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reran update_pickles so the models represent their true state (not a …
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…manually edited version).
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@gregmedlock
gregmedlock committed Aug 27, 2018
1 parent 220c1ed commit 8e31a60
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Showing 14 changed files with 49 additions and 49 deletions.
Binary file modified cobra/test/data/iJO1366.pickle
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4 changes: 2 additions & 2 deletions cobra/test/data/mini.json
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Expand Up @@ -1363,5 +1363,5 @@
"upper_bound": 1000.0
}
],
"version": 1
}
"version": "1"
}
Binary file modified cobra/test/data/mini.mat
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62 changes: 31 additions & 31 deletions cobra/test/data/mini_cobra.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="e" name="extracellular" size="1"/>
<compartment id="c" name="cytosol" size="1"/>
<compartment id="e" name="extracellular" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="M_13dpg_c" name="3-Phospho-D-glyceroyl phosphate" compartment="c" charge="-4">
Expand Down Expand Up @@ -201,8 +201,8 @@
<listOfReactions>
<reaction id="R_ATPM" name="ATP maintenance requirement" reversible="false">
<listOfReactants>
<speciesReference species="M_h2o_c" stoichiometry="1"/>
<speciesReference species="M_atp_c" stoichiometry="1"/>
<speciesReference species="M_h2o_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_pi_c" stoichiometry="1"/>
Expand All @@ -214,9 +214,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="8.39" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="1" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="8.39" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -228,8 +228,8 @@
</html>
</notes>
<listOfReactants>
<speciesReference species="M_h_e" stoichiometry="1"/>
<speciesReference species="M_lac__D_e" stoichiometry="1"/>
<speciesReference species="M_h_e" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_lac__D_c" stoichiometry="1"/>
Expand All @@ -240,9 +240,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -265,9 +265,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -284,9 +284,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-10" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-10" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -303,9 +303,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -322,9 +322,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -339,17 +339,17 @@
<speciesReference species="M_fdp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_g3p_c" stoichiometry="1"/>
<speciesReference species="M_dhap_c" stoichiometry="1"/>
<speciesReference species="M_g3p_c" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -366,18 +366,18 @@
<speciesReference species="M_g3p_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_13dpg_c" stoichiometry="1"/>
<speciesReference species="M_nadh_c" stoichiometry="1"/>
<speciesReference species="M_h_c" stoichiometry="1"/>
<speciesReference species="M_13dpg_c" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -389,21 +389,21 @@
</html>
</notes>
<listOfReactants>
<speciesReference species="M_pep_c" stoichiometry="1"/>
<speciesReference species="M_glc__D_e" stoichiometry="1"/>
<speciesReference species="M_pep_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_pyr_c" stoichiometry="1"/>
<speciesReference species="M_g6p_c" stoichiometry="1"/>
<speciesReference species="M_pyr_c" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -425,9 +425,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -443,18 +443,18 @@
<speciesReference species="M_nad_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_pyr_c" stoichiometry="1"/>
<speciesReference species="M_nadh_c" stoichiometry="1"/>
<speciesReference species="M_pyr_c" stoichiometry="1"/>
<speciesReference species="M_h_c" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -466,22 +466,22 @@
</html>
</notes>
<listOfReactants>
<speciesReference species="M_atp_c" stoichiometry="1"/>
<speciesReference species="M_f6p_c" stoichiometry="1"/>
<speciesReference species="M_atp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_adp_c" stoichiometry="1"/>
<speciesReference species="M_fdp_c" stoichiometry="1"/>
<speciesReference species="M_h_c" stoichiometry="1"/>
<speciesReference species="M_fdp_c" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="1" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -503,9 +503,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -517,21 +517,21 @@
</html>
</notes>
<listOfReactants>
<speciesReference species="M_3pg_c" stoichiometry="1"/>
<speciesReference species="M_atp_c" stoichiometry="1"/>
<speciesReference species="M_3pg_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_13dpg_c" stoichiometry="1"/>
<speciesReference species="M_adp_c" stoichiometry="1"/>
<speciesReference species="M_13dpg_c" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -553,9 +553,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -579,9 +579,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -593,8 +593,8 @@
</html>
</notes>
<listOfReactants>
<speciesReference species="M_adp_c" stoichiometry="1"/>
<speciesReference species="M_pep_c" stoichiometry="1"/>
<speciesReference species="M_adp_c" stoichiometry="1"/>
<speciesReference species="M_h_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
Expand All @@ -606,9 +606,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand All @@ -630,9 +630,9 @@
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
Expand Down
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