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Corrects previous notebooks and scripts, add supp analyses for cobra …
…and phylomint notebook and scripts, add normalised toy paper its objective reaction and its targets
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Chabname GHASSEMI
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Dec 23, 2024
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| R_BIOMASS |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,154 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1" sboTerm="SBO:0000624" fbc:required="false"> | ||
| <model fbc:strict="true" id="toy_stoichiometry"> | ||
| <listOfUnitDefinitions> | ||
| <unitDefinition id="mmol_per_gDW_per_hr"> | ||
| <listOfUnits> | ||
| <unit kind="mole" scale="-3" multiplier="1" exponent="1"/> | ||
| <unit kind="gram" scale="0" multiplier="1" exponent="-1"/> | ||
| <unit kind="second" scale="0" multiplier="3600" exponent="-1"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| </listOfUnitDefinitions> | ||
| <fbc:listOfObjectives fbc:activeObjective="obj"> | ||
| <fbc:objective fbc:id="obj" fbc:type="maximize"> | ||
| <fbc:listOfFluxObjectives> | ||
| <fbc:fluxObjective fbc:reaction="R_BIOMASS" fbc:coefficient="1"/> | ||
| </fbc:listOfFluxObjectives> | ||
| </fbc:objective> | ||
| </fbc:listOfObjectives> | ||
| <listOfParameters> | ||
| <parameter value="-1000" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> | ||
| <parameter value="1000" id="cobra_default_ub" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> | ||
| <parameter value="0" id="cobra_0_bound" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> | ||
| <parameter value="-10" id="cobra_10_lbound" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> | ||
| </listOfParameters> | ||
| <listOfCompartments> | ||
| <compartment id="e" name="extracellular space" constant="true"/> | ||
| <compartment id="c" name="cytosol" constant="true"/> | ||
| </listOfCompartments> | ||
| <listOfSpecies> | ||
| <species id="M_S1_e" name="M_S1_e" compartment="e" boundaryCondition="false"/> | ||
| <species id="M_S2_e" name="M_S2_e" compartment="e" boundaryCondition="false"/> | ||
| <species id="M_S1_c" name="M_S1_c" compartment="c" boundaryCondition="false"/> | ||
| <species id="M_S2_c" name="M_S2_c" compartment="c" boundaryCondition="false"/> | ||
| <species id="M_A_c" name="M_A_c" compartment="c" boundaryCondition="false"/> | ||
| <species id="M_B_c" name="M_B_c" compartment="c" boundaryCondition="false"/> | ||
| <species id="M_B_e" name="M_B_e" compartment="e" boundaryCondition="false"/> | ||
| <species id="M_C_c" name="M_C_c" compartment="c" boundaryCondition="false"/> | ||
| <species id="M_D_c" name="M_D_c" compartment="c" boundaryCondition="false"/> | ||
| <species id="M_E_c" name="M_E_c" compartment="c" boundaryCondition="false"/> | ||
| <species id="M_F_c" name="M_F_c" compartment="c" boundaryCondition="false"/> | ||
| <species id="M_G_c" name="M_G_c" compartment="c" boundaryCondition="false"/> | ||
| <species id="M_H_c" name="M_H_c" compartment="c" boundaryCondition="false"/> | ||
| <species id="M_I_c" name="M_I_c" compartment="c" boundaryCondition="false"/> | ||
| <species id="M_J_c" name="M_J_c" compartment="c" boundaryCondition="false"/> | ||
| </listOfSpecies> | ||
| <listOfReactions> | ||
| <reaction id="R_R1" name="R_R1" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_S1_c" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference species="M_A_c" stoichiometry="1.0000" /> | ||
| <speciesReference species="M_B_c" stoichiometry="1.0000" /> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <!-- <reaction id="R_R2" name="R_R2" reversible="false" fbc:upperFluxBound="cobra_0_bound" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_A_c" stoichiometry="1.0000" /> | ||
| <speciesReference species="M_J_c" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference species="M_C_c" stoichiometry="1.0000" /> | ||
| </listOfProducts> | ||
| </reaction> --> | ||
| <reaction id="R_R3" name="R_R3" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_S2_c" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference species="M_D_c" stoichiometry="1.0000" /> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction id="R_R4" name="R_R4" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_B_c" stoichiometry="1.0000" /> | ||
| <speciesReference species="M_D_c" stoichiometry="1.0000" /> | ||
| <speciesReference species="M_E_c" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference species="M_F_c" stoichiometry="12.0000" /> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction id="R_BIOMASS" name="R_BIOMASS" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_F_c" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference species="M_G_c" stoichiometry="1.0000" /> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction id="R_R5" name="R_R5" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_10_lbound"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_F_c" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference species="M_I_c" stoichiometry="1.0000" /> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction id="R_R6" name="R_R6" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_I_c" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference species="M_H_c" stoichiometry="1.0000" /> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction id="R_R7" name="R_R7" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_H_c" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference species="M_E_c" stoichiometry="1.0000" /> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction id="R_EX_S1_e" name="R_EX_S1" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_S1_e" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| </reaction> | ||
| <reaction id="R_TR_S1_e" name="R_TR_S1" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_S1_e" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference species="M_S1_c" stoichiometry="1.0000" /> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction id="R_EX_S2_e" name="R_EX_S2" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_S2_e" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| </reaction> | ||
| <reaction id="R_TR_S2_e" name="R_TR_S2" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_S2_e" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference species="M_S2_c" stoichiometry="1.0000" /> | ||
| </listOfProducts> | ||
| </reaction> | ||
| <reaction id="R_EX_C_c" name="R_EX_C" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_C_c" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| </reaction> | ||
| <reaction id="R_EX_G_c" name="R_EX_G" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> | ||
| <listOfReactants> | ||
| <speciesReference species="M_G_c" stoichiometry="1.0000" /> | ||
| </listOfReactants> | ||
| </reaction> | ||
| </listOfReactions> | ||
| </model> | ||
| </sbml> |
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