From 92ac3288ac7e0345aad3388b3577eac49693d36d Mon Sep 17 00:00:00 2001 From: Serguei Sokol Date: Thu, 23 Nov 2023 16:29:26 +0100 Subject: [PATCH 01/10] v7.0.1_1 Signed-off-by: Serguei Sokol --- tools/influx_si/README.rst | 12 +- tools/influx_si/influx_si.xml | 279 ++---- tools/influx_si/macros.xml | 321 +++++++ tools/influx_si/test-data/e_coli.ftbl | 720 --------------- tools/influx_si/test-data/e_coli.log | 38 - tools/influx_si/test-data/e_coli.zip | Bin 0 -> 5492 bytes .../test-data/e_coli_1-Glc_exact.ftbl | 713 --------------- .../test-data/e_coli_1-Glc_exact.log | 40 - .../test-data/e_coli_U-Glc_exact.ftbl | 711 --------------- tools/influx_si/test-data/e_coli_growth.ftbl | 822 ------------------ tools/influx_si/test-data/e_coli_growth.log | 45 - tools/influx_si/test-data/e_coli_i.ftbl | 789 ----------------- tools/influx_si/test-data/e_coli_i.log | 47 - tools/influx_si/test-data/e_coli_msen.txt | 62 -- 14 files changed, 382 insertions(+), 4217 deletions(-) create mode 100644 tools/influx_si/macros.xml delete mode 100755 tools/influx_si/test-data/e_coli.ftbl delete mode 100644 tools/influx_si/test-data/e_coli.log create mode 100644 tools/influx_si/test-data/e_coli.zip delete mode 100644 tools/influx_si/test-data/e_coli_1-Glc_exact.ftbl delete mode 100644 tools/influx_si/test-data/e_coli_1-Glc_exact.log delete mode 100644 tools/influx_si/test-data/e_coli_U-Glc_exact.ftbl delete mode 100644 tools/influx_si/test-data/e_coli_growth.ftbl delete mode 100644 tools/influx_si/test-data/e_coli_growth.log delete mode 100755 tools/influx_si/test-data/e_coli_i.ftbl delete mode 100644 tools/influx_si/test-data/e_coli_i.log delete mode 100644 tools/influx_si/test-data/e_coli_msen.txt diff --git a/tools/influx_si/README.rst b/tools/influx_si/README.rst index c610eaadd3..5d7726d76b 100644 --- a/tools/influx_si/README.rst +++ b/tools/influx_si/README.rst @@ -4,17 +4,17 @@ Metabolic flux estimation `influx_si` can be used for metabolic flux estimation based on labeling data from MS and/or NMR measurements. `influx_s` is used for stationary labeling and `influx_i` for instationary one (hence the '_s' and '_i' in the names). Tha name `influx_si` is used as common for both tools. -The input for `influx_si` in one or several FTBL files, each describing a given labeling experiment and options to use during estimation. In addition, for `influx_i` a file with time course data has to be provided for each FTBL file. +The input for `influx_si` in one or several MTF (Multiple Text Files) collections, each describing a given labeling experiment and options to use during estimation. -The output is a zip archive with files generated by `influx_si`. Among the most important is file ending with `_res.kvh` which contains the main information about estimated parameters, their statistics and so on. -If, in your FTBL file, you have requested ploting information, it can be found in respective .pdf file. +The output is a zip archive with files generated by `influx_si`. Among the most important are files ending with `.sim` (as 'simulated') which contains information about estimated parameters, their SD and so on. +If, in your .opt file, you have requested plotting information, it can be found in respective .pdf file. -For detailed documentation about `influx_si` and accompanying tools see https://metasys.insa-toulouse.fr/software/influx/doc/ +For detailed documentation about `influx_si` and accompanying tools see https://influx-si.readthedocs.io -For getting a standalone version of `influx_si` see https://metasys.insa-toulouse.fr/software/influx/ +For getting a standalone version of `influx_si` see https://anaconda.org/bioconda/influx_si Author: Serguei Sokol License: GPL2 -© INRAE 2020 +© INRAE/INSA/CNRS 2023 diff --git a/tools/influx_si/influx_si.xml b/tools/influx_si/influx_si.xml index 1158828d36..3e324c2b2f 100644 --- a/tools/influx_si/influx_si.xml +++ b/tools/influx_si/influx_si.xml @@ -1,232 +1,63 @@ - - metabolic flux analysis - - 5.1.0 - - - influx_si - - influx_s --version - + + Estimate metabolic fluxes and concentrations by fitting simulated labeling in metabolites to NMR/MS measurements + + + macros.xml + + + influx_si + + 'influx_${si.s_i}.stdout.txt' 2>'influx_${si.s_i}.stderr.txt'; res="\$?" && - - for f in *.ftbl *.log *.err *.R *.kvh *.attrs; do mv -f "\$f" "\$f".txt || true; done && - - for f in *.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done && + #for $inp in $input_main: + #set base = $inp.name[:-4] + --prefix "$base" + #end for + @MTF_OPT@ + > 'outdir/influx_${si.s_i}.stdout.txt' 2>'outdir/influx_${si.s_i}.stderr.txt'; - for f in *.RData; do [ -e "\$f" ] && mv -f "\$f" "\$f".RData || true; done && - [ "\$res" == "0" ] + #for $inp in $input_main: + #set base = $inp.name[:-4] + for f in "$base"_res/*.{err,log}; do mv -f "\$f" "\$f".txt || true; done; + for f in "$base"_res/*.{sim,stat}; do mv -f "\$f" "\$f".tsv || true; done; + for f in "$base"_res/*.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done; + rm -rf "$base"_res/tmp/; + mv "$base"_res/* outdir/; + #end for ]]> - - - - - - - - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @misc{githubinflux, - author = {Sokol, Serguei}, - year = {2020}, - title = {influx_s}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/sgsokol/influx}, - } - - 10.1093/bioinformatics/btr716 - + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tools/influx_si/macros.xml b/tools/influx_si/macros.xml new file mode 100644 index 0000000000..4998ded003 --- /dev/null +++ b/tools/influx_si/macros.xml @@ -0,0 +1,321 @@ + + + +.. class:: infomark + +**Authors** Serguei Sokol (sokol@insa-toulouse.fr) + +.. class:: infomark + +--------------------------------------------------- + + 7.0.1 + 1 + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + all scaling factors + are assumed to be 1 + --meth {BFGS,Nelder-Mead,nlsic,pso} + method for optimization, one of 'nlsic|BFGS|Nelder- + Mead|pso'. Default: 'nlsic'. Multiple occurrences of + this option can appear on command line. In this case, + specified minimization methods are applied + successively, e.g. '--meth pso --meth nlsic' means + that 'pso' will be used first, then 'nlsic' will take + over from the point where 'pso' ends. In case of + multiple methods, it is recommended to start with non- + gradient methods like 'pso' or 'Nelder-Mead' and make + them follow by gradient based methods like 'nlsic' or + 'BFGS'. If 'pso' or 'Nelder-Mead' are indeed used as + the first method, it is not recommended to combine + them with '--zc' option. + --fullsys calculate all cumomer set (not just the reduced one + necessary to simulate measurements) + --emu simulate labeling in EMU approach + --irand ignore initial approximation for free parameters (free + fluxes and metabolite concentrations) from the FTBL + file or from a dedicated file (cf --fseries and + --iseries option) and use random values drawn + uniformly from [0,1] interval + --sens SENS sensitivity method: SENS can be 'mc[=N]', mc stands + for Monte-Carlo. N is an optional number of Monte- + Carlo simulations. Default for N: 10 + --cupx CUPX upper limit for reverse fluxes. Must be in interval + [0, 1]. Default: 0.999 + --cupn CUPN absolute limit for net fluxes: -cupn <= netflux <= + cupn. Must be non negative. Value 0 means no limit. + Default: 1.e3 + --cupp CUPP upper limit for metabolite pool. Default: 1.e5 + --clownr CLOWNR lower limit for not reversible free and dependent + fluxes. Zero value (default) means no lower limit + --cinout CINOUT lower limit for input/output free and dependent + fluxes. Must be non negative. Default: 0 + --clowp CLOWP lower limit for free metabolite pools. Must be + positive. Default 1.e-8 + --np NP When integer >= 1, it is a number of parallel + subprocesses used in Monte-Carlo (MC) simulations or + for multiple FTBL inputs. When NP is a float number + between 0 and 1, it gives a fraction of available + cores (rounded to closest integer) to be used. Without + this option or for NP=0, all available cores in a + given node are used for MC simulations. + --ln Least norm solution is used for increments during the + non-linear iterations when Jacobian is rank deficient + --sln Least norm of the solution of linearized problem (and + not just of increments) is used when Jacobian is rank + deficient + --tikhreg Approximate least norm solution is used for increments + during the non-linear iterations when Jacobian is rank + deficient + --lim The same as --ln but with a function limSolve::lsei() + --zc ZC Apply zero crossing strategy with non negative + threshold for net fluxes + --ffguess Don't use free/dependent flux definitions from FTBL + file(s). Make an automatic guess. + --fseries FSERIES File name with free parameter values for multiple + starting points. Default: '' (empty, i.e. only one + starting point from the FTBL file is used) + --iseries ISERIES Indexes of starting points to use. Format: '1:10' -- + use only first ten starting points; '1,3' -- use the + the first and third starting points; '1:10,15,91:100' + -- a mix of both formats is allowed. Default: '' + (empty, i.e. all provided starting points are used) + --seed SEED Integer (preferably a prime integer) used for + reproducible random number generating. It makes + reproducible random starting points (--irand) but also + Monte-Carlo simulations for sensitivity analysis. + Default: none, i.e. current system value is used, so + random drawing will be varying at each run. + --excl_outliers [EXCL_OUTLIERS] + This option takes an optional argument, a p-value + between 0 and 1 which is used to filter out + measurement outliers. The filtering is based on Z + statistics calculated on reduced residual + distribution. Default: 0.01. + --nocalc generate an R code but not execute it. + --addnoise Add centered gaussian noise to simulated measurements + written to _res.kvh file. SD of this noise is taken + from FTBL file + --time_order {None,1,2,1,2} + Time order for ODE solving (1 (default), 2 or 1,2). + Order 2 is more precise but more time consuming. The + value '1,2' makes to start solving the ODE with the + first order scheme then continues with the order 2. + --version show program's version number and exit + --mtf MTF option passed to txt2ftbl. See help there. + --prefix PREFIX option passed to txt2ftbl. See help there. + --eprl EPRL option passed to txt2ftbl. See help there. + --force FORCE option passed to txt2ftbl. See help there. + -o OUT, --out OUT output directory. Default: basename of input file + without suffix + '_res'. If empty, no output directory + is created. In this case log and error messages are + directed to standard output/error channels. Non empty + OUT can be used when only one input file or MTF set is + given. + --copy_doc copy documentation directory in the current directory + and exit. If ./doc exists, its content is silently + overwritten. + --copy_test copy test directory in the current directory and exit. + If ./test exists, its content is silently overwritten. + --install_rdep install R dependencies and exit. + --TIMEIT developer option: measure cpu time or not + --prof developer option: do time profiling or not + --tblimit TBLIMIT developer option: set trace back limit for python + error messages + +]]> + + + + +@misc{githubinflux, + author = {Sokol, Serguei}, + year = {2023}, + title = {influx_s}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/sgsokol/influx}, +} + + 10.1093/bioinformatics/btr716 + + + diff --git a/tools/influx_si/test-data/e_coli.ftbl b/tools/influx_si/test-data/e_coli.ftbl deleted file mode 100755 index 51c8849eee..0000000000 --- a/tools/influx_si/test-data/e_coli.ftbl +++ /dev/null @@ -1,720 +0,0 @@ -PROJECT - NAME VERSION FORMAT DATE COMMENT - K12_MG1655.ftbl 1 101109 modele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees - -NETWORK - FLUX_NAME EDUCT_1 EDUCT_2 PRODUCT_1 PRODUCT_2 - -// Glycolyse. -// PPP -// TCA -// voies anaplerotiques: pepc. enz malique -// voie glyoxylate -// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre) -// saisie differentielle des substrats marques - - -//## Uptake substrats - - Glucupt_1 Gluc_1 Glc6P // fehlt bei wolfgang - #ABCDEF #ABCDEF // fehlt bei wolfgang - - Glucupt_U Gluc_U Glc6P // fehlt bei wolfgang - #ABCDEF #ABCDEF // fehlt bei wolfgang - -// CO2upt CO2_ext CO2 // entree de CO2 non marque -// #A #A // ce flux est a laisser libre - -// FTHF0 FTHF_0 FTHF // prise en charge de FTHF non marque -// #A #A - -// FTHF1 FTHF_1 FTHF // prise en charge de FTHF marque -// #a #a - - -//## Embden Meyerhof Parnas Pathway - - pgi Glc6P Fru6P - #ABCDEF #ABCDEF - - pfk Fru6P FruBP - #ABCDEF #ABCDEF - - ald FruBP GA3P GA3P - #ABCDEF #CBA #DEF - -// tpi DHAP GA3P -// #ABC #CBA - - pgk GA3P PGA - #ABC #ABC - - eno PGA PEP - #ABC #ABC - - pyk PEP Pyr - #ABC #ABC - - -//## Methylglyoxal Pathway - -// mgs DHAP Pyr -// #ABC #ABC - - -//## Pentose Phosphate Pathway - - zwf Glc6P Gnt6P - #ABCDEF #ABCDEF - - gnd Gnt6P CO2 Rib5P - #ABCDEF #A #BCDEF - - edd Gnt6P Pyr GA3P - #ABCDEF #ABC #DEF - -// ta Ery4P Fru6P GA3P Sed7P -// #ABCD #abcdef #def #abcABCD - -// tk1 GA3P Sed7P Rib5P Rib5P -// #ABC #abcdefg #abABC #cdefg - -// tk2 GA3P Fru6P Rib5P Ery4P -// #ABC #abcdef #abABC #cdef - - ta GA3P Sed7P Ery4P Fru6P - #ABC #abcdefg #defg #abcABC - - tk1 Rib5P Rib5P GA3P Sed7P - #ABCDE #abcde #CDE #ABabcde - - tk2 Rib5P Ery4P GA3P Fru6P - #ABCDE #abcd #CDE #ABabcd - - -//## Tricarboxylic Acid Cycle - - pdh Pyr AcCoA CO2 - #ABC #BC #A - - citsynth AcCoA OAA ICit - #AB #abcd #dcbaBA - - idh ICit AKG CO2 - #ABCDEF #ABCEF #D - - akgdh AKG Suc CO2 - #ABCDE #BCDE #A - - fum_a Suc Mal - #ABCD #ABCD - - fum_b Suc Mal - #ABCD #DCBA - - maldh Mal OAA - #ABCD #ABCD - - -//## Glyoxylate Shunt - -// gs1 ICit GlyOx Suc -// #ABCDEF #AB #DCEF - -// gs2 GlyOx AcCoA OAA -// #AB #ab #ABba - - -//## Anaplerotic Reactions - - ppc PEP CO2 OAA // PEPcarboxylase - #ABC #a #ABCa - - mae Mal Pyr CO2 // enzyme malique - #ABCD #ABC #D - -// pck OAA PEP CO2 // PEP carboxykinase -// #ABCD #ABC #D - - -//## Biosynthetic Pathways - - // Glucose-6-Phosphate Family - - bs_glc6P Glc6P BM_Glc6P - #ABCDEF #ABCDEF - - // Fructose-6-Phosphate Family - - bs_fru6P Fru6P BM_Fru6P // sortie de Fru6P pour biomasse - #ABCDEF #ABCDEF - - // Phosphoglycerate Family - - bs_pga PGA BM_PGA - #ABC #ABC - - bs_pga_aux BM_PGA PGA_Aux - #ABC #ABC - - bs_pga1 BM_PGA Ser - #ABC #ABC - - bs_pga1_aux Ser Ser_Aux - #ABC #ABC - - bs_pga2 Ser Cys // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga2_aux Cys Cys_Aux // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga3 Ser Gly FTHF // formation de gly pour biomasse - #ABC #AB #C // ce flux est reversible - - bs_pga3_aux Gly Gly_Aux // pour conserver Gly comme metabolite intracellulaire - #AB #AB - - // TrioseP Family - - bs_DHAP GA3P Glp // formation glycerolP pour lipides - #ABC #ABC - - // Pyruvate Family - - bs_pyr Pyr BM_Pyr - #ABC #ABC - - bs_pyr1 BM_Pyr Ala - #ABC #ABC - - bs_pyr1_aux Ala Ala_Aux // pour conserver Ala comme metabolite intracellulaire - #ABC #ABC - - bs_pyr2 BM_Pyr BM_Pyr AKV CO2 // AKV et Val ont le meme squelette C - #ABC #abc #ABbcC #a // cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val - - bs_pyr4 AKV Val // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr4_aux Val Val_Aux // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr3 AKV BM_AcCoA Leu CO2 - #ABCDE #ab #abBCDE #A - - bs_pyr3_aux Leu Leu_Aux // pour conserver Leu comme metabolite intracellulaire - #ABCDEF #ABCDEF - - - // Erythrose-4-Phosphate Family - - bs_e4p Ery4P BM_Ery4P // pour utiliser les donnees sur Ery4P - #ABCD #ABCD - -// bs_e4p_aux