Mercurial > repos > metexplore > met4j

annotate build/tools/SbmlSetChargesFromFile/test-data/toy_model.xml @ 8:1274e2a62479 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
author metexplore
date Wed, 26 Jul 2023 15:33:45 +0000
parents 7a6f2380fc1d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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6
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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1 <?xml version="1.0" encoding='UTF-8' ?>
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2 <sbml fbc:required="false" groups:required="false" level="3" version="1"
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3 xmlns="http://www.sbml.org/sbml/level3/version1/core"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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4 xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"
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5 xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1">
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6 <model fbc:strict="true" name="toy model">
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7 <listOfUnitDefinitions>
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8 <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr">
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9 <listOfUnits>
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10 <unit exponent="-1" kind="gram" multiplier="1" scale="0"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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11 <unit exponent="1" kind="mole" multiplier="1" scale="-3"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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12 <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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13 </listOfUnits>
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14 </unitDefinition>
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15 </listOfUnitDefinitions>
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16 <listOfCompartments>
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17 <compartment constant="false" id="c" name="Cytosol"/>
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18 <compartment constant="false" id="e" name="Extracellular"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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19 </listOfCompartments>
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20 <listOfSpecies>
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21 <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext">
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22 <notes>
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23 <body xmlns="http://www.w3.org/1999/xhtml">
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24 <p>SMILES: C[C@@H](C(=O)O)NC</p>
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25 </body>
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26 </notes>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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27 <annotation>
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28 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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29 xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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30 <rdf:Description rdf:about="#A_ext">
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31 <bqbiol:is>
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32 <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi>
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33 </bqbiol:is>
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34 </rdf:Description>
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35 </rdf:RDF>
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36 </annotation>
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37
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38 </species>
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39 <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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40 <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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41 <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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42 <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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43 <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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44 <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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45 <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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46 </listOfSpecies>
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47 <listOfParameters>
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48 <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/>
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49 <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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50 <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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51 <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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52 <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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53 <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
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54 <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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55 <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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56 <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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57 <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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58 </listOfParameters>
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59 <listOfReactions>
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60 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false">
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61 <listOfReactants>
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62 <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/>
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63 </listOfReactants>
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64 <listOfProducts>
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65 <speciesReference constant="true" species="A" stoichiometry="1.0"/>
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66 </listOfProducts>
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67 </reaction>
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68 <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true">
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69 <listOfReactants>
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70 <speciesReference constant="true" species="A" stoichiometry="1.0"/>
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71 </listOfReactants>
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72 <listOfProducts>
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73 <speciesReference constant="true" species="B" stoichiometry="1.0"/>
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74 </listOfProducts>
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75 </reaction>
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76 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false">
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77 <listOfReactants>
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78 <speciesReference constant="true" species="A" stoichiometry="1.0"/>
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79 </listOfReactants>
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80 <listOfProducts>
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81 <speciesReference constant="true" species="C" stoichiometry="1.0"/>
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82 </listOfProducts>
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83 </reaction>
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84 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false">
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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85 <listOfReactants>
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86 <speciesReference constant="true" species="B" stoichiometry="1.0"/>
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87 <speciesReference constant="true" species="C" stoichiometry="1.0"/>
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88 </listOfReactants>
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89 <listOfProducts>
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90 <speciesReference constant="true" species="D" stoichiometry="1.5"/>
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91 </listOfProducts>
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92 </reaction>
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93 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false">
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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94 <listOfReactants>
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95 <speciesReference constant="true" species="D" stoichiometry="1.0"/>
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96 </listOfReactants>
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97 <listOfProducts>
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98 <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/>
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99 </listOfProducts>
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100 </reaction>
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101 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false">
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102 <listOfReactants>
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103 <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/>
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104 </listOfReactants>
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105 <listOfProducts>
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106 <speciesReference constant="true" species="E" stoichiometry="1.0"/>
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107 </listOfProducts>
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108 </reaction>
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109 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false">
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110 <listOfReactants>
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111 <speciesReference constant="true" species="E" stoichiometry="2.0"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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112 </listOfReactants>
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113 <listOfProducts>
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114 <speciesReference constant="true" species="D" stoichiometry="1.0"/>
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115 </listOfProducts>
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116 </reaction>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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117 </listOfReactions>
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118 </model>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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119 </sbml>