Mercurial > repos > workflow4metabolomics > influx_si
changeset 0:9b03a930b08b draft
"planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"
| author | workflow4metabolomics |
|---|---|
| date | Mon, 04 May 2020 03:24:12 -0400 |
| parents | |
| children | 4e3d4318113b |
| files | README.rst influx_si.xml test-data/e_coli.ftbl test-data/e_coli.log test-data/e_coli_1-Glc_exact.ftbl test-data/e_coli_1-Glc_exact.log test-data/e_coli_U-Glc_exact.ftbl test-data/e_coli_growth.ftbl test-data/e_coli_growth.log test-data/e_coli_i.ftbl test-data/e_coli_i.log test-data/e_coli_msen.txt |
| diffstat | 12 files changed, 4220 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,20 @@ + +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 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. + +For detailed documentation about `influx_si` and accompanying tools see https://metasys.insa-toulouse.fr/software/influx/doc/ + +For getting a standalone version of `influx_si` see https://metasys.insa-toulouse.fr/software/influx/ + +Author: Serguei Sokol + +License: GPL2 + +© INRAE 2020
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/influx_si.xml Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,213 @@ +<tool id="influx_si" name="influx_si" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5"> + <description>metabolic flux analysis</description> + <macros> + <token name="@TOOL_VERSION@">5.1.0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">influx_si</requirement> + </requirements> + <version_command>influx_s --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + #set $inp_all = [$input_main, ($prlexp.input_aux if $prlexp.input_aux else [])] + #if $si.s_i == 'i': + #silent $inp_all.append($si.input_ti) + #end if + + mkdir outdir && cd outdir && + + #for $inp in $inp_all: + #for $i in $inp: + ln -s '$i' '$i.name' && + #end for + #end for + + influx_$si.s_i + $opt.noopt + $opt.noscale + #if $opt.meth != 'None': + $opt.meth + #end if + $opt.fullsys + $opt.emu + $opt.irand + #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 + $opt.ln + $opt.sln + $opt.tikhreg + $opt.lim + #if $opt.zc: + --zc='$opt.zc' + #end if + $opt.ffguess + #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 + $opt.nocalc + $opt.addnoise + $opt.TIMEIT + #if $opt.tblimit: + --tblimit='$opt.tblimit' + #end if + + #if $si.s_i == 'i' and $si.time_order: + --time_order='$si.time_order' + #end if + '${"' '".join([str($in_m.name) for $in_m in $input_main])}' + > 'influx_${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 f in *.RData; do [ -e "\$f" ] && mv -f "\$f" "\$f".RData || true; done && + [ "\$res" == "0" ] + ]]></command> + <inputs> + <param type="data" name="input_main" format="ftbl" multiple="true" label="main FTBL(s): network+data"/> + <conditional name="si"> + <param name="s_i" type="select" label="labeling type" display="radio"> + <option value="s">stationary</option> + <option value="i">instationary</option> + </param> + <when value="s"/> + <when value="i"> + <param type="data" name="input_ti" label="time course data" format="txt,tsv" multiple="true"/> + <param argument="--time_order" type="select" label="time order for ODE solving" display="radio" optional="true" help="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."> + <option value="None">None</option> + <option value="1">1</option> + <option value="2">2</option> + <option value="1,2">1,2</option> + </param> + </when> + </conditional> + <section name="prlexp" title="Parallel labeling experiments" expanded="false"> + <param optional="true" type="data" name="input_aux" format="ftbl" multiple="True" label="auxiliary FTBL(s): data only"/> + </section> + <section name="opt" title="Advanced Options" expanded="false"> + <param argument="--noopt" type="boolean" checked="false" truevalue="--noopt" falsevalue="" label="no optimization" optional="true" help=", just use free parameters as is (after a projection on feasibility domain), to calculate dependent fluxes, cumomers, stats and so on" /> + <param argument="--noscale" type="boolean" checked="false" truevalue="--noscale" falsevalue="" label="no scaling factors to optimize" optional="true" help="all scaling factors are assumed to be 1" /> + <param argument="--meth" type="select" label="method for optimization" optional="true"> + <option value="--meth=BFGS">BFGS</option> + <option value="--meth=Nelder-Mead">Nelder-Mead</option> + <option value="--meth=nlsic">nlsic</option> + </param> + <param