Mercurial > repos > workflow4metabolomics > influx_si
comparison test-data/e_coli_i.ftbl @ 0:9b03a930b08b draft
"planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
| author | workflow4metabolomics |
|---|---|
| date | Mon, 04 May 2020 03:24:12 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:9b03a930b08b |
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| 1 PROJECT | |
| 2 NAME VERSION FORMAT DATE COMMENT | |
| 3 K12_MG1655.ftbl 1 101109 modele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees | |
| 4 | |
| 5 NETWORK | |
| 6 FLUX_NAME EDUCT_1 EDUCT_2 PRODUCT_1 PRODUCT_2 | |
| 7 | |
| 8 // Glycolyse. | |
| 9 // PPP | |
| 10 // TCA | |
| 11 // voies anaplerotiques: pepc. enz malique | |
| 12 // voie glyoxylate | |
| 13 // avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre) | |
| 14 // saisie differentielle des substrats marques | |
| 15 | |
| 16 | |
| 17 // Uptake substrats | |
| 18 | |
| 19 Glucupt_1 Gluc_1 Glc6P // fehlt bei wolfgang | |
| 20 #ABCDEF #ABCDEF // fehlt bei wolfgang | |
| 21 | |
| 22 Glucupt_U Gluc_U Glc6P // fehlt bei wolfgang | |
| 23 #ABCDEF #ABCDEF // fehlt bei wolfgang | |
| 24 | |
| 25 // CO2upt CO2_ext CO2 // entree de CO2 non marque | |
| 26 // #A #A // ce flux est a laisser libre | |
| 27 | |
| 28 // FTHF0 FTHF_0 FTHF // prise en charge de FTHF non marque | |
| 29 // #A #A | |
| 30 | |
| 31 // FTHF1 FTHF_1 FTHF // prise en charge de FTHF marque | |
| 32 // #a #a | |
| 33 | |
| 34 | |
| 35 // Embden Meyerhof Parnas Pathway | |
| 36 | |
| 37 pgi Glc6P Fru6P | |
| 38 #ABCDEF #ABCDEF | |
| 39 | |
| 40 pfk Fru6P FruBP | |
| 41 #ABCDEF #ABCDEF | |
| 42 | |
| 43 ald FruBP GA3P GA3P | |
| 44 #ABCDEF #CBA #DEF | |
| 45 | |
| 46 // tpi DHAP GA3P | |
| 47 // #ABC #CBA | |
| 48 | |
| 49 pgk GA3P PGA | |
| 50 #ABC #ABC | |
| 51 | |
| 52 eno PGA PEP | |
| 53 #ABC #ABC | |
| 54 | |
| 55 pyk PEP Pyr | |
| 56 #ABC #ABC | |
| 57 | |
| 58 | |
| 59 // Methylglyoxal Pathway | |
| 60 | |
| 61 // mgs DHAP Pyr | |
| 62 // #ABC #ABC | |
| 63 | |
| 64 | |
| 65 // Pentose Phosphate Pathway | |
| 66 | |
| 67 zwf Glc6P Gnt6P | |
| 68 #ABCDEF #ABCDEF | |
| 69 | |
| 70 gnd Gnt6P CO2 Rib5P | |
| 71 #ABCDEF #A #BCDEF | |
| 72 | |
| 73 edd Gnt6P Pyr GA3P | |
| 74 #ABCDEF #ABC #DEF | |
| 75 | |
| 76 // ta Ery4P Fru6P GA3P Sed7P | |
| 77 // #ABCD #abcdef #def #abcABCD | |
| 78 | |
| 79 // tk1 GA3P Sed7P Rib5P Rib5P | |
| 80 // #ABC #abcdefg #abABC #cdefg | |
| 81 | |
| 82 // tk2 GA3P Fru6P Rib5P Ery4P | |
| 83 // #ABC #abcdef #abABC #cdef | |
| 84 | |
| 85 ta GA3P Sed7P Ery4P Fru6P | |
| 86 #ABC #abcdefg #defg #abcABC | |
| 87 | |
| 88 tk1 Rib5P Rib5P GA3P Sed7P | |
| 89 #ABCDE #abcde #CDE #ABabcde | |
| 90 | |
| 91 tk2 Rib5P Ery4P GA3P Fru6P | |
| 92 #ABCDE #abcd #CDE #ABabcd | |
| 93 | |
| 94 | |
| 95 // Tricarboxylic Acid Cycle | |
| 96 | |
| 97 pdh Pyr AcCoA CO2 | |
| 98 #ABC #BC #A | |
| 99 | |
| 100 citsynth AcCoA OAA ICit | |