BM_Ery4P Ery4P_aux // pour utiliser les donnees sur Ery4P -// #ABCD #ABCD - - - // Ribose-5-Phosphate Family - - bs_rib5p Rib5P BM_Rib5P // pour utiliser les donnees sur Rib5P - #ABCDE #ABCDE - - bs_rib5p1 BM_Rib5P FTHF His // pour utiliser les donnees sur Rib5P - #ABCDE #a #EDCBAa - - bs_rib5p1_aux His His_Aux // sortie pour conserver His comme metabolite intracellulaire - #ABCDEF #ABCDEF - - bs_rib5p2 BM_Rib5P Ri5P_Aux // sortie de Ri5P pour autres besoins que His - #ABCDE #ABCDE // ce flux est important pour ne pas imposer de fausses contraintes sur FTHF si on considerait His comme seule sortie - - - // Aromatic Amino Acids - - bs_pep PEP BM_PEP - #ABC #ABC - - bs_pep1 BM_PEP BM_Ery4P DAHP - #ABC #abcd #ABCabcd - - bs_pep2 BM_PEP DAHP Chor - #ABC #abcdefg #ABCabcdefg - - bs_pep3a Chor Phe CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep3b Chor Phe CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep3_aux Phe Phe_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep4a Chor Tyr CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep4b Chor Tyr CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep4_aux Tyr Tyr_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep5 BM_PEP PEP_Aux - #ABC #ABC - - bs_pep6 Chor BM_Rib5P Trp PyrCO2 - #ABCDEFGHIJ #abcde #edcbaJEFGHI #ABCD - - bs_pep6_aux Trp Trp_Aux - #ABCDEFGHIJK #ABCDEFGHIJK - - bs_pep7 PyrCO2 Pyr CO2 - #ABCD #ABC #D - - - // Acetyl-CoA - - bs_accoa AcCoA BM_AcCoA - #AB #AB - - bs_accoa_aux BM_AcCoA AcCoA_Aux - #AB #AB - - - // Alpha-Ketoglutarate Family - - bs_akg AKG BM_AKG // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg1 BM_AKG Glu // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg2 Glu Pro // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg3 Glu Gln // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg4 Glu CO2 Arg // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #a #ABCDEa - - bs_akg4_aux Arg Arg_Aux // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDEF #ABCDEF - - - // Oxaloacetate Family - - bs_oaa OAA BM_OAA - #ABCD #ABCD - - bs_oaa1 BM_OAA Asp - #ABCD #ABCD - - bs_oaa1_aux Asp Asp_Aux - #ABCD #ABCD - - bs_oaa2 Thr BM_Pyr Ile CO2 - #ABCD #abc #ABbCDc #a - - bs_oaa2_aux Ile Ile_Aux - #ABCDEF #ABCDEF - - bs_oaa3a BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #ABCDcb #a - - bs_oaa3b BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #abcDCB #A - - bs_oaa3_aux Lys Lys_Aux - #ABCDEF #ABCDEF - - bs_oaa4 BM_OAA OAA_Aux - #ABCD #ABCD - - bs_oaa5 BM_OAA Thr - #ABCD #ABCD - - bs_oaa5_aux Thr Thr_Aux - #ABCD #ABCD - - bs_oaa6 BM_OAA FTHF Met - #ABCD #a #ABCDa - - bs_oaa6_aux Met Met_Aux - #ABCDE #ABCDE - - bs_oaa7 BM_OAA Asn - #ABCD #ABCD - - bs_oaa7_aux Asn Asn_Aux - #ABCD #ABCD - - -//## Flux de sortie - - out_co2 CO2 CO2_out // Sortie de CO2 - #A #A - - out_Ac AcCoA Acetate // Sortie d'acetate - #AB #AB - - out_FTHF FTHF FTHF_out - #A #A - -FLUXES - NET - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt_1 F 0.7 //0.807194 - Glucupt_U D -// CO2upt F 0.669589 -// FTHF0 F 0.00224836 -// FTHF1 F 0.001 - - pgi D - pfk D - ald D -// tpi D - pgk D - eno D - pyk F 1.4 - - zwf F 0.2 - gnd F 0.15062 - edd D - ta D - tk1 D - tk2 D - - pdh D - citsynth D - idh D - akgdh D - fum_a D - fum_b D - maldh D - -// gs1 C 0 -// gs2 D - - ppc D - mae D -// pck D - - // flux de biomasse - - bs_glc6P C 0.0109 // sortie de G6P - bs_fru6P C 0.0038 // sortie de F6P - bs_pga C 0.0791 // sortie de PGA pour formation de biomasse - bs_pga_aux D // sortie de PGA pour formation de biomasse - bs_pga1 D // conversion PGA donne ser - bs_pga1_aux C 0.0109 // conversion PGA donne ser - bs_pga2 D - bs_pga2_aux C 0.0046 // conversion PGA donne Cys - bs_pga3 D // reaction de synthese de Gly - bs_pga3_aux C 0.0308 // sortie de Gly - bs_DHAP C 0.0068 // formation de glycerolP pour lipides - bs_pyr C 0.1501 // avant : 0.1547 // sortie de Pyr pour formation de biomasse - bs_pyr1 D // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Leu - bs_pyr2 D // synthese d'AKV. consomme 2 Pyr - bs_pyr4 D - bs_pyr4_aux C 0.0213 // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 D // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux C 0.0227 // sortie de Leu - bs_e4p D // sortie d'Ery4p pour biomasse -// bs_e4p_aux C 0 // sortie d'Ery4p pour Trp - bs_rib5p C 0.0476 // synthese d'His - bs_rib5p1 D // synthese d'His - bs_rib5p1_aux C 0.0048 // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_pep C 0.0381 // sortie de PEP - bs_pep1 D // sortie de PEP - bs_pep2 D - bs_pep3a D - bs_pep3b D - bs_pep3_aux C 0.0093 - bs_pep4a D - bs_pep4b D - bs_pep4_aux C 0.0069 - bs_pep5 C 0.0027 - bs_pep6 D - bs_pep6_aux D - bs_pep7 D - bs_accoa C 0.1565 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_akg C 0.0571 // sortie d'AKG - bs_akg1 D - bs_akg2 C 0.0111 - bs_akg3 C 0.0132 - bs_akg4 D - bs_akg4_aux D - bs_oaa C 0.0947 // sortie d'OAA pour formation de biomasse - bs_oaa1 D // sortie d'OAA pour Asp - bs_oaa1_aux C 0.0121 // sortie d'Asp - bs_oaa2 D // synthese d'Ile - bs_oaa2_aux C 0.0146 // sortie d'Ile - bs_oaa3a D - bs_oaa3b D - bs_oaa3_aux C 0.0173 - bs_oaa4 D - bs_oaa5 D - bs_oaa5_aux C 0.0128 - bs_oaa6 D - bs_oaa6_aux C 0.0077 - bs_oaa7 D - bs_oaa7_aux C 0.0121 - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac F 0.213 // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - - XCH - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt_1 D - Glucupt_U D -// CO2upt D -// FTHF0 D -// FTHF1 D - - pgi C 0.752386 // 2011-02-22 ssg: was F => often unresolved with --irand option - pfk C 0 - ald F 0.413926 -// tpi F 0.5 - pgk C 0.984718 // 2011-02-22 ssg: was F => often unresolved with --irand option - eno F 0.800962 - pyk C 0.0109591 // 2010-10-01 ssg: was F => unresolved if co2 uptake is unlimited - - zwf C 0 - gnd C 0 - edd C 0 - ta F 0.359468 - tk1 F 0.166316 - tk2 F 2.11559e-03 - - pdh C 0.0322745 // 2010-10-02 ssg: was F, otherwise unsolvable in monte-carlo - citsynth C 0 - idh C 0 - akgdh C 0 - fum_a F 0.395958 - fum_b D - maldh C 0.647115 //********************************************** C pour analyse de sensibilite, F pour minimisation - -// gs1 C 0 -// gs2 C 0 - - ppc F 0.256772 - mae C 0 -// pck C 0 - - bs_glc6P D // sortie de G6P - bs_fru6P D // sortie de F6P - bs_pga C 0 // conversion PGA donne Ser - bs_pga_aux D // conversion PGA donne Ser - bs_pga1 C 0 // conversion PGA donne Ser - bs_pga1_aux D // conversion PGA donne Ser - bs_pga2 C 0 // ser donne Cys. correspond a la sortie de PGA pour biomasse autre que formation Gly - bs_pga2_aux D - bs_pga3 C 0.011799 // reaction de synthese de Gly. cette reaction est reversible - bs_pga3_aux D // sortie de Gly - bs_DHAP D // formation de glycerolP pour lipides - bs_pyr C 0 // formation d'Ala - bs_pyr1 C 0 // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Ile - bs_pyr2 C 0 // synthese d'AKV. consomme 2 Pyr - bs_pyr4 C 0 - bs_pyr4_aux D // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 C 0 // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux D // sortie de Leu - bs_e4p C 0 // sortie d'Ery4p -// bs_e4p_aux D // sortie d'Ery4p pour Trp - bs_rib5p C 0 // synthese d'His - bs_rib5p1 C 0 // synthese d'His - bs_rib5p1_aux D // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_accoa C 0 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_pep C 0 // sortie de PEP - bs_pep1 C 0 // sortie de PEP - bs_pep2 C 0 - bs_pep3a C 0 - bs_pep3b C 0 - bs_pep3_aux D - bs_pep4a C 0 - bs_pep4b C 0 - bs_pep4_aux D - bs_pep5 D - bs_pep6 C 0 - bs_pep6_aux D - bs_pep7 C 0 - bs_akg C 0 // sortie d'AKG - bs_akg1 C 0 - bs_akg2 D - bs_akg3 D - bs_akg4 C 0 - bs_akg4_aux D - bs_oaa C 0 - bs_oaa1 C 0 // sortie d'OAA autres que Met - bs_oaa1_aux D // sortie d'OAA autres que Met - bs_oaa2 C 0 // synthese de Met - bs_oaa2_aux D // sortie de Met - bs_oaa3a C 0 - bs_oaa3b C 0 - bs_oaa3_aux D - bs_oaa4 D - bs_oaa5 C 0 - bs_oaa5_aux D - bs_oaa6 C 0 - bs_oaa6_aux D - bs_oaa7 C 0 - bs_oaa7_aux D - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac D // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - -EQUALITIES - NET - VALUE FORMULA - - 0 fum_a-fum_b // scrambling reaction - 1 Glucupt_1+Glucupt_U - 0 bs_oaa3a-bs_oaa3b - 0 bs_pep3a-bs_pep3b - 0 bs_pep4a-bs_pep4b - - XCH - VALUE FORMULA - - 0 fum_a-fum_b - -INEQUALITIES - NET - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - 1 <= pyk - 0.0001 <= edd - 0.0001 <= gnd - 0.0001 <= zwf - 0.0001 <= ppc - 0.0001 <= mae -// 2 >= CO2upt // 2010-08-18 too high value makes jacobian rank deficient - XCH - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - - -FLUX_MEASUREMENTS - FLUX_NAME VALUE DEVIATION // Val Dev - out_Ac 0.213 0.0001 - -LABEL_INPUT - META_NAME ISOTOPOMER VALUE - - Gluc_U #111111 1 - #000000 0. - Gluc_1 #100000 1. - #000000 0. -// CO2_ext #0 0.989 -// #1 0.011 - -// FTHF_0 #0 1 -// FTHF_1 #1 1 - - -LABEL_MEASUREMENTS - META_NAME CUM_GROUP VALUE DEVIATION CUM_CONSTRAINTS - // Example - -PEAK_MEASUREMENTS - META_NAME PEAK_NO VALUE_S VALUE_D- VALUE_D+ VALUE_DD VALUE_T DEVIATION_S DEVIATION_D- DEVIATION_D+ DEVIATION_DD/T - - -MASS_SPECTROMETRY - META_NAME FRAGMENT WEIGHT VALUE DEVIATION - -// Deviation fixee a 0.02 // correction inoc 0.062 - - - - Suc 1,2,3,4 1 0.371605319 0.01 - 2 0.360829749 0.01 - 3 0.208425325 0.01 - 4 0.059139607 0.01 -// Mal 1,2,3,4 0 0.164619329483 0.02 -// 1 0.110072868518 0.02 -// 2 0.637801316225333 0.02 -// 3 0.0863461044204333 0.02 -// 4 0.00116038135315367 0.02 - ICit 1,2,3,4,5,6 0 0.131864539419667 0.02 - 1 0.225857638569 0.02 - 2 0.256421170949333 0.02 - 3 0.209230210478667 0.02 - 4 0.116863585449667 0.02 - 5 0.0457727744643333 0.02 - 6 0.0139900806697867 0.02 - PEP 1,2,3 0 0.421359839367667 0.01 - 1 0.358998301162333 0.01 - 2 0.0348521859365667 0.01 - 3 0.184789673534 0.01 - PGA 1,2,3 0 0.434335785072667 0.01 - 1 0.352829683224667 0.01 - 2 0.0323479804176 0.01 - 3 0.180486551285333 0.01 - FruBP 1,2,3,4,5,6 0 0.0738121029259333 0.01 - 1 0.454450017158667 0.01 - 2 0.160823529969333 0.01 - 3 0.0944468077710667 0.01 - 4 0.105281338489667 0.01 - 5 0.0155016033633 0.01 - 6 0.0956846003217333 0.01 - Glc6P 1,2,3,4,5,6 0 0.0160587173349 0.01 - 1 0.673510772480667 0.01 - 2 0.0930110047641 0.01 - 3 0.0280359937297 0.01 - 4 0.0397315614067667 0.01 - 5 0.0145524520950667 0.01 - 6 0.135099498189 0.01 - Fru6P 1,2,3,4,5,6 0 0.0235029951295 0.01 - 1 0.624253565357667 0.01 - 2 0.113068441282333 0.01 - 3 0.0456605631765 0.01 - 4 0.0516089447155667 0.01 - 5 0.0185881765378333 0.01 - 6 0.123317313800333 0.01 - Rib5P 1,2,3,4,5 0 0.341615670498667 0.01 - 1 0.25454117519 0.01 - 2 0.159027180368333 0.01 - 3 0.113789577528667 0.01 - 4 0.0615266612553333 0.01 - 5 0.0694997351590667 0.01 - Gnt6P 1,2,3,4,5,6 0 0.0249552273874 0.01 - 1 0.672556163913 0.01 - 2 0.0866890773125333 0.01 - 3 0.0313987199704333 0.01 - 4 0.0314691889898667 0.01 - 5 0.0138168327362333 0.01 - 6 0.139114789690333 0.01 -// Ery4P 1,2,3,4 0 0.178453461108 0.01 -// 1 0.412398433968333 0.01 -// 2 0.273694508221667 0.01 -// 3 0.116142498670667 0.01 -// 4 0.0193110980315 0.01 - -OPTIONS - OPT_NAME OPT_VALUE - //MATLAB_FOR_FLUX_EQ_CONSTR_MATR 1 - //optctrl_history 1 // nlsic - //optctrl_trace 3 // BFGS - //optctrl_reltol 1.e-10 // BFGS - //optctrl_maxit 1000 // BFGS - commandArgs --TIMEIT - posttreat_R plot_smeas.R diff --git a/tools/influx_si/test-data/e_coli.log b/tools/influx_si/test-data/e_coli.log deleted file mode 100644 index daea5e4255..0000000000 --- a/tools/influx_si/test-data/e_coli.log +++ /dev/null @@ -1,38 +0,0 @@ -"/home/sokol/miniconda3/envs/__influx_si@5.0.3/bin/influx_s" "e_coli.ftbl" -code gen: 2020-03-26 18:33:45 -executing: "/usr/local/miniconda3/envs/__influx_si@5.0.3/bin/python3.8" "/home/STORAGE/local/miniconda3/envs/__influx_si@5.0.3/bin/ftbl2optR.py" "--tblimit" "0" "--ropts" "TIMEIT=TRUE" "e_coli.ftbl" -executing: R --vanilla --slave < e_coli.R -calcul : 2020-03-26 18:33:49 -load : 2020-03-26 18:33:51.07 cpu=1.016 -rinit : 2020-03-26 18:33:51.07 cpu=1.018 -r_flux : 2020-03-26 18:33:51.07 cpu=1.018 -Afl qr(): 2020-03-26 18:33:51.14 cpu=1.083 -dfl_dffg: 2020-03-26 18:33:51.20 cpu=1.123 -spAbr : 2020-03-26 18:33:51.20 cpu=1.125 -weight 1: 2020-03-26 18:33:51.20 cpu=1.125 -weight 2: 2020-03-26 18:33:51.44 cpu=1.191 -weight 3: 2020-03-26 18:33:51.59 cpu=1.258 -weight 4: 2020-03-26 18:33:51.65 cpu=1.311 -weight 5: 2020-03-26 18:33:51.67 cpu=1.338 -weight 6: 2020-03-26 18:33:51.68 cpu=1.348 -measure : 2020-03-26 18:33:51.80 cpu=1.435 -ineq : 2020-03-26 18:33:51.94 cpu=1.515 -preopt : 2020-03-26 18:33:52.02 cpu=1.595 -labargs : 2020-03-26 18:33:52.04 cpu=1.618 -run 1: 2020-03-26 18:33:56.49 cpu=4.72 -Starting point -res esti: 2020-03-26 18:33:56.50 cpu=4.722 -kvh init: 2020-03-26 18:33:56.52 cpu=4.742 -check ja: 2020-03-26 18:33:56.57 cpu=4.763 -optim : 2020-03-26 18:33:56.66 cpu=4.814 -it=0 res=33.60668 -it=1 res=8.537147 normstep=0.372971 btk=1 -it=2 res=7.844899 normstep=0.1372184 btk=1 -it=3 res=7.843106 normstep=0.005504594 btk=1 -it=4 res=7.843096 normstep=0.0004985717 btk=1 -it=5 res=7.843096 normstep=2.725573e-05 btk=1 -it=6 res=7.843096 normstep=3.688583e-06 btk=1 -postopt : 2020-03-26 18:33:57.15 cpu=5.321 -linstats: 2020-03-26 18:33:57.38 cpu=5.528 -rend : 2020-03-26 18:33:57.76 cpu=5.753 -end : 2020-03-26 18:33:58 diff --git a/tools/influx_si/test-data/e_coli.zip b/tools/influx_si/test-data/e_coli.zip new file mode 100644 index 0000000000000000000000000000000000000000..b09a4cde2b466550d41f4fa97048c20d975a61c9 GIT binary 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deleted file mode 100644 index b3fbbd04d1..0000000000 --- a/tools/influx_si/test-data/e_coli_1-Glc_exact.ftbl +++ /dev/null @@ -1,713 +0,0 @@ -PROJECT - NAME VERSION FORMAT DATE COMMENT - K12_MG1655.ftbl 1 101109 modele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees - -NETWORK - FLUX_NAME EDUCT_1 EDUCT_2 PRODUCT_1 PRODUCT_2 - -// Glycolyse. -// PPP -// TCA -// voies anaplerotiques: pepc. enz malique -// voie glyoxylate -// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre) -// saisie differentielle des substrats marques - - -// Uptake substrats - - Glucupt Gluc Glc6P - #ABCDEF #ABCDEF -// CO2upt CO2_ext CO2 // entree de CO2 non marque -// #A #A // ce flux est a laisser libre - -// FTHF0 FTHF_0 FTHF // prise en charge de FTHF non marque -// #A #A - -// FTHF1 FTHF_1 FTHF // prise en charge de FTHF marque -// #a #a - - -// Embden Meyerhof Parnas Pathway - - pgi Glc6P Fru6P - #ABCDEF #ABCDEF - - pfk Fru6P FruBP - #ABCDEF #ABCDEF - - ald FruBP GA3P GA3P - #ABCDEF #CBA #DEF - -// tpi DHAP GA3P -// #ABC #CBA - - pgk GA3P PGA - #ABC #ABC - - eno PGA PEP - #ABC #ABC - - pyk PEP Pyr - #ABC #ABC - - -// Methylglyoxal Pathway - -// mgs DHAP Pyr -// #ABC #ABC - - -// Pentose Phosphate Pathway - - zwf Glc6P Gnt6P - #ABCDEF #ABCDEF - - gnd Gnt6P CO2 Rib5P - #ABCDEF #A #BCDEF - - edd Gnt6P Pyr GA3P - #ABCDEF #ABC #DEF - -// ta Ery4P Fru6P GA3P Sed7P -// #ABCD #abcdef #def #abcABCD - -// tk1 GA3P Sed7P Rib5P Rib5P -// #ABC #abcdefg #abABC #cdefg - -// tk2 GA3P Fru6P Rib5P Ery4P -// #ABC #abcdef #abABC #cdef - - ta GA3P Sed7P Ery4P Fru6P - #ABC #abcdefg #defg #abcABC - - tk1 Rib5P Rib5P GA3P Sed7P - #ABCDE #abcde #CDE #ABabcde - - tk2 Rib5P Ery4P GA3P Fru6P - #ABCDE #abcd #CDE #ABabcd - - -// Tricarboxylic Acid Cycle - - pdh Pyr AcCoA CO2 - #ABC #BC #A - - citsynth AcCoA OAA ICit - #AB #abcd #dcbaBA - - idh ICit AKG CO2 - #ABCDEF #ABCEF #D - - akgdh AKG Suc CO2 - #ABCDE #BCDE #A - - fum_a Suc Mal - #ABCD #ABCD - - fum_b Suc Mal - #ABCD #DCBA - - maldh Mal OAA - #ABCD #ABCD - - -// Glyoxylate Shunt - -// gs1 ICit GlyOx Suc -// #ABCDEF #AB #DCEF - -// gs2 GlyOx AcCoA OAA -// #AB #ab #ABba - - -// Anaplerotic