argument="--fullsys" type="boolean" checked="false" truevalue="--fullsys" falsevalue="" label="full cumomer system" optional="true" help="calculate all cumomer set (not just the reduced one necesary to simulate measurements)" /> + <param argument="--emu" type="boolean" checked="false" truevalue="--emu" falsevalue="" label="simulate labeling in EMU approach" optional="true" /> + <param argument="--irand" type="boolean" checked="false" truevalue="--irand" falsevalue="" label="random initial approximation" optional="true" help="ignore initial approximation for free parameters (free fluxes and metabolite concentrations) from the FTBL file (cf. also --iseries option) and use random values drawn uniformly from [0,1] interval" /> + <param argument="--sens" type="text" value="" label="sensitivity method" optional="true" help="can be 'mc[=N]', mc stands for Monte-Carlo. N is an optional number of Monte-Carlo simulations. Default for N: 10" /> + <param argument="--cupx" type="float" min="0" max="1" value="" label="upper limit for reverse fluxes" optional="true" help="Must be in interval [0, 1]. Default: 0.999" /> + <param argument="--cupn" type="float" min="0" value="" label="absolute limit for net fluxes" optional="true" help="-cupn <= netflux <= cupn. Must be non negative. Value 0 means no limit. Default: 1.e3" /> + <param argument="--cupp" type="float" min="0" value="" label="upper limit for metabolite pool" optional="true" help="Default: 1.e5" /> + <param argument="--clownr" type="float" min="0" value="" label="lower limit for not reversible free and dependent fluxes" optional="true" help="Zero value (default) means no lower limit" /> + <param argument="--cinout" type="float" min="0" value="" label="lower limit for input/output free and dependent fluxes" optional="true" help="Must be non negative. Default: 0" /> + <param argument="--clowp" type="float" min="0" value="" label="lower limit for free metabolite pools" optional="true" help="Must be positive. Default 1.e-8" /> + <param argument="--np" type="float" min="0" value="" label="process number" optional="true" help="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." /> + <param argument="--ln" type="boolean" checked="false" truevalue="--ln" falsevalue="" label="least norm" optional="true" help="Least norm solution is used for increments during the non-linear iterations when Jacobian is rank deficient" /> + <param argument="--sln" type="boolean" checked="false" truevalue="--sln" falsevalue="" label="solution least norm" optional="true" help="Least norm of the solution of linearized problem (and not just of increments) is used when Jacobian is rank deficient" /> + <param argument="--tikhreg" type="boolean" checked="false" truevalue="--tikhreg" falsevalue="" label="use Tikhonov regularization" optional="true" help="Approximate least norm solution is used for increments during the non-linear iterations when Jacobian is rank deficient" /> + <param argument="--lim" type="boolean" checked="false" truevalue="--lim" falsevalue="" label="least norm from limSolve package" optional="true" help="The same as --ln but with a function limSolve::lsei()" /> + <param argument="--zc" type="float" min="0" value="" label="zero crossing" optional="true" help="Apply zero crossing strategy with non negative threshold for net fluxes" /> + <param argument="--ffguess" type="boolean" checked="false" truevalue="--ffguess" falsevalue="" label="free fluxes guess" optional="true" help="Don't use free/dependent flux definitions from FTBL file(s). Make an automatic guess." /> + <param argument="--iseries" type="text" value="" label="indexes of starting points" optional="true" help="When used jointly with --irand, allows generating multiple random starting points. 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)" /> + <param argument="--seed" type="integer" min="0" value="" label="random seed" optional="true" help="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." /> + <param argument="--excl_outliers" type="float" min="0" max="1" value="" label="threshold for excluding outliers" optional="true" help="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." /> + <param argument="--nocalc" type="boolean" checked="false" truevalue="--nocalc" falsevalue="" label="no calculation" optional="true" help="generate an R code but not execute it." /> + <param argument="--addnoise" type="boolean" checked="false" truevalue="--addnoise" falsevalue="" label="add