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comparison test-data/rp_002_0001.xml @ 0:e95370d2e5f9 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Mon, 13 Dec 2021 18:19:24 +0000
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-1:000000000000 0:e95370d2e5f9
1 <?xml version="1.0" encoding="UTF-8"?>
2 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false">
3 <model metaid="f9b1ff022aa2133fc1e5e5d1fbac90ac29a744e960a2774be646bc71471ed597" id="RP_model_002_0001" name="002_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
4 <listOfCompartments>
5 <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">
6 <annotation>
7 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
8 <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">
9 <bqbiol:is>
10 <rdf:Bag>
11 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
12 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
13 <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
14 <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
15 <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
16 <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
17 <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
18 </rdf:Bag>
19 </bqbiol:is>
20 </rdf:Description>
21 </rdf:RDF>
22 </annotation>
23 </compartment>
24 </listOfCompartments>
25 <listOfSpecies>
26 <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
27 <annotation>
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37 <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
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42 <brsynth:fba_fraction_shadow_price>
43 <brsynth:value value="-1.0"/>
44 </brsynth:fba_fraction_shadow_price>
45 <brsynth:thermo_standard_dg_formation>
46 <brsynth:value value="936.7141451846444"/>
47 <brsynth:units value="kilojoule / mole"/>
48 </brsynth:thermo_standard_dg_formation>
49 </brsynth:brsynth>
50 </rdf:BRSynth>
51 </rdf:RDF>
52 </annotation>
53 </species>
54 <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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65 <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
66 <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
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68 <brsynth:value value="-0.0018808381539567876"/>
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70 <brsynth:fba_fraction_shadow_price>
71 <brsynth:value value="-0.9946091644204852"/>
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73 <brsynth:thermo_standard_dg_formation>
74 <brsynth:value value="-1495.8281099920857"/>
75 <brsynth:units value="kilojoule / mole"/>
76 </brsynth:thermo_standard_dg_formation>
77 </brsynth:brsynth>
78 </rdf:BRSynth>
79 </rdf:RDF>
80 </annotation>
81 </species>
82 <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
83 <annotation>
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85 <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
86 <bqbiol:is>
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93 <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
94 <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
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98 <brsynth:fba_fraction_shadow_price>
99 <brsynth:value value="-1.0"/>
100 </brsynth:fba_fraction_shadow_price>
101 <brsynth:thermo_standard_dg_formation>
102 <brsynth:value value="1245.5794452419402"/>
103 <brsynth:units value="kilojoule / mole"/>
104 </brsynth:thermo_standard_dg_formation>
105 </brsynth:brsynth>
106 </rdf:BRSynth>
107 </rdf:RDF>
108 </annotation>
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111 <annotation>
112 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
113 <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
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119 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
120 <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
121 <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
122 <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
123 <brsynth:fba_biomass_shadow_price>
124 <brsynth:value value="None"/>
125 </brsynth:fba_biomass_shadow_price>
126 <brsynth:fba_fraction_shadow_price>
127 <brsynth:value value="None"/>
128 </brsynth:fba_fraction_shadow_price>
129 <brsynth:thermo_standard_dg_formation>
130 <brsynth:value value="-1828.3274439664424"/>
131 <brsynth:units value="kilojoule / mole"/>
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133 </brsynth:brsynth>
134 </rdf:BRSynth>
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136 </annotation>
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139 <annotation>
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148 <brsynth:smiles/>
149 <brsynth:inchi/>
150 <brsynth:inchikey/>
151 <brsynth:fba_biomass_shadow_price>
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153 </brsynth:fba_biomass_shadow_price>
154 <brsynth:fba_fraction_shadow_price>
155 <brsynth:value value="None"/>
156 </brsynth:fba_fraction_shadow_price>
157 <brsynth:thermo_standard_dg_formation>
158 <brsynth:value value="-2256.1898491337233"/>
159 <brsynth:units value="kilojoule / mole"/>
160 </brsynth:thermo_standard_dg_formation>
161 </brsynth:brsynth>
162 </rdf:BRSynth>
163 </rdf:RDF>
164 </annotation>
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167 <annotation>
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170 <bqbiol:is>
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175 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
176 <brsynth:smiles/>