| 101 #AB #abcd #dcbaBA | |
| 102 | |
| 103 idh ICit AKG CO2 | |
| 104 #ABCDEF #ABCEF #D | |
| 105 | |
| 106 akgdh AKG Suc CO2 | |
| 107 #ABCDE #BCDE #A | |
| 108 | |
| 109 fum_a Suc Mal | |
| 110 #ABCD #ABCD | |
| 111 | |
| 112 fum_b Suc Mal | |
| 113 #ABCD #DCBA | |
| 114 | |
| 115 maldh Mal OAA | |
| 116 #ABCD #ABCD | |
| 117 | |
| 118 | |
| 119 // Glyoxylate Shunt | |
| 120 | |
| 121 // gs1 ICit GlyOx Suc | |
| 122 // #ABCDEF #AB #DCEF | |
| 123 | |
| 124 // gs2 GlyOx AcCoA OAA | |
| 125 // #AB #ab #ABba | |
| 126 | |
| 127 | |
| 128 // Anaplerotic Reactions | |
| 129 | |
| 130 ppc PEP CO2 OAA // PEPcarboxylase | |
| 131 #ABC #a #ABCa | |
| 132 | |
| 133 mae Mal Pyr CO2 // enzyme malique | |
| 134 #ABCD #ABC #D | |
| 135 | |
| 136 // pck OAA PEP CO2 // PEP carboxykinase | |
| 137 // #ABCD #ABC #D | |
| 138 | |
| 139 | |
| 140 // Biosynthetic Pathways | |
| 141 | |
| 142 // Glucose-6-Phosphate Family | |
| 143 | |
| 144 bs_glc6P Glc6P BM_Glc6P | |
| 145 #ABCDEF #ABCDEF | |
| 146 | |
| 147 // Fructose-6-Phosphate Family | |
| 148 | |
| 149 bs_fru6P Fru6P BM_Fru6P // sortie de Fru6P pour biomasse | |
| 150 #ABCDEF #ABCDEF | |
| 151 | |
| 152 // Phosphoglycerate Family | |
| 153 | |
| 154 bs_pga PGA BM_PGA | |
| 155 #ABC #ABC | |
| 156 | |
| 157 bs_pga_aux BM_PGA PGA_Aux | |
| 158 #ABC #ABC | |
| 159 | |
| 160 bs_pga1 BM_PGA Ser | |
| 161 #ABC #ABC | |
| 162 | |
| 163 bs_pga1_aux Ser Ser_Aux | |
| 164 #ABC #ABC | |
| 165 | |
| 166 bs_pga2 Ser Cys // ce flux sert de sortie pour PGA hors formation de Gly | |
| 167 #ABC #ABC | |
| 168 | |
| 169 bs_pga2_aux Cys Cys_Aux // ce flux sert de sortie pour PGA hors formation de Gly | |
| 170 #ABC #ABC | |
| 171 | |
| 172 bs_pga3 Ser Gly FTHF // formation de gly pour biomasse | |
| 173 #ABC #AB #C // ce flux est reversible | |
| 174 | |
| 175 bs_pga3_aux Gly Gly_Aux // pour conserver Gly comme metabolite intracellulaire | |
| 176 #AB #AB | |
| 177 | |
| 178 // TrioseP Family | |
| 179 | |
| 180 bs_DHAP GA3P Glp // formation glycerolP pour lipides | |
| 181 #ABC #ABC | |
| 182 | |
| 183 // Pyruvate Family | |
| 184 | |
| 185 bs_pyr Pyr BM_Pyr | |
| 186 #ABC #ABC | |
| 187 | |
| 188 bs_pyr1 BM_Pyr Ala | |
| 189 #ABC #ABC | |
| 190 | |
| 191 bs_pyr1_aux Ala Ala_Aux // pour conserver Ala comme metabolite intracellulaire | |
| 192 #ABC #ABC | |
| 193 | |
| 194 bs_pyr2 BM_Pyr BM_Pyr AKV CO2 // AKV et Val ont le meme squelette C | |
| 195 #ABC #abc #ABbcC #a // cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val | |
| 196 | |
| 197 bs_pyr4 AKV Val // permet de tenir compte de la sortie de Val | |
| 198 #ABCDE #ABCDE | |
| 199 | |
| 200 bs_pyr4_aux Val Val_Aux // permet de tenir compte de la sortie de Val | |
| 201 #ABCDE #ABCDE | |
| 202 | |
| 203 bs_pyr3 AKV BM_AcCoA Leu CO2 | |
| 204 #ABCDE #ab #abBCDE #A | |
| 205 | |
| 206 bs_pyr3_aux Leu Leu_Aux // pour conserver Leu comme metabolite intracellulaire | |