noise" optional="true" help="Add centered gaussian noise to simulated measurements written to _res.kvh file. SD of this noise is taken from FTBL file" /> + <param argument="--TIMEIT" type="boolean" checked="false" truevalue="--TIMEIT" falsevalue="" label="measure timings" optional="true" help="developer option: measure cpu time or not" /> + <param argument="--tblimit" type="integer" min="0" value="0" label="Python traceback limit" optional="true" help="developer option: set trace back limit for Python error messages" /> + </section> + </inputs> + <outputs> + <collection name="influx_si_output" type="list" label="influx_${si.s_i}_on_${on_string}"> + <discover_datasets pattern="__name_and_ext__" directory="outdir" visible="false"/> + </collection> + </outputs> + <tests> + <test> + <param name="input_main" value="e_coli.ftbl" /> + <conditional name="si"> + <param name="s_i" value="s" /> + </conditional> + <output_collection name="influx_si_output" type="list"> + <element name="e_coli.log" ftype="txt" file="e_coli.log" compare="sim_size" delta="100" /> + </output_collection> + </test> + <test> + <param name="input_main" value="e_coli.ftbl,e_coli_growth.ftbl" /> + <conditional name="si"> + <param name="s_i" value="s" /> + </conditional> + <output_collection name="influx_si_output" type="list"> + <element name="e_coli_growth.log" ftype="txt" file="e_coli_growth.log" compare="sim_size" delta="100" /> + </output_collection> + </test> + <test> + <param name="input_main" value="e_coli_i.ftbl" /> + <conditional name="si"> + <param name="s_i" value="i" /> + <param name="input_ti" value="e_coli_msen.txt" /> + <!--param name="time_order" value="1,2" /--> <!--How to pass single value with comma in it?--> + </conditional> + <output_collection name="influx_si_output" type="list"> + <element name="e_coli_i.log" ftype="txt" file="e_coli_i.log" compare="sim_size" delta="100" /> + </output_collection> + </test> + <test> + <param name="input_main" value="e_coli_1-Glc_exact.ftbl" /> + <param name="input_aux" value="e_coli_U-Glc_exact.ftbl" /> + <conditional name="si"> + <param name="s_i" value="s" /> + </conditional> + <output_collection name="influx_si_output" type="list"> + <element name="e_coli_1-Glc_exact.log" file="e_coli_1-Glc_exact.log" compare="sim_size" delta="100" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ + Usage: influx_s [options] /path/to/FTBL_file1 [FTBL_file2 [...]] + + Optimize free fluxes and optionaly metabolite concentrations of a given static metabolic network defined in an FTBL file to fit 13C data provided in the same FTBL file. + ]]></help> + <citations> + <citation type="bibtex"> + @misc{githubinflux, + author = {Sokol, Serguei}, + year = {2020}, + title = {influx_s}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/sgsokol/influx}, + } + </citation> + <citation type="doi">10.1093/bioinformatics/btr716</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli.ftbl Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,720 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli.log Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,38 @@ +"/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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli_1-Glc_exact.ftbl Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,713 @@ +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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli_1-Glc_exact.log Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,40 @@ +"/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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli_U-Glc_exact.ftbl Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,711 @@ +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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli_growth.ftbl Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,822 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli_growth.log Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,45 @@ +"/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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli_i.ftbl Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,789 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli_i.log Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,47 @@ +"/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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli_msen.txt Mon May 04 03:24:12 2020 -0400 @@ -0,0 +1,62 @@ +# 