Mercurial > repos > workflow4metabolomics > influx_si
changeset 2:57f199aa07e4 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
| author | workflow4metabolomics |
|---|---|
| date | Wed, 13 Dec 2023 08:56:04 +0000 |
| parents | 4e3d4318113b |
| children | |
| files | README.rst influx_si.xml macros.xml test-data/e_coli.ftbl test-data/e_coli.log test-data/e_coli.zip 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 | 14 files changed, 190 insertions(+), 4198 deletions(-) [+] |
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--- a/README.rst Wed Sep 13 19:52:44 2023 +0000 +++ b/README.rst Wed Dec 13 08:56:04 2023 +0000 @@ -2,19 +2,22 @@ Metabolic flux estimation ------------------------- -`influx_si` can be used for metabolic flux estimation based on labeling data from MS and/or NMR measurements. `influx_s` is used for stationary labeling and `influx_i` for instationary one (hence the '_s' and '_i' in the names). Tha name `influx_si` is used as common for both tools. +`influx_si` can be used for estimation of metabolic fluxes and concentrations based on labeling data from MS and/or NMR measurements. `influx_s` is used for stationary labeling and `influx_i` for instationary one (hence the '_s' and '_i' in the names). The name `influx_si` is used as common for both tools. -The input for `influx_si` in one or several FTBL files, each describing a given labeling experiment and options to use during estimation. In addition, for `influx_i` a file with time course data has to be provided for each FTBL file. +The input for `influx_si` is an MTF (Multiple TSV Files) collection describing metabolic network, label transition, labeling data and options to use during estimation. + +The output is a zip archive with files generated by `influx_si`. File ending with `.tvar.sim` which contains the estimated fluxes and concentrations. Other files ending with `.sim` contain simulated measurements. File ending with `.stat` has results of chi2 test assessing quality of fit. -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. +If, in your `.opt` file, you have requested plotting information (`plot_smeas.R` or `plot_ilab.R`), it can be found in the respective `.pdf` file. + +For detailed documentation about `influx_si` and accompanying tools see https://influx-si.readthedocs.io -For 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 <https://anaconda.org/bioconda/influx_si>`_, you can install it e.g. with `conda <https://docs.conda.io/en/latest/miniconda.html>`_ package manager: :: -For getting a standalone version of `influx_si` see https://metasys.insa-toulouse.fr/software/influx/ + conda install -c conda-forge -c bioconda influx_si Author: Serguei Sokol License: GPL2 -© INRAE 2020 +© INRAE/INSA/CNRS 2023
--- a/influx_si.xml Wed Sep 13 19:52:44 2023 +0000 +++ b/influx_si.xml Wed Dec 13 08:56:04 2023 +0000 @@ -1,232 +1,204 @@ -<tool id="influx_si" name="influx_si" version="@TOOL_VERSION@+galaxy1"> - <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' '$i.element_identifier' && - #end for - #end for - - influx_$si.s_i - $opt.noopt - $opt.noscale - #if $opt.meth != 'None': - $opt.meth +<tool id="influx_si" name="influx_si" version="@TOOL_VERSION@+galaxy1" profile="21.09"> + <description> + Estimate metabolic fluxes and concentrations by fitting simulated labeling in metabolites to NMR/MS measurements + </description> + <creator> + <person givenName="Serguei" familyName="Sokol" email="sokol@insa-toulouse.fr" url="https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/cellule-mathematiques/" /> + <organization name="INRAE" url="https://www.inrae.fr/" /> + <organization name="TBI" url="https://www.toulouse-biotechnology-institute.fr/" /> + <organization name="Mathematics Cell" url="https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/cellule-mathematiques/" /> + <organization name="MetaToul-FluxoMet" url="https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/metatoul/" /> + <organization name="MetaboHub2" url="https://www.metabohub.fr/" /> + </creator> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">influx_si</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #for $inp in $input_main: + unzip $inp; + #end for + + ret=0; + influx_$si.s_i + $noopt + $noscale + $fullsys + $emu + $irand + $ln + $sln + $tikhreg + $lim + $ffguess + $nocalc + $addnoise + $TIMEIT + $prof + #if $opt.meth: + --meth='$opt.meth' #end if - $opt.fullsys - $opt.emu - $opt.irand #if $opt.sens: - --sens='$opt.sens' + --sens='$opt.sens' #end if #if $opt.cupx: - --cupx='$opt.cupx' + --cupx='$opt.cupx' #end if #if $opt.cupn: - --cupn='$opt.cupn' + --cupn='$opt.cupn' #end if #if $opt.cupp: - --cupp='$opt.cupp' + --cupp='$opt.cupp' #end if #if $opt.clownr: - --clownr='$opt.clownr' + --clownr='$opt.clownr' #end if #if $opt.cinout: - --cinout='$opt.cinout' + --cinout='$opt.cinout' #end if #if $opt.clowp: - --clowp='$opt.clowp' + --clowp='$opt.clowp' #end if #if $opt.np: - --np='$opt.np' + --np='$opt.np' + #end if + #if $opt.zc: + --zc='$opt.zc' #end if - $opt.ln - $opt.sln - $opt.tikhreg - $opt.lim - #if $opt.zc: - --zc='$opt.zc' + #if $opt.fseries: + --fseries='$opt.fseries' #end if - $opt.ffguess #if $opt.iseries: - --iseries='$opt.iseries' + --iseries='$opt.iseries' #end if #if $opt.seed: - --seed='$opt.seed' + --seed='$opt.seed' #end if #if $opt.excl_outliers: - --excl_outliers '$opt.excl_outliers' + --excl_outliers $opt.excl_outliers + #end if + #if $opt.tblimit: + --tblimit='$opt.tblimit' + #end if + #if $si.s_i == 'i' and $si.time_order != 'None': + --time_order='$si.time_order' #end if - $opt.nocalc - $opt.addnoise - $opt.TIMEIT - #if $opt.tblimit: - --tblimit='$opt.tblimit' + #for $inp in $input_main: + #set base = $inp.name[:-4] + --prefix "$base" + #end for + #if $opt.mtf: + --mtf '$opt.mtf' #end if + + || ret=\$?; - #if $si.s_i == 'i' and $si.time_order: - --time_order='$si.time_order' - #end if - '${"' '".join([str($in_m.element_identifier) 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" ] + #for $inp in $input_main: + #set base = $inp.name[:-4] + for f in "$base"_res/*.{err,log}; do mv -f "\$f" "\$f".txt || true; done; + for f in "$base"_res/*.{sim,stat}; do mv -f "\$f" "\$f".tsv || true; done; + for f in "$base"_res/*.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done; + rm -rf "$base"_res/tmp || true; + #end for + exit \$ret; ]]></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" 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> - <!-- TODO: this should probably not be a collection, also name_and_ext probably does not work correctly for all elements--> - <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" count="11"> - <element name="e_coli.log" ftype="txt"> - <assert_contents> - <has_n_lines n="38"/> - <has_line_matching expression="^end.*"/> - </assert_contents> - </element> - </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"> - <assert_contents> - <has_n_lines n="45"/> - <has_line_matching expression="^end.*"/> - </assert_contents> - </element> - </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"> - <assert_contents> - <has_n_lines n="47"/> - <has_line_matching expression="^end.*"/> - </assert_contents> - </element> - </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" ftype="txt"> - <assert_contents> - <has_n_lines n="40"/> - <has_line_matching expression="^end.*"/> - </assert_contents> - </element> - </output_collection> - </test> - </tests> - <help><![CDATA[ - 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> + <inputs> + <param type="data" format="zip" name="input_main" multiple="true" label="At least one MTF collection (.netw, .miso, ...)"/> + <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 argument="--time_order" type="select" display="radio" label="Time order for ODE solving" help="Order 2 is more precise but more time consuming than order 1. The value '1,2' makes to start solving the ODE with the first order scheme then continues with the order 2."> + <option value="None">From .opt file or Default</option> + <option value="1">1 (Default)</option> + <option value="2">2</option> + <option value="1,2">1,2</option> + </param> + </when> + </conditional> + <section name="opt" title="Advanced Options" expanded="false"> + <param argument="--noopt" type="boolean" checked="false" truevalue="--noopt" falsevalue="" label="--noopt" help="no optimization, 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="--noscale" help="no scaling factors to optimize => all scaling factors are assumed to be 1" /> + <param argument="--fullsys" type="boolean" checked="false" truevalue="--fullsys" falsevalue="" label="--fullsys" help="calculate all cumomer set (not just the reduced one necessary to simulate measurements)" /> + <param argument="--emu" type="boolean" checked="false" truevalue="--emu" falsevalue="" label="--emu" help="simulate labeling in EMU approach" /> + <param argument="--irand" type="boolean" checked="false" truevalue="--irand" falsevalue="" label="--irand" help="ignore initial approximation for free parameters (free fluxes and metabolite concentrations) from the FTBL file or from a dedicated file (cf --fseries and --iseries option) and use random values drawn uniformly from [0,1] interval" /> + <param argument="--ln" type="boolean" checked="false" truevalue="--ln" falsevalue="" label="--ln" 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="--sln" 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="--tikhreg" 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="--lim" help="The same as --ln but with a function limSolve::lsei()" /> + <param argument="--ffguess" type="boolean" checked="false" truevalue="--ffguess" falsevalue="" label="--ffguess" help="Don't use free/dependent flux definitions from FTBL file(s). Make an automatic guess." /> + <param argument="--nocalc" type="boolean" checked="false" truevalue="--nocalc" falsevalue="" label="--nocalc" help="generate an R code but not execute it." /> + <param argument="--addnoise" type="boolean" checked="false" truevalue="--addnoise" falsevalue="" label="--addnoise" 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="--TIMEIT" help="developer option: measure cpu time or not" /> + <param argument="--prof" type="boolean" checked="false" truevalue="--prof" falsevalue="" label="--prof" help="developer option: do time profiling or not" /> + + <param argument="--meth" type="select" label="--meth" optional="true" help="method for optimization, one of nlsic|BFGS|Nelder-Mead|pso. Default: nlsic"> + <option value="BFGS">BFGS</option> + <option value="Nelder-Mead">Nelder-Mead</option> + <option value="nlsic">nlsic</option> + <option value="pso">pso</option> + </param> + <param argument="--sens" type="text" value="" label="--sens" optional="true" help="sensitivity method: SENS can be 'mc[=N]', mc stands for Monte-Carlo. N is an optional number of Monte-Carlo simulations. Default for N: 10" /> + <param argument="--cupx" type="float" min="0" max="1" value="" label="--cupx" optional="true" help="upper limit for reverse fluxes. Must be in interval [0, 1]. Default: 0.999" /> + <param argument="--cupn" type="float" min="0" value="" label="--cupn" optional="true" help="absolute limit for net fluxes: -cupn <= netflux <= cupn. Must be non negative. Value 0 means no limit. Default: 1.e3" /> + <param argument="--cupp" type="float" min="0" value="" label="--cupp" optional="true" help="upper limit for metabolite pool. Default: 1.e5" /> + <param argument="--clownr" type="float" min="0" value="" label="--clownr" optional="true" help="lower limit for not reversible free and dependent fluxes. Zero value (default) means no lower limit" /> + <param argument="--cinout" type="float" min="0" value="" label="--cinout" optional="true" help="lower limit for input/output free and dependent fluxes. Must be non negative. Default: 0" /> + <param argument="--clowp" type="float" min="0" value="" label="--clowp" optional="true" help="lower limit for free metabolite pools. Must be positive. Default 1.e-8" /> + <param argument="--np" type="float" min="0" value="" label="--np" 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="--zc" type="float" min="0" value="" label="--zc" optional="true" help="Apply zero crossing strategy with non negative threshold for net fluxes" /> + <param argument="--fseries" type="text" value="" label="--fseries" optional="true" help="File name with free parameter values for multiple starting points. Default: '' (empty, i.e. only one starting point from the FTBL file is used)" /> + <param argument="--iseries" type="text" value="" label="--iseries" optional="true" help="Indexes of starting points to use. Format: '1:10' -- use only first ten starting points; '1,3' -- use the the first and third starting points; '1:10,15,91:100' -- a mix of both formats is allowed. Default: '' (empty, i.e. all provided starting points are used)" /> + <param argument="--seed" type="integer" min="0" value="" label="--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="--excl_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="--tblimit" type="integer" min="0" value="0" label="--tblimit" optional="true" help="developer option: set trace back limit for python error messages" /> + <param argument="--mtf" type="text" value="" label="--mtf MTF" optional="true" help="MTF is a coma separated list of files with following extensions: netw, linp, miso, mflux, mmet, tvar, cnstr, ftbl, vmtf. Only first 3 files are necessary to obtain a workable FTBL file, others are optional."/> + </section> + </inputs> + <outputs> + <collection name="influx_si_output" type="list:list" label="influx_${si.s_i}_on_${on_string}"> + <discover_datasets match_relative_path="true" recurse="true" pattern="(?P<identifier_0>[^/]+)_res/(?P<identifier_1>[^/]+)\.(?P<ext>[^.]+)" visible="false"/> + </collection> + </outputs> + <tests> + <test> + <param name="input_main" value="e_coli.zip" /> + <conditional name="si"> + <param name="s_i" value="s" /> + </conditional> + <output_collection name="influx_si_output" type="list:list" count="1"> + <element name="e_coli" count="7"> + <element name="e_coli.log"> + <assert_contents> + <has_n_lines n="38"/> + <has_line_matching expression="^end.*"/> + </assert_contents> + </element> + </element> + </output_collection> + </test> + </tests> + <help><![CDATA[ +Select one or several zip archives with MTF (Multiple TSV Files) sets, stationary/instationary labeling type and possibly some advanced option to run the tool. + +Detailed documentation is available on https://influx-si.readthedocs.io +]]></help> + <citations> + <citation type="bibtex"> + @misc{githubinflux, + author = {Sokol, Serguei}, + year = {2023}, + 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/macros.xml Wed Dec 13 08:56:04 2023 +0000 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">7.0.1</token> +</macros>
