Repository 'influx_si'
hg clone https://toolshed.g2.bx.psu.edu/repos/workflow4metabolomics/influx_si

Changeset 2:57f199aa07e4 (2023-12-13)
Previous changeset 1:4e3d4318113b (2023-09-13)
Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
modified:
README.rst
influx_si.xml
added:
macros.xml
test-data/e_coli.zip
removed:
test-data/e_coli.ftbl
test-data/e_coli.log
test-data/e_coli_1-Glc_exact.ftbl
test-data/e_coli_1-Glc_exact.log
test-data/e_coli_U-Glc_exact.ftbl
test-data/e_coli_growth.ftbl
test-data/e_coli_growth.log
test-data/e_coli_i.ftbl
test-data/e_coli_i.log
test-data/e_coli_msen.txt
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diff -r 4e3d4318113b -r 57f199aa07e4 README.rst
--- a/README.rst Wed Sep 13 19:52:44 2023 +0000
+++ b/README.rst Wed Dec 13 08:56:04 2023 +0000
b
@@ -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
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diff -r 4e3d4318113b -r 57f199aa07e4 influx_si.xml
--- a/influx_si.xml Wed Sep 13 19:52:44 2023 +0000
+++ b/influx_si.xml Wed Dec 13 08:56:04 2023 +0000
[
b'@@ -1,232 +1,204 @@\n-<tool id="influx_si" name="influx_si" version="@TOOL_VERSION@+galaxy1">\n-   <description>metabolic flux analysis</description>\n-   <macros>\n-        <token name="@TOOL_VERSION@">5.1.0</token>\n-   </macros>\n-   <requirements>\n-      <requirement type="package" version="@TOOL_VERSION@">influx_si</requirement>\n-   </requirements>\n-   <version_command>influx_s --version</version_command>\n-   <command detect_errors="exit_code"><![CDATA[\n-       #set $inp_all = [$input_main, ($prlexp.input_aux if $prlexp.input_aux else [])]\n-       #if $si.s_i == \'i\':\n-         #silent $inp_all.append($si.input_ti)\n-       #end if\n-\n-       mkdir outdir && cd outdir &&\n-\n-       #for $inp in $inp_all:\n-         #for $i in $inp:\n-           ln -s \'$i\' \'$i.element_identifier\' &&\n-         #end for\n-       #end for\n-\n-       influx_$si.s_i\n-            $opt.noopt\n-            $opt.noscale\n-            #if $opt.meth != \'None\':\n-               $opt.meth\n+<tool id="influx_si" name="influx_si" version="@TOOL_VERSION@+galaxy1" profile="21.09">\n+    <description>\n+        Estimate metabolic fluxes and concentrations by fitting simulated labeling in metabolites to NMR/MS measurements\n+    </description>\n+    <creator>\n+        <person givenName="Serguei" familyName="Sokol" email="sokol@insa-toulouse.fr" url="https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/cellule-mathematiques/" />\n+        <organization name="INRAE" url="https://www.inrae.fr/" />\n+        <organization name="TBI" url="https://www.toulouse-biotechnology-institute.fr/" />\n+        <organization name="Mathematics Cell" url="https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/cellule-mathematiques/" />\n+        <organization name="MetaToul-FluxoMet" url="https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/metatoul/" />\n+        <organization name="MetaboHub2" url="https://www.metabohub.fr/" />\n+    </creator>\n+    <macros>\n+        <import>macros.xml</import>\n+    </macros>\n+    <requirements>\n+        <requirement type="package" version="@TOOL_VERSION@">influx_si</requirement>\n+    </requirements>\n+    <command detect_errors="exit_code"><![CDATA[\n+        #for $inp in $input_main:\n+            unzip $inp;\n+        #end for\n+               \n+        ret=0;\n+        influx_$si.s_i\n+            $noopt\n+            $noscale\n+            $fullsys\n+            $emu\n+            $irand\n+            $ln\n+            $sln\n+            $tikhreg\n+            $lim\n+            $ffguess\n+            $nocalc\n+            $addnoise\n+            $TIMEIT\n+            $prof\n+            #if $opt.meth:\n+              --meth=\'$opt.meth\'\n             #end if\n-            $opt.fullsys\n-            $opt.emu\n-            $opt.irand\n             #if $opt.sens:\n-             --sens=\'$opt.sens\'\n+              --sens=\'$opt.sens\'\n             #end if\n             #if $opt.cupx:\n-             --cupx=\'$opt.cupx\'\n+              --cupx=\'$opt.cupx\'\n             #end if\n             #if $opt.cupn:\n-             --cupn=\'$opt.cupn\'\n+              --cupn=\'$opt.cupn\'\n             #end if\n             #if $opt.cupp:\n-             --cupp=\'$opt.cupp\'\n+              --cupp=\'$opt.cupp\'\n             #end if\n             #if $opt.clownr:\n-             --clownr=\'$opt.clownr\'\n+              --clownr=\'$opt.clownr\'\n             #end if\n             #if $opt.cinout:\n-             --cinout=\'$opt.cinout\'\n+              --cinout=\'$opt.cinout\'\n             #end if\n             #if $opt.clowp:\n-             --clowp=\'$opt.clowp\'\n+              --clowp=\'$opt.clowp\'\n             #end if\n             #if $opt.np:\n-             --np=\'$opt.np\'\n+              --np=\'$opt.np\'\n+            #end if\n+            #if $opt.zc:\n+              --zc=\'$opt.zc\'\n             #end if\n-            $opt.ln\n-            $opt.sln\n-            $opt.tikhreg\n-            $opt.lim\n-            #if $opt.zc:\n-             --zc=\'$opt.zc\'\n+            #if $opt.fseries:\n+              --fseries=\'$o'..b'able cores in a given node are used for MC simulations." />\n+            <param argument="--zc" type="float" min="0" value="" label="--zc" optional="true" help="Apply zero crossing strategy with non negative threshold for net fluxes" />\n+            <param argument="--fseries" type="text" value="" label="--fseries" optional="true" help="File name with free parameter values for multiple starting points. Default: &#x27;&#x27; (empty, i.e. only one starting point from the FTBL file is used)" />\n+            <param argument="--iseries" type="text" value="" label="--iseries" optional="true" help="Indexes of starting points to use. Format: &#x27;1:10&#x27; -- use only first ten starting points; &#x27;1,3&#x27; -- use the the first and third starting points; &#x27;1:10,15,91:100&#x27; -- a mix of both formats is allowed. Default: &#x27;&#x27; (empty, i.e. all provided starting points are used)" />\n+            <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." />\n+            <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." />\n+            <param argument="--tblimit" type="integer" min="0" value="0" label="--tblimit" optional="true" help="developer option: set trace back limit for python error messages" />\n+            <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."/>\n+        </section>\n+    </inputs>\n+    <outputs>\n+        <collection name="influx_si_output" type="list:list" label="influx_${si.s_i}_on_${on_string}">\n+            <discover_datasets match_relative_path="true" recurse="true" pattern="(?P&lt;identifier_0&gt;[^/]+)_res/(?P&lt;identifier_1&gt;[^/]+)\\.(?P&lt;ext&gt;[^.]+)" visible="false"/>\n+        </collection>\n+    </outputs>\n+    <tests>\n+        <test>\n+            <param name="input_main" value="e_coli.zip" />\n+            <conditional name="si">\n+                <param name="s_i" value="s" />\n+            </conditional>\n+            <output_collection name="influx_si_output" type="list:list" count="1">\n+                <element name="e_coli" count="7">\n+                    <element name="e_coli.log">\n+                        <assert_contents>\n+                            <has_n_lines n="38"/>\n+                            <has_line_matching expression="^end.