| 207 #ABCDEF #ABCDEF | |
| 208 | |
| 209 | |
| 210 // Erythrose-4-Phosphate Family | |
| 211 | |
| 212 bs_e4p Ery4P BM_Ery4P // pour utiliser les donnees sur Ery4P | |
| 213 #ABCD #ABCD | |
| 214 | |
| 215 // bs_e4p_aux BM_Ery4P Ery4P_aux // pour utiliser les donnees sur Ery4P | |
| 216 // #ABCD #ABCD | |
| 217 | |
| 218 | |
| 219 // Ribose-5-Phosphate Family | |
| 220 | |
| 221 bs_rib5p Rib5P BM_Rib5P // pour utiliser les donnees sur Rib5P | |
| 222 #ABCDE #ABCDE | |
| 223 | |
| 224 bs_rib5p1 BM_Rib5P FTHF His // pour utiliser les donnees sur Rib5P | |
| 225 #ABCDE #a #EDCBAa | |
| 226 | |
| 227 bs_rib5p1_aux His His_Aux // sortie pour conserver His comme metabolite intracellulaire | |
| 228 #ABCDEF #ABCDEF | |
| 229 | |
| 230 bs_rib5p2 BM_Rib5P Ri5P_Aux // sortie de Ri5P pour autres besoins que His | |
| 231 #ABCDE #ABCDE // ce flux est important pour ne pas imposer de fausses contraintes sur FTHF si on considerait His comme seule sortie | |
| 232 | |
| 233 | |
| 234 // Aromatic Amino Acids | |
| 235 | |
| 236 bs_pep PEP BM_PEP | |
| 237 #ABC #ABC | |
| 238 | |
| 239 bs_pep1 BM_PEP BM_Ery4P DAHP | |
| 240 #ABC #abcd #ABCabcd | |
| 241 | |
| 242 bs_pep2 BM_PEP DAHP Chor | |
| 243 #ABC #abcdefg #ABCabcdefg | |
| 244 | |
| 245 bs_pep3a Chor Phe CO2 | |
| 246 #ABCDEFGHIJ #ABCEFGHIJ #D | |
| 247 | |
| 248 bs_pep3b Chor Phe CO2 | |
| 249 #ABCDEFGHIJ #ABCEJIHGF #D | |
| 250 | |
| 251 bs_pep3_aux Phe Phe_Aux | |
| 252 #ABCEFGHIJ #ABCEFGHIJ | |
| 253 | |
| 254 bs_pep4a Chor Tyr CO2 | |
| 255 #ABCDEFGHIJ #ABCEFGHIJ #D | |
| 256 | |
| 257 bs_pep4b Chor Tyr CO2 | |
| 258 #ABCDEFGHIJ #ABCEJIHGF #D | |
| 259 | |
| 260 bs_pep4_aux Tyr Tyr_Aux | |
| 261 #ABCEFGHIJ #ABCEFGHIJ | |
| 262 | |
| 263 bs_pep5 BM_PEP PEP_Aux | |
| 264 #ABC #ABC | |
| 265 | |
| 266 bs_pep6 Chor BM_Rib5P Trp PyrCO2 | |
| 267 #ABCDEFGHIJ #abcde #edcbaJEFGHI #ABCD | |
| 268 | |
| 269 bs_pep6_aux Trp Trp_Aux | |
| 270 #ABCDEFGHIJK #ABCDEFGHIJK | |
| 271 | |
| 272 bs_pep7 PyrCO2 Pyr CO2 | |
| 273 #ABCD #ABC #D | |
| 274 | |
| 275 | |
| 276 // Acetyl-CoA | |
| 277 | |
| 278 bs_accoa AcCoA BM_AcCoA | |
| 279 #AB #AB | |
| 280 | |
| 281 bs_accoa_aux BM_AcCoA AcCoA_Aux | |
| 282 #AB #AB | |
| 283 | |
| 284 | |
| 285 // Alpha-Ketoglutarate Family | |
| 286 | |
| 287 bs_akg AKG BM_AKG // Les donnees sur Glu peuvent etre assimilee a AKG | |
| 288 #ABCDE #ABCDE | |
| 289 | |
| 290 bs_akg1 BM_AKG Glu // Les donnees sur Glu peuvent etre assimilee a AKG | |
| 291 #ABCDE #ABCDE | |
| 292 | |
| 293 bs_akg2 Glu Pro // Les donnees sur Glu peuvent etre assimilee a AKG | |
| 294 #ABCDE #ABCDE | |
| 295 | |
| 296 bs_akg3 Glu Gln // Les donnees sur Glu peuvent etre assimilee a AKG | |
| 297 #ABCDE #ABCDE | |
| 298 | |
| 299 bs_akg4 Glu CO2 Arg // Les donnees sur Glu peuvent etre assimilee a AKG | |
| 300 #ABCDE #a #ABCDEa | |
| 301 | |
| 302 bs_akg4_aux Arg Arg_Aux // Les donnees sur Glu peuvent etre assimilee a AKG | |