--- a/test-data/e_coli.ftbl Wed Sep 13 19:52:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,720 +0,0 @@ -PROJECT - NAME VERSION FORMAT DATE COMMENT - K12_MG1655.ftbl 1 101109 modele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees - -NETWORK - FLUX_NAME EDUCT_1 EDUCT_2 PRODUCT_1 PRODUCT_2 - -// Glycolyse. -// PPP -// TCA -// voies anaplerotiques: pepc. enz malique -// voie glyoxylate -// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre) -// saisie differentielle des substrats marques - - -//## Uptake substrats - - Glucupt_1 Gluc_1 Glc6P // fehlt bei wolfgang - #ABCDEF #ABCDEF // fehlt bei wolfgang - - Glucupt_U Gluc_U Glc6P // fehlt bei wolfgang - #ABCDEF #ABCDEF // fehlt bei wolfgang - -// CO2upt CO2_ext CO2 // entree de CO2 non marque -// #A #A // ce flux est a laisser libre - -// FTHF0 FTHF_0 FTHF // prise en charge de FTHF non marque -// #A #A - -// FTHF1 FTHF_1 FTHF // prise en charge de FTHF marque -// #a #a - - -//## Embden Meyerhof Parnas Pathway - - pgi Glc6P Fru6P - #ABCDEF #ABCDEF - - pfk Fru6P FruBP - #ABCDEF #ABCDEF - - ald FruBP GA3P GA3P - #ABCDEF #CBA #DEF - -// tpi DHAP GA3P -// #ABC #CBA - - pgk GA3P PGA - #ABC #ABC - - eno PGA PEP - #ABC #ABC - - pyk PEP Pyr - #ABC #ABC - - -//## Methylglyoxal Pathway - -// mgs DHAP Pyr -// #ABC #ABC - - -//## Pentose Phosphate Pathway - - zwf Glc6P Gnt6P - #ABCDEF #ABCDEF - - gnd Gnt6P CO2 Rib5P - #ABCDEF #A #BCDEF - - edd Gnt6P Pyr GA3P - #ABCDEF #ABC #DEF - -// ta Ery4P Fru6P GA3P Sed7P -// #ABCD #abcdef #def #abcABCD - -// tk1 GA3P Sed7P Rib5P Rib5P -// #ABC #abcdefg #abABC #cdefg - -// tk2 GA3P Fru6P Rib5P Ery4P -// #ABC #abcdef #abABC #cdef - - ta GA3P Sed7P Ery4P Fru6P - #ABC #abcdefg #defg #abcABC - - tk1 Rib5P Rib5P GA3P Sed7P - #ABCDE #abcde #CDE #ABabcde - - tk2 Rib5P Ery4P GA3P Fru6P - #ABCDE #abcd #CDE #ABabcd - - -//## Tricarboxylic Acid Cycle - - pdh Pyr AcCoA CO2 - #ABC #BC #A - - citsynth AcCoA OAA ICit - #AB #abcd #dcbaBA - - idh ICit AKG CO2 - #ABCDEF #ABCEF #D - - akgdh AKG Suc CO2 - #ABCDE #BCDE #A - - fum_a Suc Mal - #ABCD #ABCD - - fum_b Suc Mal - #ABCD #DCBA - - maldh Mal OAA - #ABCD #ABCD - - -//## Glyoxylate Shunt - -// gs1 ICit GlyOx Suc -// #ABCDEF #AB #DCEF - -// gs2 GlyOx AcCoA OAA -// #AB #ab #ABba - - -//## Anaplerotic Reactions - - ppc PEP CO2 OAA // PEPcarboxylase - #ABC #a #ABCa - - mae Mal Pyr CO2 // enzyme malique - #ABCD #ABC #D - -// pck OAA PEP CO2 // PEP carboxykinase -// #ABCD #ABC #D - - -//## Biosynthetic Pathways - - // Glucose-6-Phosphate Family - - bs_glc6P Glc6P BM_Glc6P - #ABCDEF #ABCDEF - - // Fructose-6-Phosphate Family - - bs_fru6P Fru6P BM_Fru6P // sortie de Fru6P pour biomasse - #ABCDEF #ABCDEF - - // Phosphoglycerate Family - - bs_pga PGA BM_PGA - #ABC #ABC - - bs_pga_aux BM_PGA PGA_Aux - #ABC #ABC - - bs_pga1 BM_PGA Ser - #ABC #ABC - - bs_pga1_aux Ser Ser_Aux - #ABC #ABC - - bs_pga2 Ser Cys // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga2_aux Cys Cys_Aux // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga3 Ser Gly FTHF // formation de gly pour biomasse - #ABC #AB #C // ce flux est reversible - - bs_pga3_aux Gly Gly_Aux // pour conserver Gly comme metabolite intracellulaire - #AB #AB - - // TrioseP Family - - bs_DHAP GA3P Glp // formation glycerolP pour lipides - #ABC #ABC - - // Pyruvate Family - - bs_pyr Pyr BM_Pyr - #ABC #ABC - - bs_pyr1 BM_Pyr Ala - #ABC #ABC - - bs_pyr1_aux Ala Ala_Aux // pour conserver Ala comme metabolite intracellulaire - #ABC #ABC - - bs_pyr2 BM_Pyr BM_Pyr AKV CO2 // AKV et Val ont le meme squelette C - #ABC #abc #ABbcC #a // cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val - - bs_pyr4 AKV Val // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr4_aux Val Val_Aux // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr3 AKV BM_AcCoA Leu CO2 - #ABCDE #ab #abBCDE #A - - bs_pyr3_aux Leu Leu_Aux // pour conserver Leu comme metabolite intracellulaire - #ABCDEF #ABCDEF - - - // Erythrose-4-Phosphate Family - - bs_e4p Ery4P BM_Ery4P // pour utiliser les donnees sur Ery4P - #ABCD #ABCD - -// bs_e4p_aux BM_Ery4P Ery4P_aux // pour utiliser les donnees sur Ery4P -// #ABCD #ABCD - - - // Ribose-5-Phosphate Family - - bs_rib5p Rib5P BM_Rib5P // pour utiliser les donnees sur Rib5P - #ABCDE #ABCDE - - bs_rib5p1 BM_Rib5P FTHF His // pour utiliser les donnees sur Rib5P - #ABCDE #a #EDCBAa - - bs_rib5p1_aux His His_Aux // sortie pour conserver His comme metabolite intracellulaire - #ABCDEF #ABCDEF - - bs_rib5p2 BM_Rib5P Ri5P_Aux // sortie de Ri5P pour autres besoins que His - #ABCDE #ABCDE // ce flux est important pour ne pas imposer de fausses contraintes sur FTHF si on considerait His comme seule sortie - - - // Aromatic Amino Acids - - bs_pep PEP BM_PEP - #ABC #ABC - - bs_pep1 BM_PEP BM_Ery4P DAHP - #ABC #abcd #ABCabcd - - bs_pep2 BM_PEP DAHP Chor - #ABC #abcdefg #ABCabcdefg - - bs_pep3a Chor Phe CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep3b Chor Phe CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep3_aux Phe Phe_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep4a Chor Tyr CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep4b Chor Tyr CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep4_aux Tyr Tyr_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep5 BM_PEP PEP_Aux - #ABC #ABC - - bs_pep6 Chor BM_Rib5P Trp PyrCO2 - #ABCDEFGHIJ #abcde #edcbaJEFGHI #ABCD - - bs_pep6_aux Trp Trp_Aux - #ABCDEFGHIJK #ABCDEFGHIJK - - bs_pep7 PyrCO2 Pyr CO2 - #ABCD #ABC #D - - - // Acetyl-CoA - - bs_accoa AcCoA BM_AcCoA - #AB #AB - - bs_accoa_aux BM_AcCoA AcCoA_Aux - #AB #AB - - - // Alpha-Ketoglutarate Family - - bs_akg AKG BM_AKG // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg1 BM_AKG Glu // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg2 Glu Pro // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg3 Glu Gln // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg4 Glu CO2 Arg // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #a #ABCDEa - - bs_akg4_aux Arg Arg_Aux // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDEF #ABCDEF - - - // Oxaloacetate Family - - bs_oaa OAA BM_OAA - #ABCD #ABCD - - bs_oaa1 BM_OAA Asp - #ABCD #ABCD - - bs_oaa1_aux Asp Asp_Aux - #ABCD #ABCD - - bs_oaa2 Thr BM_Pyr Ile CO2 - #ABCD #abc #ABbCDc #a - - bs_oaa2_aux Ile Ile_Aux - #ABCDEF #ABCDEF - - bs_oaa3a BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #ABCDcb #a - - bs_oaa3b BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #abcDCB #A - - bs_oaa3_aux Lys Lys_Aux - #ABCDEF #ABCDEF - - bs_oaa4 BM_OAA OAA_Aux - #ABCD #ABCD - - bs_oaa5 BM_OAA Thr - #ABCD #ABCD - - bs_oaa5_aux Thr Thr_Aux - #ABCD #ABCD - - bs_oaa6 BM_OAA FTHF Met - #ABCD #a #ABCDa - - bs_oaa6_aux Met Met_Aux - #ABCDE #ABCDE - - bs_oaa7 BM_OAA Asn - #ABCD #ABCD - - bs_oaa7_aux Asn Asn_Aux - #ABCD #ABCD - - -//## Flux de sortie - - out_co2 CO2 CO2_out // Sortie de CO2 - #A #A - - out_Ac AcCoA Acetate // Sortie d'acetate - #AB #AB - - out_FTHF FTHF FTHF_out - #A #A - -FLUXES - NET - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt_1 F 0.7 //0.807194 - Glucupt_U D -// CO2upt F 0.669589 -// FTHF0 F 0.00224836 -// FTHF1 F 0.001 - - pgi D - pfk D - ald D -// tpi D - pgk D - eno D - pyk F 1.4 - - zwf F 0.2 - gnd F 0.15062 - edd D - ta D - tk1 D - tk2 D - - pdh D - citsynth D - idh D - akgdh D - fum_a D - fum_b D - maldh D - -// gs1 C 0 -// gs2 D - - ppc D - mae D -// pck D - - // flux de biomasse - - bs_glc6P C 0.0109 // sortie de G6P - bs_fru6P C 0.0038 // sortie de F6P - bs_pga C 0.0791 // sortie de PGA pour formation de biomasse - bs_pga_aux D // sortie de PGA pour formation de biomasse - bs_pga1 D // conversion PGA donne ser - bs_pga1_aux C 0.0109 // conversion PGA donne ser - bs_pga2 D - bs_pga2_aux C 0.0046 // conversion PGA donne Cys - bs_pga3 D // reaction de synthese de Gly - bs_pga3_aux C 0.0308 // sortie de Gly - bs_DHAP C 0.0068 // formation de glycerolP pour lipides - bs_pyr C 0.1501 // avant : 0.1547 // sortie de Pyr pour formation de biomasse - bs_pyr1 D // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Leu - bs_pyr2 D // synthese d'AKV. consomme 2 Pyr - bs_pyr4 D - bs_pyr4_aux C 0.0213 // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 D // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux C 0.0227 // sortie de Leu - bs_e4p D // sortie d'Ery4p pour biomasse -// bs_e4p_aux C 0 // sortie d'Ery4p pour Trp - bs_rib5p C 0.0476 // synthese d'His - bs_rib5p1 D // synthese d'His - bs_rib5p1_aux C 0.0048 // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_pep C 0.0381 // sortie de PEP - bs_pep1 D // sortie de PEP - bs_pep2 D - bs_pep3a D - bs_pep3b D - bs_pep3_aux C 0.0093 - bs_pep4a D - bs_pep4b D - bs_pep4_aux C 0.0069 - bs_pep5 C 0.0027 - bs_pep6 D - bs_pep6_aux D - bs_pep7 D - bs_accoa C 0.1565 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_akg C 0.0571 // sortie d'AKG - bs_akg1 D - bs_akg2 C 0.0111 - bs_akg3 C 0.0132 - bs_akg4 D - bs_akg4_aux D - bs_oaa C 0.0947 // sortie d'OAA pour formation de biomasse - bs_oaa1 D // sortie d'OAA pour Asp - bs_oaa1_aux C 0.0121 // sortie d'Asp - bs_oaa2 D // synthese d'Ile - bs_oaa2_aux C 0.0146 // sortie d'Ile - bs_oaa3a D - bs_oaa3b D - bs_oaa3_aux C 0.0173 - bs_oaa4 D - bs_oaa5 D - bs_oaa5_aux C 0.0128 - bs_oaa6 D - bs_oaa6_aux C 0.0077 - bs_oaa7 D - bs_oaa7_aux C 0.0121 - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac F 0.213 // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - - XCH - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt_1 D - Glucupt_U D -// CO2upt D -// FTHF0 D -// FTHF1 D - - pgi C 0.752386 // 2011-02-22 ssg: was F => often unresolved with --irand option - pfk C 0 - ald F 0.413926 -// tpi F 0.5 - pgk C 0.984718 // 2011-02-22 ssg: was F => often unresolved with --irand option - eno F 0.800962 - pyk C 0.0109591 // 2010-10-01 ssg: was F => unresolved if co2 uptake is unlimited - - zwf C 0 - gnd C 0 - edd C 0 - ta F 0.359468 - tk1 F 0.166316 - tk2 F 2.11559e-03 - - pdh C 0.0322745 // 2010-10-02 ssg: was F, otherwise unsolvable in monte-carlo - citsynth C 0 - idh C 0 - akgdh C 0 - fum_a F 0.395958 - fum_b D - maldh C 0.647115 //********************************************** C pour analyse de sensibilite, F pour minimisation - -// gs1 C 0 -// gs2 C 0 - - ppc F 0.256772 - mae C 0 -// pck C 0 - - bs_glc6P D // sortie de G6P - bs_fru6P D // sortie de F6P - bs_pga C 0 // conversion PGA donne Ser - bs_pga_aux D // conversion PGA donne Ser - bs_pga1 C 0 // conversion PGA donne Ser - bs_pga1_aux D // conversion PGA donne Ser - bs_pga2 C 0 // ser donne Cys. correspond a la sortie de PGA pour biomasse autre que formation Gly - bs_pga2_aux D - bs_pga3 C 0.011799 // reaction de synthese de Gly. cette reaction est reversible - bs_pga3_aux D // sortie de Gly - bs_DHAP D // formation de glycerolP pour lipides - bs_pyr C 0 // formation d'Ala - bs_pyr1 C 0 // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Ile - bs_pyr2 C 0 // synthese d'AKV. consomme 2 Pyr - bs_pyr4 C 0 - bs_pyr4_aux D // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 C 0 // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux D // sortie de Leu - bs_e4p C 0 // sortie d'Ery4p -// bs_e4p_aux D // sortie d'Ery4p pour Trp - bs_rib5p C 0 // synthese d'His - bs_rib5p1 C 0 // synthese d'His - bs_rib5p1_aux D // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_accoa C 0 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_pep C 0 // sortie de PEP - bs_pep1 C 0 // sortie de PEP - bs_pep2 C 0 - bs_pep3a C 0 - bs_pep3b C 0 - bs_pep3_aux D - bs_pep4a C 0 - bs_pep4b C 0 - bs_pep4_aux D - bs_pep5 D - bs_pep6 C 0 - bs_pep6_aux D - bs_pep7 C 0 - bs_akg C 0 // sortie d'AKG - bs_akg1 C 0 - bs_akg2 D - bs_akg3 D - bs_akg4 C 0 - bs_akg4_aux D - bs_oaa C 0 - bs_oaa1 C 0 // sortie d'OAA autres que Met - bs_oaa1_aux D // sortie d'OAA autres que Met - bs_oaa2 C 0 // synthese de Met - bs_oaa2_aux D // sortie de Met - bs_oaa3a C 0 - bs_oaa3b C 0 - bs_oaa3_aux D - bs_oaa4 D - bs_oaa5 C 0 - bs_oaa5_aux D - bs_oaa6 C 0 - bs_oaa6_aux D - bs_oaa7 C 0 - bs_oaa7_aux D - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac D // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - -EQUALITIES - NET - VALUE FORMULA - - 0 