Mercurial > repos > metexplore > met4j
comparison build/tools/ExtractSubBipNetwork/test-data/toy_model.xml @ 6:7a6f2380fc1d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author | metexplore |
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date | Wed, 17 May 2023 13:26:37 +0000 |
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5:35c9abcd8934 | 6:7a6f2380fc1d |
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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> |