| 303 #ABCDEF #ABCDEF | |
| 304 | |
| 305 | |
| 306 // Oxaloacetate Family | |
| 307 | |
| 308 bs_oaa OAA BM_OAA | |
| 309 #ABCD #ABCD | |
| 310 | |
| 311 bs_oaa1 BM_OAA Asp | |
| 312 #ABCD #ABCD | |
| 313 | |
| 314 bs_oaa1_aux Asp Asp_Aux | |
| 315 #ABCD #ABCD | |
| 316 | |
| 317 bs_oaa2 Thr BM_Pyr Ile CO2 | |
| 318 #ABCD #abc #ABbCDc #a | |
| 319 | |
| 320 bs_oaa2_aux Ile Ile_Aux | |
| 321 #ABCDEF #ABCDEF | |
| 322 | |
| 323 bs_oaa3a BM_OAA BM_Pyr Lys CO2 | |
| 324 #ABCD #abc #ABCDcb #a | |
| 325 | |
| 326 bs_oaa3b BM_OAA BM_Pyr Lys CO2 | |
| 327 #ABCD #abc #abcDCB #A | |
| 328 | |
| 329 bs_oaa3_aux Lys Lys_Aux | |
| 330 #ABCDEF #ABCDEF | |
| 331 | |
| 332 bs_oaa4 BM_OAA OAA_Aux | |
| 333 #ABCD #ABCD | |
| 334 | |
| 335 bs_oaa5 BM_OAA Thr | |
| 336 #ABCD #ABCD | |
| 337 | |
| 338 bs_oaa5_aux Thr Thr_Aux | |
| 339 #ABCD #ABCD | |
| 340 | |
| 341 bs_oaa6 BM_OAA FTHF Met | |
| 342 #ABCD #a #ABCDa | |
| 343 | |
| 344 bs_oaa6_aux Met Met_Aux | |
| 345 #ABCDE #ABCDE | |
| 346 | |
| 347 bs_oaa7 BM_OAA Asn | |
| 348 #ABCD #ABCD | |
| 349 | |
| 350 bs_oaa7_aux Asn Asn_Aux | |
| 351 #ABCD #ABCD | |
| 352 | |
| 353 | |
| 354 // Flux de sortie | |
| 355 | |
| 356 out_co2 CO2 CO2_out // Sortie de CO2 | |
| 357 #A #A | |
| 358 | |
| 359 out_Ac AcCoA Acetate // Sortie d'acetate | |
| 360 #AB #AB | |
| 361 | |
| 362 out_FTHF FTHF FTHF_out | |
| 363 #A #A | |
| 364 | |
| 365 FLUXES | |
| 366 NET | |
| 367 NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) | |
| 368 | |
| 369 Glucupt_1 F 0.7 //0.807194 | |
| 370 Glucupt_U D | |
| 371 // CO2upt F 0.669589 | |
| 372 // FTHF0 F 0.00224836 | |
| 373 // FTHF1 F 0.001 | |
| 374 | |
| 375 pgi D | |
| 376 pfk D | |
| 377 ald D | |
| 378 // tpi D | |
| 379 pgk D | |
| 380 eno D | |
| 381 pyk F 1.4 | |
| 382 | |
| 383 zwf F 0.2 | |
| 384 gnd F 0.15062 | |
| 385 edd D | |
| 386 ta D | |
| 387 tk1 D | |
| 388 tk2 D | |
| 389 | |
| 390 pdh D | |
| 391 citsynth D | |
| 392 idh D | |
| 393 akgdh D | |
| 394 fum_a D | |
| 395 fum_b D | |
| 396 maldh D | |
| 397 | |
| 398 // gs1 C 0 | |
| 399 // gs2 D | |
| 400 | |
| 401 ppc D | |
| 402 mae D | |
| 403 // pck D | |
| 404 | |
| 405 // flux de biomasse | |
| 406 | |
| 407 bs_glc6P C 0.0109 // sortie de G6P | |
| 408 bs_fru6P C 0.0038 // sortie de F6P | |
| 409 bs_pga C 0.0791 // sortie de PGA pour formation de biomasse | |
| 410 bs_pga_aux D // sortie de PGA pour formation de biomasse | |
| 411 bs_pga1 D // conversion PGA donne ser | |
| 412 bs_pga1_aux C 0.0109 // conversion PGA donne ser | |
| 413 bs_pga2 D | |
| 414 bs_pga2_aux C 0.0046 // conversion PGA donne Cys | |
| 415 bs_pga3 D // reaction de synthese de Gly | |
| 416 bs_pga3_aux C 0.0308 // sortie de Gly | |
| 417 bs_DHAP C 0.0068 // formation de glycerolP pour lipides | |
| 418 bs_pyr C 0.1501 // avant : 0.1547 // sortie de Pyr pour formation de biomasse | |