fum_a-fum_b // scrambling reaction - 1 Glucupt_1+Glucupt_U - 0 bs_oaa3a-bs_oaa3b - 0 bs_pep3a-bs_pep3b - 0 bs_pep4a-bs_pep4b - - XCH - VALUE FORMULA - - 0 fum_a-fum_b - -INEQUALITIES - NET - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - 1 <= pyk - 0.0001 <= edd - 0.0001 <= gnd - 0.0001 <= zwf - 0.0001 <= ppc - 0.0001 <= mae -// 2 >= CO2upt // 2010-08-18 too high value makes jacobian rank deficient - XCH - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - - -FLUX_MEASUREMENTS - FLUX_NAME VALUE DEVIATION // Val Dev - out_Ac 0.213 0.0001 - -LABEL_INPUT - META_NAME ISOTOPOMER VALUE - - Gluc_U #111111 1 - #000000 0. - Gluc_1 #100000 1. - #000000 0. -// CO2_ext #0 0.989 -// #1 0.011 - -// FTHF_0 #0 1 -// FTHF_1 #1 1 - - -LABEL_MEASUREMENTS - META_NAME CUM_GROUP VALUE DEVIATION CUM_CONSTRAINTS - // Example - -PEAK_MEASUREMENTS - META_NAME PEAK_NO VALUE_S VALUE_D- VALUE_D+ VALUE_DD VALUE_T DEVIATION_S DEVIATION_D- DEVIATION_D+ DEVIATION_DD/T - - -MASS_SPECTROMETRY - META_NAME FRAGMENT WEIGHT VALUE DEVIATION - -// Deviation fixee a 0.02 // correction inoc 0.062 - - - - Suc 1,2,3,4 1 0.371605319 0.01 - 2 0.360829749 0.01 - 3 0.208425325 0.01 - 4 0.059139607 0.01 -// Mal 1,2,3,4 0 0.164619329483 0.02 -// 1 0.110072868518 0.02 -// 2 0.637801316225333 0.02 -// 3 0.0863461044204333 0.02 -// 4 0.00116038135315367 0.02 - ICit 1,2,3,4,5,6 0 0.131864539419667 0.02 - 1 0.225857638569 0.02 - 2 0.256421170949333 0.02 - 3 0.209230210478667 0.02 - 4 0.116863585449667 0.02 - 5 0.0457727744643333 0.02 - 6 0.0139900806697867 0.02 - PEP 1,2,3 0 0.421359839367667 0.01 - 1 0.358998301162333 0.01 - 2 0.0348521859365667 0.01 - 3 0.184789673534 0.01 - PGA 1,2,3 0 0.434335785072667 0.01 - 1 0.352829683224667 0.01 - 2 0.0323479804176 0.01 - 3 0.180486551285333 0.01 - FruBP 1,2,3,4,5,6 0 0.0738121029259333 0.01 - 1 0.454450017158667 0.01 - 2 0.160823529969333 0.01 - 3 0.0944468077710667 0.01 - 4 0.105281338489667 0.01 - 5 0.0155016033633 0.01 - 6 0.0956846003217333 0.01 - Glc6P 1,2,3,4,5,6 0 0.0160587173349 0.01 - 1 0.673510772480667 0.01 - 2 0.0930110047641 0.01 - 3 0.0280359937297 0.01 - 4 0.0397315614067667 0.01 - 5 0.0145524520950667 0.01 - 6 0.135099498189 0.01 - Fru6P 1,2,3,4,5,6 0 0.0235029951295 0.01 - 1 0.624253565357667 0.01 - 2 0.113068441282333 0.01 - 3 0.0456605631765 0.01 - 4 0.0516089447155667 0.01 - 5 0.0185881765378333 0.01 - 6 0.123317313800333 0.01 - Rib5P 1,2,3,4,5 0 0.341615670498667 0.01 - 1 0.25454117519 0.01 - 2 0.159027180368333 0.01 - 3 0.113789577528667 0.01 - 4 0.0615266612553333 0.01 - 5 0.0694997351590667 0.01 - Gnt6P 1,2,3,4,5,6 0 0.0249552273874 0.01 - 1 0.672556163913 0.01 - 2 0.0866890773125333 0.01 - 3 0.0313987199704333 0.01 - 4 0.0314691889898667 0.01 - 5 0.0138168327362333 0.01 - 6 0.139114789690333 0.01 -// Ery4P 1,2,3,4 0 0.178453461108 0.01 -// 1 0.412398433968333 0.01 -// 2 0.273694508221667 0.01 -// 3 0.116142498670667 0.01 -// 4 0.0193110980315 0.01 - -OPTIONS - OPT_NAME OPT_VALUE - //MATLAB_FOR_FLUX_EQ_CONSTR_MATR 1 - //optctrl_history 1 // nlsic - //optctrl_trace 3 // BFGS - //optctrl_reltol 1.e-10 // BFGS - //optctrl_maxit 1000 // BFGS - commandArgs --TIMEIT - posttreat_R plot_smeas.R
--- a/test-data/e_coli.log Wed Sep 13 19:52:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -"/home/sokol/miniconda3/envs/__influx_si@5.0.3/bin/influx_s" "e_coli.ftbl" -code gen: 2020-03-26 18:33:45 -executing: "/usr/local/miniconda3/envs/__influx_si@5.0.3/bin/python3.8" "/home/STORAGE/local/miniconda3/envs/__influx_si@5.0.3/bin/ftbl2optR.py" "--tblimit" "0" "--ropts" "TIMEIT=TRUE" "e_coli.ftbl" -executing: R --vanilla --slave < e_coli.R -calcul : 2020-03-26 18:33:49 -load : 2020-03-26 18:33:51.07 cpu=1.016 -rinit : 2020-03-26 18:33:51.07 cpu=1.018 -r_flux : 2020-03-26 18:33:51.07 cpu=1.018 -Afl qr(): 2020-03-26 18:33:51.14 cpu=1.083 -dfl_dffg: 2020-03-26 18:33:51.20 cpu=1.123 -spAbr : 2020-03-26 18:33:51.20 cpu=1.125 -weight 1: 2020-03-26 18:33:51.20 cpu=1.125 -weight 2: 2020-03-26 18:33:51.44 cpu=1.191 -weight 3: 2020-03-26 18:33:51.59 cpu=1.258 -weight 4: 2020-03-26 18:33:51.65 cpu=1.311 -weight 5: 2020-03-26 18:33:51.67 cpu=1.338 -weight 6: 2020-03-26 18:33:51.68 cpu=1.348 -measure : 2020-03-26 18:33:51.80 cpu=1.435 -ineq : 2020-03-26 18:33:51.94 cpu=1.515 -preopt : 2020-03-26 18:33:52.02 cpu=1.595 -labargs : 2020-03-26 18:33:52.04 cpu=1.618 -run 1: 2020-03-26 18:33:56.49 cpu=4.72 -Starting point -res esti: 2020-03-26 18:33:56.50 cpu=4.722 -kvh init: 2020-03-26 18:33:56.52 cpu=4.742 -check ja: 2020-03-26 18:33:56.57 cpu=4.763 -optim : 2020-03-26 18:33:56.66 cpu=4.814 -it=0 res=33.60668 -it=1 res=8.537147 normstep=0.372971 btk=1 -it=2 res=7.844899 normstep=0.1372184 btk=1 -it=3 res=7.843106 normstep=0.005504594 btk=1 -it=4 res=7.843096 normstep=0.0004985717 btk=1 -it=5 res=7.843096 normstep=2.725573e-05 btk=1 -it=6 res=7.843096 normstep=3.688583e-06 btk=1 -postopt : 2020-03-26 18:33:57.15 cpu=5.321 -linstats: 2020-03-26 18:33:57.38 cpu=5.528 -rend : 2020-03-26 18:33:57.76 cpu=5.753 -end : 2020-03-26 18:33:58
--- a/test-data/e_coli_1-Glc_exact.ftbl Wed Sep 13 19:52:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,713 +0,0 @@ -PROJECT - NAME VERSION FORMAT DATE COMMENT - K12_MG1655.ftbl 1 101109 modele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees - -NETWORK - FLUX_NAME EDUCT_1 EDUCT_2 PRODUCT_1 PRODUCT_2 - -// Glycolyse. -// PPP -// TCA -// voies anaplerotiques: pepc. enz malique -// voie glyoxylate -// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre) -// saisie differentielle des substrats marques - - -// Uptake substrats - - Glucupt Gluc Glc6P - #ABCDEF #ABCDEF -// CO2upt CO2_ext CO2 // entree de CO2 non marque -// #A #A // ce flux est a laisser libre - -// FTHF0 FTHF_0 FTHF // prise en charge de FTHF non marque -// #A #A - -// FTHF1 FTHF_1 FTHF // prise en charge de FTHF marque -// #a #a - - -// Embden Meyerhof Parnas Pathway - - pgi Glc6P Fru6P - #ABCDEF #ABCDEF - - pfk Fru6P FruBP - #ABCDEF #ABCDEF - - ald FruBP GA3P GA3P - #ABCDEF #CBA #DEF - -// tpi DHAP GA3P -// #ABC #CBA - - pgk GA3P PGA - #ABC #ABC - - eno PGA PEP - #ABC #ABC - - pyk PEP Pyr - #ABC #ABC - - -// Methylglyoxal Pathway - -// mgs DHAP Pyr -// #ABC #ABC - - -// Pentose Phosphate Pathway - - zwf Glc6P Gnt6P - #ABCDEF #ABCDEF - - gnd Gnt6P CO2 Rib5P - #ABCDEF #A #BCDEF - - edd Gnt6P Pyr GA3P - #ABCDEF #ABC #DEF - -// ta Ery4P Fru6P GA3P Sed7P -// #ABCD #abcdef #def #abcABCD - -// tk1 GA3P Sed7P Rib5P Rib5P -// #ABC #abcdefg #abABC #cdefg - -// tk2 GA3P Fru6P Rib5P Ery4P -// #ABC #abcdef #abABC #cdef - - ta GA3P Sed7P Ery4P Fru6P - #ABC #abcdefg #defg #abcABC - - tk1 Rib5P Rib5P GA3P Sed7P - #ABCDE #abcde #CDE #ABabcde - - tk2 Rib5P Ery4P GA3P Fru6P - #ABCDE #abcd #CDE #ABabcd - - -// Tricarboxylic Acid Cycle - - pdh Pyr AcCoA CO2 - #ABC #BC #A - - citsynth AcCoA OAA ICit - #AB #abcd #dcbaBA - - idh ICit AKG CO2 - #ABCDEF #ABCEF #D - - akgdh AKG Suc CO2 - #ABCDE #BCDE #A - - fum_a Suc Mal - #ABCD #ABCD - - fum_b Suc Mal - #ABCD #DCBA - - maldh Mal OAA - #ABCD #ABCD - - -// Glyoxylate Shunt - -// gs1 ICit GlyOx Suc -// #ABCDEF #AB #DCEF - -// gs2 GlyOx AcCoA OAA -// #AB #ab #ABba - - -// Anaplerotic Reactions - - ppc PEP CO2 OAA // PEPcarboxylase - #ABC #a #ABCa - - mae Mal Pyr CO2 // enzyme malique - #ABCD #ABC #D - -// pck OAA PEP CO2 // PEP carboxykinase -// #ABCD #ABC #D - - -// Biosynthetic Pathways - - // Glucose-6-Phosphate Family - - bs_glc6P Glc6P BM_Glc6P - #ABCDEF #ABCDEF - - // Fructose-6-Phosphate Family - - bs_fru6P Fru6P BM_Fru6P // sortie de Fru6P pour biomasse - #ABCDEF #ABCDEF - - // Phosphoglycerate Family - - bs_pga PGA BM_PGA - #ABC #ABC - - bs_pga_aux BM_PGA PGA_Aux - #ABC #ABC - - bs_pga1 BM_PGA Ser - #ABC #ABC - - bs_pga1_aux Ser Ser_Aux - #ABC #ABC - - bs_pga2 Ser Cys // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga2_aux Cys Cys_Aux // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga3 Ser Gly FTHF // formation de gly pour biomasse - #ABC #AB #C // ce flux est reversible - - bs_pga3_aux Gly Gly_Aux // pour conserver Gly comme metabolite intracellulaire - #AB #AB - - // TrioseP Family - - bs_DHAP GA3P Glp // formation glycerolP pour lipides - #ABC #ABC - - // Pyruvate Family - - bs_pyr Pyr BM_Pyr - #ABC #ABC - - bs_pyr1 BM_Pyr Ala - #ABC #ABC - - bs_pyr1_aux Ala Ala_Aux // pour conserver Ala comme metabolite intracellulaire - #ABC #ABC - - bs_pyr2 BM_Pyr BM_Pyr AKV CO2 // AKV et Val ont le meme squelette C - #ABC #abc #ABbcC #a // cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val - - bs_pyr4 AKV Val // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr4_aux Val Val_Aux // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr3 AKV BM_AcCoA Leu CO2 - #ABCDE #ab #abBCDE #A - - bs_pyr3_aux Leu Leu_Aux // pour conserver Leu comme metabolite intracellulaire - #ABCDEF #ABCDEF - - - // Erythrose-4-Phosphate Family - - bs_e4p Ery4P BM_Ery4P // pour utiliser les donnees sur Ery4P - #ABCD #ABCD - -// bs_e4p_aux BM_Ery4P Ery4P_aux // pour utiliser les donnees sur Ery4P -// #ABCD #ABCD - - - // Ribose-5-Phosphate Family - - bs_rib5p Rib5P BM_Rib5P // pour utiliser les donnees sur Rib5P - #ABCDE #ABCDE - - bs_rib5p1 BM_Rib5P FTHF His // pour utiliser les donnees sur Rib5P - #ABCDE #a #EDCBAa - - bs_rib5p1_aux His His_Aux // sortie pour conserver His comme metabolite intracellulaire - #ABCDEF #ABCDEF - - bs_rib5p2 BM_Rib5P Ri5P_Aux // sortie de Ri5P pour autres besoins que His - #ABCDE #ABCDE // ce flux est important pour ne pas imposer de fausses contraintes sur FTHF si on considerait His comme seule sortie - - - // Aromatic Amino Acids - - bs_pep PEP BM_PEP - #ABC #ABC - - bs_pep1 BM_PEP BM_Ery4P DAHP - #ABC #abcd #ABCabcd - - bs_pep2 BM_PEP DAHP Chor - #ABC #abcdefg #ABCabcdefg - - bs_pep3a Chor Phe CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep3b Chor Phe CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep3_aux Phe Phe_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep4a Chor Tyr CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep4b Chor Tyr CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep4_aux Tyr Tyr_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep5 BM_PEP PEP_Aux - #ABC #ABC - - bs_pep6 Chor BM_Rib5P Trp PyrCO2 - #ABCDEFGHIJ #abcde #edcbaJEFGHI #ABCD - - bs_pep6_aux Trp Trp_Aux - #ABCDEFGHIJK #ABCDEFGHIJK - - bs_pep7 PyrCO2 Pyr CO2 - #ABCD #ABC #D - - - // Acetyl-CoA - - bs_accoa AcCoA BM_AcCoA - #AB #AB - - bs_accoa_aux BM_AcCoA AcCoA_Aux - #AB #AB - - - // Alpha-Ketoglutarate Family - - bs_akg AKG BM_AKG // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg1 BM_AKG Glu // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg2 Glu Pro // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg3 Glu Gln // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg4 Glu CO2 Arg // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #a #ABCDEa - - bs_akg4_aux Arg Arg_Aux // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDEF #ABCDEF - - - // Oxaloacetate Family - - bs_oaa OAA BM_OAA - #ABCD #ABCD - - bs_oaa1 BM_OAA Asp - #ABCD #ABCD - - bs_oaa1_aux Asp Asp_Aux - #ABCD #ABCD - - bs_oaa2 Thr BM_Pyr Ile CO2 - #ABCD #abc #ABbCDc #a - - bs_oaa2_aux Ile Ile_Aux - #ABCDEF #ABCDEF - - bs_oaa3a BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #ABCDcb #a - - bs_oaa3b BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #abcDCB #A - - bs_oaa3_aux Lys Lys_Aux - #ABCDEF #ABCDEF - - bs_oaa4 BM_OAA OAA_Aux - #ABCD #ABCD - - bs_oaa5 BM_OAA Thr - #ABCD #ABCD - - bs_oaa5_aux Thr Thr_Aux - #ABCD #ABCD - - bs_oaa6 BM_OAA FTHF Met - #ABCD #a #ABCDa - - bs_oaa6_aux Met Met_Aux - #ABCDE #ABCDE - - bs_oaa7 BM_OAA Asn - #ABCD #ABCD - - bs_oaa7_aux Asn Asn_Aux - #ABCD #ABCD - - -// Flux de sortie - - out_co2 CO2 CO2_out // Sortie de CO2 - #A #A - - out_Ac AcCoA Acetate // Sortie d'acetate - #AB #AB - - out_FTHF FTHF FTHF_out - #A #A - -FLUXES - NET - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt C 1 -// CO2upt F 0.669589 -// FTHF0 F 0.00224836 -// FTHF1 F 0.001 - - pgi D - pfk D - ald D -// tpi D - pgk D - eno D - pyk F 1.54425507 - - zwf F 0.14233479 - gnd F 0.14223479 - edd D - ta D - tk1 D - tk2 D - - pdh D - citsynth D - idh D - akgdh D - fum_a D - fum_b D - maldh D - -// gs1 C 0 -// gs2 D - - ppc D - mae D -// pck D - - // flux de biomasse - - bs_glc6P C 0.0109 // sortie de G6P - bs_fru6P C 0.0038 // sortie de F6P - bs_pga C 0.0791 // sortie de PGA pour formation de biomasse - bs_pga_aux D // sortie de PGA pour formation de biomasse - bs_pga1 D // conversion PGA donne ser - bs_pga1_aux C 0.0109 // conversion PGA donne ser - bs_pga2 D - bs_pga2_aux C 0.0046 // conversion PGA donne Cys - bs_pga3 D // reaction de synthese de Gly - bs_pga3_aux C 0.0308 // sortie de Gly - bs_DHAP C 0.0068 // formation de glycerolP pour lipides - bs_pyr C 0.1501 // avant : 0.1547 // sortie de Pyr pour formation de biomasse - bs_pyr1 D // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Leu - bs_pyr2 D // synthese d'AKV. consomme 2 Pyr - bs_pyr4 D - bs_pyr4_aux C 0.0213 // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 D // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux C 0.0227 // sortie de Leu - bs_e4p D // sortie d'Ery4p pour biomasse -// bs_e4p_aux C 0 // sortie d'Ery4p pour Trp - bs_rib5p C 0.0476 // synthese d'His - bs_rib5p1 D // synthese d'His - bs_rib5p1_aux C 0.0048 // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_pep C 0.0381 // sortie de PEP - bs_pep1 D // sortie de PEP - bs_pep2 D - bs_pep3a D - bs_pep3b D - bs_pep3_aux C 0.0093 - bs_pep4a D - bs_pep4b D - bs_pep4_aux C 0.0069 - bs_pep5 C 0.0027 - bs_pep6 D - bs_pep6_aux D - bs_pep7 D - bs_accoa C 0.1565 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_akg C 0.0571 // sortie d'AKG - bs_akg1 D - bs_akg2 C 0.0111 - bs_akg3 C 0.0132 - bs_akg4 D - bs_akg4_aux D - bs_oaa C 0.0947 // sortie d'OAA pour formation de biomasse - bs_oaa1 D // sortie d'OAA pour Asp - bs_oaa1_aux C 0.0121 // sortie d'Asp - bs_oaa2 D // synthese d'Ile - bs_oaa2_aux C 0.0146 // sortie d'Ile - bs_oaa3a D - bs_oaa3b D - bs_oaa3_aux C 0.0173 - bs_oaa4 D - bs_oaa5 D - bs_oaa5_aux C 0.0128 - bs_oaa6 D - bs_oaa6_aux C 0.0077 - bs_oaa7 D - bs_oaa7_aux C 0.0121 - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac F 0.213000005 - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - - XCH - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt C 0 -// CO2upt D -// FTHF0 D -// FTHF1 D - - pgi C 0.752386 // 2011-02-22 ssg: was F => often unresolved with --irand option - pfk C 0 - ald F 0.420281957 -// tpi F 0.5 - pgk C 0.984718 // 2011-02-22 ssg: was F => often unresolved with --irand option - eno F 0.999 - pyk C 0.0109591 // 2010-10-01 ssg: was F => unresolved if co2 uptake is unlimited - - zwf C 0 - gnd C 0 - edd C 0 - ta F 0.361648085 - tk1 F 0.151671492 - tk2 F 0 - - pdh C 0.0322745 // 2010-10-02 ssg: was F, otherwise unsolvable in monte-carlo - citsynth C 0 - idh C 0 - akgdh C 0 - fum_a F 0.3013683 - fum_b D - maldh C 0.647115 //********************************************** C pour analyse de sensibilite, F pour minimisation - -// gs1 C 0 -// gs2 C 0 - - ppc F 0.147615337 - mae C 0 -// pck C 0 - - bs_glc6P D // sortie de G6P - bs_fru6P D // sortie de F6P - bs_pga C 0 // conversion PGA donne Ser - bs_pga_aux D // conversion PGA donne Ser - bs_pga1 C 0 // conversion PGA donne Ser - bs_pga1_aux D // conversion PGA donne Ser - bs_pga2 C 0 // ser donne Cys. correspond a la sortie de PGA pour biomasse autre que formation Gly - bs_pga2_aux D - bs_pga3 C 0.011799 // reaction de synthese de Gly. cette reaction est reversible - bs_pga3_aux D // sortie de Gly - bs_DHAP D // formation de glycerolP pour lipides - bs_pyr C 0 // formation d'Ala - bs_pyr1 C 0 // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Ile - bs_pyr2 C 0 // synthese d'AKV. consomme 2 Pyr - bs_pyr4 C 0 - bs_pyr4_aux D // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 C 0 // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux D // sortie de Leu - bs_e4p C 0 // sortie d'Ery4p -// bs_e4p_aux D // sortie d'Ery4p pour Trp - bs_rib5p C 0 // synthese d'His - bs_rib5p1 C 0 // synthese d'His - bs_rib5p1_aux D // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_accoa C 0 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_pep C 0 // sortie de PEP - bs_pep1 C 0 // sortie de PEP - bs_pep2 C 0 - bs_pep3a C 0 - bs_pep3b C 0 - bs_pep3_aux D - bs_pep4a C 0 - bs_pep4b C 0 - bs_pep4_aux D - bs_pep5 D - bs_pep6 C 0 - bs_pep6_aux D - bs_pep7 C 0 - bs_akg C 0 // sortie d'AKG - bs_akg1 C 0 - bs_akg2 D - bs_akg3 D - bs_akg4 C 0 - bs_akg4_aux D - bs_oaa C 0 - bs_oaa1 C 0 // sortie d'OAA autres que Met - bs_oaa1_aux D // sortie d'OAA autres que Met - bs_oaa2 C 0 // synthese de Met - bs_oaa2_aux D // sortie de Met - bs_oaa3a C 0 - bs_oaa3b C 0 - bs_oaa3_aux D - bs_oaa4 D - bs_oaa5 C 0 - bs_oaa5_aux D - bs_oaa6 C 0 - bs_oaa6_aux D - bs_oaa7 C 0 - bs_oaa7_aux D - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac D // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - -EQUALITIES - NET - VALUE FORMULA - - 0 fum_a-fum_b // scrambling reaction - 0 bs_oaa3a-bs_oaa3b - 0 bs_pep3a-bs_pep3b - 0 bs_pep4a-bs_pep4b - - XCH - VALUE FORMULA - - 0 fum_a-fum_b - -INEQUALITIES - NET - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - 1 <= pyk - 0.0001 <= edd - 0.0001 <= gnd - 0.0001 <= zwf - 0.0001 <= ppc - 0.0001 <= mae -// 2 >= CO2upt // 2010-08-18 too high value makes jacobian rank deficient - XCH - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - - -FLUX_MEASUREMENTS - FLUX_NAME VALUE DEVIATION // Val Dev - out_Ac 0.213 0.0001 - -LABEL_INPUT - META_NAME ISOTOPOMER VALUE - - Gluc #100000 0.8 - #000000 0.2 -// CO2_ext #0 0.989 -// #1 0.011 - -// FTHF_0 #0 1 -// FTHF_1 #1 1 - - -LABEL_MEASUREMENTS - META_NAME CUM_GROUP VALUE DEVIATION CUM_CONSTRAINTS - // Example - -PEAK_MEASUREMENTS - META_NAME PEAK_NO VALUE_S VALUE_D- VALUE_D+ VALUE_DD VALUE_T DEVIATION_S DEVIATION_D- DEVIATION_D+ DEVIATION_DD/T - - -MASS_SPECTROMETRY - META_NAME FRAGMENT WEIGHT VALUE DEVIATION - -// Deviation fixee a 0.02 // correction inoc 0.062 - - - - Suc 1,2,3,4 1 0.371605319 0.01 - 2 0.360829749 0.01 - 3 0.208425325 0.01 - 4 0.059139607 0.01 -// Mal 1,2,3,4 0 0.164619329483 0.02 -// 1 0.110072868518 0.02 -// 2 0.637801316225333 0.02 -// 3 0.0863461044204333 0.02 -// 4 0.00116038135315367 0.02 - ICit 1,2,3,4,5,6 0 0.131864539419667 0.02 - 1 0.225857638569 0.02 - 2 0.256421170949333 0.02 - 3 0.209230210478667 0.02 - 4 0.116863585449667 0.02 - 5 0.0457727744643333 0.02 - 6 0.0139900806697867 0.02 - PEP 1,2,3 0 0.421359839367667 0.01 - 1 0.358998301162333 0.01 - 2 0.0348521859365667 0.01 - 3 0.184789673534 0.01 - PGA 1,2,3 0 0.434335785072667 0.01 - 1 0.352829683224667 0.01 - 2 0.0323479804176 0.01 - 3 0.180486551285333 0.01 - FruBP 1,2,3,4,5,6 0 0.0738121029259333 0.01 - 1 0.454450017158667 0.01 - 2 0.160823529969333 0.01 - 3 0.0944468077710667 0.01 - 4 0.105281338489667 0.01 - 5 0.0155016033633 0.01 - 6 0.0956846003217333 0.01 - Glc6P 1,2,3,4,5,6 0 0.0160587173349 0.01 - 1 0.673510772480667 0.01 - 2 0.0930110047641 0.01 - 3 0.0280359937297 0.01 - 4 0.0397315614067667 0.01 - 5 0.0145524520950667 0.01 - 6 0.135099498189 0.01 - Fru6P 1,2,3,4,5,6 0 0.0235029951295 0.01 - 1 0.624253565357667 0.01 - 2 0.113068441282333 0.01 - 3 0.0456605631765 0.01 - 4 0.0516089447155667 0.01 - 5 0.0185881765378333 0.01 - 6 0.123317313800333 0.01 - Rib5P 1,2,3,4,5 0 0.341615670498667 0.01 - 1 0.25454117519 0.01 - 2 0.159027180368333 0.01 - 3 0.113789577528667 0.01 - 4 0.0615266612553333 0.01 - 5 0.0694997351590667 0.01 - Gnt6P 1,2,3,4,5,6 0 0.0249552273874 0.01 - 1 0.672556163913 0.01 - 2 0.0866890773125333 0.01 - 3 0.0313987199704333 0.01 - 4 0.0314691889898667 0.01 - 5 0.0138168327362333 0.01 - 6 0.139114789690333 0.01 -// Ery4P 1,2,3,4 0 0.178453461108 0.01 -// 1 0.412398433968333 0.01 -// 2 0.273694508221667 0.01 -// 3 0.116142498670667 0.01 -// 4 0.0193110980315 0.01 - -OPTIONS - OPT_NAME OPT_VALUE - MATLAB_FOR_FLUX_EQ_CONSTR_MATR 1 - //optctrl_history 1 // nlsic - //optctrl_trace 3 // BFGS - //optctrl_reltol 1.e-10 // BFGS - //optctrl_maxit 1000 // BFGS - posttreat_R plot_smeas.R - prl_exp e_coli_U-Glc_exact.ftbl - commandArgs --TIMEIT --noscale -
--- a/test-data/e_coli_1-Glc_exact.log Wed Sep 13 19:52:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -"/usr/local/miniconda3/bin/influx_s" "e_coli_1-Glc_exact.ftbl" -code gen: 2020-03-25 16:47:11 -executing: "/usr/local/miniconda3/bin/python3.7" "/home/STORAGE/local/miniconda3/bin/ftbl2optR.py" "--tblimit" "0" "--ropts" "noscale=TRUE; TIMEIT=TRUE" "e_coli_1-Glc_exact.ftbl" -executing: R --vanilla --slave < e_coli_1-Glc_exact.R -calcul : 2020-03-25 16:47:12 -load : 2020-03-25 16:47:13.55 cpu=0.945 -rinit : 2020-03-25 16:47:13.56 cpu=0.947 -r_flux : 2020-03-25 16:47:13.56 cpu=0.948 -Afl qr(): 2020-03-25 16:47:13.62 cpu=1.008 -dfl_dffg: 2020-03-25 16:47:13.73 cpu=1.042 -spAbr : 2020-03-25 16:47:13.73 cpu=1.045 -weight 1: 2020-03-25 16:47:13.73 cpu=1.046 -weight 2: 2020-03-25 16:47:13.77 cpu=1.123 -weight 3: 2020-03-25 16:47:13.84 cpu=1.251 -weight 4: 2020-03-25 16:47:13.89 cpu=1.354 -weight 5: 2020-03-25 16:47:13.91 cpu=1.402 -weight 6: 2020-03-25 16:47:13.92 cpu=1.421 -measure : 2020-03-25 16:47:14.00 cpu=1.506 -ineq : 2020-03-25 16:47:14.15 cpu=1.649 -preopt : 2020-03-25 16:47:14.20 cpu=1.718 -labargs : 2020-03-25 16:47:14.21 cpu=1.741 -run 1: 2020-03-25 16:47:17.10 cpu=4.779 -Starting point -The following 4 ineqalitie(s) are active at starting point: -n:0.0001<=edd -n:0.0001<=mae -f.x.tk2>=0 -f.x.eno<=0.999 -kvh init: 2020-03-25 16:47:17.10 cpu=4.781 -check ja: 2020-03-25 16:47:17.17 cpu=4.832 -optim : 2020-03-25 16:47:17.31 cpu=4.968 -it=0 res=211.2524 -it=1 res=162.3825 normstep=1.36222 btk=1 -it=2 res=143.6255 normstep=1.508085 btk=1 -it=3 res=143.4337 normstep=0.1225691 btk=1 -it=4 res=143.4337 normstep=2.429788e-08 btk=1 -postopt : 2020-03-25 16:47:17.64 cpu=5.279 -linstats: 2020-03-25 16:47:17.83 cpu=5.426 -rend : 2020-03-25 16:47:18.17 cpu=5.792 -end : 2020-03-25 16:47:18
--- a/test-data/e_coli_U-Glc_exact.ftbl Wed Sep 13 19:52:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,711 +0,0 @@ -PROJECT - NAME VERSION FORMAT DATE COMMENT - K12_MG1655.ftbl 1 101109 modele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees - -NETWORK - FLUX_NAME EDUCT_1 EDUCT_2 PRODUCT_1 PRODUCT_2 - -// Glycolyse. -// PPP -// TCA -// voies anaplerotiques: pepc. enz malique -// voie glyoxylate -// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre) -// saisie differentielle des substrats marques - - -// Uptake substrats - - Glucupt Gluc Glc6P - #ABCDEF #ABCDEF -// CO2upt CO2_ext CO2 // entree de CO2 non marque -// #A #A // ce flux est a laisser libre - -// FTHF0 FTHF_0 FTHF // prise en charge de FTHF non marque -// #A #A - -// FTHF1 FTHF_1 FTHF // prise en charge de FTHF marque -// #a #a - - -// Embden Meyerhof Parnas Pathway - - pgi Glc6P Fru6P - #ABCDEF #ABCDEF - - pfk Fru6P FruBP - #ABCDEF #ABCDEF - - ald FruBP GA3P GA3P - #ABCDEF #CBA #DEF - -// tpi DHAP GA3P -// #ABC #CBA - - pgk GA3P PGA - #ABC #ABC - - eno PGA PEP - #ABC #ABC - - pyk PEP Pyr - #ABC #ABC - - -// Methylglyoxal Pathway - -// mgs DHAP Pyr -// #ABC #ABC - - -// Pentose Phosphate Pathway - - zwf Glc6P Gnt6P - #ABCDEF #ABCDEF - - gnd Gnt6P CO2 Rib5P - #ABCDEF #A #BCDEF - - edd Gnt6P Pyr GA3P - #ABCDEF #ABC #DEF - -// ta Ery4P Fru6P GA3P Sed7P -// #ABCD #abcdef #def #abcABCD - -// tk1 GA3P Sed7P Rib5P Rib5P -// #ABC #abcdefg #abABC #cdefg - -// tk2 GA3P Fru6P Rib5P Ery4P -// #ABC #abcdef #abABC #cdef - - ta GA3P Sed7P Ery4P Fru6P - #ABC #abcdefg #defg #abcABC - - tk1 Rib5P Rib5P GA3P Sed7P - #ABCDE #abcde #CDE #ABabcde - - tk2 Rib5P Ery4P GA3P Fru6P - #ABCDE #abcd #CDE #ABabcd - - -// Tricarboxylic Acid Cycle - - pdh Pyr AcCoA CO2 - #ABC #BC #A - - citsynth AcCoA OAA ICit - #AB #abcd #dcbaBA - - idh ICit AKG CO2 - #ABCDEF #ABCEF #D - - akgdh AKG Suc CO2 - #ABCDE #BCDE #A - - fum_a Suc Mal - #ABCD #ABCD - - fum_b Suc Mal - #ABCD #DCBA - - maldh Mal OAA - #ABCD #ABCD - - -// Glyoxylate Shunt - -// gs1 ICit GlyOx Suc -// #ABCDEF #AB #DCEF - -// gs2 GlyOx AcCoA OAA -// #AB #ab #ABba - - -// Anaplerotic Reactions - - ppc PEP CO2 OAA // PEPcarboxylase - #ABC #a #ABCa - - mae Mal Pyr CO2 // enzyme malique - #ABCD #ABC #D - -// pck OAA PEP CO2 // PEP carboxykinase -// #ABCD #ABC #D - - -// Biosynthetic Pathways - - // Glucose-6-Phosphate Family - - bs_glc6P Glc6P BM_Glc6P - #ABCDEF #ABCDEF - - // Fructose-6-Phosphate Family - - bs_fru6P Fru6P BM_Fru6P // sortie de Fru6P pour biomasse - #ABCDEF #ABCDEF - - // Phosphoglycerate Family - - bs_pga PGA BM_PGA - #ABC #ABC - - bs_pga_aux BM_PGA PGA_Aux - #ABC #ABC - - bs_pga1 BM_PGA Ser - #ABC #ABC - - bs_pga1_aux Ser Ser_Aux - #ABC #ABC - - bs_pga2 Ser Cys // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga2_aux Cys Cys_Aux // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga3 Ser Gly FTHF // formation de gly pour biomasse - #ABC #AB #C // ce flux est reversible - - bs_pga3_aux Gly Gly_Aux // pour conserver Gly comme metabolite intracellulaire - #AB #AB - - // TrioseP Family - - bs_DHAP GA3P Glp // formation glycerolP pour lipides - #ABC #ABC - - // Pyruvate Family - - bs_pyr Pyr BM_Pyr - #ABC #ABC - - bs_pyr1 BM_Pyr Ala - #ABC #ABC - - bs_pyr1_aux Ala Ala_Aux // pour conserver Ala comme metabolite intracellulaire - #ABC #ABC - - bs_pyr2 BM_Pyr BM_Pyr AKV CO2 // AKV et Val ont le meme squelette C - #ABC #abc #ABbcC #a // cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val - - bs_pyr4 AKV Val // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr4_aux Val Val_Aux // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr3 AKV BM_AcCoA Leu CO2 - #ABCDE #ab #abBCDE #A - - bs_pyr3_aux Leu Leu_Aux // pour conserver Leu comme metabolite intracellulaire - #ABCDEF #ABCDEF - - - // Erythrose-4-Phosphate Family - - bs_e4p Ery4P BM_Ery4P // pour utiliser les donnees sur Ery4P - #ABCD #ABCD - -// bs_e4p_aux BM_Ery4P Ery4P_aux // pour utiliser les donnees sur Ery4P -// #ABCD #ABCD - - - // Ribose-5-Phosphate Family - - bs_rib5p Rib5P BM_Rib5P // pour utiliser les donnees sur Rib5P - #ABCDE #ABCDE - - bs_rib5p1 BM_Rib5P FTHF His // pour utiliser les donnees sur Rib5P - #ABCDE #a #EDCBAa - - bs_rib5p1_aux His His_Aux // sortie pour conserver His comme metabolite intracellulaire - #ABCDEF #ABCDEF - - bs_rib5p2 BM_Rib5P Ri5P_Aux // sortie de Ri5P pour autres besoins que His - #ABCDE #ABCDE // ce flux est important pour ne pas imposer de fausses contraintes sur FTHF si on considerait His comme seule sortie - - - // Aromatic Amino Acids - - bs_pep PEP BM_PEP - #ABC #ABC - - bs_pep1 BM_PEP BM_Ery4P DAHP - #ABC #abcd #ABCabcd - - bs_pep2 BM_PEP DAHP Chor - #ABC #abcdefg #ABCabcdefg - - bs_pep3a Chor Phe CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep3b Chor Phe CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep3_aux Phe Phe_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep4a Chor Tyr CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep4b Chor Tyr CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep4_aux