Reactions - - ppc PEP CO2 OAA // PEPcarboxylase - #ABC #a #ABCa - - mae Mal Pyr CO2 // enzyme malique - #ABCD #ABC #D - -// pck OAA PEP CO2 // PEP carboxykinase -// #ABCD #ABC #D - - -// Biosynthetic Pathways - - // Glucose-6-Phosphate Family - - bs_glc6P Glc6P BM_Glc6P - #ABCDEF #ABCDEF - - // Fructose-6-Phosphate Family - - bs_fru6P Fru6P BM_Fru6P // sortie de Fru6P pour biomasse - #ABCDEF #ABCDEF - - // Phosphoglycerate Family - - bs_pga PGA BM_PGA - #ABC #ABC - - bs_pga_aux BM_PGA PGA_Aux - #ABC #ABC - - bs_pga1 BM_PGA Ser - #ABC #ABC - - bs_pga1_aux Ser Ser_Aux - #ABC #ABC - - bs_pga2 Ser Cys // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga2_aux Cys Cys_Aux // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga3 Ser Gly FTHF // formation de gly pour biomasse - #ABC #AB #C // ce flux est reversible - - bs_pga3_aux Gly Gly_Aux // pour conserver Gly comme metabolite intracellulaire - #AB #AB - - // TrioseP Family - - bs_DHAP GA3P Glp // formation glycerolP pour lipides - #ABC #ABC - - // Pyruvate Family - - bs_pyr Pyr BM_Pyr - #ABC #ABC - - bs_pyr1 BM_Pyr Ala - #ABC #ABC - - bs_pyr1_aux Ala Ala_Aux // pour conserver Ala comme metabolite intracellulaire - #ABC #ABC - - bs_pyr2 BM_Pyr BM_Pyr AKV CO2 // AKV et Val ont le meme squelette C - #ABC #abc #ABbcC #a // cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val - - bs_pyr4 AKV Val // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr4_aux Val Val_Aux // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr3 AKV BM_AcCoA Leu CO2 - #ABCDE #ab #abBCDE #A - - bs_pyr3_aux Leu Leu_Aux // pour conserver Leu comme metabolite intracellulaire - #ABCDEF #ABCDEF - - - // Erythrose-4-Phosphate Family - - bs_e4p Ery4P BM_Ery4P // pour utiliser les donnees sur Ery4P - #ABCD #ABCD - -// bs_e4p_aux BM_Ery4P Ery4P_aux // pour utiliser les donnees sur Ery4P -// #ABCD #ABCD - - - // Ribose-5-Phosphate Family - - bs_rib5p Rib5P BM_Rib5P // pour utiliser les donnees sur Rib5P - #ABCDE #ABCDE - - bs_rib5p1 BM_Rib5P FTHF His // pour utiliser les donnees sur Rib5P - #ABCDE #a #EDCBAa - - bs_rib5p1_aux His His_Aux // sortie pour conserver His comme metabolite intracellulaire - #ABCDEF #ABCDEF - - bs_rib5p2 BM_Rib5P Ri5P_Aux // sortie de Ri5P pour autres besoins que His - #ABCDE #ABCDE // ce flux est important pour ne pas imposer de fausses contraintes sur FTHF si on considerait His comme seule sortie - - - // Aromatic Amino Acids - - bs_pep PEP BM_PEP - #ABC #ABC - - bs_pep1 BM_PEP BM_Ery4P DAHP - #ABC #abcd #ABCabcd - - bs_pep2 BM_PEP DAHP Chor - #ABC #abcdefg #ABCabcdefg - - bs_pep3a Chor Phe CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep3b Chor Phe CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep3_aux Phe Phe_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep4a Chor Tyr CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep4b Chor Tyr CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep4_aux Tyr Tyr_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep5 BM_PEP PEP_Aux - #ABC #ABC - - bs_pep6 Chor BM_Rib5P Trp PyrCO2 - #ABCDEFGHIJ #abcde #edcbaJEFGHI #ABCD - - bs_pep6_aux Trp Trp_Aux - #ABCDEFGHIJK #ABCDEFGHIJK - - bs_pep7 PyrCO2 Pyr CO2 - #ABCD #ABC #D - - - // Acetyl-CoA - - bs_accoa AcCoA BM_AcCoA - #AB #AB - - bs_accoa_aux BM_AcCoA AcCoA_Aux - #AB #AB - - - // Alpha-Ketoglutarate Family - - bs_akg AKG BM_AKG // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg1 BM_AKG Glu // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg2 Glu Pro // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg3 Glu Gln // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg4 Glu CO2 Arg // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #a #ABCDEa - - bs_akg4_aux Arg Arg_Aux // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDEF #ABCDEF - - - // Oxaloacetate Family - - bs_oaa OAA BM_OAA - #ABCD #ABCD - - bs_oaa1 BM_OAA Asp - #ABCD #ABCD - - bs_oaa1_aux Asp Asp_Aux - #ABCD #ABCD - - bs_oaa2 Thr BM_Pyr Ile CO2 - #ABCD #abc #ABbCDc #a - - bs_oaa2_aux Ile Ile_Aux - #ABCDEF #ABCDEF - - bs_oaa3a BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #ABCDcb #a - - bs_oaa3b BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #abcDCB #A - - bs_oaa3_aux Lys Lys_Aux - #ABCDEF #ABCDEF - - bs_oaa4 BM_OAA OAA_Aux - #ABCD #ABCD - - bs_oaa5 BM_OAA Thr - #ABCD #ABCD - - bs_oaa5_aux Thr Thr_Aux - #ABCD #ABCD - - bs_oaa6 BM_OAA FTHF Met - #ABCD #a #ABCDa - - bs_oaa6_aux Met Met_Aux - #ABCDE #ABCDE - - bs_oaa7 BM_OAA Asn - #ABCD #ABCD - - bs_oaa7_aux Asn Asn_Aux - #ABCD #ABCD - - -// Flux de sortie - - out_co2 CO2 CO2_out // Sortie de CO2 - #A #A - - out_Ac AcCoA Acetate // Sortie d'acetate - #AB #AB - - out_FTHF FTHF FTHF_out - #A #A - -FLUXES - NET - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt C 1 -// CO2upt F 0.669589 -// FTHF0 F 0.00224836 -// FTHF1 F 0.001 - - pgi D - pfk D - ald D -// tpi D - pgk D - eno D - pyk F 1.54425507 - - zwf F 0.14233479 - gnd F 0.14223479 - edd D - ta D - tk1 D - tk2 D - - pdh D - citsynth D - idh D - akgdh D - fum_a D - fum_b D - maldh D - -// gs1 C 0 -// gs2 D - - ppc D - mae D -// pck D - - // flux de biomasse - - bs_glc6P C 0.0109 // sortie de G6P - bs_fru6P C 0.0038 // sortie de F6P - bs_pga C 0.0791 // sortie de PGA pour formation de biomasse - bs_pga_aux D // sortie de PGA pour formation de biomasse - bs_pga1 D // conversion PGA donne ser - bs_pga1_aux C 0.0109 // conversion PGA donne ser - bs_pga2 D - bs_pga2_aux C 0.0046 // conversion PGA donne Cys - bs_pga3 D // reaction de synthese de Gly - bs_pga3_aux C 0.0308 // sortie de Gly - bs_DHAP C 0.0068 // formation de glycerolP pour lipides - bs_pyr C 0.1501 // avant : 0.1547 // sortie de Pyr pour formation de biomasse - bs_pyr1 D // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Leu - bs_pyr2 D // synthese d'AKV. consomme 2 Pyr - bs_pyr4 D - bs_pyr4_aux C 0.0213 // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 D // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux C 0.0227 // sortie de Leu - bs_e4p D // sortie d'Ery4p pour biomasse -// bs_e4p_aux C 0 // sortie d'Ery4p pour Trp - bs_rib5p C 0.0476 // synthese d'His - bs_rib5p1 D // synthese d'His - bs_rib5p1_aux C 0.0048 // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_pep C 0.0381 // sortie de PEP - bs_pep1 D // sortie de PEP - bs_pep2 D - bs_pep3a D - bs_pep3b D - bs_pep3_aux C 0.0093 - bs_pep4a D - bs_pep4b D - bs_pep4_aux C 0.0069 - bs_pep5 C 0.0027 - bs_pep6 D - bs_pep6_aux D - bs_pep7 D - bs_accoa C 0.1565 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_akg C 0.0571 // sortie d'AKG - bs_akg1 D - bs_akg2 C 0.0111 - bs_akg3 C 0.0132 - bs_akg4 D - bs_akg4_aux D - bs_oaa C 0.0947 // sortie d'OAA pour formation de biomasse - bs_oaa1 D // sortie d'OAA pour Asp - bs_oaa1_aux C 0.0121 // sortie d'Asp - bs_oaa2 D // synthese d'Ile - bs_oaa2_aux C 0.0146 // sortie d'Ile - bs_oaa3a D - bs_oaa3b D - bs_oaa3_aux C 0.0173 - bs_oaa4 D - bs_oaa5 D - bs_oaa5_aux C 0.0128 - bs_oaa6 D - bs_oaa6_aux C 0.0077 - bs_oaa7 D - bs_oaa7_aux C 0.0121 - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac F 0.213000005 - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - - XCH - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt C 0 -// CO2upt D -// FTHF0 D -// FTHF1 D - - pgi C 0.752386 // 2011-02-22 ssg: was F => often unresolved with --irand option - pfk C 0 - ald F 0.420281957 -// tpi F 0.5 - pgk C 0.984718 // 2011-02-22 ssg: was F => often unresolved with --irand option - eno F 0.999 - pyk C 0.0109591 // 2010-10-01 ssg: was F => unresolved if co2 uptake is unlimited - - zwf C 0 - gnd C 0 - edd C 0 - ta F 0.361648085 - tk1 F 0.151671492 - tk2 F 0 - - pdh C 0.0322745 // 2010-10-02 ssg: was F, otherwise unsolvable in monte-carlo - citsynth C 0 - idh C 0 - akgdh C 0 - fum_a F 0.3013683 - fum_b D - maldh C 0.647115 //********************************************** C pour analyse de sensibilite, F pour minimisation - -// gs1 C 0 -// gs2 C 0 - - ppc F 0.147615337 - mae C 0 -// pck C 0 - - bs_glc6P D // sortie de G6P - bs_fru6P D // sortie de F6P - bs_pga C 0 // conversion PGA donne Ser - bs_pga_aux D // conversion PGA donne Ser - bs_pga1 C 0 // conversion PGA donne Ser - bs_pga1_aux D // conversion PGA donne Ser - bs_pga2 C 0 // ser donne Cys. correspond a la sortie de PGA pour biomasse autre que formation Gly - bs_pga2_aux D - bs_pga3 C 0.011799 // reaction de synthese de Gly. cette reaction est reversible - bs_pga3_aux D // sortie de Gly - bs_DHAP D // formation de glycerolP pour lipides - bs_pyr C 0 // formation d'Ala - bs_pyr1 C 0 // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Ile - bs_pyr2 C 0 // synthese d'AKV. consomme 2 Pyr - bs_pyr4 C 0 - bs_pyr4_aux D // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 C 0 // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux D // sortie de Leu - bs_e4p C 0 // sortie d'Ery4p -// bs_e4p_aux D // sortie d'Ery4p pour Trp - bs_rib5p C 0 // synthese d'His - bs_rib5p1 C 0 // synthese d'His - bs_rib5p1_aux D // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_accoa C 0 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_pep C 0 // sortie de PEP - bs_pep1 C 0 // sortie de PEP - bs_pep2 C 0 - bs_pep3a C 0 - bs_pep3b C 0 - bs_pep3_aux D - bs_pep4a C 0 - bs_pep4b C 0 - bs_pep4_aux D - bs_pep5 D - bs_pep6 C 0 - bs_pep6_aux D - bs_pep7 C 0 - bs_akg C 0 // sortie d'AKG - bs_akg1 C 0 - bs_akg2 D - bs_akg3 D - bs_akg4 C 0 - bs_akg4_aux D - bs_oaa C 0 - bs_oaa1 C 0 // sortie d'OAA autres que Met - bs_oaa1_aux D // sortie d'OAA autres que Met - bs_oaa2 C 0 // synthese de Met - bs_oaa2_aux D // sortie de Met - bs_oaa3a C 0 - bs_oaa3b C 0 - bs_oaa3_aux D - bs_oaa4 D - bs_oaa5 C 0 - bs_oaa5_aux D - bs_oaa6 C 0 - bs_oaa6_aux D - bs_oaa7 C 0 - bs_oaa7_aux D - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac D // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - -EQUALITIES - NET - VALUE FORMULA - - 0 fum_a-fum_b // scrambling reaction - 0 bs_oaa3a-bs_oaa3b - 0 bs_pep3a-bs_pep3b - 0 bs_pep4a-bs_pep4b - - XCH - VALUE FORMULA - - 0 fum_a-fum_b - -INEQUALITIES - NET - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - 1 <= pyk - 0.0001 <= edd - 0.0001 <= gnd - 0.0001 <= zwf - 0.0001 <= ppc - 0.0001 <= mae -// 2 >= CO2upt // 2010-08-18 too high value makes jacobian rank deficient - XCH - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - - -FLUX_MEASUREMENTS - FLUX_NAME VALUE DEVIATION // Val Dev - out_Ac 0.213 0.0001 - -LABEL_INPUT - META_NAME ISOTOPOMER VALUE - - Gluc #100000 0.8 - #000000 0.2 -// CO2_ext #0 0.989 -// #1 0.011 - -// FTHF_0 #0 1 -// FTHF_1 #1 1 - - -LABEL_MEASUREMENTS - META_NAME CUM_GROUP VALUE DEVIATION CUM_CONSTRAINTS - // Example - -PEAK_MEASUREMENTS - META_NAME PEAK_NO VALUE_S VALUE_D- VALUE_D+ VALUE_DD VALUE_T DEVIATION_S DEVIATION_D- DEVIATION_D+ DEVIATION_DD/T - - -MASS_SPECTROMETRY - META_NAME FRAGMENT WEIGHT VALUE DEVIATION - -// Deviation fixee a 0.02 // correction inoc 0.062 - - - - Suc 1,2,3,4 1 0.371605319 0.01 - 2 0.360829749 0.01 - 3 0.208425325 0.01 - 4 0.059139607 0.01 -// Mal 1,2,3,4 0 0.164619329483 0.02 -// 1 0.110072868518 0.02 -// 2 0.637801316225333 0.02 -// 3 0.0863461044204333 0.02 -// 4 0.00116038135315367 0.02 - ICit 1,2,3,4,5,6 0 0.131864539419667 0.02 - 1 0.225857638569 0.02 - 2 0.256421170949333 0.02 - 3 0.209230210478667 0.02 - 4 0.116863585449667 0.02 - 5 0.0457727744643333 0.02 - 6 0.0139900806697867 0.02 - PEP 1,2,3 0 0.421359839367667 0.01 - 1 0.358998301162333 0.01 - 2 0.0348521859365667 0.01 - 3 0.184789673534 0.01 - PGA 1,2,3 0 0.434335785072667 0.01 - 1 0.352829683224667 0.01 - 2 0.0323479804176 0.01 - 3 0.180486551285333 0.01 - FruBP 1,2,3,4,5,6 0 0.0738121029259333 0.01 - 1 0.454450017158667 0.01 - 2 0.160823529969333 0.01 - 3 0.0944468077710667 0.01 - 4 0.105281338489667 0.01 - 5 0.0155016033633 0.01 - 6 0.0956846003217333 0.01 - Glc6P 1,2,3,4,5,6 0 0.0160587173349 0.01 - 1 0.673510772480667 0.01 - 2 0.0930110047641 0.01 - 3 0.0280359937297 0.01 - 4 0.0397315614067667 0.01 - 5 0.0145524520950667 0.01 - 6 0.135099498189 0.01 - Fru6P 1,2,3,4,5,6 0 0.0235029951295 0.01 - 1 0.624253565357667 0.01 - 2 0.113068441282333 0.01 - 3 0.0456605631765 0.01 - 4 0.0516089447155667 0.01 - 5 0.0185881765378333 0.01 - 6 0.123317313800333 0.01 - Rib5P 1,2,3,4,5 0 0.341615670498667 0.01 - 1 0.25454117519 0.01 - 2 0.159027180368333 0.01 - 3 0.113789577528667 0.01 - 4 0.0615266612553333 0.01 - 5 0.0694997351590667 0.01 - Gnt6P 1,2,3,4,5,6 0 0.0249552273874 0.01 - 1 0.672556163913 0.01 - 2 0.0866890773125333 0.01 - 3 0.0313987199704333 0.01 - 4 0.0314691889898667 0.01 - 5 0.0138168327362333 0.01 - 6 0.139114789690333 0.01 -// Ery4P 1,2,3,4 0 0.178453461108 0.01 -// 1 0.412398433968333 0.01 -// 2 0.273694508221667 0.01 -// 3 0.116142498670667 0.01 -// 4 0.0193110980315 0.01 - -OPTIONS - OPT_NAME OPT_VALUE - MATLAB_FOR_FLUX_EQ_CONSTR_MATR 1 - //optctrl_history 1 // nlsic - //optctrl_trace 3 // BFGS - //optctrl_reltol 1.e-10 // BFGS - //optctrl_maxit 1000 // BFGS - posttreat_R plot_smeas.R - prl_exp e_coli_U-Glc_exact.ftbl - commandArgs --TIMEIT --noscale - diff --git a/tools/influx_si/test-data/e_coli_1-Glc_exact.log b/tools/influx_si/test-data/e_coli_1-Glc_exact.log deleted file mode 100644 index 45dcc70e30..0000000000 --- a/tools/influx_si/test-data/e_coli_1-Glc_exact.log +++ /dev/null @@ -1,40 +0,0 @@ -"/usr/local/miniconda3/bin/influx_s" "e_coli_1-Glc_exact.ftbl" -code gen: 2020-03-25 16:47:11 -executing: "/usr/local/miniconda3/bin/python3.7" "/home/STORAGE/local/miniconda3/bin/ftbl2optR.py" "--tblimit" "0" "--ropts" "noscale=TRUE; TIMEIT=TRUE" "e_coli_1-Glc_exact.ftbl" -executing: R --vanilla --slave < e_coli_1-Glc_exact.R -calcul : 2020-03-25 16:47:12 -load : 2020-03-25 16:47:13.55 cpu=0.945 -rinit : 2020-03-25 16:47:13.56 cpu=0.947 -r_flux : 2020-03-25 16:47:13.56 cpu=0.948 -Afl qr(): 2020-03-25 16:47:13.62 cpu=1.008 -dfl_dffg: 2020-03-25 16:47:13.73 cpu=1.042 -spAbr : 2020-03-25 16:47:13.73 cpu=1.045 -weight 1: 2020-03-25 16:47:13.73 cpu=1.046 -weight 2: 2020-03-25 16:47:13.77 cpu=1.123 -weight 3: 2020-03-25 16:47:13.84 cpu=1.251 -weight 4: 2020-03-25 16:47:13.89 cpu=1.354 -weight 5: 2020-03-25 16:47:13.91 cpu=1.402 -weight 6: 2020-03-25 16:47:13.92 cpu=1.421 -measure : 2020-03-25 16:47:14.00 cpu=1.506 -ineq : 2020-03-25 16:47:14.15 cpu=1.649 -preopt : 2020-03-25 16:47:14.20 cpu=1.718 -labargs : 2020-03-25 16:47:14.21 cpu=1.741 -run 1: 2020-03-25 16:47:17.10 cpu=4.779 -Starting point -The following 4 ineqalitie(s) are active at starting point: -n:0.0001<=edd -n:0.0001<=mae -f.x.tk2>=0 -f.x.eno<=0.999 -kvh init: 2020-03-25 16:47:17.10 cpu=4.781 -check ja: 2020-03-25 16:47:17.17 cpu=4.832 -optim : 2020-03-25 16:47:17.31 cpu=4.968 -it=0 res=211.2524 -it=1 res=162.3825 normstep=1.36222 btk=1 -it=2 res=143.6255 normstep=1.508085 btk=1 -it=3 res=143.4337 normstep=0.1225691 btk=1 -it=4 res=143.4337 normstep=2.429788e-08 btk=1 -postopt : 2020-03-25 16:47:17.64 cpu=5.279 -linstats: 2020-03-25 16:47:17.83 cpu=5.426 -rend : 2020-03-25 16:47:18.17 cpu=5.792 -end : 2020-03-25 16:47:18 diff --git a/tools/influx_si/test-data/e_coli_U-Glc_exact.ftbl b/tools/influx_si/test-data/e_coli_U-Glc_exact.ftbl deleted file mode 100644 index 1a36ac9cd4..0000000000 --- a/tools/influx_si/test-data/e_coli_U-Glc_exact.ftbl +++ /dev/null @@ -1,711 +0,0 @@ -PROJECT - NAME VERSION FORMAT DATE COMMENT - K12_MG1655.ftbl 1 101109 modele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees - -NETWORK - FLUX_NAME EDUCT_1 EDUCT_2 PRODUCT_1 PRODUCT_2 - -// Glycolyse. -// PPP -// TCA -// voies anaplerotiques: pepc. enz malique -// voie glyoxylate -// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre) -// saisie differentielle des substrats