| 419 bs_pyr1 D // formation d'Ala | |
| 420 bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Leu | |
| 421 bs_pyr2 D // synthese d'AKV. consomme 2 Pyr | |
| 422 bs_pyr4 D | |
| 423 bs_pyr4_aux C 0.0213 // sortie correspondant a l'utilisation de Val pour la biomasse | |
| 424 bs_pyr3 D // synthese de Leu (AKV+AcCoA consommes) | |
| 425 bs_pyr3_aux C 0.0227 // sortie de Leu | |
| 426 bs_e4p D // sortie d'Ery4p pour biomasse | |
| 427 // bs_e4p_aux C 0 // sortie d'Ery4p pour Trp | |
| 428 bs_rib5p C 0.0476 // synthese d'His | |
| 429 bs_rib5p1 D // synthese d'His | |
| 430 bs_rib5p1_aux C 0.0048 // sortie d'His | |
| 431 bs_rib5p2 D // sortie de Rib5P autre que His | |
| 432 bs_pep C 0.0381 // sortie de PEP | |
| 433 bs_pep1 D // sortie de PEP | |
| 434 bs_pep2 D | |
| 435 bs_pep3a D | |
| 436 bs_pep3b D | |
| 437 bs_pep3_aux C 0.0093 | |
| 438 bs_pep4a D | |
| 439 bs_pep4b D | |
| 440 bs_pep4_aux C 0.0069 | |
| 441 bs_pep5 C 0.0027 | |
| 442 bs_pep6 D | |
| 443 bs_pep6_aux D | |
| 444 bs_pep7 D | |
| 445 bs_accoa C 0.1565 // sortie d'AcCoA pour biomasse | |
| 446 bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu | |
| 447 bs_akg C 0.0571 // sortie d'AKG | |
| 448 bs_akg1 D | |
| 449 bs_akg2 C 0.0111 | |
| 450 bs_akg3 C 0.0132 | |
| 451 bs_akg4 D | |
| 452 bs_akg4_aux D | |
| 453 bs_oaa C 0.0947 // sortie d'OAA pour formation de biomasse | |
| 454 bs_oaa1 D // sortie d'OAA pour Asp | |
| 455 bs_oaa1_aux C 0.0121 // sortie d'Asp | |
| 456 bs_oaa2 D // synthese d'Ile | |
| 457 bs_oaa2_aux C 0.0146 // sortie d'Ile | |
| 458 bs_oaa3a D | |
| 459 bs_oaa3b D | |
| 460 bs_oaa3_aux C 0.0173 | |
| 461 bs_oaa4 D | |
| 462 bs_oaa5 D | |
| 463 bs_oaa5_aux C 0.0128 | |
| 464 bs_oaa6 D | |
| 465 bs_oaa6_aux C 0.0077 | |
| 466 bs_oaa7 D | |
| 467 bs_oaa7_aux C 0.0121 | |
| 468 | |
| 469 // Flux de sortie | |
| 470 | |
| 471 out_co2 D // sortie de CO2 | |
| 472 out_Ac F 0.213 // sortie d'acetate | |
| 473 out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF | |
| 474 | |
| 475 | |
| 476 XCH | |
| 477 NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) | |
| 478 | |
| 479 Glucupt_1 D | |
| 480 Glucupt_U D | |
| 481 // CO2upt D | |
| 482 // FTHF0 D | |
| 483 // FTHF1 D | |
| 484 | |
| 485 pgi C 0.752386 // 2011-02-22 ssg: was F => often unresolved with --irand option | |
| 486 pfk C 0 | |
| 487 ald F 0.413926 | |
| 488 // tpi F 0.5 | |
| 489 pgk C 0.984718 // 2011-02-22 ssg: was F => often unresolved with --irand option | |
| 490 eno F 0.800962 | |
| 491 pyk C 0.0109591 // 2010-10-01 ssg: was F => unresolved if co2 uptake is unlimited | |
| 492 | |
| 493 zwf C 0 | |
| 494 gnd C 0 | |
| 495 edd C 0 | |
| 496 ta F 0.359468 | |
| 497 tk1 F 0.166316 | |
| 498 tk2 F 2.11559e-03 | |
| 499 | |
| 500 pdh C 0.0322745 // 2010-10-02 ssg: was F, otherwise unsolvable in monte-carlo | |
| 501 citsynth C 0 | |
| 502 idh C 0 | |
| 503 akgdh C 0 | |
| 504 fum_a F 0.395958 | |