Tyr Tyr_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep5 BM_PEP PEP_Aux - #ABC #ABC - - bs_pep6 Chor BM_Rib5P Trp PyrCO2 - #ABCDEFGHIJ #abcde #edcbaJEFGHI #ABCD - - bs_pep6_aux Trp Trp_Aux - #ABCDEFGHIJK #ABCDEFGHIJK - - bs_pep7 PyrCO2 Pyr CO2 - #ABCD #ABC #D - - - // Acetyl-CoA - - bs_accoa AcCoA BM_AcCoA - #AB #AB - - bs_accoa_aux BM_AcCoA AcCoA_Aux - #AB #AB - - - // Alpha-Ketoglutarate Family - - bs_akg AKG BM_AKG // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg1 BM_AKG Glu // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg2 Glu Pro // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg3 Glu Gln // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg4 Glu CO2 Arg // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #a #ABCDEa - - bs_akg4_aux Arg Arg_Aux // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDEF #ABCDEF - - - // Oxaloacetate Family - - bs_oaa OAA BM_OAA - #ABCD #ABCD - - bs_oaa1 BM_OAA Asp - #ABCD #ABCD - - bs_oaa1_aux Asp Asp_Aux - #ABCD #ABCD - - bs_oaa2 Thr BM_Pyr Ile CO2 - #ABCD #abc #ABbCDc #a - - bs_oaa2_aux Ile Ile_Aux - #ABCDEF #ABCDEF - - bs_oaa3a BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #ABCDcb #a - - bs_oaa3b BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #abcDCB #A - - bs_oaa3_aux Lys Lys_Aux - #ABCDEF #ABCDEF - - bs_oaa4 BM_OAA OAA_Aux - #ABCD #ABCD - - bs_oaa5 BM_OAA Thr - #ABCD #ABCD - - bs_oaa5_aux Thr Thr_Aux - #ABCD #ABCD - - bs_oaa6 BM_OAA FTHF Met - #ABCD #a #ABCDa - - bs_oaa6_aux Met Met_Aux - #ABCDE #ABCDE - - bs_oaa7 BM_OAA Asn - #ABCD #ABCD - - bs_oaa7_aux Asn Asn_Aux - #ABCD #ABCD - - -// Flux de sortie - - out_co2 CO2 CO2_out // Sortie de CO2 - #A #A - - out_Ac AcCoA Acetate // Sortie d'acetate - #AB #AB - - out_FTHF FTHF FTHF_out - #A #A - -FLUXES - NET - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt C 1 -// CO2upt F 0.669589 -// FTHF0 F 0.00224836 -// FTHF1 F 0.001 - - pgi D - pfk D - ald D -// tpi D - pgk D - eno D - pyk F 1.54425507 - - zwf F 0.14233479 - gnd F 0.14223479 - edd D - ta D - tk1 D - tk2 D - - pdh D - citsynth D - idh D - akgdh D - fum_a D - fum_b D - maldh D - -// gs1 C 0 -// gs2 D - - ppc D - mae D -// pck D - - // flux de biomasse - - bs_glc6P C 0.0109 // sortie de G6P - bs_fru6P C 0.0038 // sortie de F6P - bs_pga C 0.0791 // sortie de PGA pour formation de biomasse - bs_pga_aux D // sortie de PGA pour formation de biomasse - bs_pga1 D // conversion PGA donne ser - bs_pga1_aux C 0.0109 // conversion PGA donne ser - bs_pga2 D - bs_pga2_aux C 0.0046 // conversion PGA donne Cys - bs_pga3 D // reaction de synthese de Gly - bs_pga3_aux C 0.0308 // sortie de Gly - bs_DHAP C 0.0068 // formation de glycerolP pour lipides - bs_pyr C 0.1501 // avant : 0.1547 // sortie de Pyr pour formation de biomasse - bs_pyr1 D // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Leu - bs_pyr2 D // synthese d'AKV. consomme 2 Pyr - bs_pyr4 D - bs_pyr4_aux C 0.0213 // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 D // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux C 0.0227 // sortie de Leu - bs_e4p D // sortie d'Ery4p pour biomasse -// bs_e4p_aux C 0 // sortie d'Ery4p pour Trp - bs_rib5p C 0.0476 // synthese d'His - bs_rib5p1 D // synthese d'His - bs_rib5p1_aux C 0.0048 // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_pep C 0.0381 // sortie de PEP - bs_pep1 D // sortie de PEP - bs_pep2 D - bs_pep3a D - bs_pep3b D - bs_pep3_aux C 0.0093 - bs_pep4a D - bs_pep4b D - bs_pep4_aux C 0.0069 - bs_pep5 C 0.0027 - bs_pep6 D - bs_pep6_aux D - bs_pep7 D - bs_accoa C 0.1565 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_akg C 0.0571 // sortie d'AKG - bs_akg1 D - bs_akg2 C 0.0111 - bs_akg3 C 0.0132 - bs_akg4 D - bs_akg4_aux D - bs_oaa C 0.0947 // sortie d'OAA pour formation de biomasse - bs_oaa1 D // sortie d'OAA pour Asp - bs_oaa1_aux C 0.0121 // sortie d'Asp - bs_oaa2 D // synthese d'Ile - bs_oaa2_aux C 0.0146 // sortie d'Ile - bs_oaa3a D - bs_oaa3b D - bs_oaa3_aux C 0.0173 - bs_oaa4 D - bs_oaa5 D - bs_oaa5_aux C 0.0128 - bs_oaa6 D - bs_oaa6_aux C 0.0077 - bs_oaa7 D - bs_oaa7_aux C 0.0121 - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac F 0.213000005 - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - - XCH - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt C 0 -// CO2upt D -// FTHF0 D -// FTHF1 D - - pgi C 0.752386 // 2011-02-22 ssg: was F => often unresolved with --irand option - pfk C 0 - ald F 0.420281957 -// tpi F 0.5 - pgk C 0.984718 // 2011-02-22 ssg: was F => often unresolved with --irand option - eno F 0.999 - pyk C 0.0109591 // 2010-10-01 ssg: was F => unresolved if co2 uptake is unlimited - - zwf C 0 - gnd C 0 - edd C 0 - ta F 0.361648085 - tk1 F 0.151671492 - tk2 F 0 - - pdh C 0.0322745 // 2010-10-02 ssg: was F, otherwise unsolvable in monte-carlo - citsynth C 0 - idh C 0 - akgdh C 0 - fum_a F 0.3013683 - fum_b D - maldh C 0.647115 //********************************************** C pour analyse de sensibilite, F pour minimisation - -// gs1 C 0 -// gs2 C 0 - - ppc F 0.147615337 - mae C 0 -// pck C 0 - - bs_glc6P D // sortie de G6P - bs_fru6P D // sortie de F6P - bs_pga C 0 // conversion PGA donne Ser - bs_pga_aux D // conversion PGA donne Ser - bs_pga1 C 0 // conversion PGA donne Ser - bs_pga1_aux D // conversion PGA donne Ser - bs_pga2 C 0 // ser donne Cys. correspond a la sortie de PGA pour biomasse autre que formation Gly - bs_pga2_aux D - bs_pga3 C 0.011799 // reaction de synthese de Gly. cette reaction est reversible - bs_pga3_aux D // sortie de Gly - bs_DHAP D // formation de glycerolP pour lipides - bs_pyr C 0 // formation d'Ala - bs_pyr1 C 0 // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Ile - bs_pyr2 C 0 // synthese d'AKV. consomme 2 Pyr - bs_pyr4 C 0 - bs_pyr4_aux D // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 C 0 // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux D // sortie de Leu - bs_e4p C 0 // sortie d'Ery4p -// bs_e4p_aux D // sortie d'Ery4p pour Trp - bs_rib5p C 0 // synthese d'His - bs_rib5p1 C 0 // synthese d'His - bs_rib5p1_aux D // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_accoa C 0 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_pep C 0 // sortie de PEP - bs_pep1 C 0 // sortie de PEP - bs_pep2 C 0 - bs_pep3a C 0 - bs_pep3b C 0 - bs_pep3_aux D - bs_pep4a C 0 - bs_pep4b C 0 - bs_pep4_aux D - bs_pep5 D - bs_pep6 C 0 - bs_pep6_aux D - bs_pep7 C 0 - bs_akg C 0 // sortie d'AKG - bs_akg1 C 0 - bs_akg2 D - bs_akg3 D - bs_akg4 C 0 - bs_akg4_aux D - bs_oaa C 0 - bs_oaa1 C 0 // sortie d'OAA autres que Met - bs_oaa1_aux D // sortie d'OAA autres que Met - bs_oaa2 C 0 // synthese de Met - bs_oaa2_aux D // sortie de Met - bs_oaa3a C 0 - bs_oaa3b C 0 - bs_oaa3_aux D - bs_oaa4 D - bs_oaa5 C 0 - bs_oaa5_aux D - bs_oaa6 C 0 - bs_oaa6_aux D - bs_oaa7 C 0 - bs_oaa7_aux D - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac D // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - -EQUALITIES - NET - VALUE FORMULA - - 0 fum_a-fum_b // scrambling reaction - 0 bs_oaa3a-bs_oaa3b - 0 bs_pep3a-bs_pep3b - 0 bs_pep4a-bs_pep4b - - XCH - VALUE FORMULA - - 0 fum_a-fum_b - -INEQUALITIES - NET - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - 1 <= pyk - 0.0001 <= edd - 0.0001 <= gnd - 0.0001 <= zwf - 0.0001 <= ppc - 0.0001 <= mae -// 2 >= CO2upt // 2010-08-18 too high value makes jacobian rank deficient - XCH - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - - -FLUX_MEASUREMENTS - FLUX_NAME VALUE DEVIATION // Val Dev - out_Ac 0.213 0.0001 - -LABEL_INPUT - META_NAME ISOTOPOMER VALUE - - Gluc #111111 0.2 - #000000 0.8 -// CO2_ext #0 0.989 -// #1 0.011 - -// FTHF_0 #0 1 -// FTHF_1 #1 1 - - -LABEL_MEASUREMENTS - META_NAME CUM_GROUP VALUE DEVIATION CUM_CONSTRAINTS - // Example - -PEAK_MEASUREMENTS - META_NAME PEAK_NO VALUE_S VALUE_D- VALUE_D+ VALUE_DD VALUE_T DEVIATION_S DEVIATION_D- DEVIATION_D+ DEVIATION_DD/T - - -MASS_SPECTROMETRY - META_NAME FRAGMENT WEIGHT VALUE DEVIATION - -// Deviation fixee a 0.02 // correction inoc 0.062 - - - - Suc 1,2,3,4 1 0.371605319 0.01 - 2 0.360829749 0.01 - 3 0.208425325 0.01 - 4 0.059139607 0.01 -// Mal 1,2,3,4 0 0.164619329483 0.02 -// 1 0.110072868518 0.02 -// 2 0.637801316225333 0.02 -// 3 0.0863461044204333 0.02 -// 4 0.00116038135315367 0.02 - ICit 1,2,3,4,5,6 0 0.131864539419667 0.02 - 1 0.225857638569 0.02 - 2 0.256421170949333 0.02 - 3 0.209230210478667 0.02 - 4 0.116863585449667 0.02 - 5 0.0457727744643333 0.02 - 6 0.0139900806697867 0.02 - PEP 1,2,3 0 0.421359839367667 0.01 - 1 0.358998301162333 0.01 - 2 0.0348521859365667 0.01 - 3 0.184789673534 0.01 - PGA 1,2,3 0 0.434335785072667 0.01 - 1 0.352829683224667 0.01 - 2 0.0323479804176 0.01 - 3 0.180486551285333 0.01 - FruBP 1,2,3,4,5,6 0 0.0738121029259333 0.01 - 1 0.454450017158667 0.01 - 2 0.160823529969333 0.01 - 3 0.0944468077710667 0.01 - 4 0.105281338489667 0.01 - 5 0.0155016033633 0.01 - 6 0.0956846003217333 0.01 - Glc6P 1,2,3,4,5,6 0 0.0160587173349 0.01 - 1 0.673510772480667 0.01 - 2 0.0930110047641 0.01 - 3 0.0280359937297 0.01 - 4 0.0397315614067667 0.01 - 5 0.0145524520950667 0.01 - 6 0.135099498189 0.01 - Fru6P 1,2,3,4,5,6 0 0.0235029951295 0.01 - 1 0.624253565357667 0.01 - 2 0.113068441282333 0.01 - 3 0.0456605631765 0.01 - 4 0.0516089447155667 0.01 - 5 0.0185881765378333 0.01 - 6 0.123317313800333 0.01 - Rib5P 1,2,3,4,5 0 0.341615670498667 0.01 - 1 0.25454117519 0.01 - 2 0.159027180368333 0.01 - 3 0.113789577528667 0.01 - 4 0.0615266612553333 0.01 - 5 0.0694997351590667 0.01 - Gnt6P 1,2,3,4,5,6 0 0.0249552273874 0.01 - 1 0.672556163913 0.01 - 2 0.0866890773125333 0.01 - 3 0.0313987199704333 0.01 - 4 0.0314691889898667 0.01 - 5 0.0138168327362333 0.01 - 6 0.139114789690333 0.01 -// Ery4P 1,2,3,4 0 0.178453461108 0.01 -// 1 0.412398433968333 0.01 -// 2 0.273694508221667 0.01 -// 3 0.116142498670667 0.01 -// 4 0.0193110980315 0.01 - -OPTIONS - OPT_NAME OPT_VALUE - MATLAB_FOR_FLUX_EQ_CONSTR_MATR 1 - //optctrl_history 1 // nlsic - //optctrl_trace 3 // BFGS - //optctrl_reltol 1.e-10 // BFGS - //optctrl_maxit 1000 // BFGS - posttreat_R plot_smeas.R -
--- a/test-data/e_coli_growth.ftbl Wed Sep 13 19:52:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,822 +0,0 @@ -PROJECT - NAME VERSION FORMAT DATE COMMENT - Nissle.ftbl 1 100910 modele E coli Nissle WT avec voies centrales completes et voies biomasse - Nissle.ftbl 2 121025 growth fluxes+pooled penthoses - Nissle.ftbl 3 121123 concentration measurements - -NETWORK - FLUX_NAME EDUCT_1 EDUCT_2 PRODUCT_1 PRODUCT_2 - -// Glycolyse. -// PPP -// TCA -// voies anaplerotiques: pepc. enz malique -// voie glyoxylate -// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre) -// saisie differentielle des substrats marques - - -// Uptake substrats - - Glucupt_1 Gluc_1 Glc - #ABCDEF #ABCDEF - - Glucupt_U Gluc_U Glc - #ABCDEF #ABCDEF - - Glucupt Glc Glc6P - #ABCDEF #ABCDEF - - CO2upt CO2_ext CO2 // entree de CO2 non marque - #A #A // ce flux est a laisser libre - -// FTHF0 FTHF_0 FTHF // prise en charge de FTHF non marque -// #A #A - -// FTHF1 FTHF_1 FTHF // prise en charge de FTHF marque -// #a #a - - -// Embden Meyerhof Parnas Pathway - - pgi Glc6P Fru6P - #ABCDEF #ABCDEF - - pfk Fru6P FruBP - #ABCDEF #ABCDEF - - ald FruBP GA3P GA3P - #ABCDEF #CBA #DEF - -// tpi DHAP GA3P -// #ABC #CBA - - pgk GA3P PGA - #ABC #ABC - - eno PGA PEP - #ABC #ABC - - pyk PEP Pyr - #ABC #ABC - - -// Methylglyoxal Pathway - -// mgs DHAP Pyr -// #ABC #ABC - - -// Pentose Phosphate Pathway - - zwf Glc6P Gnt6P - #ABCDEF #ABCDEF - - gnd Gnt6P CO2 Rub5P - #ABCDEF #A #BCDEF - - rib Rub5P Rib5P - #ABCDE #ABCDE - - xul Rub5P Xul5P - #ABCDE #ABCDE - - edd Gnt6P Pyr GA3P - #ABCDEF #ABC #DEF - -// ta GA3P Sed7P Ery4P Fru6P -// #ABC #abcdefg #defg #abcABC - -// tk1 Rib5P Rib5P GA3P Sed7P -// #ABCDE #abcde #CDE #ABabcde - -// tk2 Rib5P Ery4P GA3P Fru6P -// #ABCDE #abcd #CDE #ABabcd - - HR1 GA3P E2 Xul5P - #CDE #AB #ABCDE - - HR2 Fru6P Ery4P E2 - #ABCDEF #CDEF #AB - - HR3 Fru6P GA3P E3 - #ABCDEF #DEF #ABC - - HR4 Sed7P Rib5P E2 - #abABCDE #ABCDE #ab - - HR5 Ery4P E3 Sed7P - #ABCD #abc #abcABCD - - -// Tricarboxylic Acid Cycle - - pdh Pyr AcCoA CO2 - #ABC #BC #A - - citsynth AcCoA OAA Cit - #AB #abcd #dcbaBA - - idh Cit AKG CO2 - #ABCDEF #ABCEF #D - - akgdh AKG Suc CO2 - #ABCDE #BCDE #A - - fum_a Suc Mal - #ABCD #ABCD - - fum_b Suc Mal - #ABCD #DCBA - - maldh Mal OAA - #ABCD #ABCD - - -// Glyoxylate Shunt - -// gs1 Cit GlyOx Suc -// #ABCDEF #AB #DCEF - -// gs2 GlyOx AcCoA OAA -// #AB #ab #ABba - - -// Anaplerotic Reactions - - ppc PEP CO2 OAA // PEPcarboxylase - #ABC #a #ABCa - -// mae Mal Pyr CO2 // enzyme malique -// #ABCD #ABC #D - -// pck OAA PEP CO2 // PEP carboxykinase -// #ABCD #ABC #D - - -// Biosynthetic Pathways - - // Glucose-6-Phosphate Family - - bs_glc6P Glc6P BM_Glc6P - #ABCDEF #ABCDEF - - // Fructose-6-Phosphate Family - - bs_fru6P Fru6P BM_Fru6P - #ABCDEF #ABCDEF - - // Phosphoglycerate Family - - bs_pga PGA BM_PGA - #ABC #ABC - -// bs_pga_aux BM_PGA PGA_Aux -// #ABC #ABC - -// bs_pga1 BM_PGA Ser -// #ABC #ABC - -// bs_pga1_aux Ser Ser_Aux -// #ABC #ABC - -// bs_pga2 Ser Cys -// #ABC #ABC - -// bs_pga2_aux Cys Cys_Aux -// #ABC #ABC - -// bs_pga3 Ser Gly FTHF -// #ABC #AB #C - -// bs_pga3_aux Gly Gly_Aux -// #AB #AB - - // TrioseP Family - - bs_DHAP GA3P Glp - #ABC #ABC - - // Pyruvate Family - - bs_pyr Pyr BM_Pyr - #ABC #ABC - -// bs_pyr1 BM_Pyr Ala -// #ABC #ABC - -// bs_pyr1_aux Ala Ala_Aux -// #ABC #ABC - -// bs_pyr2 BM_Pyr BM_Pyr AKV CO2 -// #ABC #abc #ABbcC #a - -// bs_pyr4 AKV Val -// #ABCDE #ABCDE - -// bs_pyr4_aux