338 | ||
| D-Ribose_C1-C5,m2,0.0091,0.0758,0.0062,44.439 | ||
| D-Ribose_C1-C5,m3,0.0005,0.0102,0.0005,0.935 | ||
| D-Ribose_C1-C5,m4,0.0,0.0149,0.0016,2.195 | ||
| D-Ribose_C1-C5,m5,0.0,0.0002,0.0,0.0 | ||
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| D-Ribose_C1-C5,m1/Sm,0.9367,0.34,0.0294 | ||
| D-Ribose_C1-C5,m2/Sm,0.0595,0.4951,0.0405 | ||
| D-Ribose_C1-C5,m3/Sm,0.0035,0.0667,0.0031 | ||
| D-Ribose_C1-C5,m4/Sm,0.0002,0.097,0.0101 | ||
| D-Ribose_C1-C5,m5/Sm,0.0,0.0012,0.0002 | ||
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| <?xml version='1.0' encoding='UTF-8'?> | ||
| <sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" sboTerm="SBO:0000624" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false"> | ||
| <model fbc:strict="true" id="Constraint based model"> | ||
| <listOfUnitDefinitions> | ||
| <unitDefinition id="mmol_per_gDW_per_hr"> | ||
| <listOfUnits> | ||
| <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> | ||
| <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> | ||
| <unit exponent="-1" kind="second" multiplier="3600" scale="0"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| </listOfUnitDefinitions> | ||
| <fbc:listOfObjectives fbc:activeObjective="obj"> | ||
| <fbc:objective fbc:id="obj" fbc:type="maximize"> | ||
| <fbc:listOfFluxObjectives/> | ||
| </fbc:objective> | ||
| </fbc:listOfObjectives> | ||
| <listOfParameters> | ||
| <parameter constant="true" id="cobra_default_lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-1000"/> | ||
| <parameter constant="true" id="cobra_default_ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="1000"/> | ||
| <parameter constant="true" id="cobra_0_bound" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="0"/> | ||
| </listOfParameters> | ||
| <listOfCompartments/> | ||
| <listOfSpecies> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Glc" name="Glucose" compartment="None" fbc:chemicalFormula="C6H12O6"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Lac" name="Lactate" compartment="None" fbc:chemicalFormula="C3H5O3"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Glc6p_a" name="Glucose 6-phosphate (pool A)" compartment="None" fbc:chemicalFormula="C6H11O9P"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Glc6p_b" name="Glucose 6-phosphate (pool B)" compartment="None" fbc:chemicalFormula="C6H11O9P"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Fru6p" name="Fructose 6-phosphate" compartment="None" fbc:chemicalFormula="C6H11O9P"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Fru16bp" name="Fructose 1-6 biphosphate" compartment="None" fbc:chemicalFormula="C6H10O12P2"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Dhap" name="Dihydroxyacetone phsophate" compartment="None" fbc:chemicalFormula="C3H5O6P"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Gap" name="Glyceraldehyde 3-phosphate" compartment="None" fbc:chemicalFormula="C3H5O6P"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Pep" name="Posphoenolpyruvate" compartment="None" fbc:chemicalFormula="C3H2O6P"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Pyr" name="Pyruvate" compartment="None" fbc:chemicalFormula="C3H3O3"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Rul5p" name="Ribulose 5-phosphate" compartment="None" fbc:chemicalFormula="C5H9O8P"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Rib5p" name="Ribose 5-phosphate" compartment="None" fbc:chemicalFormula="C5H9O8P"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Xyl5p" name="Xylulose 5-phosphate" compartment="None" fbc:chemicalFormula="C5H9O8P"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_Sed7p" name="Sedoheptulose 7-phosphate" compartment="None" fbc:chemicalFormula="C7H13O10P"/> | ||
| <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_E4p" name="Erythrose 4-phosphate" compartment="None" fbc:chemicalFormula="C4H7O7P"/> | ||
| </listOfSpecies> | ||
| <listOfReactions> | ||
| <reaction fast="false" id="R_RglcEx" reversible="false" name="Glucose uptake" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Glc" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_RlacEx" reversible="false" name="Lactate release" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Lac" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rhex1" reversible="false" name="Hexokinase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Glc" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Glc6p_a" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_RglycEx" reversible="false" name="Glycogen utilization" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Glc6p_a" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rglc6p_pdif" reversible="true" name="Difussion between Glucose 6-phosphate pools" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Glc6p_a" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Glc6p_b" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rpgi" reversible="true" name="Glucose-6-phosphate isomerase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Glc6p_b" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Fru6p" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rpfk" reversible="false" name="Phosphofructokinase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Fru6p" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Fru16bp" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rfba" reversible="true" name="Aldolase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Fru16bp" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Dhap" stoichiometry="1"/> | ||
| <speciesReference constant="true" species="M_Gap" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rtpi" reversible="true" name="Triose-phosphate isomerase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Dhap" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Gap" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rbottom_Glc" reversible="true" name="Glyceraldehyde phosphate dehydrogenase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Gap" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Pep" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rpyk" reversible="false" name="Pyruvate Kinase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Pep" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Pyr" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rldh_l" reversible="true" name="L-lactate dehydrogenase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Pyr" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Lac" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_RoxPPP" reversible="false" name="Glucose 6-Phosphate dehydrogenase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Glc6p_b" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Rul5p" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rrpi" reversible="true" name="Ribose phosphate isomerase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Rul5p" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Rib5p" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rrpe" reversible="true" name="Ribulose 5 phosphate epimerase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Rul5p" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Xyl5p" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rtkt1" reversible="true" name="Transketolase 1" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Rib5p" stoichiometry="1"/> | ||
| <speciesReference constant="true" species="M_Xyl5p" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Gap" stoichiometry="1"/> | ||
| <speciesReference constant="true" species="M_Sed7p" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rtkt2" reversible="true" name="Transketolase 2" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_E4p" stoichiometry="1"/> | ||
| <speciesReference constant="true" species="M_Xyl5p" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Fru6p" stoichiometry="1"/> | ||
| <speciesReference constant="true" species="M_Gap" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_Rtala" reversible="true" name="Transaldolase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference constant="true" species="M_Gap" stoichiometry="1"/> | ||
| <speciesReference constant="true" species="M_Sed7p" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_E4p" stoichiometry="1"/> | ||
| <speciesReference constant="true" species="M_Fru6p" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction fast="false" id="R_RextraPyr" reversible="false" name="extra pyruvate" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfProducts> | ||
| <speciesReference constant="true" species="M_Pyr" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| </reaction> | ||
| </listOfReactions> | ||
| </model> | ||
| </sbml> |
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