| 505 fum_b D | |
| 506 maldh C 0.647115 //********************************************** C pour analyse de sensibilite, F pour minimisation | |
| 507 | |
| 508 // gs1 C 0 | |
| 509 // gs2 C 0 | |
| 510 | |
| 511 ppc F 0.256772 | |
| 512 mae C 0 | |
| 513 // pck C 0 | |
| 514 | |
| 515 bs_glc6P D // sortie de G6P | |
| 516 bs_fru6P D // sortie de F6P | |
| 517 bs_pga C 0 // conversion PGA donne Ser | |
| 518 bs_pga_aux D // conversion PGA donne Ser | |
| 519 bs_pga1 C 0 // conversion PGA donne Ser | |
| 520 bs_pga1_aux D // conversion PGA donne Ser | |
| 521 bs_pga2 C 0 // ser donne Cys. correspond a la sortie de PGA pour biomasse autre que formation Gly | |
| 522 bs_pga2_aux D | |
| 523 bs_pga3 C 0.011799 // reaction de synthese de Gly. cette reaction est reversible | |
| 524 bs_pga3_aux D // sortie de Gly | |
| 525 bs_DHAP D // formation de glycerolP pour lipides | |
| 526 bs_pyr C 0 // formation d'Ala | |
| 527 bs_pyr1 C 0 // formation d'Ala | |
| 528 bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Ile | |
| 529 bs_pyr2 C 0 // synthese d'AKV. consomme 2 Pyr | |
| 530 bs_pyr4 C 0 | |
| 531 bs_pyr4_aux D // sortie correspondant a l'utilisation de Val pour la biomasse | |
| 532 bs_pyr3 C 0 // synthese de Leu (AKV+AcCoA consommes) | |
| 533 bs_pyr3_aux D // sortie de Leu | |
| 534 bs_e4p C 0 // sortie d'Ery4p | |
| 535 // bs_e4p_aux D // sortie d'Ery4p pour Trp | |
| 536 bs_rib5p C 0 // synthese d'His | |
| 537 bs_rib5p1 C 0 // synthese d'His | |
| 538 bs_rib5p1_aux D // sortie d'His | |
| 539 bs_rib5p2 D // sortie de Rib5P autre que His | |
| 540 bs_accoa C 0 // sortie d'AcCoA pour biomasse | |
| 541 bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu | |
| 542 bs_pep C 0 // sortie de PEP | |
| 543 bs_pep1 C 0 // sortie de PEP | |
| 544 bs_pep2 C 0 | |
| 545 bs_pep3a C 0 | |
| 546 bs_pep3b C 0 | |
| 547 bs_pep3_aux D | |
| 548 bs_pep4a C 0 | |
| 549 bs_pep4b C 0 | |
| 550 bs_pep4_aux D | |
| 551 bs_pep5 D | |
| 552 bs_pep6 C 0 | |
| 553 bs_pep6_aux D | |
| 554 bs_pep7 C 0 | |
| 555 bs_akg C 0 // sortie d'AKG | |
| 556 bs_akg1 C 0 | |
| 557 bs_akg2 D | |
| 558 bs_akg3 D | |
| 559 bs_akg4 C 0 | |
| 560 bs_akg4_aux D | |
| 561 bs_oaa C 0 | |
| 562 bs_oaa1 C 0 // sortie d'OAA autres que Met | |
| 563 bs_oaa1_aux D // sortie d'OAA autres que Met | |
| 564 bs_oaa2 C 0 // synthese de Met | |
| 565 bs_oaa2_aux D // sortie de Met | |
| 566 bs_oaa3a C 0 | |
| 567 bs_oaa3b C 0 | |
| 568 bs_oaa3_aux D | |
| 569 bs_oaa4 D | |
| 570 bs_oaa5 C 0 | |
| 571 bs_oaa5_aux D | |
| 572 bs_oaa6 C 0 | |
| 573 bs_oaa6_aux D | |
| 574 bs_oaa7 C 0 | |
| 575 bs_oaa7_aux D | |
| 576 | |
| 577 // Flux de sortie | |
| 578 | |
| 579 out_co2 D // sortie de CO2 | |
| 580 out_Ac D // sortie d'acetate | |
| 581 out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF | |
| 582 | |
| 583 | |
| 584 EQUALITIES | |
| 585 NET | |
| 586 VALUE FORMULA | |
| 587 | |