Val Val_Aux -// #ABCDE #ABCDE - -// bs_pyr3 AKV BM_AcCoA Leu CO2 -// #ABCDE #ab #abBCDE #A - -// bs_pyr3_aux Leu Leu_Aux -// #ABCDEF #ABCDEF - - // Erythrose-4-Phosphate Family - - bs_e4p Ery4P BM_Ery4P - #ABCD #ABCD - -// bs_e4p_aux BM_Ery4P Ery4P_aux -// #ABCD #ABCD - - // Ribose-5-Phosphate Family - - bs_rib5P Rib5P BM_Rib5P - #ABCDE #ABCDE - -// bs_rib5P1 BM_Rib5P FTHF His -// #ABCDE #a #EDCBAa - -// bs_rib5P1_aux His His_Aux -// #ABCDEF #ABCDEF - -// bs_rib5P2 BM_Rib5P Ri5P_Aux -// #ABCDE #ABCDE - - - // Aromatic Amino Acids - - bs_pep PEP BM_PEP - #ABC #ABC - -// bs_pep1 BM_PEP BM_Ery4P DAHP -// #ABC #abcd #ABCabcd - -// bs_pep2 BM_PEP DAHP Chor -// #ABC #abcdefg #ABCabcdefg - -// bs_pep3a Chor Phe CO2 -// #ABCDEFGHIJ #ABCEFGHIJ #D - -// bs_pep3b Chor Phe CO2 -// #ABCDEFGHIJ #ABCEJIHGF #D - -// bs_pep3_aux Phe Phe_Aux -// #ABCEFGHIJ #ABCEFGHIJ - -// bs_pep4a Chor Tyr CO2 -// #ABCDEFGHIJ #ABCEFGHIJ #D - -// bs_pep4b Chor Tyr CO2 -// #ABCDEFGHIJ #ABCEJIHGF #D - -// bs_pep4_aux Tyr Tyr_Aux -// #ABCEFGHIJ #ABCEFGHIJ - -// bs_pep5 BM_PEP PEP_Aux -// #ABC #ABC - -// bs_pep6 Chor BM_Rib5P Trp PyrCO2 -// #ABCDEFGHIJ #abcde #edcbaJEFGHI #ABCD - -// bs_pep6_aux Trp Trp_Aux -// #ABCDEFGHIJK #ABCDEFGHIJK - -// bs_pep7 PyrCO2 Pyr CO2 -// #ABCD #ABC #D - - // Acetyl-CoA - - bs_accoa AcCoA BM_AcCoA - #AB #AB - -// bs_accoa_aux BM_AcCoA AcCoA_Aux -// #AB #AB - - // Alpha-Ketoglutarate Family - - bs_akg AKG BM_AKG - #ABCDE #ABCDE - -// bs_akg1 BM_AKG Glu -// #ABCDE #ABCDE - -// bs_akg2 Glu Pro -// #ABCDE #ABCDE - -// bs_akg3 Glu Gln -// #ABCDE #ABCDE - -// bs_akg4 Glu CO2 Arg -// #ABCDE #a #ABCDEa - -// bs_akg4_aux Arg Arg_Aux -// #ABCDEF #ABCDEF - -// bs_akg2_aux Pro Pro_Aux -// #ABCDE #ABCDE - - - // Oxaloacetate Family - - bs_oaa OAA BM_OAA - #ABCD #ABCD - -// bs_oaa1 BM_OAA Asp -// #ABCD #ABCD - -// bs_oaa1_aux Asp Asp_Aux -// #ABCD #ABCD - -// bs_oaa2 Thr BM_Pyr Ile CO2 -// #ABCD #abc #ABbCDc #a - -// bs_oaa2_aux Ile Ile_Aux -// #ABCDEF #ABCDEF - -// bs_oaa3a BM_OAA BM_Pyr Lys CO2 -// #ABCD #abc #ABCDcb #a - -// bs_oaa3b BM_OAA BM_Pyr Lys CO2 -// #ABCD #abc #abcDCB #A - -// bs_oaa3_aux Lys Lys_Aux -// #ABCDEF #ABCDEF - -// bs_oaa4 BM_OAA OAA_Aux -// #ABCD #ABCD - -// bs_oaa5 BM_OAA Thr -// #ABCD #ABCD - -// bs_oaa5_aux Thr Thr_Aux -// #ABCD #ABCD - -// bs_oaa6 BM_OAA FTHF Met -// #ABCD #a #ABCDa - -// bs_oaa6_aux Met Met_Aux -// #ABCDE #ABCDE - -// bs_oaa7 BM_OAA Asn -// #ABCD #ABCD - -// bs_oaa7_aux Asn Asn_Aux -// #ABCD #ABCD - - -// Extracellular fluxes - - out_co2 CO2 CO2_out // CO2 output - #A #A - - out_Ac AcCoA Acetate // Acetate output - #AB #AB - -// out_FTHF FTHF FTHF_out -// #A #A - -FLUXES - NET - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - // INPUT - Glucupt_1 F 0.8128 - Glucupt_U D - Glucupt D - CO2upt C 0.77 // fixed arbitrary -// FTHF0 F 0.00224836 -// FTHF1 F 0.001 - - // Glycolysis - pgi F 0.1 - pfk D - ald D -// tpi D - pgk D 0.1 - eno D - pyk D 1.21144 - - // PPP + EDP - zwf D 0.4 - gnd D - edd F 0.1 - rib D - xul D -// ta D -// tk1 D -// tk2 D - HR1 D - HR2 D - HR3 D - HR4 D - HR5 D - - // TCA - pdh D - citsynth D - idh D - akgdh D - fum_a D - fum_b D - maldh D -// gs1 C 0 -// gs2 D - ppc D -// mae D -// pck D - - // Biosynthetic pathways - bs_glc6P C 0.0132 // sortie de G6P - bs_fru6P C 0.0045 // sortie de F6P - bs_pga C 0.0958 // sortie de PGA -// bs_pga_aux D -// bs_pga1 D -// bs_pga1_aux C 0.0132 // sortie de Ser -// bs_pga2 D -// bs_pga2_aux C 0.0056 // sortie de Cys -// bs_pga3 D -// bs_pga3_aux C 0.0373 // sortie de Gly - bs_DHAP C 0.0083 - bs_pyr C 0.1818 // sortie de Pyr -// bs_pyr1 D -// bs_pyr1_aux D // sortie d'Ala -// bs_pyr2 D -// bs_pyr4 D -// bs_pyr4_aux C 0.0258 // sortie de Val -// bs_pyr3 D -// bs_pyr3_aux C 0.0275 // sortie de Leu - bs_e4p C 0.0247 // sortie d'E4P - bs_rib5P C 0.0576 // sortie de R5P -// bs_rib5P1 D -// bs_rib5P1_aux C 0.0058 // sortie d'His -// bs_rib5P2 D - bs_pep C 0.0461 // sortie de PEP -// bs_pep1 D -// bs_pep2 D -// bs_pep3a D -// bs_pep3b D -// bs_pep3_aux C 0.0113 // sortie de Phe -// bs_pep4a D -// bs_pep4b D -// bs_pep4_aux C 0.0084 // sortie de Tyr -// bs_pep5 C 0.0033 // sorties autres que ac. amines -// bs_pep6 D -// bs_pep6_aux D -// bs_pep7 D - bs_accoa C 0.1895 // sortie d'AcCoA -// bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_akg C 0.0692 // sortie d'AcCoA -// bs_akg1 D -// bs_akg2 D // sortie de Pro -// bs_akg3 C 0.0160 // sortie de Gln -// bs_akg4 D -// bs_akg2_aux C 0.013475 -// bs_akg4_aux D - bs_oaa C 0.1146 -// bs_oaa1 D -// bs_oaa1_aux C 0.0147 // sortie d'Asp -// bs_oaa2 D -// bs_oaa2_aux C 0.0177 // sortie d'Ile -// bs_oaa3a D -// bs_oaa3b D -// bs_oaa3_aux C 0.0209 // sortie de Lys -// bs_oaa4 D -// bs_oaa5 D -// bs_oaa5_aux C 0.0155 // sortie de Thr -// bs_oaa6 D -// bs_oaa6_aux C 0.0094 // sortie de Met -// bs_oaa7 D -// bs_oaa7_aux C 0.0147 // sortie d'Asn - - // Extracellular fluxes - - out_co2 D 0.1 // sortie de CO2 - out_Ac F 0.48 // sortie d'acetate -// out_FTHF D // sortie de FTHF - - - XCH - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - // INPUT - Glucupt_1 D - Glucupt_U D - Glucupt C 0 - CO2upt D -// FTHF0 D -// FTHF1 D - - // Glycolysis - pgi F 0.4 - pfk F 0.01 - ald F 0.4 -// tpi F 0.5 - pgk F 0.99 - eno F 0.99 - pyk F 0.4 - - // PPP + EDP - zwf C 0 - gnd C 0 - edd C 0 - rib C 0.99 // fixed arbitrary big - xul F 0 -// ta F 0.35468 -// tk1 F 0.0960538 -// tk2 F 0.0521646 - HR1 C 0.24 // fixed arbitrary - HR2 F 0.0151117 - HR3 F 0.14 - HR4 C 0.04 // fixed arbitrary - HR5 F 0.02 - - // TCA - pdh C 0.01 - citsynth C 0 - idh C 0 - akgdh C 0 - fum_a C 0.01 // fixed arbitrary - fum_b D -// maldh F 0.99 - maldh C 0.42 // fixed arbitrary -// gs1 C 0 -// gs2 C 0 - ppc F 0.2 -// mae C 0 -// pck C 0 - - // Biosynthetic pathways - bs_glc6P D - bs_fru6P D - bs_pga D -// bs_pga_aux D -// bs_pga1 C 0 -// bs_pga1_aux D -// bs_pga2 C 0 -// bs_pga2_aux D -// bs_pga3 C 0.00824415 -// bs_pga3_aux D - bs_DHAP D - bs_pyr D -// bs_pyr1 C 0 -// bs_pyr1_aux D -// bs_pyr2 C 0 -// bs_pyr4 C 0 -// bs_pyr4_aux D -// bs_pyr3 C 0 -// bs_pyr3_aux D - bs_e4p D 0 -// bs_e4p_aux D - bs_rib5P D 0 -// bs_rib5P1 C 0 -// bs_rib5P1_aux D -// bs_rib5P2 D - bs_accoa D 0 -// bs_accoa_aux D - bs_pep D 0 -// bs_pep1 C 0 -// bs_pep2 C 0 -// bs_pep3a C 0 -// bs_pep3b C 0 -// bs_pep3_aux D -// bs_pep4a C 0 -// bs_pep4b C 0 -// bs_pep4_aux D -// bs_pep5 D -// bs_pep6 C 0 -// bs_pep6_aux D -// bs_pep7 C 0 - bs_akg D 0 -// bs_akg1 C 0 -// bs_akg2 C 0 -// bs_akg3 D -// bs_akg4 C 0 -// bs_akg4_aux D -// bs_akg2_aux D - bs_oaa D 0 -// bs_oaa1 C 0 -// bs_oaa1_aux D -// bs_oaa2 C 0 -// bs_oaa2_aux D -// bs_oaa3a C 0 -// bs_oaa3b C 0 -// bs_oaa3_aux D -// bs_oaa4 D -// bs_oaa5 C 0 -// bs_oaa5_aux D -// bs_oaa6 C 0 -// bs_oaa6_aux D -// bs_oaa7 C 0 -// bs_oaa7_aux D - - // Flux de sortie - out_co2 C 0 // sortie de CO2 - out_Ac C 0 // sortie d'acetate -// out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - -EQUALITIES - NET - VALUE FORMULA - - 0 fum_a-fum_b // scrambling reaction - 1 Glucupt_1+Glucupt_U -// 0 bs_oaa3a-bs_oaa3b -// 0 bs_pep3a-bs_pep3b -// 0 bs_pep4a-bs_pep4b - - XCH - VALUE FORMULA - - 0 fum_a-fum_b - -INEQUALITIES - NET - VALUE COMP FORMULA -// 1 <= pyk - 0 <= edd - 0 <= gnd - 0 <= zwf - 0 <= ppc - 0 <= idh - 0 <= akgdh -// 0 <= mae - - XCH - VALUE COMP FORMULA - -FLUX_MEASUREMENTS - FLUX_NAME VALUE DEVIATION - out_Ac 0.497 0.04 - -LABEL_INPUT - META_NAME ISOTOPOMER VALUE - - Gluc_U #111111 0.952 - #011111 0.008 - #101111 0.008 - #110111 0.008 - #111011 0.008 - #111101 0.008 - #111110 0.008 - - Gluc_1 #100000 0.9465 - #110000 0.0107 - #101000 0.0107 - #100100 0.0107 - #100010 0.0107 - #100001 0.0107 - - CO2_ext #0 0.9893 - #1 0.0107 - -// FTHF_0 #0 1 -// FTHF_1 #1 1 - - -LABEL_MEASUREMENTS - META_NAME CUM_GROUP VALUE DEVIATION CUM_CONSTRAINTS - - AcCoA 1 0.495 0.02 #00 - 2 0.303 0.02 #01 // CH3 specific enrichment - 3 0.012 0.02 #10 - 4 0.190 0.02 #11 - -PEAK_MEASUREMENTS - - META_NAME PEAK_NO VALUE_S VALUE_D- VALUE_D+ VALUE_DD VALUE_T DEVIATION_S DEVIATION_D- DEVIATION_D+ DEVIATION_DD/T - -METAB_MEASUREMENTS - META_NAME VALUE DEVIATION - // source: p.millard 2010/12/03 Nissle_Glc_conc.xlsx sent by email - Suc 15.8893144279264*1.e-3/10.7 1.e-2 - Mal 6.47828321758155*1.e-3/10.7 1.e-2 - PEP 0.588638938013844*1.e-3/10.7 1.e-2 - PGA 5.35922289028553*1.e-3/10.7 1.e-2 - Cit 17.4452511107891*1.e-3/10.7 1.e-2 - Gnt6P 1.54945619497337*1.e-3/10.7 1.e-2 - FruBP 5.27278870110121*1.e-3/10.7 1.e-2 - Fru6P 1.07071770798187*1.e-3/10.7 1.e-2 - Glc6P 5.24845556085526*1.e-3/10.7 1.e-2 - Rub5P+Rib5P+Xul5P 1.66034545348219*1.e-3/10.7 1.e-2 - -MASS_SPECTROMETRY - META_NAME FRAGMENT WEIGHT VALUE DEVIATION - Mal 1,2,3,4 1 0.587391867374382 0.0493159626907812 - 2 0.216493214407424 0.0306546571894417 - 3 0.159494782909672 0.03 - 4 0.0366201353085213 0.03 - PEP 1,2,3 0 0.462166666666667 0.01 - 1 0.340003333333333 0.01 - 2 0.0273166666666667 0.01 - 3 0.170513333333333 0.01 - PGA 1,2,3 0 0.447066666666667 0.0180848260520618 - 1 0.34127 0.018075350619006 - 2 0.02441 0.01 - 3 0.187253333333333 0.01 - Gnt6P 1,2,3,4,5,6 0 0.0195533333333333 0.01 - 1 0.72562 0.0120547874307264 - 2 0.0571233333333333 0.01 - 3 0.0135033333333333 0.01 - 4 0.01331 0.01 - 5 0.0131033333333333 0.01 - 6 0.157793333333333 0.01 - Sed7P 1,2,3,4,5,6,7 0 0.272433333333333 0.0122309539012022 - 1 0.23752 0.01 - 2 0.180446666666667 0.01 - 3 0.12744 0.01 - 4 0.06321 0.01 - 5 0.0839233333333333 0.01 - 6 0.01751 0.01 - 7 0.0175266666666667 0.01 - FruBP 1,2,3,4,5,6 0 0.0853733333333333 0.02 - 1 0.482283333333333 0.02 - 2 0.140086666666667 0.02 - 3 0.0953466666666667 0.02 - 4 0.09712 0.02 - 5 0.0120166666666667 0.02 - 6 0.0877666666666667 0.02 - Rib5P+Xul5P+Rub5P 1,2,3,4,5 0 0.433956666666667 0.0115292555411585 - 1 0.215956666666667 0.01 - 2 0.09658 0.01 - 3 0.129033333333333 0.01 - 4 0.0272733333333333 0.01 - 5 0.0971933333333333 0.01 - Glc6P 1,2,3,4,5,6 0 0.0167633333333333 0.01 - 1 0.716826666666667 0.01 - 2 0.0578233333333333 0.01 - 3 0.0122433333333333 0.01 - 4 0.01151 0.01 - 5 0.01089 0.01 - 6 0.173946666666667 0.01 - Fru6P 1,2,3,4,5,6 0 0.04716 0.01 - 1 0.623343333333333 0.0106878170518274 - 2 0.0820266666666667 0.01 - 3 0.03604 0.01 - 4 0.0315766666666667 0.01 - 5 0.0149133333333333 0.01 - 6 0.164943333333333 0.0111688555068697 - - Cit 1,2,3,4,5,6 1 0.322208057034832 0.03 - 2 0.288291305558056 0.03 - 3 0.212855540659154 0.03 - 4 0.117626468347467 0.03 - 5 0.0484839619377435 0.03 - 6 0.0105346664627478 0.03 - -OPTIONS - OPT_NAME OPT_VALUE - MATLAB_FOR_FLUX_EQ_CONSTR_MATR 1 - include_growth_flux 1 - mu 0.8 - optctrl_maxit 50 - commandArgs --TIMEIT - //optctrl_btdesc 0.1 - posttreat_R plot_smeas.R -METABOLITE_POOLS - META_NAME META_SIZE // size is in units of metab_scale option defined before - // source: p.millard 2010/12/03 Nissle_Glc_conc.xlsx sent by email - //Fum -2.47158569399681*1.e-3/10.7 - Suc -15.8893144279264*1.e-3/10.7 - Mal -6.47828321758155*1.e-3/10.7 - PEP -0.588638938013844*1.e-3/10.7 - //Aco -0.871035781090548*1.e-3/10.7 - PGA -5.35922289028553*1.e-3/10.7 - Cit -17.4452511107891*1.e-3/10.7 - //1-3diPG -7.31670971749174*1.e-3/10.7 - Gnt6P -1.54945619497337*1.e-3/10.7 - //Sed7P -11.5512490274248*1.e-3/10.7 conc - //PRPP -2.74943425027474*1.e-3/10.7 - //CMP -0.433742769835568*1.e-3/10.7 - //UMP -4.69421895911195*1.e-3/10.7 - //cAMP -0.109838817225867*1.e-3/10.7 - FruBP -5.27278870110121*1.e-3/10.7 - //AMP -0.801372321192278*1.e-3/10.7 - //GMP -0.394103922207334*1.e-3/10.7 - //dCDP -4.41071909173208*1.e-3/10.7 - //CDP -0.204009683016196*1.e-3/10.7 - //UDP -0.528949008341637*1.e-3/10.7 - //ADP -2.0246124170601*1.e-3/10.7 - //GDP -1.02724694822302*1.e-3/10.7 - //CTP -1.39055711133101*1.e-3/10.7 - //UTP -1.73433655893259*1.e-3/10.7 - //ATP -6.32820169657847*1.e-3/10.7 - //UDP-Glc -9.93608536663137*1.e-3/10.7 conc - //ADP-Glc -0*1.e-3/10.7 - //GDP-Man -5.52555199979534*1.e-3/10.7 - //G1P -72.1756241692542*1.e-3/10.7 conc - //F1P -0.0942291270750201*1.e-3/10.7 - Fru6P -1.07071770798187*1.e-3/10.7 - Glc6P -5.24845556085526*1.e-3/10.7 - //M6P -0.642830603277483*1.e-3/10.7 - //Rib1P -0.0558080128279041*1.e-3/10.7 - Rub5P -1.66034545348219/3*1.e-3/10.7 -// Rib5P -1.66034545348219/3*1.e-3/10.7 - Rib5P 1.e-7 // fixed arbitrary low - Xul5P -4*1.66034545348219/3*1.e-3/10.7 - //dADP -5.86959266616353*1.e-3/10.7 conc - //dATP -13.1542008577561*1.e-3/10.7 conc - //dTDP -9.52423600696743*1.e-3/10.7 conc - //dTTP -19.9757914243397*1.e-3/10.7 conc
--- a/test-data/e_coli_growth.log Wed Sep 13 19:52:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ -"/usr/local/miniconda3/bin/influx_s" "e_coli.ftbl" "e_coli_growth.ftbl" -code gen: 2020-03-25 14:32:15 -executing: "/usr/local/miniconda3/bin/python3.7" "/home/STORAGE/local/miniconda3/bin/ftbl2optR.py" "--tblimit" "0" "--ropts" "TIMEIT=TRUE" "e_coli_growth.ftbl" -calcul : 2020-03-25 14:32:22 -load : 2020-03-25 14:32:24.17 cpu=1.207 -rinit : 2020-03-25 14:32:24.17 cpu=1.21 -r_flux : 2020-03-25 14:32:24.17 cpu=1.21 -Afl qr(): 2020-03-25 14:32:24.21 cpu=1.248 -dfl_dffg: 2020-03-25 14:32:24.45 cpu=1.258 -spAbr : 2020-03-25 14:32:24.45 cpu=1.262 -weight 1: 2020-03-25 14:32:24.45 cpu=1.263 -weight 2: 2020-03-25 14:32:24.45 cpu=1.265 -weight 3: 2020-03-25 14:32:24.45 cpu=1.267 -weight 4: 2020-03-25 14:32:24.46 cpu=1.272 -weight 5: 2020-03-25 14:32:24.47 cpu=1.274 -weight 6: 2020-03-25 14:32:24.47 cpu=1.275 -weight 7: 2020-03-25 14:32:24.47 cpu=1.277 -measure : 2020-03-25 14:32:24.56 cpu=1.343 -ineq : 2020-03-25 14:32:24.60 cpu=1.368 -preopt : 2020-03-25 14:32:24.66 cpu=1.413 -labargs : 2020-03-25 14:32:24.66 cpu=1.416 -run 1: 2020-03-25 14:32:24.66 cpu=1.417 -Starting point -res esti: 2020-03-25 14:32:24.67 cpu=1.419 -The following 1 ineqalitie(s) are active at starting point: -f.x.xul>=0 -kvh init: 2020-03-25 14:32:24.80 cpu=1.438 -check ja: 2020-03-25 14:32:24.85 cpu=1.454 -optim : 2020-03-25 14:32:24.94 cpu=1.515 -it=0 res=45.2102 -it=1 res=12.83995 normstep=1.515861 btk=1 -it=2 res=12.25994 normstep=1.259661 btk=1 -it=3 res=8.098585 normstep=0.5463658 btk=1 -it=4 res=7.960851 normstep=0.0589933 btk=1 -it=5 res=7.959322 normstep=0.03050743 btk=1 -it=6 res=7.959081 normstep=0.004902886 btk=1 -it=7 res=7.959029 normstep=0.003060732 btk=1 -it=8 res=7.959017 normstep=0.001367668 btk=1 -it=9 res=7.959014 normstep=0.0006590508 btk=1 -it=10 res=7.959014 normstep=0.0003104052 btk=1 -it=15 res=7.959014 normstep=7.292328e-06 btk=1 -postopt : 2020-03-25 14:32:26.48 cpu=3.125 -linstats: 2020-03-25 14:32:26.77 cpu=3.377 -rend : 2020-03-25 14:32:27.07 cpu=3.706 -end : 2020-03-25 14:32:27