marques - - -// Uptake substrats - - Glucupt Gluc Glc6P - #ABCDEF #ABCDEF -// CO2upt CO2_ext CO2 // entree de CO2 non marque -// #A #A // ce flux est a laisser libre - -// FTHF0 FTHF_0 FTHF // prise en charge de FTHF non marque -// #A #A - -// FTHF1 FTHF_1 FTHF // prise en charge de FTHF marque -// #a #a - - -// Embden Meyerhof Parnas Pathway - - pgi Glc6P Fru6P - #ABCDEF #ABCDEF - - pfk Fru6P FruBP - #ABCDEF #ABCDEF - - ald FruBP GA3P GA3P - #ABCDEF #CBA #DEF - -// tpi DHAP GA3P -// #ABC #CBA - - pgk GA3P PGA - #ABC #ABC - - eno PGA PEP - #ABC #ABC - - pyk PEP Pyr - #ABC #ABC - - -// Methylglyoxal Pathway - -// mgs DHAP Pyr -// #ABC #ABC - - -// Pentose Phosphate Pathway - - zwf Glc6P Gnt6P - #ABCDEF #ABCDEF - - gnd Gnt6P CO2 Rib5P - #ABCDEF #A #BCDEF - - edd Gnt6P Pyr GA3P - #ABCDEF #ABC #DEF - -// ta Ery4P Fru6P GA3P Sed7P -// #ABCD #abcdef #def #abcABCD - -// tk1 GA3P Sed7P Rib5P Rib5P -// #ABC #abcdefg #abABC #cdefg - -// tk2 GA3P Fru6P Rib5P Ery4P -// #ABC #abcdef #abABC #cdef - - ta GA3P Sed7P Ery4P Fru6P - #ABC #abcdefg #defg #abcABC - - tk1 Rib5P Rib5P GA3P Sed7P - #ABCDE #abcde #CDE #ABabcde - - tk2 Rib5P Ery4P GA3P Fru6P - #ABCDE #abcd #CDE #ABabcd - - -// Tricarboxylic Acid Cycle - - pdh Pyr AcCoA CO2 - #ABC #BC #A - - citsynth AcCoA OAA ICit - #AB #abcd #dcbaBA - - idh ICit AKG CO2 - #ABCDEF #ABCEF #D - - akgdh AKG Suc CO2 - #ABCDE #BCDE #A - - fum_a Suc Mal - #ABCD #ABCD - - fum_b Suc Mal - #ABCD #DCBA - - maldh Mal OAA - #ABCD #ABCD - - -// Glyoxylate Shunt - -// gs1 ICit GlyOx Suc -// #ABCDEF #AB #DCEF - -// gs2 GlyOx AcCoA OAA -// #AB #ab #ABba - - -// Anaplerotic Reactions - - ppc PEP CO2 OAA // PEPcarboxylase - #ABC #a #ABCa - - mae Mal Pyr CO2 // enzyme malique - #ABCD #ABC #D - -// pck OAA PEP CO2 // PEP carboxykinase -// #ABCD #ABC #D - - -// Biosynthetic Pathways - - // Glucose-6-Phosphate Family - - bs_glc6P Glc6P BM_Glc6P - #ABCDEF #ABCDEF - - // Fructose-6-Phosphate Family - - bs_fru6P Fru6P BM_Fru6P // sortie de Fru6P pour biomasse - #ABCDEF #ABCDEF - - // Phosphoglycerate Family - - bs_pga PGA BM_PGA - #ABC #ABC - - bs_pga_aux BM_PGA PGA_Aux - #ABC #ABC - - bs_pga1 BM_PGA Ser - #ABC #ABC - - bs_pga1_aux Ser Ser_Aux - #ABC #ABC - - bs_pga2 Ser Cys // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga2_aux Cys Cys_Aux // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga3 Ser Gly FTHF // formation de gly pour biomasse - #ABC #AB #C // ce flux est reversible - - bs_pga3_aux Gly Gly_Aux // pour conserver Gly comme metabolite intracellulaire - #AB #AB - - // TrioseP Family - - bs_DHAP GA3P Glp // formation glycerolP pour lipides - #ABC #ABC - - // Pyruvate Family - - bs_pyr Pyr BM_Pyr - #ABC #ABC - - bs_pyr1 BM_Pyr Ala - #ABC #ABC - - bs_pyr1_aux Ala Ala_Aux // pour conserver Ala comme metabolite intracellulaire - #ABC #ABC - - bs_pyr2 BM_Pyr BM_Pyr AKV CO2 // AKV et Val ont le meme squelette C - #ABC #abc #ABbcC #a // cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val - - bs_pyr4 AKV Val // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr4_aux Val Val_Aux // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr3 AKV BM_AcCoA Leu CO2 - #ABCDE #ab #abBCDE #A - - bs_pyr3_aux Leu Leu_Aux // pour conserver Leu comme metabolite intracellulaire - #ABCDEF #ABCDEF - - - // Erythrose-4-Phosphate Family - - bs_e4p Ery4P BM_Ery4P // pour utiliser les donnees sur Ery4P - #ABCD #ABCD - -// bs_e4p_aux BM_Ery4P Ery4P_aux // pour utiliser les donnees sur Ery4P -// #ABCD #ABCD - - - // Ribose-5-Phosphate Family - - bs_rib5p Rib5P BM_Rib5P // pour utiliser les donnees sur Rib5P - #ABCDE #ABCDE - - bs_rib5p1 BM_Rib5P FTHF His // pour utiliser les donnees sur Rib5P - #ABCDE #a #EDCBAa - - bs_rib5p1_aux His His_Aux // sortie pour conserver His comme metabolite intracellulaire - #ABCDEF #ABCDEF - - bs_rib5p2 BM_Rib5P Ri5P_Aux // sortie de Ri5P pour autres besoins que His - #ABCDE #ABCDE // ce flux est important pour ne pas imposer de fausses contraintes sur FTHF si on considerait His comme seule sortie - - - // Aromatic Amino Acids - - bs_pep PEP BM_PEP - #ABC #ABC - - bs_pep1 BM_PEP BM_Ery4P DAHP - #ABC #abcd #ABCabcd - - bs_pep2 BM_PEP DAHP Chor - #ABC #abcdefg #ABCabcdefg - - bs_pep3a Chor Phe CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep3b Chor Phe CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep3_aux Phe Phe_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep4a Chor Tyr CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep4b Chor Tyr CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep4_aux Tyr Tyr_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep5 BM_PEP PEP_Aux - #ABC #ABC - - bs_pep6 Chor BM_Rib5P Trp PyrCO2 - #ABCDEFGHIJ #abcde #edcbaJEFGHI #ABCD - - bs_pep6_aux Trp Trp_Aux - #ABCDEFGHIJK #ABCDEFGHIJK - - bs_pep7 PyrCO2 Pyr CO2 - #ABCD #ABC #D - - - // Acetyl-CoA - - bs_accoa AcCoA BM_AcCoA - #AB #AB - - bs_accoa_aux BM_AcCoA AcCoA_Aux - #AB #AB - - - // Alpha-Ketoglutarate Family - - bs_akg AKG BM_AKG // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg1 BM_AKG Glu // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg2 Glu Pro // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg3 Glu Gln // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg4 Glu CO2 Arg // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #a #ABCDEa - - bs_akg4_aux Arg Arg_Aux // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDEF #ABCDEF - - - // Oxaloacetate Family - - bs_oaa OAA BM_OAA - #ABCD #ABCD - - bs_oaa1 BM_OAA Asp - #ABCD #ABCD - - bs_oaa1_aux Asp Asp_Aux - #ABCD #ABCD - - bs_oaa2 Thr BM_Pyr Ile CO2 - #ABCD #abc #ABbCDc #a - - bs_oaa2_aux Ile Ile_Aux - #ABCDEF #ABCDEF - - bs_oaa3a BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #ABCDcb #a - - bs_oaa3b BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #abcDCB #A - - bs_oaa3_aux Lys Lys_Aux - #ABCDEF #ABCDEF - - bs_oaa4 BM_OAA OAA_Aux - #ABCD #ABCD - - bs_oaa5 BM_OAA Thr - #ABCD #ABCD - - bs_oaa5_aux Thr Thr_Aux - #ABCD #ABCD - - bs_oaa6 BM_OAA FTHF Met - #ABCD #a #ABCDa - - bs_oaa6_aux Met Met_Aux - #ABCDE #ABCDE - - bs_oaa7 BM_OAA Asn - #ABCD #ABCD - - bs_oaa7_aux Asn Asn_Aux - #ABCD #ABCD - - -// Flux de sortie - - out_co2 CO2 CO2_out // Sortie de CO2 - #A #A - - out_Ac AcCoA Acetate // Sortie d'acetate - #AB #AB - - out_FTHF FTHF FTHF_out - #A #A - -FLUXES - NET - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt C 1 -// CO2upt F 0.669589 -// FTHF0 F 0.00224836 -// FTHF1 F 0.001 - - pgi D - pfk D - ald D -// tpi D - pgk D - eno D - pyk F 1.54425507 - - zwf F 0.14233479 - gnd F 0.14223479 - edd D - ta D - tk1 D - tk2 D - - pdh D - citsynth D - idh D - akgdh D - fum_a D - fum_b D - maldh D - -// gs1 C 0 -// gs2 D - - ppc D - mae D -// pck D - - // flux de biomasse - - bs_glc6P C 0.0109 // sortie de G6P - bs_fru6P C 0.0038 // sortie de F6P - bs_pga C 0.0791 // sortie de PGA pour formation de biomasse - bs_pga_aux D // sortie de PGA pour formation de biomasse - bs_pga1 D // conversion PGA donne ser - bs_pga1_aux C 0.0109 // conversion PGA donne ser - bs_pga2 D - bs_pga2_aux C 0.0046 // conversion PGA donne Cys - bs_pga3 D // reaction de synthese de Gly - bs_pga3_aux C 0.0308 // sortie de Gly - bs_DHAP C 0.0068 // formation de glycerolP pour lipides - bs_pyr C 0.1501 // avant : 0.1547 // sortie de Pyr pour formation de biomasse - bs_pyr1 D // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Leu - bs_pyr2 D // synthese d'AKV. consomme 2 Pyr - bs_pyr4 D - bs_pyr4_aux C 0.0213 // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 D // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux C 0.0227 // sortie de Leu - bs_e4p D // sortie d'Ery4p pour biomasse -// bs_e4p_aux C 0 // sortie d'Ery4p pour Trp - bs_rib5p C 0.0476 // synthese d'His - bs_rib5p1 D // synthese d'His - bs_rib5p1_aux C 0.0048 // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_pep C 0.0381 // sortie de PEP - bs_pep1 D // sortie de PEP - bs_pep2 D - bs_pep3a D - bs_pep3b D - bs_pep3_aux C 0.0093 - bs_pep4a D - bs_pep4b D - bs_pep4_aux C 0.0069 - bs_pep5 C 0.0027 - bs_pep6 D - bs_pep6_aux D - bs_pep7 D - bs_accoa C 0.1565 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_akg C 0.0571 // sortie d'AKG - bs_akg1 D - bs_akg2 C 0.0111 - bs_akg3 C 0.0132 - bs_akg4 D - bs_akg4_aux D - bs_oaa C 0.0947 // sortie d'OAA pour formation de biomasse - bs_oaa1 D // sortie d'OAA pour Asp - bs_oaa1_aux C 0.0121 // sortie d'Asp - bs_oaa2 D // synthese d'Ile - bs_oaa2_aux C 0.0146 // sortie d'Ile - bs_oaa3a D - bs_oaa3b D - bs_oaa3_aux C 0.0173 - bs_oaa4 D - bs_oaa5 D - bs_oaa5_aux C 0.0128 - bs_oaa6 D - bs_oaa6_aux C 0.0077 - bs_oaa7 D - bs_oaa7_aux C 0.0121 - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac F 0.213000005 - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - - XCH - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt C 0 -// CO2upt D -// FTHF0 D -// FTHF1 D - - pgi C 0.752386 // 2011-02-22 ssg: was F => often unresolved with --irand option - pfk C 0 - ald F 0.420281957 -// tpi F 0.5 - pgk C 0.984718 // 2011-02-22 ssg: was F => often unresolved with --irand option - eno F 0.999 - pyk C 0.0109591 // 2010-10-01 ssg: was F => unresolved if co2 uptake is unlimited - - zwf C 0 - gnd C 0 - edd C 0 - ta F 0.361648085 - tk1 F 0.151671492 - tk2 F 0 - - pdh C 0.0322745 // 2010-10-02 ssg: was F, otherwise unsolvable in monte-carlo - citsynth C 0 - idh C 0 - akgdh C 0 - fum_a F 0.3013683 - fum_b D - maldh C 0.647115 //********************************************** C pour analyse de sensibilite, F pour minimisation - -// gs1 C 0 -// gs2 C 0 - - ppc F 0.147615337 - mae C 0 -// pck C 0 - - bs_glc6P D // sortie de G6P - bs_fru6P D // sortie de F6P - bs_pga C 0 // conversion PGA donne Ser - bs_pga_aux D // conversion PGA donne Ser - bs_pga1 C 0 // conversion PGA donne Ser - bs_pga1_aux D // conversion PGA donne Ser - bs_pga2 C 0 // ser donne Cys. correspond a la sortie de PGA pour biomasse autre que formation Gly - bs_pga2_aux D - bs_pga3 C 0.011799 // reaction de synthese de Gly. cette reaction est reversible - bs_pga3_aux D // sortie de Gly - bs_DHAP D // formation de glycerolP pour lipides - bs_pyr C 0 // formation d'Ala - bs_pyr1 C 0 // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Ile - bs_pyr2 C 0 // synthese d'AKV. consomme 2 Pyr - bs_pyr4 C 0 - bs_pyr4_aux D // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 C 0 // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux D // sortie de Leu - bs_e4p C 0 // sortie d'Ery4p -// bs_e4p_aux D // sortie d'Ery4p pour Trp - bs_rib5p C 0 // synthese d'His - bs_rib5p1 C 0 // synthese d'His - bs_rib5p1_aux D // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_accoa C 0 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_pep C 0 // sortie de PEP - bs_pep1 C 0 // sortie de PEP - bs_pep2 C 0 - bs_pep3a C 0 - bs_pep3b C 0 - bs_pep3_aux D - bs_pep4a C 0 - bs_pep4b C 0 - bs_pep4_aux D - bs_pep5 D - bs_pep6 C 0 - bs_pep6_aux D - bs_pep7 C 0 - bs_akg C 0 // sortie d'AKG - bs_akg1 C 0 - bs_akg2 D - bs_akg3 D - bs_akg4 C 0 - bs_akg4_aux D - bs_oaa C 0 - bs_oaa1 C 0 // sortie d'OAA autres que Met - bs_oaa1_aux D // sortie d'OAA autres que Met - bs_oaa2 C 0 // synthese de Met - bs_oaa2_aux D // sortie de Met - bs_oaa3a C 0 - bs_oaa3b C 0 - bs_oaa3_aux D - bs_oaa4 D - bs_oaa5 C 0 - bs_oaa5_aux D - bs_oaa6 C 0 - bs_oaa6_aux D - bs_oaa7 C 0 - bs_oaa7_aux D - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac D // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - -EQUALITIES - NET - VALUE FORMULA - - 0 fum_a-fum_b // scrambling reaction - 0 bs_oaa3a-bs_oaa3b - 0 bs_pep3a-bs_pep3b - 0 bs_pep4a-bs_pep4b - - XCH - VALUE FORMULA - - 0 fum_a-fum_b - -INEQUALITIES - NET - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - 1 <= pyk - 0.0001 <= edd - 0.0001 <= gnd - 0.0001 <= zwf - 0.0001 <= ppc - 0.0001 <= mae -// 2 >= CO2upt // 2010-08-18 too high value makes jacobian rank deficient - XCH - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - - -FLUX_MEASUREMENTS - FLUX_NAME VALUE DEVIATION // Val Dev - out_Ac 0.213 0.0001 - -LABEL_INPUT - META_NAME ISOTOPOMER VALUE - - Gluc #111111 0.2 - #000000 0.8 -// CO2_ext #0 0.989 -// #1 0.011 - -// FTHF_0 #0 1 -// FTHF_1 #1 1 - - -LABEL_MEASUREMENTS - META_NAME CUM_GROUP VALUE DEVIATION CUM_CONSTRAINTS - // Example - -PEAK_MEASUREMENTS - META_NAME PEAK_NO VALUE_S VALUE_D- VALUE_D+ VALUE_DD VALUE_T DEVIATION_S DEVIATION_D- DEVIATION_D+ DEVIATION_DD/T - - -MASS_SPECTROMETRY - META_NAME FRAGMENT WEIGHT VALUE DEVIATION - -// Deviation fixee a 0.02 // correction inoc 0.062 - - - - Suc 1,2,3,4 1 0.371605319 0.01 - 2 0.360829749 0.01 - 3 0.208425325 0.01 - 4 0.059139607 0.01 -// Mal 1,2,3,4 0 0.164619329483 0.02 -// 1 0.110072868518 0.02 -// 2 0.637801316225333 0.02 -// 3 0.0863461044204333 0.02 -// 4 0.00116038135315367 0.02 - ICit 1,2,3,4,5,6 0 0.131864539419667 0.02 - 1 0.225857638569 0.02 - 2 0.256421170949333 0.02 - 3 0.209230210478667 0.02 - 4 0.116863585449667 0.02 - 5 0.0457727744643333 0.02 - 6 0.0139900806697867 0.02 - PEP 1,2,3 0 0.421359839367667 0.01 - 1 0.358998301162333 0.01 - 2 0.0348521859365667 0.01 - 3 0.184789673534 0.01 - PGA 1,2,3 0 0.434335785072667 0.01 - 1 0.352829683224667 0.01 - 2 0.0323479804176 0.01 - 3 0.180486551285333 0.01 - FruBP 1,2,3,4,5,6 0 0.0738121029259333 0.01 - 1 0.454450017158667 0.01 - 2 0.160823529969333 0.01 - 3 0.0944468077710667 0.01 - 4 0.105281338489667 0.01 - 5 0.0155016033633 0.01 - 6 0.0956846003217333 0.01 - Glc6P 1,2,3,4,5,6 0 0.0160587173349 0.01 - 1 0.673510772480667 0.01 - 2 0.0930110047641 0.01 - 3 0.0280359937297 0.01 - 4 0.0397315614067667 0.01 - 5 0.0145524520950667 0.01 - 6 0.135099498189 0.01 - Fru6P 1,2,3,4,5,6 0 0.0235029951295 0.01 - 1 0.624253565357667 0.01 - 2 0.113068441282333 0.01 - 3 0.0456605631765 0.01 - 4 0.0516089447155667 0.01 - 5 0.0185881765378333 0.01 - 6 0.123317313800333 0.01 - Rib5P 1,2,3,4,5 0 0.341615670498667 0.01 - 1 0.25454117519 0.01 - 2 0.159027180368333 0.01 - 3 0.113789577528667 0.01 - 4 0.0615266612553333 0.01 - 5 0.0694997351590667 0.01 - Gnt6P 1,2,3,4,5,6 0 0.0249552273874 0.01 - 1 0.672556163913 0.01 - 2 0.0866890773125333 0.01 - 3 0.0313987199704333 0.01 - 4 0.0314691889898667 0.01 - 5 0.0138168327362333 0.01 - 6 0.139114789690333 0.01 -// Ery4P 1,2,3,4 0 0.178453461108 0.01 -// 1 0.412398433968333 0.01 -// 2 0.273694508221667 0.01 -// 3 0.116142498670667 0.01 -// 4 0.0193110980315 0.01 - -OPTIONS - OPT_NAME OPT_VALUE - MATLAB_FOR_FLUX_EQ_CONSTR_MATR 1 - //optctrl_history 1 // nlsic - //optctrl_trace 3 // BFGS - //optctrl_reltol 1.e-10 // BFGS - //optctrl_maxit 1000 // BFGS - posttreat_R plot_smeas.R - diff --git a/tools/influx_si/test-data/e_coli_growth.ftbl b/tools/influx_si/test-data/e_coli_growth.ftbl deleted file mode 100644 index 5b6d25465c..0000000000 --- a/tools/influx_si/test-data/e_coli_growth.ftbl +++ /dev/null @@ -1,822 +0,0 @@ -PROJECT - NAME VERSION FORMAT DATE COMMENT - Nissle.ftbl 1 100910 modele E coli Nissle WT avec voies centrales completes et voies biomasse - Nissle.ftbl 2 121025 growth fluxes+pooled penthoses - Nissle.ftbl 3 121123 concentration measurements - -NETWORK - FLUX_NAME EDUCT_1 EDUCT_2 PRODUCT_1 PRODUCT_2 - -// Glycolyse. -// PPP -// TCA -// voies anaplerotiques: pepc. enz malique -// voie glyoxylate -// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre) -// saisie differentielle des substrats marques - - -// Uptake substrats - - Glucupt_1 Gluc_1 Glc - #ABCDEF #ABCDEF - - Glucupt_U Gluc_U Glc - #ABCDEF #ABCDEF - - Glucupt Glc Glc6P - #ABCDEF #ABCDEF - - CO2upt CO2_ext CO2 // entree de CO2 non marque - #A #A // ce flux est a laisser libre - -// FTHF0 FTHF_0 FTHF // prise en charge de FTHF non marque -// #A #A - -// FTHF1 