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 + +m:PEP:1,2,3:0:664 0.959305356621255 0.899429291001306 0.793091742198796 0.727694639632051 0.661797176142203 0.610886177732735 0.582532494113683 0.530442722689088 0.529050805368866 0.534367517591899 +m:PEP:1,2,3:1:665 0.0208665230365796 0.0529703549691902 0.105744546377435 0.182105641800708 0.218798900635198 0.25211771929553 0.260661349516476 0.293792896551455 0.303805124775345 0.330443567281624 +m:PEP:1,2,3:2:666 0.00810159190910743 0.00857003057280515 0.0164616569826104 -0.00580284991874017 -0.0063738169583666 0.00439384742710785 0.00782240375778176 0.00823428016898976 0.0225480831085196 0.00540316722852868 +m:PEP:1,2,3:3:667 0.0160174417665648 0.0673268207131409 0.0737601703050139 0.0784050704969314 0.117536949383343 0.125388990412662 0.152013381581937 0.13491538119973 0.150036045107799 0.152979924474585 + +m:Gnt6P:1,2,3,4,5,6:0:699 0.980348768364065 0.887065707402045 0.775412601358149 0.682721033571734 0.638019427572899 0.537217635545053 0.46397661247481 0.40841020722789 0.354996545552177 0.328852241202942 +m:Gnt6P:1,2,3,4,5,6:1:700 0.0280915336431533 0.0900207235146178 0.178718976529483 0.238199954663426 0.297651174309232 0.377668812920342 0.406206528759584 0.43139141657629 0.463288334282323 0.498910430969407 +m:Gnt6P:1,2,3,4,5,6:2:701 -0.0118658948310887 0.00587644250607669 -0.000171197622197317 0.0283613357792838 -0.00121861221678132 0.0190972740079335 0.0203873738550575 0.043882002295937 0.00895785739811282 0.029492638878724 +m:Gnt6P:1,2,3,4,5,6:3:702 0.00419604783069589 0.017811925924337 0.00288410451231084 -0.00278521719286527 -0.00346833577593073 0.00824367096436317 0.0308084876487389 0.00684988634924229 0.00342583492597715 0.0231271068836901 +m:Gnt6P:1,2,3,4,5,6:4:703 0.0117131384422775 0.00130463713177113 0.00810930185180439 0.0119236165114781 0.0058578264597987 0.00992587860273877 0.00960534666262163 0.0178935788593294 0.00634540914627665 0.0161416252798136 +m:Gnt6P:1,2,3,4,5,6:5:704 0.020546992817452 -0.0124359940415735 -0.00492561472492338 0.00338433309336889 0.00879451474297676 -0.00775625913406869 -0.0155108586142624 -0.00491469372051669 0.0102530236644356 0.000435656001570747 +m:Gnt6P:1,2,3,4,5,6:6:705 0.0123813174021481 0.026469487723487 0.0383202157383438 0.0457935417210038 0.0641838950995448 0.0775084104251395 0.0719800594322437 0.0689150899176442 0.104305456142958 0.100296931509246 + +m:Suc:1,2,3,4:1:648 -0.00740536579943663 -0.0071005977123083 0.0116361522025203 0.0155529939694648 0.0614369267187886 0.080653519229227 0.126488314467457 0.175267908031439 0.213998958328793 0.253963529986229 +m:Suc:1,2,3,4:2:649 0.00035329920798099 0.000375561367706547 0.0213616438244359 0.00541204837458218 0.0402702326634204 0.0498260948480971 0.0767447890046914 0.0924200973134789 0.12505390376649 0.124911685829664 +m:Suc:1,2,3,4:3:650 0.00871527066853332 -0.00316297484652509 0.0104909186040306 -0.00900495372166635 0.00261827267948352 0.0085349378032622 0.0109475170837865 0.0232501338991491 0.0206200755625722 0.0296011617670213 +m:Suc:1,2,3,4:4:651 -0.00993736466764629 0.00196472438489081 -0.00484695474256728 0.0153408517532834 0.0041592776106311 -0.00430377880030445 -0.00244362524377602 0.0109534229782509 0.0137604488833386 0.00586316823546521 +m:PGA:1,2,3:0:668 0.971624233727786 0.88105488804591 0.813066699228851 0.740599622946611 0.655913445307991 0.631749494323584 0.576140697543343 0.557971599084521 0.51860388489637 0.51803381029278 +m:PGA:1,2,3:1:669 0.00220541233021583 0.0757210734343468 0.12052269067551 0.162191306191376 0.223937545869529 0.241442753352368 0.258583425386211 0.30259748123379 0.315427978552718 0.321801842964539 +m:PGA:1,2,3:2:670 -0.00600635453904946 0.0103004820964093 0.000507682594582335 -0.012889899397529 0.0102382227596737 0.00870989588467711 0.0150594342872339 0.0101818907371649 0.0215484107926831 0.0184451709580988 +m:PGA:1,2,3:3:671 0.0222666463570966 0.0396053154740378 0.0652581947362937 0.108004619157695 0.110623893009565 0.138973931054194 0.131470119271174 0.137869954971786 0.136658102046298 0.135855362678781 + +m:FruBP:1,2,3,4,5,6:0:672 0.915100660678142 0.710538255628495 0.539707264234807 0.410485596290365 0.316133497140404 0.260353766957447 0.203404008159282 0.182459522045085 0.164876978870191 0.148857194981653 +m:FruBP:1,2,3,4,5,6:1:673 0.0678013467712298 0.226304674965867 0.336541856973518 0.416051058082716 0.464564802241236 0.485336774391881 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