--- a/test-data/e_coli_i.ftbl Wed Sep 13 19:52:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,789 +0,0 @@ -PROJECT - NAME VERSION FORMAT DATE COMMENT - K12_MG1655.ftbl 1 101109 modele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees - -NETWORK - FLUX_NAME EDUCT_1 EDUCT_2 PRODUCT_1 PRODUCT_2 - -// Glycolyse. -// PPP -// TCA -// voies anaplerotiques: pepc. enz malique -// voie glyoxylate -// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre) -// saisie differentielle des substrats marques - - -// Uptake substrats - - Glucupt_1 Gluc_1 Glc6P // fehlt bei wolfgang - #ABCDEF #ABCDEF // fehlt bei wolfgang - - Glucupt_U Gluc_U Glc6P // fehlt bei wolfgang - #ABCDEF #ABCDEF // fehlt bei wolfgang - -// CO2upt CO2_ext CO2 // entree de CO2 non marque -// #A #A // ce flux est a laisser libre - -// FTHF0 FTHF_0 FTHF // prise en charge de FTHF non marque -// #A #A - -// FTHF1 FTHF_1 FTHF // prise en charge de FTHF marque -// #a #a - - -// Embden Meyerhof Parnas Pathway - - pgi Glc6P Fru6P - #ABCDEF #ABCDEF - - pfk Fru6P FruBP - #ABCDEF #ABCDEF - - ald FruBP GA3P GA3P - #ABCDEF #CBA #DEF - -// tpi DHAP GA3P -// #ABC #CBA - - pgk GA3P PGA - #ABC #ABC - - eno PGA PEP - #ABC #ABC - - pyk PEP Pyr - #ABC #ABC - - -// Methylglyoxal Pathway - -// mgs DHAP Pyr -// #ABC #ABC - - -// Pentose Phosphate Pathway - - zwf Glc6P Gnt6P - #ABCDEF #ABCDEF - - gnd Gnt6P CO2 Rib5P - #ABCDEF #A #BCDEF - - edd Gnt6P Pyr GA3P - #ABCDEF #ABC #DEF - -// ta Ery4P Fru6P GA3P Sed7P -// #ABCD #abcdef #def #abcABCD - -// tk1 GA3P Sed7P Rib5P Rib5P -// #ABC #abcdefg #abABC #cdefg - -// tk2 GA3P Fru6P Rib5P Ery4P -// #ABC #abcdef #abABC #cdef - - ta GA3P Sed7P Ery4P Fru6P - #ABC #abcdefg #defg #abcABC - - tk1 Rib5P Rib5P GA3P Sed7P - #ABCDE #abcde #CDE #ABabcde - - tk2 Rib5P Ery4P GA3P Fru6P - #ABCDE #abcd #CDE #ABabcd - - -// Tricarboxylic Acid Cycle - - pdh Pyr AcCoA CO2 - #ABC #BC #A - - citsynth AcCoA OAA ICit - #AB #abcd #dcbaBA - - idh ICit AKG CO2 - #ABCDEF #ABCEF #D - - akgdh AKG Suc CO2 - #ABCDE #BCDE #A - - fum_a Suc Mal - #ABCD #ABCD - - fum_b Suc Mal - #ABCD #DCBA - - maldh Mal OAA - #ABCD #ABCD - - -// Glyoxylate Shunt - -// gs1 ICit GlyOx Suc -// #ABCDEF #AB #DCEF - -// gs2 GlyOx AcCoA OAA -// #AB #ab #ABba - - -// Anaplerotic Reactions - - ppc PEP CO2 OAA // PEPcarboxylase - #ABC #a #ABCa - - mae Mal Pyr CO2 // enzyme malique - #ABCD #ABC #D - -// pck OAA PEP CO2 // PEP carboxykinase -// #ABCD #ABC #D - - -// Biosynthetic Pathways - - // Glucose-6-Phosphate Family - - bs_glc6P Glc6P BM_Glc6P - #ABCDEF #ABCDEF - - // Fructose-6-Phosphate Family - - bs_fru6P Fru6P BM_Fru6P // sortie de Fru6P pour biomasse - #ABCDEF #ABCDEF - - // Phosphoglycerate Family - - bs_pga PGA BM_PGA - #ABC #ABC - - bs_pga_aux BM_PGA PGA_Aux - #ABC #ABC - - bs_pga1 BM_PGA Ser - #ABC #ABC - - bs_pga1_aux Ser Ser_Aux - #ABC #ABC - - bs_pga2 Ser Cys // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga2_aux Cys Cys_Aux // ce flux sert de sortie pour PGA hors formation de Gly - #ABC #ABC - - bs_pga3 Ser Gly FTHF // formation de gly pour biomasse - #ABC #AB #C // ce flux est reversible - - bs_pga3_aux Gly Gly_Aux // pour conserver Gly comme metabolite intracellulaire - #AB #AB - - // TrioseP Family - - bs_DHAP GA3P Glp // formation glycerolP pour lipides - #ABC #ABC - - // Pyruvate Family - - bs_pyr Pyr BM_Pyr - #ABC #ABC - - bs_pyr1 BM_Pyr Ala - #ABC #ABC - - bs_pyr1_aux Ala Ala_Aux // pour conserver Ala comme metabolite intracellulaire - #ABC #ABC - - bs_pyr2 BM_Pyr BM_Pyr AKV CO2 // AKV et Val ont le meme squelette C - #ABC #abc #ABbcC #a // cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val - - bs_pyr4 AKV Val // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr4_aux Val Val_Aux // permet de tenir compte de la sortie de Val - #ABCDE #ABCDE - - bs_pyr3 AKV BM_AcCoA Leu CO2 - #ABCDE #ab #abBCDE #A - - bs_pyr3_aux Leu Leu_Aux // pour conserver Leu comme metabolite intracellulaire - #ABCDEF #ABCDEF - - - // Erythrose-4-Phosphate Family - - bs_e4p Ery4P BM_Ery4P // pour utiliser les donnees sur Ery4P - #ABCD #ABCD - -// bs_e4p_aux BM_Ery4P Ery4P_aux // pour utiliser les donnees sur Ery4P -// #ABCD #ABCD - - - // Ribose-5-Phosphate Family - - bs_rib5p Rib5P BM_Rib5P // pour utiliser les donnees sur Rib5P - #ABCDE #ABCDE - - bs_rib5p1 BM_Rib5P FTHF His // pour utiliser les donnees sur Rib5P - #ABCDE #a #EDCBAa - - bs_rib5p1_aux His His_Aux // sortie pour conserver His comme metabolite intracellulaire - #ABCDEF #ABCDEF - - bs_rib5p2 BM_Rib5P Ri5P_Aux // sortie de Ri5P pour autres besoins que His - #ABCDE #ABCDE // ce flux est important pour ne pas imposer de fausses contraintes sur FTHF si on considerait His comme seule sortie - - - // Aromatic Amino Acids - - bs_pep PEP BM_PEP - #ABC #ABC - - bs_pep1 BM_PEP BM_Ery4P DAHP - #ABC #abcd #ABCabcd - - bs_pep2 BM_PEP DAHP Chor - #ABC #abcdefg #ABCabcdefg - - bs_pep3a Chor Phe CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep3b Chor Phe CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep3_aux Phe Phe_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep4a Chor Tyr CO2 - #ABCDEFGHIJ #ABCEFGHIJ #D - - bs_pep4b Chor Tyr CO2 - #ABCDEFGHIJ #ABCEJIHGF #D - - bs_pep4_aux Tyr Tyr_Aux - #ABCEFGHIJ #ABCEFGHIJ - - bs_pep5 BM_PEP PEP_Aux - #ABC #ABC - - bs_pep6 Chor BM_Rib5P Trp PyrCO2 - #ABCDEFGHIJ #abcde #edcbaJEFGHI #ABCD - - bs_pep6_aux Trp Trp_Aux - #ABCDEFGHIJK #ABCDEFGHIJK - - bs_pep7 PyrCO2 Pyr CO2 - #ABCD #ABC #D - - - // Acetyl-CoA - - bs_accoa AcCoA BM_AcCoA - #AB #AB - - bs_accoa_aux BM_AcCoA AcCoA_Aux - #AB #AB - - - // Alpha-Ketoglutarate Family - - bs_akg AKG BM_AKG // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg1 BM_AKG Glu // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg2 Glu Pro // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg3 Glu Gln // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #ABCDE - - bs_akg4 Glu CO2 Arg // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDE #a #ABCDEa - - bs_akg4_aux Arg Arg_Aux // Les donnees sur Glu peuvent etre assimilee a AKG - #ABCDEF #ABCDEF - - - // Oxaloacetate Family - - bs_oaa OAA BM_OAA - #ABCD #ABCD - - bs_oaa1 BM_OAA Asp - #ABCD #ABCD - - bs_oaa1_aux Asp Asp_Aux - #ABCD #ABCD - - bs_oaa2 Thr BM_Pyr Ile CO2 - #ABCD #abc #ABbCDc #a - - bs_oaa2_aux Ile Ile_Aux - #ABCDEF #ABCDEF - - bs_oaa3a BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #ABCDcb #a - - bs_oaa3b BM_OAA BM_Pyr Lys CO2 - #ABCD #abc #abcDCB #A - - bs_oaa3_aux Lys Lys_Aux - #ABCDEF #ABCDEF - - bs_oaa4 BM_OAA OAA_Aux - #ABCD #ABCD - - bs_oaa5 BM_OAA Thr - #ABCD #ABCD - - bs_oaa5_aux Thr Thr_Aux - #ABCD #ABCD - - bs_oaa6 BM_OAA FTHF Met - #ABCD #a #ABCDa - - bs_oaa6_aux Met Met_Aux - #ABCDE #ABCDE - - bs_oaa7 BM_OAA Asn - #ABCD #ABCD - - bs_oaa7_aux Asn Asn_Aux - #ABCD #ABCD - - -// Flux de sortie - - out_co2 CO2 CO2_out // Sortie de CO2 - #A #A - - out_Ac AcCoA Acetate // Sortie d'acetate - #AB #AB - - out_FTHF FTHF FTHF_out - #A #A - -FLUXES - NET - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt_1 F 0.7 //0.807194 - Glucupt_U D -// CO2upt F 0.669589 -// FTHF0 F 0.00224836 -// FTHF1 F 0.001 - - pgi D - pfk D - ald D -// tpi D - pgk D - eno D - pyk F 1.4 - - zwf F 0.2 - gnd F 0.15062 - edd D - ta D - tk1 D - tk2 D - - pdh D - citsynth D - idh D - akgdh D - fum_a D - fum_b D - maldh D - -// gs1 C 0 -// gs2 D - - ppc D - mae D -// pck D - - // flux de biomasse - - bs_glc6P C 0.0109 // sortie de G6P - bs_fru6P C 0.0038 // sortie de F6P - bs_pga C 0.0791 // sortie de PGA pour formation de biomasse - bs_pga_aux D // sortie de PGA pour formation de biomasse - bs_pga1 D // conversion PGA donne ser - bs_pga1_aux C 0.0109 // conversion PGA donne ser - bs_pga2 D - bs_pga2_aux C 0.0046 // conversion PGA donne Cys - bs_pga3 D // reaction de synthese de Gly - bs_pga3_aux C 0.0308 // sortie de Gly - bs_DHAP C 0.0068 // formation de glycerolP pour lipides - bs_pyr C 0.1501 // avant : 0.1547 // sortie de Pyr pour formation de biomasse - bs_pyr1 D // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Leu - bs_pyr2 D // synthese d'AKV. consomme 2 Pyr - bs_pyr4 D - bs_pyr4_aux C 0.0213 // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 D // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux C 0.0227 // sortie de Leu - bs_e4p D // sortie d'Ery4p pour biomasse -// bs_e4p_aux C 0 // sortie d'Ery4p pour Trp - bs_rib5p C 0.0476 // synthese d'His - bs_rib5p1 D // synthese d'His - bs_rib5p1_aux C 0.0048 // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_pep C 0.0381 // sortie de PEP - bs_pep1 D // sortie de PEP - bs_pep2 D - bs_pep3a D - bs_pep3b D - bs_pep3_aux C 0.0093 - bs_pep4a D - bs_pep4b D - bs_pep4_aux C 0.0069 - bs_pep5 C 0.0027 - bs_pep6 D - bs_pep6_aux D - bs_pep7 D - bs_accoa C 0.1565 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_akg C 0.0571 // sortie d'AKG - bs_akg1 D - bs_akg2 C 0.0111 - bs_akg3 C 0.0132 - bs_akg4 D - bs_akg4_aux D - bs_oaa C 0.0947 // sortie d'OAA pour formation de biomasse - bs_oaa1 D // sortie d'OAA pour Asp - bs_oaa1_aux C 0.0121 // sortie d'Asp - bs_oaa2 D // synthese d'Ile - bs_oaa2_aux C 0.0146 // sortie d'Ile - bs_oaa3a D - bs_oaa3b D - bs_oaa3_aux C 0.0173 - bs_oaa4 D - bs_oaa5 D - bs_oaa5_aux C 0.0128 - bs_oaa6 D - bs_oaa6_aux C 0.0077 - bs_oaa7 D - bs_oaa7_aux C 0.0121 - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac F 0.213 // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - - XCH - NAME FCD VALUE(F/C) ED_WEIGHT LOW(F) INC(F) UP(F) - - Glucupt_1 D - Glucupt_U D -// CO2upt D -// FTHF0 D -// FTHF1 D - - pgi C 0.752386 // 2011-02-22 ssg: was F => often unresolved with --irand option - pfk C 0 - ald F 0.413926 -// tpi F 0.5 - pgk C 0.984718 // 2011-02-22 ssg: was F => often unresolved with --irand option - eno F 0.800962 - pyk C 0.0109591 // 2010-10-01 ssg: was F => unresolved if co2 uptake is unlimited - - zwf C 0 - gnd C 0 - edd C 0 - ta F 0.359468 - tk1 F 0.166316 - tk2 F 2.11559e-03 - - pdh C 0.0322745 // 2010-10-02 ssg: was F, otherwise unsolvable in monte-carlo - citsynth C 0 - idh C 0 - akgdh C 0 - fum_a F 0.395958 - fum_b D - maldh C 0.647115 //********************************************** C pour analyse de sensibilite, F pour minimisation - -// gs1 C 0 -// gs2 C 0 - - ppc F 0.256772 - mae C 0 -// pck C 0 - - bs_glc6P D // sortie de G6P - bs_fru6P D // sortie de F6P - bs_pga C 0 // conversion PGA donne Ser - bs_pga_aux D // conversion PGA donne Ser - bs_pga1 C 0 // conversion PGA donne Ser - bs_pga1_aux D // conversion PGA donne Ser - bs_pga2 C 0 // ser donne Cys. correspond a la sortie de PGA pour biomasse autre que formation Gly - bs_pga2_aux D - bs_pga3 C 0.011799 // reaction de synthese de Gly. cette reaction est reversible - bs_pga3_aux D // sortie de Gly - bs_DHAP D // formation de glycerolP pour lipides - bs_pyr C 0 // formation d'Ala - bs_pyr1 C 0 // formation d'Ala - bs_pyr1_aux D // sortie d'Ala. correspond aux sorties de Pyr qui ne sont pas associees a Val et Ile - bs_pyr2 C 0 // synthese d'AKV. consomme 2 Pyr - bs_pyr4 C 0 - bs_pyr4_aux D // sortie correspondant a l'utilisation de Val pour la biomasse - bs_pyr3 C 0 // synthese de Leu (AKV+AcCoA consommes) - bs_pyr3_aux D // sortie de Leu - bs_e4p C 0 // sortie d'Ery4p -// bs_e4p_aux D // sortie d'Ery4p pour Trp - bs_rib5p C 0 // synthese d'His - bs_rib5p1 C 0 // synthese d'His - bs_rib5p1_aux D // sortie d'His - bs_rib5p2 D // sortie de Rib5P autre que His - bs_accoa C 0 // sortie d'AcCoA pour biomasse - bs_accoa_aux D // sortie d'AcCoA pour biomasse en dehors de synthese Leu - bs_pep C 0 // sortie de PEP - bs_pep1 C 0 // sortie de PEP - bs_pep2 C 0 - bs_pep3a C 0 - bs_pep3b C 0 - bs_pep3_aux D - bs_pep4a C 0 - bs_pep4b C 0 - bs_pep4_aux D - bs_pep5 D - bs_pep6 C 0 - bs_pep6_aux D - bs_pep7 C 0 - bs_akg C 0 // sortie d'AKG - bs_akg1 C 0 - bs_akg2 D - bs_akg3 D - bs_akg4 C 0 - bs_akg4_aux D - bs_oaa C 0 - bs_oaa1 C 0 // sortie d'OAA autres que Met - bs_oaa1_aux D // sortie d'OAA autres que Met - bs_oaa2 C 0 // synthese de Met - bs_oaa2_aux D // sortie de Met - bs_oaa3a C 0 - bs_oaa3b C 0 - bs_oaa3_aux D - bs_oaa4 D - bs_oaa5 C 0 - bs_oaa5_aux D - bs_oaa6 C 0 - bs_oaa6_aux D - bs_oaa7 C 0 - bs_oaa7_aux D - - // Flux de sortie - - out_co2 D // sortie de CO2 - out_Ac D // sortie d'acetate - out_FTHF D // sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF - - -EQUALITIES - NET - VALUE FORMULA - - 0 fum_a-fum_b // scrambling reaction - 1 Glucupt_1+Glucupt_U - 0 bs_oaa3a-bs_oaa3b - 0 bs_pep3a-bs_pep3b - 0 bs_pep4a-bs_pep4b - - XCH - VALUE FORMULA - - 0 