177 <brsynth:inchi/>
178 <brsynth:inchikey/>
179 <brsynth:fba_biomass_shadow_price>
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181 </brsynth:fba_biomass_shadow_price>
182 <brsynth:fba_fraction_shadow_price>
183 <brsynth:value value="None"/>
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185 <brsynth:thermo_standard_dg_formation>
186 <brsynth:value value="-2261.3806478863044"/>
187 <brsynth:units value="kilojoule / mole"/>
188 </brsynth:thermo_standard_dg_formation>
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190 </rdf:BRSynth>
191 </rdf:RDF>
192 </annotation>
193 </species>
194 <species metaid="_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36" id="MNXM100" name="MNXM100" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
195 <annotation>
196 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
197 <rdf:Description rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
198 <bqbiol:is>
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202 <rdf:BRSynth rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
203 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
204 <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
205 <brsynth:inchi value="InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)"/>
206 <brsynth:inchikey value="GVVPGTZRZFNKDS-UHFFFAOYSA-N"/>
207 <brsynth:fba_biomass_shadow_price>
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210 <brsynth:fba_fraction_shadow_price>
211 <brsynth:value value="None"/>
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213 <brsynth:thermo_standard_dg_formation>
214 <brsynth:value value="-1719.970141951422"/>
215 <brsynth:units value="kilojoule / mole"/>
216 </brsynth:thermo_standard_dg_formation>
217 </brsynth:brsynth>
218 </rdf:BRSynth>
219 </rdf:RDF>
220 </annotation>
221 </species>
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223 <annotation>
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233 <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
234 <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
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238 <brsynth:fba_fraction_shadow_price>
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240 </brsynth:fba_fraction_shadow_price>
241 <brsynth:thermo_standard_dg_formation>
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243 <brsynth:units value="kilojoule / mole"/>
244 </brsynth:thermo_standard_dg_formation>
245 </brsynth:brsynth>
246 </rdf:BRSynth>
247 </rdf:RDF>
248 </annotation>
249 </species>
250 </listOfSpecies>
251 <listOfParameters>
252 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000_0" value="10000" constant="true"/>
253 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0_0" value="0" constant="true"/>
254 </listOfParameters>
255 <listOfReactions>
256 <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0">
257 <annotation>
258 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
259 <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
260 <bqbiol:is>
261 <rdf:Bag>
262 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.82"/>
263 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.29"/>
264 </rdf:Bag>
265 </bqbiol:is>
266 </rdf:Description>
267 <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
268 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
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270 <brsynth:rp2_transfo_id value="TRS_0_2_740"/>
271 <brsynth:rule_ids>
272 <brsynth:RR-02-0c33a3bfd9bf5ad5-14-F/>
273 <brsynth:RR-02-6692e4af37fbca2d-14-F/>
274 </brsynth:rule_ids>
275 <brsynth:tmpl_rxn_ids>
276 <brsynth:MNXR132231/>
277 <brsynth:MNXR112683/>
278 </brsynth:tmpl_rxn_ids>
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281 <brsynth:selenzy/>
282 <brsynth:fba_biomass>
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293 <brsynth:units value="kilojoule / mole"/>
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295 <brsynth:thermo_dGm_prime>
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298 <brsynth:units value="kilojoule / mole"/>
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300 <brsynth:thermo_dG_prime>
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302 <brsynth:error value="4.6679220722885155"/>
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305 <brsynth:thermo_dG>
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307 <brsynth:error value="4.6679220722885155"/>
308 <brsynth:units value="kilojoule / mole"/>
309 </brsynth:thermo_dG>
310 </brsynth:brsynth>
311 </rdf:BRSynth>
312 </rdf:RDF>
313 </annotation>
314 <listOfReactants>
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316 <speciesReference species="MNXM83" stoichiometry="1" constant="true"/>
317 </listOfReactants>
318 <listOfProducts>
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362 <brsynth:error value="11.000567449695138"/>
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380 </brsynth:brsynth>
381 </rdf:BRSynth>
382 </rdf:RDF>
383 </annotation>
384 <listOfReactants>
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386 </listOfReactants>
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451 <listOfProducts>
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453 <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
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455 </reaction>
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585 </groups:group>
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587 </model>
588 </sbml>