FTHF_1 FTHF // prise en charge de FTHF marque -// #a #a - - -// Embden Meyerhof Parnas Pathway - - pgi Glc6P Fru6P - #ABCDEF #ABCDEF - - pfk Fru6P FruBP - #ABCDEF #ABCDEF - - ald FruBP GA3P GA3P - #ABCDEF #CBA #DEF - -// tpi DHAP GA3P -// #ABC #CBA - - pgk GA3P PGA - #ABC #ABC - - eno PGA PEP - #ABC #ABC - - pyk PEP Pyr - #ABC #ABC - - -// Methylglyoxal Pathway - -// mgs DHAP Pyr -// #ABC #ABC - - -// Pentose Phosphate Pathway - - zwf Glc6P Gnt6P - #ABCDEF #ABCDEF - - gnd Gnt6P CO2 Rub5P - #ABCDEF #A #BCDEF - - rib Rub5P Rib5P - #ABCDE #ABCDE - - xul Rub5P Xul5P - #ABCDE #ABCDE - - edd Gnt6P Pyr GA3P - #ABCDEF #ABC #DEF - -// ta GA3P Sed7P Ery4P Fru6P -// #ABC #abcdefg #defg #abcABC - -// tk1 Rib5P Rib5P GA3P Sed7P -// #ABCDE #abcde #CDE #ABabcde - -// tk2 Rib5P Ery4P GA3P Fru6P -// #ABCDE #abcd #CDE #ABabcd - - HR1 GA3P E2 Xul5P - #CDE #AB #ABCDE - - HR2 Fru6P Ery4P E2 - #ABCDEF #CDEF #AB - - HR3 Fru6P GA3P E3 - #ABCDEF #DEF #ABC - - HR4 Sed7P Rib5P E2 - #abABCDE #ABCDE #ab - - HR5 Ery4P E3 Sed7P - #ABCD #abc #abcABCD - - -// Tricarboxylic Acid Cycle - - pdh Pyr AcCoA CO2 - #ABC #BC #A - - citsynth AcCoA OAA Cit - #AB #abcd #dcbaBA - - idh Cit AKG CO2 - #ABCDEF #ABCEF #D - - akgdh AKG Suc CO2 - #ABCDE #BCDE #A - - fum_a Suc Mal - #ABCD #ABCD - - fum_b Suc Mal - #ABCD #DCBA - - maldh Mal OAA - #ABCD #ABCD - - -// Glyoxylate Shunt - -// gs1 Cit GlyOx Suc -// #ABCDEF #AB #DCEF - -// gs2 GlyOx AcCoA OAA -// #AB #ab #ABba - - -// Anaplerotic Reactions - - ppc PEP CO2 OAA // PEPcarboxylase - #ABC #a #ABCa - -// mae Mal Pyr CO2 // enzyme malique -// #ABCD #ABC #D - -// pck OAA PEP CO2 // PEP carboxykinase -// #ABCD #ABC #D - - -// Biosynthetic Pathways - - // Glucose-6-Phosphate Family - - bs_glc6P Glc6P BM_Glc6P - #ABCDEF #ABCDEF - - // Fructose-6-Phosphate Family - - bs_fru6P Fru6P BM_Fru6P - #ABCDEF #ABCDEF - - // Phosphoglycerate Family - - bs_pga PGA BM_PGA - #ABC #ABC - -// bs_pga_aux BM_PGA PGA_Aux -// #ABC #ABC - -// bs_pga1 BM_PGA Ser -// #ABC #ABC - -// bs_pga1_aux Ser Ser_Aux -// #ABC #ABC - -// bs_pga2 Ser Cys -// #ABC #ABC - -// bs_pga2_aux Cys Cys_Aux -// #ABC #ABC - -// bs_pga3 Ser Gly FTHF -// #ABC #AB #C - -// bs_pga3_aux Gly Gly_Aux -// #AB #AB - - // TrioseP Family - - bs_DHAP GA3P Glp - #ABC #ABC - - // Pyruvate Family - - bs_pyr Pyr BM_Pyr - #ABC #ABC - -// bs_pyr1 BM_Pyr Ala -// #ABC #ABC - -// bs_pyr1_aux Ala Ala_Aux -// #ABC #ABC - -// bs_pyr2 BM_Pyr BM_Pyr AKV CO2 -// #ABC #abc #ABbcC #a - -// bs_pyr4 AKV Val -// #ABCDE #ABCDE - -// bs_pyr4_aux Val Val_Aux -// #ABCDE #ABCDE - -// bs_pyr3 AKV BM_AcCoA Leu CO2 -// #ABCDE #ab #abBCDE #A - -// bs_pyr3_aux Leu Leu_Aux -// #ABCDEF #ABCDEF - - // Erythrose-4-Phosphate Family - - bs_e4p Ery4P BM_Ery4P - #ABCD #ABCD - -// bs_e4p_aux BM_Ery4P Ery4P_aux -// #ABCD #ABCD - - // Ribose-5-Phosphate Family - - bs_rib5P Rib5P BM_Rib5P - #ABCDE #ABCDE - -// bs_rib5P1 BM_Rib5P FTHF His -// #ABCDE #a #EDCBAa - -// bs_rib5P1_aux His His_Aux -// #ABCDEF #ABCDEF - -// bs_rib5P2 BM_Rib5P Ri5P_Aux -// #ABCDE #ABCDE - - - // Aromatic Amino Acids - - bs_pep PEP BM_PEP - #ABC #ABC - -// bs_pep1 BM_PEP BM_Ery4P DAHP -// #ABC #abcd #ABCabcd - -// bs_pep2 BM_PEP DAHP Chor -// #ABC #abcdefg #ABCabcdefg - -// bs_pep3a Chor Phe CO2 -// #ABCDEFGHIJ #ABCEFGHIJ #D - -// bs_pep3b Chor Phe CO2 -// #ABCDEFGHIJ #ABCEJIHGF #D - -// bs_pep3_aux Phe Phe_Aux -// #ABCEFGHIJ #ABCEFGHIJ - -// bs_pep4a Chor Tyr CO2 -// #ABCDEFGHIJ #ABCEFGHIJ #D - -// bs_pep4b Chor Tyr CO2 -// #ABCDEFGHIJ #ABCEJIHGF #D - -// bs_pep4_aux Tyr Tyr_Aux -// #ABCEFGHIJ #ABCEFGHIJ - -// bs_pep5 BM_PEP PEP_Aux -// #ABC #ABC - -// bs_pep6 Chor BM_Rib5P Trp PyrCO2 -// #ABCDEFGHIJ #abcde #edcbaJEFGHI #ABCD - -// bs_pep6_aux Trp Trp_Aux -// #ABCDEFGHIJK #ABCDEFGHIJK - -// bs_pep7 PyrCO2 Pyr CO2 -// #ABCD #ABC #D - - // Acetyl-CoA - - bs_accoa AcCoA BM_AcCoA - #AB #AB - -// bs_accoa_aux BM_AcCoA AcCoA_Aux -// #AB #AB - - // Alpha-Ketoglutarate Family - - bs_akg AKG BM_AKG - #ABCDE #ABCDE - -// bs_akg1 BM_AKG Glu -// #ABCDE #ABCDE - -// bs_akg2 Glu Pro -// #ABCDE #ABCDE - -// bs_akg3 Glu Gln -// #ABCDE #ABCDE - -// bs_akg4 Glu CO2 Arg -// #ABCDE #a #ABCDEa - -// bs_akg4_aux Arg Arg_Aux -// #ABCDEF #ABCDEF - -// bs_akg2_aux Pro Pro_Aux -// #ABCDE #ABCDE - - - // Oxaloacetate Family - - bs_oaa OAA BM_OAA - #ABCD #ABCD - -// bs_oaa1 BM_OAA Asp -// #ABCD #ABCD - -// bs_oaa1_aux Asp Asp_Aux -// #ABCD #ABCD - -// bs_oaa2 Thr BM_Pyr Ile CO2 -// #ABCD #abc #ABbCDc #a - -// bs_oaa2_aux Ile Ile_Aux -// #ABCDEF #ABCDEF - -// bs_oaa3a BM_OAA BM_Pyr Lys CO2 -// #ABCD #abc #ABCDcb #a - -// bs_oaa3b BM_OAA BM_Pyr Lys CO2 -// #ABCD #abc #abcDCB #A - -// bs_oaa3_aux Lys Lys_Aux -// #ABCDEF #ABCDEF - -// bs_oaa4 BM_OAA OAA_Aux -// #ABCD #ABCD - -// bs_oaa5 BM_OAA Thr -// #ABCD #ABCD - -// bs_oaa5_aux Thr Thr_Aux -// #ABCD #ABCD - -// bs_oaa6 BM_OAA FTHF Met -// #ABCD #a #ABCDa - -// bs_oaa6_aux Met Met_Aux -// #ABCDE #ABCDE - -// bs_oaa7 BM_OAA Asn -// #ABCD #ABCD - -// bs_oaa7_aux Asn Asn_Aux -// #ABCD #ABCD - - -// Extracellular fluxes - - out_co2 CO2 CO2_out // CO2 output - #A #A - - out_Ac AcCoA Acetate // Acetate output - #AB #AB - -// out_FTHF FTHF FTHF_out -// #A #A - -FLUXES - NET - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - // INPUT - Glucupt_1 F 0.8128 - Glucupt_U D - Glucupt D - CO2upt C 0.77 // fixed arbitrary -// FTHF0 F 0.00224836 -// FTHF1 F 0.001 - - // Glycolysis - pgi F 0.1 - pfk D - ald D -// tpi D - pgk D 0.1 - eno D - pyk D 1.21144 - - // PPP + EDP - zwf D 0.4 - gnd D - edd F 0.1 - rib D - xul D -// ta D -// tk1 D -// tk2 D - HR1 D - HR2 D - HR3 D - HR4 D - HR5 D - - // TCA - pdh D - citsynth D - idh D - akgdh D - fum_a D - fum_b D - maldh D -// gs1 C 0 -// gs2 D - ppc D -// mae D -// pck D - - // Biosynthetic pathways - bs_glc6P C 0.0132 // sortie de G6P - bs_fru6P C 0.0045 // sortie de F6P - bs_pga C 0.0958 // sortie de PGA -// bs_pga_aux D -// bs_pga1 D -// bs_pga1_aux C 0.0132 // sortie de Ser -// bs_pga2 D -// bs_pga2_aux C 0.0056 // sortie de Cys -// bs_pga3 D -// bs_pga3_aux C 0.0373 // sortie de Gly - bs_DHAP C 0.0083 - bs_pyr C 0.1818 // sortie de Pyr -// bs_pyr1 D -// bs_pyr1_aux D // sortie d'Ala -// bs_pyr2 D -// bs_pyr4 D -// bs_pyr4_aux C 0.0258 // sortie de Val -// bs_pyr3 D -// bs_pyr3_aux C 0.0275 // sortie de Leu - bs_e4p C 0.0247 // sortie d'E4P - bs_rib5P C 0.0576 // sortie de R5P -// bs_rib5P1 D -// bs_rib5P1_aux C 0.0058 // sortie d'His -// bs_rib5P2 D - bs_pep C 0.0461 // sortie de PEP -// bs_pep1 D -// bs_pep2 D -// bs_pep3a D -// bs_pep3b D -// bs_pep3_aux C 0.0113 // sortie de Phe -// bs_pep4a D -// bs_pep4b D -// bs_pep4_aux C 0.0084 // sortie de Tyr -// bs_pep5 C 0.0033 // sorties autres que ac. amines -// bs_pep6 D -// bs_pep6_aux D -// bs_pep7 D - bs_accoa C 0.1895 // sortie d'AcCoA -// bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_akg C 0.0692 // sortie d'AcCoA -// bs_akg1 D -// bs_akg2 D // sortie de Pro -// bs_akg3 C 0.0160 // sortie de Gln -// bs_akg4 D -// bs_akg2_aux C 0.013475 -// bs_akg4_aux D - bs_oaa C 0.1146 -// bs_oaa1 D -// bs_oaa1_aux C 0.0147 // sortie d'Asp -// bs_oaa2 D -// bs_oaa2_aux C 0.0177 // sortie d'Ile -// bs_oaa3a D -// bs_oaa3b D -// bs_oaa3_aux C 0.0209 // sortie de Lys -// bs_oaa4 D -// bs_oaa5 D -// bs_oaa5_aux C 0.0155 // sortie de Thr -// bs_oaa6 D -// bs_oaa6_aux C 0.0094 // sortie de Met -// bs_oaa7 D -// bs_oaa7_aux C 0.0147 // sortie d'Asn - - // Extracellular fluxes - - out_co2 D 0.1 // sortie de CO2 - out_Ac F 0.48 // sortie d'acetate -// out_FTHF D // sortie de FTHF - - - XCH - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - // INPUT - Glucupt_1 D - Glucupt_U D - Glucupt C 0 - CO2upt D -// FTHF0 D -// FTHF1 D - - // Glycolysis - pgi F 0.4 - pfk F 0.01 - ald F 0.4 -// tpi F 0.5 - pgk F 0.99 - eno F 0.99 - pyk F 0.4 - - // PPP + EDP - zwf C 0 - gnd C 0 - edd C 0 - rib C 0.99 // fixed arbitrary big - xul F 0 -// ta F 0.35468 -// tk1 F 0.0960538 -// tk2 F 0.0521646 - HR1 C 0.24 // fixed arbitrary - HR2 F 0.0151117 - HR3 F 0.14 - HR4 C 0.04 // fixed arbitrary - HR5 F 0.02 - - // TCA - pdh C 0.01 - citsynth C 0 - idh C 0 - akgdh C 0 - fum_a C 0.01 // fixed arbitrary - fum_b D -// maldh F 0.99 - maldh C 0.42 // fixed arbitrary -// gs1 C 0 -// gs2 C 0 - ppc F 0.2 -// mae C 0 -// pck C 0 - - // Biosynthetic pathways - bs_glc6P D - bs_fru6P D - bs_pga D -// bs_pga_aux D -// bs_pga1 C 0 -// bs_pga1_aux D -// bs_pga2 C 0 -// bs_pga2_aux D -// bs_pga3 C 0.00824415 -// bs_pga3_aux D - bs_DHAP D - bs_pyr D -// bs_pyr1 C 0 -// bs_pyr1_aux D -// bs_pyr2 C 0 -// bs_pyr4 C 0 -// bs_pyr4_aux D -// bs_pyr3 C 0 -// bs_pyr3_aux D - bs_e4p D 0 -// bs_e4p_aux D - bs_rib5P D 0 -// bs_rib5P1 C 0 -// bs_rib5P1_aux D -// bs_rib5P2 D - bs_accoa D 0 -// bs_accoa_aux D - bs_pep D 0 -// bs_pep1 C 0 -// bs_pep2 C 0 -// bs_pep3a C 0 -// bs_pep3b C 0 -// bs_pep3_aux D -// bs_pep4a C 0 -// bs_pep4b C 0 -// bs_pep4_aux D -// bs_pep5 D -// bs_pep6 C 0 -// bs_pep6_aux D -// bs_pep7 C 0 - bs_akg D 0 -// bs_akg1 C 0 -// bs_akg2 C 0 -// bs_akg3 D -// bs_akg4 C 0 -// bs_akg4_aux D -// bs_akg2_aux D - bs_oaa D 0 -// bs_oaa1 C 0 -// bs_oaa1_aux D -// bs_oaa2 C 0 -// bs_oaa2_aux D -// bs_oaa3a C 0 -// bs_oaa3b C 0 -// bs_oaa3_aux D -// bs_oaa4 D -// bs_oaa5 C 0 -// bs_oaa5_aux D -// bs_oaa6 C 0 -// bs_oaa6_aux D -// bs_oaa7 C 0 -// bs_oaa7_aux D - - // Flux de sortie - out_co2 C 0 // sortie de CO2 - out_Ac C 0 // sortie d'acetate -// out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - -EQUALITIES - NET - VALUE FORMULA - - 0 fum_a-fum_b // scrambling reaction - 1 Glucupt_1+Glucupt_U -// 0 bs_oaa3a-bs_oaa3b -// 0 bs_pep3a-bs_pep3b -// 0 bs_pep4a-bs_pep4b - - XCH - VALUE FORMULA - - 0 fum_a-fum_b - -INEQUALITIES - NET - VALUE COMP FORMULA -// 1 <= pyk - 0 <= edd - 0 <= gnd - 0 <= zwf - 0 <= ppc - 0 <= idh - 0 <= akgdh -// 0 <= mae - - XCH - VALUE COMP FORMULA - -FLUX_MEASUREMENTS - FLUX_NAME VALUE DEVIATION - out_Ac 0.497 0.04 - -LABEL_INPUT - META_NAME ISOTOPOMER VALUE - - Gluc_U #111111 0.952 - #011111 0.008 - #101111 0.008 - #110111 0.008 - #111011 0.008 - #111101 0.008 - #111110 0.008 - - Gluc_1 #100000 0.9465 - #110000 0.0107 - #101000 0.0107 - #100100 0.0107 - #100010 0.0107 - #100001 0.0107 - - CO2_ext #0 0.9893 - #1 0.0107 - -// FTHF_0 #0 1 -// FTHF_1 #1 1 - - -LABEL_MEASUREMENTS - META_NAME CUM_GROUP VALUE DEVIATION CUM_CONSTRAINTS - - AcCoA 1 0.495 0.02 #00 - 2 0.303 0.02 #01 // CH3 specific enrichment - 3 0.012 0.02 #10 - 4 0.190 0.02 #11 - -PEAK_MEASUREMENTS - - META_NAME PEAK_NO VALUE_S VALUE_D- VALUE_D+ VALUE_DD VALUE_T DEVIATION_S DEVIATION_D- DEVIATION_D+ DEVIATION_DD/T - -METAB_MEASUREMENTS - META_NAME VALUE DEVIATION - // source: p.millard 2010/12/03 Nissle_Glc_conc.xlsx sent by email - Suc 15.8893144279264*1.e-3/10.7 1.e-2 - Mal 6.47828321758155*1.e-3/10.7 1.e-2 - PEP 0.588638938013844*1.e-3/10.7 1.e-2 - PGA 5.35922289028553*1.e-3/10.7 1.e-2 - Cit 17.4452511107891*1.e-3/10.7 1.e-2 - Gnt6P 1.54945619497337*1.e-3/10.7 1.e-2 - FruBP 5.27278870110121*1.e-3/10.7 1.e-2 - Fru6P 1.07071770798187*1.e-3/10.7 1.e-2 - Glc6P 5.24845556085526*1.e-3/10.7 1.e-2 - Rub5P+Rib5P+Xul5P 1.66034545348219*1.e-3/10.7 1.e-2 - -MASS_SPECTROMETRY - META_NAME FRAGMENT WEIGHT VALUE DEVIATION - Mal 1,2,3,4 1 0.587391867374382 0.0493159626907812 - 2 0.216493214407424 0.0306546571894417 - 3 0.159494782909672 0.03 - 4 0.0366201353085213 0.03 - PEP 1,2,3 0 0.462166666666667 0.01 - 1 0.340003333333333 0.01 - 2 0.0273166666666667 0.01 - 3 0.170513333333333 0.01 - PGA 1,2,3 0 0.447066666666667 0.0180848260520618 - 1 0.34127 0.018075350619006 - 2 0.02441 0.01 - 3 0.187253333333333 0.01 - Gnt6P 1,2,3,4,5,6 0 0.0195533333333333 0.01 - 1 0.72562 0.0120547874307264 - 2 0.0571233333333333 0.01 - 3 0.0135033333333333 0.01 - 4 0.01331 0.01 - 5 0.0131033333333333 0.01 - 6 0.157793333333333 0.01 - Sed7P 1,2,3,4,5,6,7 0 0.272433333333333 0.0122309539012022 - 1 0.23752 0.01 - 2 0.180446666666667 0.01 - 3 0.12744 0.01 - 4 0.06321 0.01 - 5 0.0839233333333333 0.01 - 6 0.01751 0.01 - 7 0.0175266666666667 0.01 - FruBP 1,2,3,4,5,6 0 0.0853733333333333 0.02 - 1 0.482283333333333 0.02 - 2 0.140086666666667 0.02 - 3 0.0953466666666667 0.02 - 4 0.09712 0.02 - 5 0.0120166666666667 0.02 - 6 0.0877666666666667 0.02 - Rib5P+Xul5P+Rub5P 1,2,3,4,5 0 0.433956666666667 0.0115292555411585 - 1 0.215956666666667 0.01 - 2 0.09658 0.01 - 3 0.129033333333333 0.01 - 4 0.0272733333333333 0.01 - 5 0.0971933333333333 0.01 - Glc6P 1,2,3,4,5,6 0 0.0167633333333333 0.01 - 1 0.716826666666667 0.01 - 2 0.0578233333333333 0.01 - 3 0.0122433333333333 0.01 - 4 0.01151 0.01 - 5 0.01089 0.01 - 6 0.173946666666667 0.01 - Fru6P 1,2,3,4,5,6 0 0.04716 0.01 - 1 0.623343333333333 0.0106878170518274 - 2 0.0820266666666667 0.01 - 3 0.03604 0.01 - 4 0.0315766666666667 0.01 - 5 0.0149133333333333 0.01 - 6 0.164943333333333 0.0111688555068697 - - Cit 1,2,3,4,5,6 1 0.322208057034832 0.03 - 2 0.288291305558056 0.03 - 3 0.212855540659154 0.03 - 4 0.117626468347467 0.03 - 5 0.0484839619377435 0.03 - 6 0.0105346664627478 0.03 - -OPTIONS - OPT_NAME OPT_VALUE - MATLAB_FOR_FLUX_EQ_CONSTR_MATR 1 - include_growth_flux 1 - mu 0.8 - optctrl_maxit 50 - commandArgs --TIMEIT - //optctrl_btdesc 0.1 - posttreat_R plot_smeas.R -METABOLITE_POOLS - META_NAME META_SIZE // size is in units of metab_scale option defined before - // source: p.millard 2010/12/03 Nissle_Glc_conc.xlsx sent by email - //Fum -2.47158569399681*1.e-3/10.7 - Suc -15.8893144279264*1.e-3/10.7 - Mal -6.47828321758155*1.e-3/10.7 - PEP -0.588638938013844*1.e-3/10.7 - //Aco -0.871035781090548*1.e-3/10.7 - PGA -5.35922289028553*1.e-3/10.7 - Cit -17.4452511107891*1.e-3/10.7 - //1-3diPG -7.31670971749174*1.e-3/10.7 - Gnt6P -1.54945619497337*1.e-3/10.7 - //Sed7P -11.5512490274248*1.e-3/10.7 conc - //PRPP -2.74943425027474*1.e-3/10.7 - //CMP -0.433742769835568*1.e-3/10.7 - //UMP -4.69421895911195*1.e-3/10.7 - //cAMP -0.109838817225867*1.e-3/10.7 - FruBP -5.27278870110121*1.e-3/10.7 - //AMP -0.801372321192278*1.e-3/10.7 - //GMP -0.394103922207334*1.e-3/10.7 - //dCDP -4.41071909173208*1.e-3/10.7 - //CDP -0.204009683016196*1.e-3/10.7 - //UDP -0.528949008341637*1.e-3/10.7 - //ADP -2.0246124170601*1.e-3/10.7 - //GDP -1.02724694822302*1.e-3/10.7 - //CTP -1.39055711133101*1.e-3/10.7 - //UTP -1.73433655893259*1.e-3/10.7 - //ATP -6.32820169657847*1.e-3/10.7 - //UDP-Glc -9.93608536663137*1.e-3/10.7 conc - //ADP-Glc -0*1.e-3/10.7 - //GDP-Man -5.52555199979534*1.e-3/10.7 - //G1P -72.1756241692542*1.e-3/10.7 conc - //F1P -0.0942291270750201*1.e-3/10.7 - Fru6P -1.07071770798187*1.e-3/10.7 - Glc6P -5.24845556085526*1.e-3/10.7 - //M6P -0.642830603277483*1.e-3/10.7 - //Rib1P -0.0558080128279041*1.e-3/10.7 - Rub5P -1.66034545348219/3*1.e-3/10.7 -// Rib5P -1.66034545348219/3*1.e-3/10.7 - Rib5P 1.e-7 // fixed arbitrary low - Xul5P -4*1.66034545348219/3*1.e-3/10.7 - //dADP -5.86959266616353*1.e-3/10.7 conc - //dATP -13.1542008577561*1.e-3/10.7 conc - //dTDP -9.52423600696743*1.e-3/10.7 conc - //dTTP -19.9757914243397*1.e-3/10.7 conc diff --git a/tools/influx_si/test-data/e_coli_growth.log b/tools/influx_si/test-data/e_coli_growth.log deleted file mode 100644 index a4bef48a51..0000000000 --- a/tools/influx_si/test-data/e_coli_growth.log +++ /dev/null @@ -1,45 +0,0 @@ -"/usr/local/miniconda3/bin/influx_s" "e_coli.ftbl" "e_coli_growth.ftbl" -code gen: 2020-03-25 14:32:15 -executing: "/usr/local/miniconda3/bin/python3.7" "/home/STORAGE/local/miniconda3/bin/ftbl2optR.py" "--tblimit" "0" "--ropts" "TIMEIT=TRUE" "e_coli_growth.ftbl" -calcul : 2020-03-25 14:32:22 -load : 2020-03-25 14:32:24.17 cpu=1.207 -rinit : 2020-03-25 14:32:24.17 cpu=1.21 -r_flux : 2020-03-25 14:32:24.17 cpu=1.21 -Afl qr(): 2020-03-25 14:32:24.21 cpu=1.248 -dfl_dffg: 2020-03-25 