*"/>\n+                        </assert_contents>\n+                    </element>\n+                </element>\n+            </output_collection>\n+        </test>\n+    </tests>\n+    <help><![CDATA[\n+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.\n+\n+Detailed documentation is available on https://influx-si.readthedocs.io\n+]]></help>\n+    <citations>\n+        <citation type="bibtex">\n+            @misc{githubinflux,\n+                author = {Sokol, Serguei},\n+                year = {2023},\n+                title = {influx_s},\n+                publisher = {GitHub},\n+                journal = {GitHub repository},\n+                url = {https://github.com/sgsokol/influx},\n+            }\n+        </citation>\n+        <citation type="doi">10.1093/bioinformatics/btr716</citation>\n+    </citations>\n </tool>\n'
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diff -r 4e3d4318113b -r 57f199aa07e4 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Dec 13 08:56:04 2023 +0000
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@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">7.0.1</token>
+</macros>
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diff -r 4e3d4318113b -r 57f199aa07e4 test-data/e_coli.ftbl
--- a/test-data/e_coli.ftbl Wed Sep 13 19:52:44 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b"@@ -1,720 +0,0 @@\n-PROJECT\n-\tNAME\tVERSION\tFORMAT\tDATE\tCOMMENT\n-\tK12_MG1655.ftbl\t1\t\t101109\tmodele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees\n-\n-NETWORK\n-\tFLUX_NAME\tEDUCT_1\tEDUCT_2\tPRODUCT_1\tPRODUCT_2\n-\n-// Glycolyse.\n-// PPP\n-// TCA\n-// voies anaplerotiques: pepc. enz malique\n-// voie glyoxylate\n-// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre)\n-// saisie differentielle des substrats marques\n-\n-\n-//## Uptake substrats\n-\n-\tGlucupt_1\tGluc_1\t\tGlc6P\t\t// fehlt bei wolfgang\n-\t\t#ABCDEF\t\t#ABCDEF\t\t// fehlt bei wolfgang\n-\n-\tGlucupt_U\tGluc_U\t\tGlc6P\t\t// fehlt bei wolfgang\n-\t\t#ABCDEF\t\t#ABCDEF\t\t// fehlt bei wolfgang\n-\n-//\tCO2upt\tCO2_ext\t\tCO2\t\t// entree de CO2 non marque\n-//\t\t#A\t\t#A\t\t// ce flux est a laisser libre\n-\n-//\tFTHF0\tFTHF_0\t\tFTHF\t\t// prise en charge de FTHF non marque\n-//\t\t#A\t\t#A\n-\n-//\tFTHF1\tFTHF_1\t\tFTHF\t\t// prise en charge de FTHF marque\n-//\t\t#a\t\t#a\n-\n-\n-//## Embden Meyerhof Parnas Pathway\n-\n-\tpgi\tGlc6P\t\tFru6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tpfk\tFru6P\t\tFruBP\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tald\tFruBP\t\tGA3P\tGA3P\n-\t\t#ABCDEF\t\t#CBA\t#DEF\n-\n-//\ttpi\tDHAP\t\tGA3P\n-//\t\t#ABC\t\t#CBA\n-\n-\tpgk\tGA3P\t\tPGA\n-\t\t#ABC\t\t#ABC\n-\n-\teno\tPGA\t\tPEP\n-\t\t#ABC\t\t#ABC\n-\n-\tpyk\tPEP\t\tPyr\n-\t\t#ABC\t\t#ABC\n-\n-\n-//## Methylglyoxal Pathway\n-\n-//\tmgs\tDHAP\t\tPyr\n-//\t\t#ABC\t\t#ABC\n-\n-\n-//## Pentose Phosphate Pathway\n-\n-\tzwf\tGlc6P\t\tGnt6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tgnd\tGnt6P\t\tCO2\tRib5P\n-\t\t#ABCDEF\t\t#A\t#BCDEF\n-\n-\tedd\tGnt6P\t\tPyr\tGA3P\n-\t\t#ABCDEF\t\t#ABC\t#DEF\n-\n-//\tta\tEry4P\tFru6P\tGA3P\tSed7P\n-//\t\t#ABCD\t#abcdef\t#def\t#abcABCD\n-\n-//\ttk1\tGA3P\tSed7P\tRib5P\tRib5P\n-//\t\t#ABC\t#abcdefg\t#abABC\t#cdefg\n-\n-//\ttk2\tGA3P\tFru6P\tRib5P\tEry4P\n-//\t\t#ABC\t#abcdef\t#abABC\t#cdef\n-\n-\tta\tGA3P\tSed7P\tEry4P\tFru6P\n-\t\t#ABC\t#abcdefg\t#defg\t#abcABC\n-\n-\ttk1\tRib5P\tRib5P\tGA3P\tSed7P\n-\t\t#ABCDE\t#abcde\t#CDE\t#ABabcde\n-\n-\ttk2\tRib5P\tEry4P\tGA3P\tFru6P\n-\t\t#ABCDE\t#abcd\t#CDE\t#ABabcd\n-\n-\n-//## Tricarboxylic Acid