Mercurial > repos > metexplore > met4j

comparison build/tools/SbmlSetChargesFromFile/test-data/toy_model.xml @ 6:7a6f2380fc1d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
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5:35c9abcd8934 6:7a6f2380fc1d
1 <?xml version="1.0" encoding='UTF-8' ?>
2 <sbml fbc:required="false" groups:required="false" level="3" version="1"
3 xmlns="http://www.sbml.org/sbml/level3/version1/core"
4 xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"
5 xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1">
6 <model fbc:strict="true" name="toy model">
7 <listOfUnitDefinitions>
8 <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr">
9 <listOfUnits>
10 <unit exponent="-1" kind="gram" multiplier="1" scale="0"/>
11 <unit exponent="1" kind="mole" multiplier="1" scale="-3"/>
12 <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/>
13 </listOfUnits>
14 </unitDefinition>
15 </listOfUnitDefinitions>
16 <listOfCompartments>
17 <compartment constant="false" id="c" name="Cytosol"/>
18 <compartment constant="false" id="e" name="Extracellular"/>
19 </listOfCompartments>
20 <listOfSpecies>
21 <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext">
22 <notes>
23 <body xmlns="http://www.w3.org/1999/xhtml">
24 <p>SMILES: C[C@@H](C(=O)O)NC</p>
25 </body>
26 </notes>
27 <annotation>
28 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
29 xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
30 <rdf:Description rdf:about="#A_ext">
31 <bqbiol:is>
32 <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi>
33 </bqbiol:is>
34 </rdf:Description>
35 </rdf:RDF>
36 </annotation>
37
38 </species>
39 <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/>
40 <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/>
41 <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/>
42 <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/>
43 <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/>
44 <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/>
45 <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/>
46 </listOfSpecies>
47 <listOfParameters>
48 <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/>
49 <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/>
50 <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/>
51 <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/>
52 <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/>
53 <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
54 <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
55 <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
56 <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
57 <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
58 </listOfParameters>
59 <listOfReactions>
60 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false">
61 <listOfReactants>
62 <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/>
63 </listOfReactants>
64 <listOfProducts>
65 <speciesReference constant="true" species="A" stoichiometry="1.0"/>
66 </listOfProducts>
67 </reaction>
68 <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true">
69 <listOfReactants>
70 <speciesReference constant="true" species="A" stoichiometry="1.0"/>
71 </listOfReactants>
72 <listOfProducts>
73 <speciesReference constant="true" species="B" stoichiometry="1.0"/>
74 </listOfProducts>
75 </reaction>
76 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false">
77 <listOfReactants>
78 <speciesReference constant="true" species="A" stoichiometry="1.0"/>
79 </listOfReactants>
80 <listOfProducts>
81 <speciesReference constant="true" species="C" stoichiometry="1.0"/>
82 </listOfProducts>
83 </reaction>
84 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false">
85 <listOfReactants>
86 <speciesReference constant="true" species="B" stoichiometry="1.0"/>
87 <speciesReference constant="true" species="C" stoichiometry="1.0"/>
88 </listOfReactants>
89 <listOfProducts>
90 <speciesReference constant="true" species="D" stoichiometry="1.5"/>
91 </listOfProducts>
92 </reaction>
93 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false">
94 <listOfReactants>
95 <speciesReference constant="true" species="D" stoichiometry="1.0"/>
96 </listOfReactants>
97 <listOfProducts>
98 <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/>
99 </listOfProducts>
100 </reaction>
101 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false">
102 <listOfReactants>
103 <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/>
104 </listOfReactants>
105 <listOfProducts>
106 <speciesReference constant="true" species="E" stoichiometry="1.0"/>
107 </listOfProducts>
108 </reaction>
109 <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false">
110 <listOfReactants>
111 <speciesReference constant="true" species="E" stoichiometry="2.0"/>
112 </listOfReactants>
113 <listOfProducts>
114 <speciesReference constant="true" species="D" stoichiometry="1.0"/>
115 </listOfProducts>
116 </reaction>
117 </listOfReactions>
118 </model>
119 </sbml>