14:32:24.45 cpu=1.258 -spAbr : 2020-03-25 14:32:24.45 cpu=1.262 -weight 1: 2020-03-25 14:32:24.45 cpu=1.263 -weight 2: 2020-03-25 14:32:24.45 cpu=1.265 -weight 3: 2020-03-25 14:32:24.45 cpu=1.267 -weight 4: 2020-03-25 14:32:24.46 cpu=1.272 -weight 5: 2020-03-25 14:32:24.47 cpu=1.274 -weight 6: 2020-03-25 14:32:24.47 cpu=1.275 -weight 7: 2020-03-25 14:32:24.47 cpu=1.277 -measure : 2020-03-25 14:32:24.56 cpu=1.343 -ineq : 2020-03-25 14:32:24.60 cpu=1.368 -preopt : 2020-03-25 14:32:24.66 cpu=1.413 -labargs : 2020-03-25 14:32:24.66 cpu=1.416 -run 1: 2020-03-25 14:32:24.66 cpu=1.417 -Starting point -res esti: 2020-03-25 14:32:24.67 cpu=1.419 -The following 1 ineqalitie(s) are active at starting point: -f.x.xul>=0 -kvh init: 2020-03-25 14:32:24.80 cpu=1.438 -check ja: 2020-03-25 14:32:24.85 cpu=1.454 -optim : 2020-03-25 14:32:24.94 cpu=1.515 -it=0 res=45.2102 -it=1 res=12.83995 normstep=1.515861 btk=1 -it=2 res=12.25994 normstep=1.259661 btk=1 -it=3 res=8.098585 normstep=0.5463658 btk=1 -it=4 res=7.960851 normstep=0.0589933 btk=1 -it=5 res=7.959322 normstep=0.03050743 btk=1 -it=6 res=7.959081 normstep=0.004902886 btk=1 -it=7 res=7.959029 normstep=0.003060732 btk=1 -it=8 res=7.959017 normstep=0.001367668 btk=1 -it=9 res=7.959014 normstep=0.0006590508 btk=1 -it=10 res=7.959014 normstep=0.0003104052 btk=1 -it=15 res=7.959014 normstep=7.292328e-06 btk=1 -postopt : 2020-03-25 14:32:26.48 cpu=3.125 -linstats: 2020-03-25 14:32:26.77 cpu=3.377 -rend : 2020-03-25 14:32:27.07 cpu=3.706 -end : 2020-03-25 14:32:27 diff --git a/tools/influx_si/test-data/e_coli_i.ftbl b/tools/influx_si/test-data/e_coli_i.ftbl deleted file mode 100755 index 01850a6d36..0000000000 --- a/tools/influx_si/test-data/e_coli_i.ftbl +++ /dev/null @@ -1,789 +0,0 @@ -PROJECT - NAME VERSION FORMAT DATE COMMENT - K12_MG1655.ftbl 1 101109 modele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees - -NETWORK - FLUX_NAME EDUCT_1 EDUCT_2 PRODUCT_1 PRODUCT_2 - -// Glycolyse. -// PPP -// TCA -// voies anaplerotiques: pepc. enz malique -// voie glyoxylate -// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre) -// saisie differentielle des substrats marques - - -// Uptake substrats - - Glucupt_1 Gluc_1 Glc6P // fehlt bei wolfgang - #ABCDEF #ABCDEF // fehlt bei wolfgang - - Glucupt_U Gluc_U Glc6P // fehlt bei wolfgang - #ABCDEF #ABCDEF // fehlt bei wolfgang - -// CO2upt CO2_ext CO2 // entree de CO2 non marque -// #A #A // ce flux est a laisser libre - -// FTHF0 FTHF_0 FTHF // prise en charge de FTHF non marque -// #A #A - -// FTHF1 FTHF_1 FTHF // prise en charge de FTHF marque -// #a #a - - -// Embden Meyerhof Parnas Pathway - - pgi Glc6P Fru6P - #ABCDEF #ABCDEF - - pfk Fru6P FruBP - #ABCDEF #ABCDEF - - ald FruBP GA3P GA3P - #ABCDEF #CBA #DEF - -// tpi DHAP GA3P -// #ABC #CBA - - pgk GA3P PGA - #ABC #ABC - - eno PGA PEP - #ABC #ABC - - pyk PEP Pyr - #ABC #ABC - - -// Methylglyoxal Pathway - -// mgs DHAP Pyr -// #ABC #ABC - - -// Pentose Phosphate Pathway - - zwf Glc6P Gnt6P - #ABCDEF #ABCDEF - - gnd Gnt6P CO2 Rib5P - #ABCDEF #A #BCDEF - - edd Gnt6P Pyr GA3P - #ABCDEF #ABC #DEF - -// ta Ery4P Fru6P GA3P Sed7P -// #ABCD #abcdef #def #abcABCD - -// tk1 GA3P Sed7P Rib5P Rib5P -// #ABC #abcdefg #abABC #cdefg - -// tk2 GA3P Fru6P Rib5P Ery4P -// #ABC #abcdef #abABC #cdef - - ta GA3P Sed7P Ery4P Fru6P - #ABC #abcdefg #defg #abcABC - - tk1 Rib5P Rib5P GA3P Sed7P - #ABCDE #abcde #CDE #ABabcde - - tk2 Rib5P Ery4P GA3P Fru6P - #ABCDE #abcd #CDE #ABabcd - - -// Tricarboxylic Acid Cycle - - pdh Pyr AcCoA CO2 - #ABC #BC #A - - citsynth AcCoA OAA ICit - #AB #abcd #dcbaBA - - idh ICit AKG CO2 - #ABCDEF #ABCEF #D - - akgdh AKG Suc CO2 - #ABCDE #BCDE #A - - fum_a Suc Mal - #ABCD #ABCD - - fum_b Suc Mal - #ABCD #DCBA - - maldh Mal OAA - #ABCD #ABCD - - -// Glyoxylate Shunt - -// gs1 ICit GlyOx Suc -// #ABCDEF #AB #DCEF - -// gs2 GlyOx AcCoA OAA -// #AB #ab #ABba - - -// Anaplerotic Reactions - - ppc PEP CO2 OAA // PEPcarboxylase - #ABC #a #ABCa - - mae Mal Pyr CO2 // enzyme malique - #ABCD #ABC #D - -// pck OAA PEP CO2 // PEP carboxykinase -// #ABCD #ABC #D - - -// Biosynthetic Pathways - - // Glucose-6-Phosphate Family - - bs_glc6P Glc6P BM_Glc6P - #ABCDEF #ABCDEF - - // Fructose-6-Phosphate Family - - bs_fru6P Fru6P BM_Fru6P // sortie de Fru6P pour biomasse - #ABCDEF #ABCDEF - - // Phosphoglycerate Family - - bs_pga PGA BM_PGA - #ABC #ABC - - bs_pga_aux BM_PGA PGA_Aux - #ABC #ABC - - bs_pga1 BM_PGA Ser - #ABC #ABC - - bs_pga1_aux Ser Ser_Aux - #ABC #ABC - - bs_pga2 Ser Cys // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga2_aux Cys Cys_Aux // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga3 Ser Gly FTHF // formation de gly pour biomasse - #ABC #AB #C // ce flux est reversible - - bs_pga3_aux Gly Gly_Aux // pour conserver Gly comme metabolite intracellulaire - #AB #AB - - // TrioseP Family - - bs_DHAP GA3P Glp // formation glycerolP pour lipides - #ABC #ABC - - // Pyruvate Family - - bs_pyr Pyr BM_Pyr - #ABC #ABC - - bs_pyr1 BM_Pyr Ala - #ABC #ABC - - bs_pyr1_aux Ala Ala_Aux // pour conserver Ala comme metabolite intracellulaire - #ABC #ABC - - bs_pyr2 BM_Pyr BM_Pyr AKV CO2 // AKV et Val ont le meme squelette C - #ABC #abc #ABbcC #a // cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val - - bs_pyr4 AKV Val // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr4_aux Val Val_Aux // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr3 AKV BM_AcCoA Leu CO2 - #ABCDE #ab #abBCDE #A - - bs_pyr3_aux Leu Leu_Aux // pour conserver Leu comme metabolite intracellulaire - #ABCDEF #ABCDEF - - - // Erythrose-4-Phosphate Family - - bs_e4p Ery4P BM_Ery4P // pour utiliser les donnees sur Ery4P - #ABCD #ABCD - -// bs_e4p_aux BM_Ery4P Ery4P_aux // pour utiliser les donnees sur Ery4P -// #ABCD #ABCD - - - // Ribose-5-Phosphate Family - - bs_rib5p Rib5P BM_Rib5P // pour utiliser les donnees sur Rib5P - #ABCDE #ABCDE - - bs_rib5p1 BM_Rib5P FTHF His // pour utiliser les donnees sur Rib5P - #ABCDE #a #EDCBAa - - bs_rib5p1_aux His His_Aux // sortie pour conserver His comme metabolite intracellulaire - #ABCDEF #ABCDEF - - bs_rib5p2 BM_Rib5P Ri5P_Aux // sortie de Ri5P pour autres besoins que His - #ABCDE #ABCDE // ce flux est important pour ne pas imposer de fausses contraintes sur FTHF si on considerait His comme seule sortie - - - // Aromatic Amino Acids - - bs_pep PEP BM_PEP - #ABC #ABC - - bs_pep1 BM_PEP BM_Ery4P DAHP - #ABC #abcd #ABCabcd - - bs_pep2 BM_PEP DAHP Chor - #ABC #abcdefg #ABCabcdefg - - bs_pep3a Chor Phe CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep3b Chor Phe CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep3_aux Phe Phe_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep4a Chor Tyr CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep4b Chor Tyr CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep4_aux Tyr Tyr_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep5 BM_PEP PEP_Aux - #ABC #ABC - - bs_pep6 Chor BM_Rib5P Trp PyrCO2 - #ABCDEFGHIJ #abcde #edcbaJEFGHI #ABCD - - bs_pep6_aux Trp Trp_Aux - #ABCDEFGHIJK #ABCDEFGHIJK - - bs_pep7 PyrCO2 Pyr CO2 - #ABCD #ABC #D - - - // Acetyl-CoA - - bs_accoa AcCoA BM_AcCoA - #AB #AB - - bs_accoa_aux BM_AcCoA AcCoA_Aux - #AB #AB - - - // Alpha-Ketoglutarate Family - - bs_akg AKG BM_AKG // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg1 BM_AKG Glu // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg2 Glu Pro // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg3 Glu Gln // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg4 Glu CO2 Arg // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #a #ABCDEa - - bs_akg4_aux Arg Arg_Aux // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDEF #ABCDEF - - - // Oxaloacetate Family - - bs_oaa OAA BM_OAA - #ABCD #ABCD - - bs_oaa1 BM_OAA Asp - #ABCD #ABCD - - bs_oaa1_aux Asp Asp_Aux - #ABCD #ABCD - - bs_oaa2 Thr BM_Pyr Ile CO2 - #ABCD #abc #ABbCDc #a - - bs_oaa2_aux Ile Ile_Aux - #ABCDEF #ABCDEF - - bs_oaa3a BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #ABCDcb #a - - bs_oaa3b BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #abcDCB #A - - bs_oaa3_aux Lys Lys_Aux - #ABCDEF #ABCDEF - - bs_oaa4 BM_OAA OAA_Aux - #ABCD #ABCD - - bs_oaa5 BM_OAA Thr - #ABCD #ABCD - - bs_oaa5_aux Thr Thr_Aux - #ABCD #ABCD - - bs_oaa6 BM_OAA FTHF Met - #ABCD #a #ABCDa - - bs_oaa6_aux Met Met_Aux - #ABCDE #ABCDE - - bs_oaa7 BM_OAA Asn - #ABCD #ABCD - - bs_oaa7_aux Asn Asn_Aux - #ABCD #ABCD - - -// Flux de sortie - - out_co2 CO2 CO2_out // Sortie de CO2 - #A #A - - out_Ac AcCoA Acetate // Sortie d'acetate - #AB #AB - - out_FTHF FTHF FTHF_out - #A #A - -FLUXES - NET - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt_1 F 0.7 //0.807194 - Glucupt_U D -// CO2upt F 0.669589 -// FTHF0 F 0.00224836 -// FTHF1 F 0.001 - - pgi D - pfk D - ald D -// tpi D - pgk D - eno D - pyk F 1.4 - - zwf F 0.2 - gnd F 0.15062 - edd D - ta D - tk1 D - tk2 D - - pdh D - citsynth D - idh D - akgdh D - fum_a D - fum_b D - maldh D - -// gs1 C 0 -// gs2 D - - ppc D - mae D -// pck D - - // flux de biomasse - - bs_glc6P C 0.0109 // sortie de G6P - bs_fru6P C 0.0038 // sortie de F6P - bs_pga C 0.0791 // sortie de PGA pour formation de biomasse - bs_pga_aux D // sortie de PGA pour formation de biomasse - bs_pga1 D // conversion PGA donne ser - bs_pga1_aux C 0.0109 // conversion PGA donne ser - bs_pga2 D - bs_pga2_aux C 0.0046 // conversion PGA donne Cys - bs_pga3 D // reaction de synthese de Gly - bs_pga3_aux C 0.0308 // sortie de Gly - bs_DHAP C 0.0068 // formation de glycerolP pour lipides - bs_pyr C 0.1501 // avant : 0.1547 // sortie de Pyr pour formation de biomasse - bs_pyr1 D // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Leu - bs_pyr2 D // synthese d'AKV. consomme 2 Pyr - bs_pyr4 D - bs_pyr4_aux C 0.0213 // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 D // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux C 0.0227 // sortie de Leu - bs_e4p D // sortie d'Ery4p pour biomasse -// bs_e4p_aux C 0 // sortie d'Ery4p pour Trp - bs_rib5p C 0.0476 // synthese d'His - bs_rib5p1 D // synthese d'His - bs_rib5p1_aux C 0.0048 // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_pep C 0.0381 // sortie de PEP - bs_pep1 D // sortie de PEP - bs_pep2 D - bs_pep3a D - bs_pep3b D - bs_pep3_aux C 0.0093 - bs_pep4a D - bs_pep4b D - bs_pep4_aux C 0.0069 - bs_pep5 C 0.0027 - bs_pep6 D - bs_pep6_aux D - bs_pep7 D - bs_accoa C 0.1565 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_akg C 0.0571 // sortie d'AKG - bs_akg1 D - bs_akg2 C 0.0111 - bs_akg3 C 0.0132 - bs_akg4 D - bs_akg4_aux D - bs_oaa C 0.0947 // sortie d'OAA pour formation de biomasse - bs_oaa1 D // sortie d'OAA pour Asp - bs_oaa1_aux C 0.0121 // sortie d'Asp - bs_oaa2 D // synthese d'Ile - bs_oaa2_aux C 0.0146 // sortie d'Ile - bs_oaa3a D - bs_oaa3b D - bs_oaa3_aux C 0.0173 - bs_oaa4 D - bs_oaa5 D - bs_oaa5_aux C 0.0128 - bs_oaa6 D - bs_oaa6_aux C 0.0077 - bs_oaa7 D - bs_oaa7_aux C 0.0121 - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac F 0.213 // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - - XCH - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt_1 D - Glucupt_U D -// CO2upt D -// FTHF0 D -// FTHF1 D - - pgi C 0.752386 // 2011-02-22 ssg: was F => often unresolved with --irand option - pfk C 0 - ald F 0.413926 -// tpi F 0.5 - pgk C 0.984718 // 2011-02-22 ssg: was F => often unresolved with --irand option - eno F 0.800962 - pyk C 0.0109591 // 2010-10-01 ssg: was F => unresolved if co2 uptake is unlimited - - zwf C 0 - gnd C 0 - edd C 0 - ta F 0.359468 - tk1 F 0.166316 - tk2 F 2.11559e-03 - - pdh C 0.0322745 // 2010-10-02 ssg: was F, otherwise unsolvable in monte-carlo - citsynth C 0 - idh C 0 - akgdh C 0 - fum_a F 0.395958 - fum_b D - maldh C 0.647115 //********************************************** C pour analyse de sensibilite, F pour minimisation - -// gs1 C 0 -// gs2 C 0 - - ppc F 0.256772 - mae C 0 -// pck C 0 - - bs_glc6P D // sortie de G6P - bs_fru6P D // sortie de F6P - bs_pga C 0 // conversion PGA donne Ser - bs_pga_aux D // conversion PGA donne Ser - bs_pga1 C 0 // conversion PGA donne Ser - bs_pga1_aux D // conversion PGA donne Ser - bs_pga2 C 0 // ser donne Cys. correspond a la sortie de PGA pour biomasse autre que formation Gly - bs_pga2_aux D - bs_pga3 C 0.011799 // reaction de synthese de Gly. cette reaction est reversible - bs_pga3_aux D // sortie de Gly - bs_DHAP D // formation de glycerolP pour lipides - bs_pyr C 0 // formation d'Ala - bs_pyr1 C 0 // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Ile - bs_pyr2 C 0 // synthese d'AKV. consomme 2 Pyr - bs_pyr4 C 0 - bs_pyr4_aux D // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 C 0 // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux D // sortie de Leu - bs_e4p C 0 // sortie d'Ery4p -// bs_e4p_aux D // sortie d'Ery4p pour Trp - bs_rib5p C 0 // synthese d'His - bs_rib5p1 C 0 // synthese d'His - bs_rib5p1_aux D // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_accoa C 0 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_pep C 0 // sortie de PEP - bs_pep1 C 0 // sortie de PEP - bs_pep2 C 0 - bs_pep3a C 0 - bs_pep3b C 0 - bs_pep3_aux D - bs_pep4a C 0 - bs_pep4b C 0 - bs_pep4_aux D - bs_pep5 D - bs_pep6 C 0 - bs_pep6_aux D - bs_pep7 C 0 - bs_akg C 0 // sortie d'AKG - bs_akg1 C 0 - bs_akg2 D - bs_akg3 D - bs_akg4 C 0 - bs_akg4_aux D - bs_oaa C 0 - bs_oaa1 C 0 // sortie d'OAA autres que Met - bs_oaa1_aux D // sortie d'OAA autres que Met - bs_oaa2 C 0 // synthese de Met - bs_oaa2_aux D // sortie de Met - bs_oaa3a C 0 - bs_oaa3b C 0 - bs_oaa3_aux D - bs_oaa4 D - bs_oaa5 C 0 - bs_oaa5_aux D - bs_oaa6 C 0 - bs_oaa6_aux D - bs_oaa7 C 0 - bs_oaa7_aux D - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac D // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - -EQUALITIES - NET - VALUE FORMULA - - 0 fum_a-fum_b // scrambling reaction - 1 Glucupt_1+Glucupt_U - 0 bs_oaa3a-bs_oaa3b - 0 bs_pep3a-bs_pep3b - 0 bs_pep4a-bs_pep4b - - XCH - VALUE FORMULA - - 0 fum_a-fum_b - -INEQUALITIES - NET - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - 1 <= pyk - 0.0001 <= edd - 0.0001 <= gnd - 0.0001 <= zwf - 0.0001 <= ppc - 0.0001 <= mae -// 2 >= CO2upt // 2010-08-18 too high value makes jacobian rank deficient - XCH - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - METAB - VALUE COMP FORMULA -// 1.2 >= AKG - - -FLUX_MEASUREMENTS - FLUX_NAME VALUE DEVIATION // Val Dev - out_Ac 0.213 0.0001 - -LABEL_INPUT - META_NAME ISOTOPOMER VALUE - - Gluc_U #111111 1 - #000000 0. - Gluc_1 #100000 1. - #000000 0. -// CO2_ext #0 0.989 -// #1 0.011 - -// FTHF_0 #0 1 -// FTHF_1 #1 1 - - -LABEL_MEASUREMENTS - META_NAME CUM_GROUP VALUE DEVIATION CUM_CONSTRAINTS - // Example - -PEAK_MEASUREMENTS - META_NAME PEAK_NO VALUE_S VALUE_D- VALUE_D+ VALUE_DD VALUE_T DEVIATION_S DEVIATION_D- DEVIATION_D+ DEVIATION_DD/T - - -MASS_SPECTROMETRY - META_NAME FRAGMENT WEIGHT VALUE DEVIATION - -// Deviation fixee a 0.02 // correction inoc 0.062 - - - - Suc 1,2,3,4 1 0.371605319 0.01 - 2 0.360829749 0.01 - 3 0.208425325 0.01 - 4 0.059139607 0.01 -// Mal 1,2,3,4 0 0.164619329483 0.02 -// 1 0.110072868518 0.02 -// 2 0.637801316225333 0.02 -// 3 0.0863461044204333 0.02 -// 4 0.00116038135315367 0.02 - ICit 1,2,3,4,5,6 0 0.131864539419667 0.02 - 1 0.225857638569 0.02 - 2 0.256421170949333 0.02 - 3 0.209230210478667 0.02 - 4 0.116863585449667 0.02 - 5 0.0457727744643333 0.02 - 6 0.0139900806697867 0.02 - PEP 1,2,3 0 0.421359839367667 0.01 - 1 0.358998301162333 0.01 - 2 0.0348521859365667 0.01 - 3 0.184789673534 0.01 - PGA 1,2,3 0 0.434335785072667 0.01 - 1 0.352829683224667 0.01 - 2 0.0323479804176 0.01 - 3 0.180486551285333 0.01 - FruBP 1,2,3,4,5,6 0 0.0738121029259333 