| 588 0 fum_a-fum_b // scrambling reaction | |
| 589 1 Glucupt_1+Glucupt_U | |
| 590 0 bs_oaa3a-bs_oaa3b | |
| 591 0 bs_pep3a-bs_pep3b | |
| 592 0 bs_pep4a-bs_pep4b | |
| 593 | |
| 594 XCH | |
| 595 VALUE FORMULA | |
| 596 | |
| 597 0 fum_a-fum_b | |
| 598 | |
| 599 INEQUALITIES | |
| 600 NET | |
| 601 VALUE COMP FORMULA | |
| 602 // Inequalities for Input and Output Fluxes are generated automatically | |
| 603 1 <= pyk | |
| 604 0.0001 <= edd | |
| 605 0.0001 <= gnd | |
| 606 0.0001 <= zwf | |
| 607 0.0001 <= ppc | |
| 608 0.0001 <= mae | |
| 609 // 2 >= CO2upt // 2010-08-18 too high value makes jacobian rank deficient | |
| 610 XCH | |
| 611 VALUE COMP FORMULA | |
| 612 // Inequalities for Input and Output Fluxes are generated automatically | |
| 613 METAB | |
| 614 VALUE COMP FORMULA | |
| 615 // 1.2 >= AKG | |
| 616 | |
| 617 | |
| 618 FLUX_MEASUREMENTS | |
| 619 FLUX_NAME VALUE DEVIATION // Val Dev | |
| 620 out_Ac 0.213 0.0001 | |
| 621 | |
| 622 LABEL_INPUT | |
| 623 META_NAME ISOTOPOMER VALUE | |
| 624 | |
| 625 Gluc_U #111111 1 | |
| 626 #000000 0. | |
| 627 Gluc_1 #100000 1. | |
| 628 #000000 0. | |
| 629 // CO2_ext #0 0.989 | |
| 630 // #1 0.011 | |
| 631 | |
| 632 // FTHF_0 #0 1 | |
| 633 // FTHF_1 #1 1 | |
| 634 | |
| 635 | |
| 636 LABEL_MEASUREMENTS | |
| 637 META_NAME CUM_GROUP VALUE DEVIATION CUM_CONSTRAINTS | |
| 638 // Example | |
| 639 | |
| 640 PEAK_MEASUREMENTS | |
| 641 META_NAME PEAK_NO VALUE_S VALUE_D- VALUE_D+ VALUE_DD VALUE_T DEVIATION_S DEVIATION_D- DEVIATION_D+ DEVIATION_DD/T | |
| 642 | |
| 643 | |
| 644 MASS_SPECTROMETRY | |
| 645 META_NAME FRAGMENT WEIGHT VALUE DEVIATION | |
| 646 | |
| 647 // Deviation fixee a 0.02 // correction inoc 0.062 | |
| 648 | |
| 649 | |
| 650 | |
| 651 Suc 1,2,3,4 1 0.371605319 0.01 | |
| 652 2 0.360829749 0.01 | |
| 653 3 0.208425325 0.01 | |
| 654 4 0.059139607 0.01 | |
| 655 // Mal 1,2,3,4 0 0.164619329483 0.02 | |
| 656 // 1 0.110072868518 0.02 | |
| 657 // 2 0.637801316225333 0.02 | |
| 658 // 3 0.0863461044204333 0.02 | |
| 659 // 4 0.00116038135315367 0.02 | |
| 660 ICit 1,2,3,4,5,6 0 0.131864539419667 0.02 | |
| 661 1 0.225857638569 0.02 | |
| 662 2 0.256421170949333 0.02 | |
| 663 3 0.209230210478667 0.02 | |
| 664 4 0.116863585449667 0.02 | |
| 665 5 0.0457727744643333 0.02 | |
| 666 6 0.0139900806697867 0.02 | |
| 667 PEP 1,2,3 0 0.421359839367667 0.01 | |
| 668 1 0.358998301162333 0.01 | |
| 669 2 0.0348521859365667 0.01 | |
| 670 3 0.184789673534 0.01 | |
| 671 PGA 1,2,3 0 0.434335785072667 0.01 | |
| 672 1 0.352829683224667 0.01 | |
| 673 2 0.0323479804176 0.01 | |
| 674 3 0.180486551285333 0.01 | |
| 675 FruBP 1,2,3,4,5,6 0 0.0738121029259333 0.01 | |
| 676 1 0.454450017158667 0.01 | |
| 677 2 0.160823529969333 0.01 | |
| 678 3 0.0944468077710667 0.01 | |
| 679 4 0.105281338489667 0.01 | |
| 680 5 0.0155016033633 0.01 | |
| 681 6 0.0956846003217333 0.01 | |