fum_a-fum_b - -INEQUALITIES - NET - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - 1 <= pyk - 0.0001 <= edd - 0.0001 <= gnd - 0.0001 <= zwf - 0.0001 <= ppc - 0.0001 <= mae -// 2 >= CO2upt // 2010-08-18 too high value makes jacobian rank deficient - XCH - VALUE COMP FORMULA -// Inequalities for Input and Output Fluxes are generated automatically - METAB - VALUE COMP FORMULA -// 1.2 >= AKG - - -FLUX_MEASUREMENTS - FLUX_NAME VALUE DEVIATION // Val Dev - out_Ac 0.213 0.0001 - -LABEL_INPUT - META_NAME ISOTOPOMER VALUE - - Gluc_U #111111 1 - #000000 0. - Gluc_1 #100000 1. - #000000 0. -// CO2_ext #0 0.989 -// #1 0.011 - -// FTHF_0 #0 1 -// FTHF_1 #1 1 - - -LABEL_MEASUREMENTS - META_NAME CUM_GROUP VALUE DEVIATION CUM_CONSTRAINTS - // Example - -PEAK_MEASUREMENTS - META_NAME PEAK_NO VALUE_S VALUE_D- VALUE_D+ VALUE_DD VALUE_T DEVIATION_S DEVIATION_D- DEVIATION_D+ DEVIATION_DD/T - - -MASS_SPECTROMETRY - META_NAME FRAGMENT WEIGHT VALUE DEVIATION - -// Deviation fixee a 0.02 // correction inoc 0.062 - - - - Suc 1,2,3,4 1 0.371605319 0.01 - 2 0.360829749 0.01 - 3 0.208425325 0.01 - 4 0.059139607 0.01 -// Mal 1,2,3,4 0 0.164619329483 0.02 -// 1 0.110072868518 0.02 -// 2 0.637801316225333 0.02 -// 3 0.0863461044204333 0.02 -// 4 0.00116038135315367 0.02 - ICit 1,2,3,4,5,6 0 0.131864539419667 0.02 - 1 0.225857638569 0.02 - 2 0.256421170949333 0.02 - 3 0.209230210478667 0.02 - 4 0.116863585449667 0.02 - 5 0.0457727744643333 0.02 - 6 0.0139900806697867 0.02 - PEP 1,2,3 0 0.421359839367667 0.01 - 1 0.358998301162333 0.01 - 2 0.0348521859365667 0.01 - 3 0.184789673534 0.01 - PGA 1,2,3 0 0.434335785072667 0.01 - 1 0.352829683224667 0.01 - 2 0.0323479804176 0.01 - 3 0.180486551285333 0.01 - FruBP 1,2,3,4,5,6 0 0.0738121029259333 0.01 - 1 0.454450017158667 0.01 - 2 0.160823529969333 0.01 - 3 0.0944468077710667 0.01 - 4 0.105281338489667 0.01 - 5 0.0155016033633 0.01 - 6 0.0956846003217333 0.01 - Glc6P 1,2,3,4,5,6 0 0.0160587173349 0.01 - 1 0.673510772480667 0.01 - 2 0.0930110047641 0.01 - 3 0.0280359937297 0.01 - 4 0.0397315614067667 0.01 - 5 0.0145524520950667 0.01 - 6 0.135099498189 0.01 - Fru6P 1,2,3,4,5,6 0 0.0235029951295 0.01 - 1 0.624253565357667 0.01 - 2 0.113068441282333 0.01 - 3 0.0456605631765 0.01 - 4 0.0516089447155667 0.01 - 5 0.0185881765378333 0.01 - 6 0.123317313800333 0.01 - Rib5P 1,2,3,4,5 0 0.341615670498667 0.01 - 1 0.25454117519 0.01 - 2 0.159027180368333 0.01 - 3 0.113789577528667 0.01 - 4 0.0615266612553333 0.01 - 5 0.0694997351590667 0.01 - Gnt6P 1,2,3,4,5,6 0 0.0249552273874 0.01 - 1 0.672556163913 0.01 - 2 0.0866890773125333 0.01 - 3 0.0313987199704333 0.01 - 4 0.0314691889898667 0.01 - 5 0.0138168327362333 0.01 - 6 0.139114789690333 0.01 -// Ery4P 1,2,3,4 0 0.178453461108 0.01 -// 1 0.412398433968333 0.01 -// 2 0.273694508221667 0.01 -// 3 0.116142498670667 0.01 -// 4 0.0193110980315 0.01 -METABOLITE_POOLS - META_NAME META_SIZE - AKG -1 - AKV 1 - AcCoA 1 - Ala 1 - Arg 1 - Asn 1 - Asp 1 - BM_AKG 1 - BM_AcCoA 1 - BM_Ery4P 1 - BM_OAA 1 - BM_PEP 1 - BM_PGA 1 - BM_Pyr 1 - BM_Rib5P 1 - CO2 1 - Chor 1 - Cys 1 - DAHP 1 - Ery4P -1 - FTHF 1 - Fru6P -1 - FruBP -1 - GA3P -1 - Glc6P 1 - Glu 1 - Gly 1 - Gnt6P -1 - His 1 - ICit -1 - Ile 1 - Leu 1 - Lys 1 - Mal 1 - Met 1 - OAA -1 - PEP -1 - PGA -1 - Phe 1 - Pyr -1 - PyrCO2 1 - Rib5P -1 - Sed7P -1 - Ser 1 - Suc -1 - Thr 1 - Trp 1 - Tyr 1 - Val 1 -METAB_MEASUREMENTS - META_NAME VALUE DEVIATION - Fru6P 0.4263681348074568 0.01 - GA3P 0.469998855791378 0.01 - FruBP 1.860001398406723 0.01 - PEP 0.1099999780931608 0.01 - Rib5P 0.01933825682263468 0.01 - Sed7P 0.05727159999541005 0.01 - -OPTIONS - OPT_NAME OPT_VALUE - dt 1 - nsubdiv_dt 4 - //tmax 10 - file_labcin e_coli_msen.txt - commandArgs --noscale --TIMEIT --time_order=2 --zc=0 --clowp 1.e-9 - optctrl_errx 1.e-3 - optctrl_maxit 50 - optctrl_btmaxit 16 - optctrl_btstart 1 - optctrl_btfrac 0.5 - //optctrl_history 1 - optctrl_adaptbt 1 - optctrl_monotone 1 - posttreat_R plot_imass.R
--- a/test-data/e_coli_i.log Wed Sep 13 19:52:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ -"/usr/local/miniconda3/bin/influx_i" "e_coli_i.ftbl" -code gen: 2020-03-25 15:40:11 -executing: "/usr/local/miniconda3/bin/python3.7" "/home/STORAGE/local/miniconda3/bin/ftbl2optR.py" "--tblimit" "0" "--ropts" "noscale=TRUE; clowp=1e-09; zc=0.0; time_order='2'; TIMEIT=TRUE" "--case_i" "e_coli_i.ftbl" -executing: R --vanilla --slave < e_coli_i.R -calcul : 2020-03-25 15:40:14 -load : 2020-03-25 15:40:18.59 cpu=1.02 -rinit : 2020-03-25 15:40:18.61 cpu=1.031 -r_flux : 2020-03-25 15:40:18.61 cpu=1.031 -Afl qr(): 2020-03-25 15:40:18.68 cpu=1.101 -dfl_dffg: 2020-03-25 15:40:18.91 cpu=1.139 -spAbr : 2020-03-25 15:40:18.91 cpu=1.143 -weight 1: 2020-03-25 15:40:18.91 cpu=1.143 -weight 2: 2020-03-25 15:40:18.95 cpu=1.225 -weight 3: 2020-03-25 15:40:19.02 cpu=1.348 -weight 4: 2020-03-25 15:40:19.07 cpu=1.456 -weight 5: 2020-03-25 15:40:19.10 cpu=1.506 -weight 6: 2020-03-25 15:40:19.17 cpu=1.574 -measure : 2020-03-25 15:40:19.25 cpu=1.602 -ineq : 2020-03-25 15:40:19.33 cpu=1.683 -preopt : 2020-03-25 15:40:19.57 cpu=2.056 -labargs : 2020-03-25 15:40:19.58 cpu=2.069 -cl expor: 2020-03-25 15:40:20.32 cpu=2.089 -cl sourc: 2020-03-25 15:40:21.20 cpu=2.204 -run 1: 2020-03-25 15:40:24.75 cpu=5.386 -Starting point -zc ineq : 2020-03-25 15:40:24.75 cpu=5.387 -kvh init: 2020-03-25 15:40:24.78 cpu=5.432 -check ja: 2020-03-25 15:40:25.27 cpu=5.625 -optim : 2020-03-25 15:40:26.47 cpu=5.632 -it=0 res=237.7947 -it=1 res=70.06248 normstep=30.47659 btk=1 -it=2 res=36.43491 normstep=31.35182 btk=1 -it=3 res=21.83319 normstep=0.2793447 btk=1 -it=4 res=21.7384 normstep=0.03332941 btk=1 -it=5 res=21.72383 normstep=0.03867587 btk=1 -it=6 res=21.6348 normstep=0.08885869 btk=1 -it=7 res=21.37745 normstep=0.4890457 btk=0.5 -it=8 res=21.24931 normstep=0.6490092 btk=1 -it=9 res=20.96647 normstep=0.3171006 btk=1 -it=10 res=20.96366 normstep=0.1287473 btk=1 -it=15 res=20.96358 normstep=5.449035e-05 btk=1 -secondzc: 2020-03-25 15:40:41.08 cpu=8.101 -After the first optimization, no zero crossing inequality was activated. So no reoptimization -postopt : 2020-03-25 15:40:41.09 cpu=8.111 -linstats: 2020-03-25 15:40:41.87 cpu=8.697 -rend : 2020-03-25 15:40:42.16 cpu=9.089 -end : 2020-03-25 15:40:43
--- a/test-data/e_coli_msen.txt Wed Sep 13 19:52:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -# simulated measurement with noise (e_coli_mse.txt+noise with sd from e_coli_ie.ftbl) -row_col 1 2 3 4 5 6 7 8 9 10 # see if ignored -m:Rib5P:1,2,3,4,5:0:693 0.8301287113482 0.705273440788489 0.630962344759146 0.599912176047555 0.573404157056382 0.549013957980969 0.544210331911793 0.508277982602693 0.499016033193777 0.485286541644114 -m:Rib5P:1,2,3,4,5:1:694 0.139499223890491 0.222339755290909 0.243819119211992 0.251856352480698 0.277951849850555 0.26624702204022 0.253318961326116 0.242251579900221 0.257243898371434 0.245894214016595 -m:Rib5P:1,2,3,4,5:2:695 0.0290070095454754 0.0533324485991101 0.0672401633923346 0.0862872836178193 0.0903657887685621 0.111438208430907 0.106264456513264 0.127665879867143 0.129695750051211 0.143194872657798 -m:Rib5P:1,2,3,4,5:3:696 0.00160408414038381 0.0229950078431453 0.0242885112480173 0.0236262011871506 0.0384713977458625 0.0395862886561061 0.0399422126310299 0.0434575340902056 0.057575220004768 0.053327058437221 -m:Rib5P:1,2,3,4,5:4:697 0.00284213879991028 0.00136220262120975 0.00945113487347922 0.0262298815476012 0.0339069314888829 0.045111483933521 0.0308238334730582 0.0483697721397453 0.0489364990171572 0.056352033597862 -m:Rib5P:1,2,3,4,5:5:698 0.00381673478018765 0.0136152393183676 0.0187948292708048 0.029237436783619 0.0340531521955641 0.0266101321627734 0.0399368276378717 0.046845505348588 0.0373560862314168 0.0462793762301527 - -m:Glc6P:1,2,3,4,5,6:0:679 0.493952162617383 0.241788346718873 0.129931016363475 0.0728422136538586 0.0555639355367493 0.0401826943349669 0.0314283807166068 0.0372888457858936 0.0241841875922507 0.030958811289491 -m:Glc6P:1,2,3,4,5,6:1:680 0.404262494562378 0.601528892652349 0.673997202888538 0.700284514239992 0.714448890273421 0.702861007777799 0.685523754578573 0.704662941393205 0.68684504474593 0.682856315908778 -m:Glc6P:1,2,3,4,5,6:2:681 -0.00971071210181876 0.00551823887717201 0.00739665415406503 0.0281297328224873 0.0374856512913617 0.0452870902703815 0.0460785142653824 0.0814776167048646 0.0659155729271299 0.0785432369222522 -m:Glc6P:1,2,3,4,5,6:3:682 0.0174215229553926 0.0170559578191188 0.025304157357846 0.0430017639175836 0.0348874311624526 0.0489484715084225 0.0351411534788991 0.0269856593772156 0.0192927092252581 0.0385779418075484 -m:Glc6P:1,2,3,4,5,6:4:683 0.0043659263104226 0.00877723557364165 0.00725821330054203 0.0126022050427868 0.0289095437215765 0.0282667499900472 0.0428080102047586 0.02592897485848 0.0333262720524978 0.0333836437820453 -m:Glc6P:1,2,3,4,5,6:5:684 -0.00295242877114927 0.0228561008765114 0.00107949443140708 0.00576924101393923 0.00359462341126682 -0.00291644895745689 -0.000650092439870991 -0.00722996134202132 -0.0148852807485112 0.00354062643070811 -m:Glc6P:1,2,3,4,5,6:6:685 0.0949417468382319 0.129448731101592 0.11756999828035 0.116834010941517 0.156652332757322 0.142614492470288 0.136775707360364 0.142247844825291 0.128888546346649 0.132781514945108 - -m:ICit:1,2,3,4,5,6:0:657 0.964808884433423 1.00382002410753 0.976023042393462 0.894194434705964 0.766995156890106 0.690445464992781 0.63176893227039 0.528124368350999 0.442923129524696 0.395459161361152 -m:ICit:1,2,3,4,5,6:1:658 0.0143600676195567 0.0436548728034513 0.0534942728405111 0.0639987878375545 0.134065776629187 0.146919412024849 0.227799495903936 0.272494318035825 0.294024445522389 0.247190260186848 -m:ICit:1,2,3,4,5,6:2:659 0.0166297755006583 -0.0125797291227997 0.0127788142463291 0.0221526869422438 0.0870629846959751 0.124622112755198 0.0805533586113773 0.124589240328517 0.174587994783957 0.20637931969854 -m:ICit:1,2,3,4,5,6:3:660 -0.0164071602748031 -0.021607873341015 0.0405857166794395 0.0067533469595018 0.00856287955464007 0.032691842098317 0.03648172445535 0.0897097881203855 0.0377806396555514 0.108435276435524 -m:ICit:1,2,3,4,5,6:4:661 -0.0311946635661311 0.0112912100867262 -0.00328434976694734 -0.0291273953557248 0.00347615542802288 0.0135048730050441 0.0071339543400162 0.004515912946923 0.00749482343750274 0.0493479770558265 -m:ICit:1,2,3,4,5,6:5:662 -0.0151243019611019 -0.010343521441609 -0.0179127774136863 -0.0106202857696235 0.00503762224320454 0.0053007176644241 0.00856924745879578 -0.0046437475961502 -0.0137565134141504 -0.00931041072969327 -m:ICit:1,2,3,4,5,6:6:663 -0.00200369348784026 -0.00117170585835455 0.0284291904473502 0.0128473467258485 0.0142796581015085 -0.0119617502140488 0.00832215559537679 0.0333737729365706 -0.0233735989156783 -0.0163687999125459 - -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 0.490207230868459 0.513759561323935 0.497418644493142 0.480282911481621 -m:FruBP:1,2,3,4,5,6:2:674 -0.00198367254664417 0.0125753789563416 0.00042629691833386 0.0251359606878703 0.0458213984942464 0.0537112170700128 0.0582455692688059 0.0732956046933924 0.0761912369338422 0.0857605693669639 -m:FruBP:1,2,3,4,5,6:3:675 -0.000392113325137966 0.0132767242245432 0.0467756022636571 0.0803441546018749 0.0732686847392194 0.100607368009337 0.100554195366947 0.0912022225582722 0.102199914711651 0.0936825194012971 -m:FruBP:1,2,3,4,5,6:4:676 -0.0120394479858482 -0.00593961237618397 -0.000971488795492516 0.00796387425034388 0.00873461737604841 0.0545832171869149 0.0565000883937298 0.0405511217315538 0.0519562886079823 0.0725381260214016 -m:FruBP:1,2,3,4,5,6:5:677 -0.00525294722682946 0.00537247522397268 -0.00380859480830061 0.00270832479079256 -0.00087264218392774 0.00494152714714406 0.00135371023071657 0.00927633370606465 0.00936073842733687 0.00788049093123055 -m:FruBP:1,2,3,4,5,6:6:678 0.00402818220901069 0.035673399588083 0.0542952441027104 0.0750899278339439 0.0689359253522637 0.0907137663313326 0.0662239468820011 0.0837284613547794 0.0741911443336369 0.0691637252843734 - -m:Fru6P:1,2,3,4,5,6:0:686 0.543315183156242 0.271442215154307 0.15342041555599 0.104226528529691 0.0601207158756622 0.0667835627698116 0.032169592051183 0.0444987186974436 0.0312424656505585 0.0371738310019649 -m:Fru6P:1,2,3,4,5,6:1:687 0.381498556157925 0.566820512279315 0.64753590777845 0.669325655114947 0.672155048267478 0.658521355463491 0.672620087099418 0.658937533256872 0.65065211800828 0.629670055679612 -m:Fru6P:1,2,3,4,5,6:2:688 -0.0102984598677217 0.00689221621662103 0.0339321967612094 0.0465421546157055 0.0571543647969092 0.0732789089821859 0.0959460289039786 0.0715783489999898 0.0926230588187283 0.0957791120020438 -m:Fru6P:1,2,3,4,5,6:3:689 0.0250657939547482 0.023460916637709 0.0473358002097497 0.0321217800543612 0.0458500181495104 0.0259668014922916 0.0305191527374548 0.0469266856851943 0.0580452840754031 0.0385375322919084 -m:Fru6P:1,2,3,4,5,6:4:690 -0.00136306896214337 0.0137397725510333 0.0170177475023465 0.0417372012671271 0.0258510180458119 0.0385973494576826 0.0622003922899037 0.0620209065758034 0.0670552727027324 0.0510832683047673 -m:Fru6P:1,2,3,4,5,6:5:691 0.0126114174874434 0.0168366636261353 0.00613625694852706 0.00646155542199223 0.00416011463957945 -0.0185323336578468 0.00502015745762575 0.0152813542807671 0.00415755701611636 0.0088205581757464 -m:Fru6P:1,2,3,4,5,6:6:692 0.0772794502106592 0.105015237675548 0.105838420467053 0.117576197845624 0.106974963083314 0.126498375256686 0.113727482281553 0.12301912138022 0.114583839516509 0.122447416359013