0.01 - 1 0.454450017158667 0.01 - 2 0.160823529969333 0.01 - 3 0.0944468077710667 0.01 - 4 0.105281338489667 0.01 - 5 0.0155016033633 0.01 - 6 0.0956846003217333 0.01 - Glc6P 1,2,3,4,5,6 0 0.0160587173349 0.01 - 1 0.673510772480667 0.01 - 2 0.0930110047641 0.01 - 3 0.0280359937297 0.01 - 4 0.0397315614067667 0.01 - 5 0.0145524520950667 0.01 - 6 0.135099498189 0.01 - Fru6P 1,2,3,4,5,6 0 0.0235029951295 0.01 - 1 0.624253565357667 0.01 - 2 0.113068441282333 0.01 - 3 0.0456605631765 0.01 - 4 0.0516089447155667 0.01 - 5 0.0185881765378333 0.01 - 6 0.123317313800333 0.01 - Rib5P 1,2,3,4,5 0 0.341615670498667 0.01 - 1 0.25454117519 0.01 - 2 0.159027180368333 0.01 - 3 0.113789577528667 0.01 - 4 0.0615266612553333 0.01 - 5 0.0694997351590667 0.01 - Gnt6P 1,2,3,4,5,6 0 0.0249552273874 0.01 - 1 0.672556163913 0.01 - 2 0.0866890773125333 0.01 - 3 0.0313987199704333 0.01 - 4 0.0314691889898667 0.01 - 5 0.0138168327362333 0.01 - 6 0.139114789690333 0.01 -// Ery4P 1,2,3,4 0 0.178453461108 0.01 -// 1 0.412398433968333 0.01 -// 2 0.273694508221667 0.01 -// 3 0.116142498670667 0.01 -// 4 0.0193110980315 0.01 -METABOLITE_POOLS - META_NAME META_SIZE - AKG -1 - AKV 1 - AcCoA 1 - Ala 1 - Arg 1 - Asn 1 - Asp 1 - BM_AKG 1 - BM_AcCoA 1 - BM_Ery4P 1 - BM_OAA 1 - BM_PEP 1 - BM_PGA 1 - BM_Pyr 1 - BM_Rib5P 1 - CO2 1 - Chor 1 - Cys 1 - DAHP 1 - Ery4P -1 - FTHF 1 - Fru6P -1 - FruBP -1 - GA3P -1 - Glc6P 1 - Glu 1 - Gly 1 - Gnt6P -1 - His 1 - ICit -1 - Ile 1 - Leu 1 - Lys 1 - Mal 1 - Met 1 - OAA -1 - PEP -1 - PGA -1 - Phe 1 - Pyr -1 - PyrCO2 1 - Rib5P -1 - Sed7P -1 - Ser 1 - Suc -1 - Thr 1 - Trp 1 - Tyr 1 - Val 1 -METAB_MEASUREMENTS - META_NAME VALUE DEVIATION - Fru6P 0.4263681348074568 0.01 - GA3P 0.469998855791378 0.01 - FruBP 1.860001398406723 0.01 - PEP 0.1099999780931608 0.01 - Rib5P 0.01933825682263468 0.01 - Sed7P 0.05727159999541005 0.01 - -OPTIONS - OPT_NAME OPT_VALUE - dt 1 - nsubdiv_dt 4 - //tmax 10 - file_labcin e_coli_msen.txt - commandArgs --noscale --TIMEIT --time_order=2 --zc=0 --clowp 1.e-9 - optctrl_errx 1.e-3 - optctrl_maxit 50 - optctrl_btmaxit 16 - optctrl_btstart 1 - optctrl_btfrac 0.5 - //optctrl_history 1 - optctrl_adaptbt 1 - optctrl_monotone 1 - posttreat_R plot_imass.R diff --git a/tools/influx_si/test-data/e_coli_i.log b/tools/influx_si/test-data/e_coli_i.log deleted file mode 100644 index 3b8d297503..0000000000 --- a/tools/influx_si/test-data/e_coli_i.log +++ /dev/null @@ -1,47 +0,0 @@ -"/usr/local/miniconda3/bin/influx_i" "e_coli_i.ftbl" -code gen: 2020-03-25 15:40:11 -executing: "/usr/local/miniconda3/bin/python3.7" "/home/STORAGE/local/miniconda3/bin/ftbl2optR.py" "--tblimit" "0" "--ropts" "noscale=TRUE; clowp=1e-09; zc=0.0; time_order='2'; TIMEIT=TRUE" "--case_i" "e_coli_i.ftbl" -executing: R --vanilla --slave < e_coli_i.R -calcul : 2020-03-25 15:40:14 -load : 2020-03-25 15:40:18.59 cpu=1.02 -rinit : 2020-03-25 15:40:18.61 cpu=1.031 -r_flux : 2020-03-25 15:40:18.61 cpu=1.031 -Afl qr(): 2020-03-25 15:40:18.68 cpu=1.101 -dfl_dffg: 2020-03-25 15:40:18.91 cpu=1.139 -spAbr : 2020-03-25 15:40:18.91 cpu=1.143 -weight 1: 2020-03-25 15:40:18.91 cpu=1.143 -weight 2: 2020-03-25 15:40:18.95 cpu=1.225 -weight 3: 2020-03-25 15:40:19.02 cpu=1.348 -weight 4: 2020-03-25 15:40:19.07 cpu=1.456 -weight 5: 2020-03-25 15:40:19.10 cpu=1.506 -weight 6: 2020-03-25 15:40:19.17 cpu=1.574 -measure : 2020-03-25 15:40:19.25 cpu=1.602 -ineq : 2020-03-25 15:40:19.33 cpu=1.683 -preopt : 2020-03-25 15:40:19.57 cpu=2.056 -labargs : 2020-03-25 15:40:19.58 cpu=2.069 -cl expor: 2020-03-25 15:40:20.32 cpu=2.089 -cl sourc: 2020-03-25 15:40:21.20 cpu=2.204 -run 1: 2020-03-25 15:40:24.75 cpu=5.386 -Starting point -zc ineq : 2020-03-25 15:40:24.75 cpu=5.387 -kvh init: 2020-03-25 15:40:24.78 cpu=5.432 -check ja: 2020-03-25 15:40:25.27 cpu=5.625 -optim : 2020-03-25 15:40:26.47 cpu=5.632 -it=0 res=237.7947 -it=1 res=70.06248 normstep=30.47659 btk=1 -it=2 res=36.43491 normstep=31.35182 btk=1 -it=3 res=21.83319 normstep=0.2793447 btk=1 -it=4 res=21.7384 normstep=0.03332941 btk=1 -it=5 res=21.72383 normstep=0.03867587 btk=1 -it=6 res=21.6348 normstep=0.08885869 btk=1 -it=7 res=21.37745 normstep=0.4890457 btk=0.5 -it=8 res=21.24931 normstep=0.6490092 btk=1 -it=9 res=20.96647 normstep=0.3171006 btk=1 -it=10 res=20.96366 normstep=0.1287473 btk=1 -it=15 res=20.96358 normstep=5.449035e-05 btk=1 -secondzc: 2020-03-25 15:40:41.08 cpu=8.101 -After the first optimization, no zero crossing inequality was activated. So no reoptimization -postopt : 2020-03-25 15:40:41.09 cpu=8.111 -linstats: 2020-03-25 15:40:41.87 cpu=8.697 -rend : 2020-03-25 15:40:42.16 cpu=9.089 -end : 2020-03-25 15:40:43 diff --git a/tools/influx_si/test-data/e_coli_msen.txt b/tools/influx_si/test-data/e_coli_msen.txt deleted file mode 100644 index 59d9ad0a5b..0000000000 --- a/tools/influx_si/test-data/e_coli_msen.txt +++ /dev/null @@ -1,62 +0,0 @@ -# simulated measurement with noise (e_coli_mse.txt+noise with sd from e_coli_ie.ftbl) -row_col 1 2 3 4 5 6 7 8 9 10 # see if ignored -m:Rib5P:1,2,3,4,5:0:693 0.8301287113482 0.705273440788489 0.630962344759146 0.599912176047555 0.573404157056382 0.549013957980969 0.544210331911793 0.508277982602693 0.499016033193777 0.485286541644114 -m:Rib5P:1,2,3,4,5:1:694 0.139499223890491 0.222339755290909 0.243819119211992 0.251856352480698 0.277951849850555 0.26624702204022 0.253318961326116 0.242251579900221 0.257243898371434 0.245894214016595 -m:Rib5P:1,2,3,4,5:2:695 0.0290070095454754 0.0533324485991101 0.0672401633923346 0.0862872836178193 0.0903657887685621 0.111438208430907 0.106264456513264 0.127665879867143 0.129695750051211 0.143194872657798 -m:Rib5P:1,2,3,4,5:3:696 0.00160408414038381 0.0229950078431453 0.0242885112480173 0.0236262011871506 0.0384713977458625 0.0395862886561061 0.0399422126310299 0.0434575340902056 0.057575220004768 0.053327058437221 -m:Rib5P:1,2,3,4,5:4:697 0.00284213879991028 0.00136220262120975 0.00945113487347922 0.0262298815476012 0.0339069314888829 0.045111483933521 0.0308238334730582 0.0483697721397453 0.0489364990171572 0.056352033597862 -m:Rib5P:1,2,3,4,5:5:698 0.00381673478018765 0.0136152393183676 0.0187948292708048 0.029237436783619 0.0340531521955641 0.0266101321627734 0.0399368276378717 0.046845505348588 0.0373560862314168 0.0462793762301527 - -m:Glc6P:1,2,3,4,5,6:0:679 0.493952162617383 0.241788346718873 0.129931016363475 0.0728422136538586 0.0555639355367493 0.0401826943349669 0.0314283807166068 0.0372888457858936 0.0241841875922507 0.030958811289491 -m:Glc6P:1,2,3,4,5,6:1:680 0.404262494562378 0.601528892652349 0.673997202888538 0.700284514239992 0.714448890273421 0.702861007777799 0.685523754578573 0.704662941393205 0.68684504474593 0.682856315908778 -m:Glc6P:1,2,3,4,5,6:2:681 -0.00971071210181876 0.00551823887717201 0.00739665415406503 0.0281297328224873 0.0374856512913617 0.0452870902703815 0.0460785142653824 0.0814776167048646 0.0659155729271299 0.0785432369222522 -m:Glc6P:1,2,3,4,5,6:3:682 0.0174215229553926 0.0170559578191188 0.025304157357846 0.0430017639175836 0.0348874311624526 0.0489484715084225 0.0351411534788991 0.0269856593772156 0.0192927092252581 0.0385779418075484 -m:Glc6P:1,2,3,4,5,6:4:683 0.0043659263104226 0.00877723557364165 0.00725821330054203 0.0126022050427868 0.0289095437215765 0.0282667499900472 0.0428080102047586 0.02592897485848 0.0333262720524978 0.0333836437820453 -m:Glc6P:1,2,3,4,5,6:5:684 -0.00295242877114927 0.0228561008765114 0.00107949443140708 0.00576924101393923 0.00359462341126682 -0.00291644895745689 -0.000650092439870991 -0.00722996134202132 -0.0148852807485112 0.00354062643070811 -m:Glc6P:1,2,3,4,5,6:6:685 0.0949417468382319 0.129448731101592 0.11756999828035 0.116834010941517 0.156652332757322 0.142614492470288 0.136775707360364 0.142247844825291 0.128888546346649 0.132781514945108 - -m:ICit:1,2,3,4,5,6:0:657 0.964808884433423 1.00382002410753 0.976023042393462 0.894194434705964 0.766995156890106 0.690445464992781 0.63176893227039 0.528124368350999 0.442923129524696 0.395459161361152 -m:ICit:1,2,3,4,5,6:1:658 0.0143600676195567 0.0436548728034513 0.0534942728405111 0.0639987878375545 0.134065776629187 0.146919412024849 0.227799495903936 0.272494318035825 0.294024445522389 0.247190260186848 -m:ICit:1,2,3,4,5,6:2:659 0.0166297755006583 -0.0125797291227997 0.0127788142463291 0.0221526869422438 0.0870629846959751 0.124622112755198 0.0805533586113773 0.124589240328517 0.174587994783957 0.20637931969854 -m:ICit:1,2,3,4,5,6:3:660 -0.0164071602748031 -0.021607873341015 0.0405857166794395 0.0067533469595018 0.00856287955464007 0.032691842098317 0.03648172445535 0.0897097881203855 0.0377806396555514 0.108435276435524 -m:ICit:1,2,3,4,5,6:4:661 -0.0311946635661311 0.0112912100867262 -0.00328434976694734 -0.0291273953557248 0.00347615542802288 0.0135048730050441 0.0071339543400162 0.004515912946923 0.00749482343750274 0.0493479770558265 -m:ICit:1,2,3,4,5,6:5:662 -0.0151243019611019 -0.010343521441609 -0.0179127774136863 -0.0106202857696235 0.00503762224320454 0.0053007176644241 0.00856924745879578 -0.0046437475961502 -0.0137565134141504 -0.00931041072969327 -m:ICit:1,2,3,4,5,6:6:663 -0.00200369348784026 -0.00117170585835455 0.0284291904473502 0.0128473467258485 0.0142796581015085 -0.0119617502140488 0.00832215559537679 0.0333737729365706 -0.0233735989156783 -0.0163687999125459 - 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-m:Fru6P:1,2,3,4,5,6:0:686 0.543315183156242 0.271442215154307 0.15342041555599 0.104226528529691 0.0601207158756622 0.0667835627698116 0.032169592051183 0.0444987186974436 0.0312424656505585 0.0371738310019649 -m:Fru6P:1,2,3,4,5,6:1:687 0.381498556157925 0.566820512279315 0.64753590777845 0.669325655114947 0.672155048267478 0.658521355463491 0.672620087099418 0.658937533256872 0.65065211800828 0.629670055679612 -m:Fru6P:1,2,3,4,5,6:2:688 -0.0102984598677217 0.00689221621662103 0.0339321967612094 0.0465421546157055 0.0571543647969092 0.0732789089821859 0.0959460289039786 0.0715783489999898 0.0926230588187283 0.0957791120020438 -m:Fru6P:1,2,3,4,5,6:3:689 0.0250657939547482 0.023460916637709 0.0473358002097497 0.0321217800543612 0.0458500181495104 0.0259668014922916 0.0305191527374548 0.0469266856851943 0.0580452840754031 0.0385375322919084 -m:Fru6P:1,2,3,4,5,6:4:690 -0.00136306896214337 0.0137397725510333 0.0170177475023465 0.0417372012671271 0.0258510180458119 0.0385973494576826 0.0622003922899037 0.0620209065758034 0.0670552727027324 0.0510832683047673 -m:Fru6P:1,2,3,4,5,6:5:691 0.0126114174874434 0.0168366636261353 0.00613625694852706 0.00646155542199223 0.00416011463957945 -0.0185323336578468 0.00502015745762575 0.0152813542807671 0.00415755701611636 0.0088205581757464 -m:Fru6P:1,2,3,4,5,6:6:692 0.0772794502106592 0.105015237675548 0.105838420467053 0.117576197845624 0.106974963083314 0.126498375256686 0.113727482281553 0.12301912138022 0.114583839516509 0.122447416359013 From 1efd60b4252b70eb02bdcbdb12b5eb294d078977 Mon Sep 17 00:00:00 2001 From: Serguei Sokol Date: Thu, 23 Nov 2023 17:15:53 +0100 Subject: [PATCH 02/10] fixed lint warnings Signed-off-by: Serguei Sokol --- tools/influx_si/macros.xml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/tools/influx_si/macros.xml b/tools/influx_si/macros.xml index 4998ded003..62a2bf0119 100644 --- a/tools/influx_si/macros.xml +++ b/tools/influx_si/macros.xml @@ -193,8 +193,7 @@ options: dependent fluxes, cumomers, stats and so on --noscale no scaling factors to optimize => all scaling factors are assumed to be 1 - --meth {BFGS,Nelder-Mead,nlsic,pso} - method for optimization, one of 'nlsic|BFGS|Nelder- + --meth METH method for optimization, one of 'nlsic|BFGS|Nelder- Mead|pso'. Default: 'nlsic'. Multiple occurrences of this option can appear on command line. In this case, specified minimization methods are applied @@ -264,8 +263,7 @@ options: Monte-Carlo simulations for sensitivity analysis. Default: none, i.e. current system value is used, so random drawing will be varying at each run. - --excl_outliers [EXCL_OUTLIERS] - This option takes an optional argument, a p-value + --excl_outliers V This option takes an optional argument V, a p-value between 0 and 1 which is used to filter out measurement outliers. The filtering is based on Z statistics calculated on reduced residual @@ -274,8 +272,7 @@ options: --addnoise Add centered gaussian noise to simulated measurements written to _res.kvh file. SD of this noise is taken from FTBL file - --time_order {None,1,2,1,2} - Time order for ODE solving (1 (default), 2 or 1,2). + --time_order TO Time order TO for ODE solving (1 (default), 2 or 1,2). Order 2 is more precise but more time consuming. The value '1,2' makes to start solving the ODE with the first order scheme then continues with the order 2. From 553d96357f673515ea469e3a713df49b728b5e75 Mon Sep 17 00:00:00 2001 From: Serguei Sokol Date: Fri, 24 Nov 2023 09:24:29 +0100 Subject: [PATCH 03/10] fixed optional time_order Signed-off-by: Serguei Sokol --- tools/influx_si/macros.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/influx_si/macros.xml b/tools/influx_si/macros.xml index 62a2bf0119..a1010f3e05 100644 --- a/tools/influx_si/macros.xml +++ b/tools/influx_si/macros.xml @@ -117,7 +117,7 @@ - + From 94edf40ad2970d2d1d7666d418d8961239984267 Mon Sep 17 00:00:00 2001 From: Serguei Sokol Date: Tue, 28 Nov 2023 16:33:10 +0100 Subject: [PATCH 04/10] fixed test config & added env.yaml Signed-off-by: Serguei Sokol --- tools/influx_si/environment.yml | 7 +++++++ tools/influx_si/influx_si.xml | 4 ++-- 2 files changed, 9 insertions(+), 2 deletions(-) create mode 100644 tools/influx_si/environment.yml diff --git a/tools/influx_si/environment.yml b/tools/influx_si/environment.yml new file mode 100644 index 0000000000..225c445c46 --- /dev/null +++ b/tools/influx_si/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - influx-si=7.0.1 +platforms: + - linux-64 diff --git a/tools/influx_si/influx_si.xml b/tools/influx_si/influx_si.xml index 3e324c2b2f..5de12a3015 100644 --- a/tools/influx_si/influx_si.xml +++ b/tools/influx_si/influx_si.xml @@ -48,10 +48,10 @@ - + - + From b446da2a279c84774142998fc35a2ab51f114304 Mon Sep 17 00:00:00 2001 From: Serguei Sokol Date: Wed, 29 Nov 2023 11:41:47 +0100 Subject: [PATCH 05/10] fixed indentation and simplified boolean parameters Signed-off-by: Serguei Sokol --- tools/influx_si/influx_si.xml | 83 ++++++----- tools/influx_si/macros.xml | 265 ++++++++++++++++------------------ 2 files changed, 162 insertions(+), 186 deletions(-) diff --git a/tools/influx_si/influx_si.xml b/tools/influx_si/influx_si.xml index 5de12a3015..68fcd51923 100644 --- a/tools/influx_si/influx_si.xml +++ b/tools/influx_si/influx_si.xml @@ -8,55 +8,54 @@ influx_si - 'outdir/influx_${si.s_i}.stdout.txt' 2>'outdir/influx_${si.s_i}.stderr.txt'; - - #for $inp in $input_main: - #set base = $inp.name[:-4] - for f in "$base"_res/*.{err,log}; do mv -f "\$f" "\$f".txt || true; done; - for f in "$base"_res/*.{sim,stat}; do mv -f "\$f" "\$f".tsv || true; done; - for f in "$base"_res/*.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done; - rm -rf "$base"_res/tmp/; - mv "$base"_res/* outdir/; - #end for + 'outdir/influx_${si.s_i}.stdout.txt' 2>'outdir/influx_${si.s_i}.stderr.txt'; + + #for $inp in $input_main: + #set base = $inp.name[:-4] + for f in "$base"_res/*.{err,log}; do mv -f "\$f" "\$f".txt || true; done; + for f in "$base"_res/*.{sim,stat}; do mv -f "\$f" "\$f".tsv || true; done; + for f in "$base"_res/*.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done; + rm -rf "$base"_res/tmp/; + mv "$base"_res/* outdir/; + #end for ]]> - - - + + + - - - - - - + + + + + + - - - - + + + + - - + + diff --git a/tools/influx_si/macros.xml b/tools/influx_si/macros.xml index a1010f3e05..48bcc90129 100644 --- a/tools/influx_si/macros.xml +++ b/tools/influx_si/macros.xml @@ -12,99 +12,74 @@ 7.0.1 1 @@ -126,58 +101,59 @@