| 682 Glc6P 1,2,3,4,5,6 0 0.0160587173349 0.01 | |
| 683 1 0.673510772480667 0.01 | |
| 684 2 0.0930110047641 0.01 | |
| 685 3 0.0280359937297 0.01 | |
| 686 4 0.0397315614067667 0.01 | |
| 687 5 0.0145524520950667 0.01 | |
| 688 6 0.135099498189 0.01 | |
| 689 Fru6P 1,2,3,4,5,6 0 0.0235029951295 0.01 | |
| 690 1 0.624253565357667 0.01 | |
| 691 2 0.113068441282333 0.01 | |
| 692 3 0.0456605631765 0.01 | |
| 693 4 0.0516089447155667 0.01 | |
| 694 5 0.0185881765378333 0.01 | |
| 695 6 0.123317313800333 0.01 | |
| 696 Rib5P 1,2,3,4,5 0 0.341615670498667 0.01 | |
| 697 1 0.25454117519 0.01 | |
| 698 2 0.159027180368333 0.01 | |
| 699 3 0.113789577528667 0.01 | |
| 700 4 0.0615266612553333 0.01 | |
| 701 5 0.0694997351590667 0.01 | |
| 702 Gnt6P 1,2,3,4,5,6 0 0.0249552273874 0.01 | |
| 703 1 0.672556163913 0.01 | |
| 704 2 0.0866890773125333 0.01 | |
| 705 3 0.0313987199704333 0.01 | |
| 706 4 0.0314691889898667 0.01 | |
| 707 5 0.0138168327362333 0.01 | |
| 708 6 0.139114789690333 0.01 | |
| 709 // Ery4P 1,2,3,4 0 0.178453461108 0.01 | |
| 710 // 1 0.412398433968333 0.01 | |
| 711 // 2 0.273694508221667 0.01 | |
| 712 // 3 0.116142498670667 0.01 | |
| 713 // 4 0.0193110980315 0.01 | |
| 714 METABOLITE_POOLS | |
| 715 META_NAME META_SIZE | |
| 716 AKG -1 | |
| 717 AKV 1 | |
| 718 AcCoA 1 | |
| 719 Ala 1 | |
| 720 Arg 1 | |
| 721 Asn 1 | |
| 722 Asp 1 | |
| 723 BM_AKG 1 | |
| 724 BM_AcCoA 1 | |
| 725 BM_Ery4P 1 | |
| 726 BM_OAA 1 | |
| 727 BM_PEP 1 | |
| 728 BM_PGA 1 | |
| 729 BM_Pyr 1 | |
| 730 BM_Rib5P 1 | |
| 731 CO2 1 | |
| 732 Chor 1 | |
| 733 Cys 1 | |
| 734 DAHP 1 | |
| 735 Ery4P -1 | |
| 736 FTHF 1 | |
| 737 Fru6P -1 | |
| 738 FruBP -1 | |
| 739 GA3P -1 | |
| 740 Glc6P 1 | |
| 741 Glu 1 | |
| 742 Gly 1 | |
| 743 Gnt6P -1 | |
| 744 His 1 | |
| 745 ICit -1 | |
| 746 Ile 1 | |
| 747 Leu 1 | |
| 748 Lys 1 | |
| 749 Mal 1 | |
| 750 Met 1 | |
| 751 OAA -1 | |
| 752 PEP -1 | |
| 753 PGA -1 | |
| 754 Phe 1 | |
| 755 Pyr -1 | |
| 756 PyrCO2 1 | |
| 757 Rib5P -1 | |
| 758 Sed7P -1 | |
| 759 Ser 1 | |
| 760 Suc -1 | |
| 761 Thr 1 | |
| 762 Trp 1 | |
| 763 Tyr 1 | |
| 764 Val 1 | |
| 765 METAB_MEASUREMENTS | |
| 766 META_NAME VALUE DEVIATION | |
| 767 Fru6P 0.4263681348074568 0.01 | |
| 768 GA3P 0.469998855791378 0.01 | |
| 769 FruBP 1.860001398406723 0.01 | |
| 770 PEP 0.1099999780931608 0.01 | |
| 771 Rib5P 0.01933825682263468 0.01 | |
| 772 Sed7P 0.05727159999541005 0.01 | |
| 773 | |
| 774 OPTIONS | |
| 775 OPT_NAME OPT_VALUE | |
| 776 dt 1 | |
| 777 nsubdiv_dt 4 | |
| 778 //tmax 10 | |
| 779 file_labcin e_coli_msen.txt | |
| 780 commandArgs --noscale --TIMEIT --time_order=2 --zc=0 --clowp 1.e-9 | |
| 781 optctrl_errx 1.e-3 | |
| 782 optctrl_maxit 50 | |
| 783 optctrl_btmaxit 16 | |
| 784 optctrl_btstart 1 | |
| 785 optctrl_btfrac 0.5 | |
| 786 //optctrl_history 1 | |
| 787 optctrl_adaptbt 1 | |
| 788 optctrl_monotone 1 | |
| 789 posttreat_R plot_imass.R |