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
- +]]> + - - + + @misc{githubinflux, author = {Sokol, Serguei}, year = {2023}, @@ -311,8 +288,8 @@ options: journal = {GitHub repository}, url = {https://github.com/sgsokol/influx}, } - - 10.1093/bioinformatics/btr716 - + + 10.1093/bioinformatics/btr716 + From fc1c985909c5a4743ef54b0b97f86271e17cd6bd Mon Sep 17 00:00:00 2001 From: Serguei Sokol Date: Wed, 29 Nov 2023 15:24:27 +0100 Subject: [PATCH 06/10] booleans are no more optional Signed-off-by: Serguei Sokol --- tools/influx_si/macros.xml | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/tools/influx_si/macros.xml b/tools/influx_si/macros.xml index 48bcc90129..5438bb095e 100644 --- a/tools/influx_si/macros.xml +++ b/tools/influx_si/macros.xml @@ -101,20 +101,20 @@
- - - - - - - - - - - - - - + + + + + + + + + + + + + + From 52e7065330b4f27272d6ef14b36252164ab1a5d0 Mon Sep 17 00:00:00 2001 From: Serguei Sokol Date: Fri, 1 Dec 2023 10:00:10 +0100 Subject: [PATCH 07/10] added creator tag; added exit $ret; fixed --time_order; simplified Help. Signed-off-by: Serguei Sokol --- tools/influx_si/README.rst | 13 +-- tools/influx_si/environment.yml | 7 -- tools/influx_si/influx_si.xml | 18 +++- tools/influx_si/macros.xml | 151 ++------------------------------ 4 files changed, 28 insertions(+), 161 deletions(-) delete mode 100644 tools/influx_si/environment.yml diff --git a/tools/influx_si/README.rst b/tools/influx_si/README.rst index 5d7726d76b..66a8925c48 100644 --- a/tools/influx_si/README.rst +++ b/tools/influx_si/README.rst @@ -2,16 +2,19 @@ Metabolic flux estimation ------------------------- -`influx_si` can be used for metabolic flux estimation based on labeling data from MS and/or NMR measurements. `influx_s` is used for stationary labeling and `influx_i` for instationary one (hence the '_s' and '_i' in the names). Tha name `influx_si` is used as common for both tools. +`influx_si` can be used for estimation of metabolic fluxes and concentrations based on labeling data from MS and/or NMR measurements. `influx_s` is used for stationary labeling and `influx_i` for instationary one (hence the '_s' and '_i' in the names). The name `influx_si` is used as common for both tools. -The input for `influx_si` in one or several MTF (Multiple Text Files) collections, each describing a given labeling experiment and options to use during estimation. +The input for `influx_si` is an MTF (Multiple TSV Files) collection describing metabolic network, label transition, labeling data and options to use during estimation. -The output is a zip archive with files generated by `influx_si`. Among the most important are files ending with `.sim` (as 'simulated') which contains information about estimated parameters, their SD and so on. -If, in your .opt file, you have requested plotting information, it can be found in respective .pdf file. +The output is a zip archive with files generated by `influx_si`. File ending with `.tvar.sim` which contains the estimated fluxes and concentrations. Other files ending with `.sim` contain simulated measurements. File ending with `.stat` has results of chi2 test assessing quality of fit. + +If, in your `.opt` file, you have requested plotting information (`plot_smeas.R` or `plot_ilab.R`), it can be found in the respective `.pdf` file. For detailed documentation about `influx_si` and accompanying tools see https://influx-si.readthedocs.io -For getting a standalone version of `influx_si` see https://anaconda.org/bioconda/influx_si +For getting a standalone version of `influx_si `_, you can install it e.g. with `conda `_ package manager: :: + + conda install -c conda-forge -c bioconda influx_si Author: Serguei Sokol diff --git a/tools/influx_si/environment.yml b/tools/influx_si/environment.yml deleted file mode 100644 index 225c445c46..0000000000 --- a/tools/influx_si/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - influx-si=7.0.1 -platforms: - - linux-64 diff --git a/tools/influx_si/influx_si.xml b/tools/influx_si/influx_si.xml index 68fcd51923..0fb52513de 100644 --- a/tools/influx_si/influx_si.xml +++ b/tools/influx_si/influx_si.xml @@ -2,6 +2,14 @@ Estimate metabolic fluxes and concentrations by fitting simulated labeling in metabolites to NMR/MS measurements + + + + + + + + macros.xml @@ -14,9 +22,10 @@ unzip $inp; #end for + ret=0; influx_$si.s_i @COMMAND_OPT@ - #if $si.s_i == 'i' and $si.time_order: + #if $si.s_i == 'i' and $si.time_order != 'None': --time_order='$si.time_order' #end if #for $inp in $input_main: @@ -24,7 +33,9 @@ --prefix "$base" #end for @MTF_OPT@ - > 'outdir/influx_${si.s_i}.stdout.txt' 2>'outdir/influx_${si.s_i}.stderr.txt'; + > 'outdir/influx_${si.s_i}.stdout.txt' 2>'outdir/influx_${si.s_i}.stderr.txt' || + ret=\${PIPESTATUS[0]}; + #for $inp in $input_main: #set base = $inp.name[:-4] @@ -32,8 +43,9 @@ for f in "$base"_res/*.{sim,stat}; do mv -f "\$f" "\$f".tsv || true; done; for f in "$base"_res/*.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done; rm -rf "$base"_res/tmp/; - mv "$base"_res/* outdir/; + mv -f "$base"_res/* outdir/; #end for + exit \$ret; ]]> diff --git a/tools/influx_si/macros.xml b/tools/influx_si/macros.xml index 5438bb095e..2c45d2e886 100644 --- a/tools/influx_si/macros.xml +++ b/tools/influx_si/macros.xml @@ -1,14 +1,5 @@ - -.. class:: infomark - -**Authors** Serguei Sokol (sokol@insa-toulouse.fr) - -.. class:: infomark - ---------------------------------------------------- - 7.0.1 1 - - - + + + @@ -142,138 +130,9 @@ all scaling factors - are assumed to be 1 - --meth METH method for optimization, one of 'nlsic|BFGS|Nelder- - Mead|pso'. Default: 'nlsic'. Multiple occurrences of - this option can appear on command line. In this case, - specified minimization methods are applied - successively, e.g. '--meth pso --meth nlsic' means - that 'pso' will be used first, then 'nlsic' will take - over from the point where 'pso' ends. In case of - multiple methods, it is recommended to start with non- - gradient methods like 'pso' or 'Nelder-Mead' and make - them follow by gradient based methods like 'nlsic' or - 'BFGS'. If 'pso' or 'Nelder-Mead' are indeed used as - the first method, it is not recommended to combine - them with '--zc' option. - --fullsys calculate all cumomer set (not just the reduced one - necessary to simulate measurements) - --emu simulate labeling in EMU approach - --irand ignore initial approximation for free parameters (free - fluxes and metabolite concentrations) from the FTBL - file or from a dedicated file (cf --fseries and - --iseries option) and use random values drawn - uniformly from [0,1] interval - --sens SENS sensitivity method: SENS can be 'mc[=N]', mc stands - for Monte-Carlo. N is an optional number of Monte- - Carlo simulations. Default for N: 10 - --cupx CUPX upper limit for reverse fluxes. Must be in interval - [0, 1]. Default: 0.999 - --cupn CUPN absolute limit for net fluxes: -cupn <= netflux <= - cupn. Must be non negative. Value 0 means no limit. - Default: 1.e3 - --cupp CUPP upper limit for metabolite pool. Default: 1.e5 - --clownr CLOWNR lower limit for not reversible free and dependent - fluxes. Zero value (default) means no lower limit - --cinout CINOUT lower limit for input/output free and dependent - fluxes. Must be non negative. Default: 0 - --clowp CLOWP lower limit for free metabolite pools. Must be - positive. Default 1.e-8 - --np NP When integer >= 1, it is a number of parallel - subprocesses used in Monte-Carlo (MC) simulations or - for multiple FTBL inputs. When NP is a float number - between 0 and 1, it gives a fraction of available - cores (rounded to closest integer) to be used. Without - this option or for NP=0, all available cores in a - given node are used for MC simulations. - --ln Least norm solution is used for increments during the - non-linear iterations when Jacobian is rank deficient - --sln Least norm of the solution of linearized problem (and - not just of increments) is used when Jacobian is rank - deficient - --tikhreg Approximate least norm solution is used for increments - during the non-linear iterations when Jacobian is rank - deficient - --lim The same as --ln but with a function limSolve::lsei() - --zc ZC Apply zero crossing strategy with non negative - threshold for net fluxes - --ffguess Don't use free/dependent flux definitions from FTBL - file(s). Make an automatic guess. - --fseries FSERIES File name with free parameter values for multiple - starting points. Default: '' (empty, i.e. only one - starting point from the FTBL file is used) - --iseries ISERIES Indexes of starting points to use. Format: '1:10' -- - use only first ten starting points; '1,3' -- use the - the first and third starting points; '1:10,15,91:100' - -- a mix of both formats is allowed. Default: '' - (empty, i.e. all provided starting points are used) - --seed SEED Integer (preferably a prime integer) used for - reproducible random number generating. It makes - reproducible random starting points (--irand) but also - Monte-Carlo simulations for sensitivity analysis. - Default: none, i.e. current system value is used, so - random drawing will be varying at each run. - --excl_outliers V This option takes an optional argument V, a p-value - between 0 and 1 which is used to filter out - measurement outliers. The filtering is based on Z - statistics calculated on reduced residual - distribution. Default: 0.01. - --nocalc generate an R code but not execute it. - --addnoise Add centered gaussian noise to simulated measurements - written to _res.kvh file. SD of this noise is taken - from FTBL file - --time_order TO Time order TO for ODE solving (1 (default), 2 or 1,2). - Order 2 is more precise but more time consuming. The - value '1,2' makes to start solving the ODE with the - first order scheme then continues with the order 2. - --version show program's version number and exit - --mtf MTF option passed to txt2ftbl. See help there. - --prefix PREFIX option passed to txt2ftbl. See help there. - --eprl EPRL option passed to txt2ftbl. See help there. - --force FORCE option passed to txt2ftbl. See help there. - -o OUT, --out OUT output directory. Default: basename of input file - without suffix + '_res'. If empty, no output directory - is created. In this case log and error messages are - directed to standard output/error channels. Non empty - OUT can be used when only one input file or MTF set is - given. - --copy_doc copy documentation directory in the current directory - and exit. If ./doc exists, its content is silently - overwritten. - --copy_test copy test directory in the current directory and exit. - If ./test exists, its content is silently overwritten. - --install_rdep install R dependencies and exit. - --TIMEIT developer option: measure cpu time or not - --prof developer option: do time profiling or not - --tblimit TBLIMIT developer option: set trace back limit for python - error messages +Select one or several zip archives with MTF (Multiple TSV Files) sets, stationary/instationary labeling type and possibly some advanced option to run the tool. +Detailed documentation is available on https://influx-si.readthedocs.io ]]> From e24b37659a5042717a369816289e0f4db700ca6d Mon Sep 17 00:00:00 2001 From: Serguei Sokol Date: Thu, 7 Dec 2023 15:40:49 +0100 Subject: [PATCH 08/10] nested list output Signed-off-by: Serguei Sokol --- tools/influx_si/influx_si.xml | 26 ++++++++++++-------------- 1 file changed, 12 insertions(+), 14 deletions(-) diff --git a/tools/influx_si/influx_si.xml b/tools/influx_si/influx_si.xml index 0fb52513de..ba4d082af5 100644 --- a/tools/influx_si/influx_si.xml +++ b/tools/influx_si/influx_si.xml @@ -17,7 +17,6 @@ influx_si 'outdir/influx_${si.s_i}.stdout.txt' 2>'outdir/influx_${si.s_i}.stderr.txt' || - ret=\${PIPESTATUS[0]}; - + || ret=\$?; #for $inp in $input_main: #set base = $inp.name[:-4] for f in "$base"_res/*.{err,log}; do mv -f "\$f" "\$f".txt || true; done; for f in "$base"_res/*.{sim,stat}; do mv -f "\$f" "\$f".tsv || true; done; for f in "$base"_res/*.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done; - rm -rf "$base"_res/tmp/; - mv -f "$base"_res/* outdir/; + rm -rf "$base"_res/tmp || true; #end for exit \$ret; ]]> - - + + @@ -59,12 +55,14 @@ - - - - - - + + + + + + + + From 9a38f6ba5a0d162855dafda4fd29cd87950e2179 Mon Sep 17 00:00:00 2001 From: Serguei Sokol Date: Thu, 7 Dec 2023 16:35:59 +0100 Subject: [PATCH 09/10] fixed discovering of file type Signed-off-by: Serguei Sokol --- tools/influx_si/influx_si.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/influx_si/influx_si.xml b/tools/influx_si/influx_si.xml index ba4d082af5..7f17de001e 100644 --- a/tools/influx_si/influx_si.xml +++ b/tools/influx_si/influx_si.xml @@ -45,8 +45,8 @@ ]]> - - + + From 67188de4af3e174675765bf544642448f1428327 Mon Sep 17 00:00:00 2001 From: sgsokol Date: Tue, 12 Dec 2023 18:37:21 +0100 Subject: [PATCH 10/10] moved stuff from macros to influx Signed-off-by: sgsokol --- tools/influx_si/influx_si.xml | 144 ++++++++++++++++++++++++++++++-- tools/influx_si/macros.xml | 150 ---------------------------------- 2 files changed, 138 insertions(+), 156 deletions(-) diff --git a/tools/influx_si/influx_si.xml b/tools/influx_si/influx_si.xml index 7f17de001e..35deefdaaf 100644 --- a/tools/influx_si/influx_si.xml +++ b/tools/influx_si/influx_si.xml @@ -1,4 +1,4 @@ - + Estimate metabolic fluxes and concentrations by fitting simulated labeling in metabolites to NMR/MS measurements @@ -23,7 +23,65 @@ ret=0; influx_$si.s_i - @COMMAND_OPT@ + $noopt + $noscale + $fullsys + $emu + $irand + $ln + $sln + $tikhreg + $lim + $ffguess + $nocalc + $addnoise + $TIMEIT + $prof + #if $opt.meth: + --meth='$opt.meth' + #end if + #if $opt.sens: + --sens='$opt.sens' + #end if + #if $opt.cupx: + --cupx='$opt.cupx' + #end if + #if $opt.cupn: + --cupn='$opt.cupn' + #end if + #if $opt.cupp: + --cupp='$opt.cupp' + #end if + #if $opt.clownr: + --clownr='$opt.clownr' + #end if + #if $opt.cinout: + --cinout='$opt.cinout' + #end if + #if $opt.clowp: + --clowp='$opt.clowp' + #end if + #if $opt.np: + --np='$opt.np' + #end if + #if $opt.zc: + --zc='$opt.zc' + #end if + #if $opt.fseries: + --fseries='$opt.fseries' + #end if + #if $opt.iseries: + --iseries='$opt.iseries' + #end if + #if $opt.seed: + --seed='$opt.seed' + #end if + #if $opt.excl_outliers: + --excl_outliers $opt.excl_outliers + #end if + #if $opt.tblimit: + --tblimit='$opt.tblimit' + #end if #if $si.s_i == 'i' and $si.time_order != 'None': --time_order='$si.time_order' #end if @@ -31,7 +89,10 @@ #set base = $inp.name[:-4] --prefix "$base" #end for - @MTF_OPT@ + #if $opt.mtf: + --mtf '$opt.mtf' + #end if + || ret=\$?; #for $inp in $input_main: @@ -43,7 +104,62 @@ #end for exit \$ret; ]]> - + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ @@ -67,6 +183,22 @@ - - + + + + @misc{githubinflux, + author = {Sokol, Serguei}, + year = {2023}, + title = {influx_s}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/sgsokol/influx}, + } + + 10.1093/bioinformatics/btr716 + diff --git a/tools/influx_si/macros.xml b/tools/influx_si/macros.xml index 2c45d2e886..c4140a716b 100644 --- a/tools/influx_si/macros.xml +++ b/tools/influx_si/macros.xml @@ -1,154 +1,4 @@ 7.0.1 - 1 - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - -@misc{githubinflux, - author = {Sokol, Serguei}, - year = {2023}, - title = {influx_s}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/sgsokol/influx}, -} - - 10.1093/bioinformatics/btr716 - -