Cycle\n-\n-\tpdh\tPyr\t\tAcCoA\tCO2\n-\t\t#ABC\t\t#BC\t#A\n-\n-\tcitsynth\tAcCoA\tOAA\tICit\n-\t\t#AB\t#abcd\t#dcbaBA\n-\n-\tidh\tICit\t\tAKG\tCO2\n-\t\t#ABCDEF\t\t#ABCEF\t#D\n-\n-\takgdh\tAKG\t\tSuc\tCO2\n-\t\t#ABCDE\t\t#BCDE\t#A\n-\n-\tfum_a\tSuc\t\tMal\n-\t\t#ABCD\t\t#ABCD\n-\n-\tfum_b\tSuc\t\tMal\n-\t\t#ABCD\t\t#DCBA\n-\n-\tmaldh\tMal\t\tOAA\n-\t\t#ABCD\t\t#ABCD\n-\n-\n-//## Glyoxylate Shunt\n-\n-//\tgs1\tICit\t\tGlyOx\tSuc\n-//\t\t#ABCDEF\t\t#AB\t#DCEF\n-\n-//\tgs2\tGlyOx\tAcCoA\tOAA\n-//\t\t#AB\t#ab\t#ABba\n-\n-\n-//## Anaplerotic Reactions\n-\n-\tppc\tPEP\tCO2\tOAA\t\t\t// PEPcarboxylase\n-\t\t#ABC\t#a\t#ABCa\n-\n-\tmae\tMal\t\tPyr\tCO2\t\t// enzyme malique\n-\t\t#ABCD\t\t#ABC\t#D\n-\n-//\tpck\tOAA\t\tPEP\tCO2\t\t// PEP carboxykinase\n-//\t\t#ABCD\t\t#ABC\t#D\n-\n-\n-//## Biosynthetic Pathways\n-\n-\t// Glucose-6-Phosphate Family\n-\n-\tbs_glc6P\tGlc6P\t\tBM_Glc6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\t// Fructose-6-Phosphate Family\n-\n-\tbs_fru6P\tFru6P\t\tBM_Fru6P\t\t// sortie de Fru6P pour biomasse\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\t// Phosphoglycerate Family\n-\n-\tbs_pga\tPGA\t\tBM_PGA\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga_aux\tBM_PGA\t\tPGA_Aux\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga1\tBM_PGA\t\tSer\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga1_aux\tSer\t\tSer_Aux\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga2\tSer\t\tCys\t\t\t// ce flux sert de sortie pour PGA hors formation de Gly\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga2_aux\tCys\t\tCys_Aux\t\t\t// ce flux sert de sortie pour PGA hors formation de Gly\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga3\tSer\t\tGly\tFTHF\t\t// formation de gly pour biomasse\n-\t\t#ABC\t\t#AB\t#C\t\t// ce flux est reversible\n-\n-\tbs_pga3_aux\tGly\t\tGly_Aux\t\t// pour conserver Gly comme metabolite intracellulaire\n-\t\t#AB\t\t#AB\n-\n-\t// TrioseP Family\n-\n-\tbs_DHAP\tGA3P\t\tGlp\t\t\t// formation glycerolP pour lipides\n-\t\t#ABC\t\t#ABC\n-\n-\t// Pyruvate Family\n-\n-\tbs_pyr\tPyr\t\tBM_Pyr\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr1\tBM_Pyr\t\tAla\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr1_aux\tAla\t\tAla_Aux\t\t// pour conserver Ala comme metabolite intracellulaire\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr2\tBM_Pyr\tBM_Pyr\tAKV\tCO2\t\t// AKV et Val ont le meme squelette C\n-\t\t#ABC\t#abc\t#ABbcC\t#a\t\t// cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val\n-\n-\tbs_pyr4\tAKV\t\tVal\t\t// permet de tenir compte de la sortie de Val\n-\t\t#ABCDE\t\t#ABCDE\n-\n-\tbs_pyr4_aux\tVal\t\tVal_Aux\t\t// permet de tenir compte de la sortie de Val\n-\t\t#ABCDE\t\t#ABCDE\n-\n-\tbs"..b"D\n-\t\tbs_akg3\tD\n-\t\tbs_akg4\tC\t0\n-\t\tbs_akg4_aux\tD\n-\t\tbs_oaa\tC\t0\n-\t\tbs_oaa1\tC\t0\t\t// sortie d'OAA autres que Met\n-\t\tbs_oaa1_aux\tD\t\t// sortie d'OAA autres que Met\n-\t\tbs_oaa2\tC\t0\t\t// synthese de Met\n-\t\tbs_oaa2_aux\tD\t\t// sortie de Met\n-\t\tbs_oaa3a\tC\t0\n-\t\tbs_oaa3b\tC\t0\n-\t\tbs_oaa3_aux\tD\n-\t\tbs_oaa4\tD\n-\t\tbs_oaa5\tC\t0\n-\t\tbs_oaa5_aux\tD\n-\t\tbs_oaa6\tC\t0\n-\t\tbs_oaa6_aux\tD\n-\t\tbs_oaa7\tC\t0\n-\t\tbs_oaa7_aux\tD\n-\n-\t\t// Flux de sortie\n-\n-\t\tout_co2\tD\t\t\t// sortie de CO2\n-\t\tout_Ac\tD\t\t\t// sortie d'acetate\n-\t\tout_FTHF\tD\t\t// sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF\n-\n-\n-EQUALITIES\n-\tNET\n-\t\tVALUE\tFORMULA\n-\n-\t\t0\tfum_a-fum_b\t\t// scrambling reaction\n-\t\t1\tGlucupt_1+Glucupt_U\n-\t\t0\tbs_oaa3a-bs_oaa3b\n-\t\t0\tbs_pep3a-bs_pep3b\n-\t\t0\tbs_pep4a-bs_pep4b\n-\n-\tXCH\n-\t\tVALUE\tFORMULA\n-\n-\t\t0\tfum_a-fum_b\n-\n-INEQUALITIES\n-\tNET\n-\t\tVALUE\tCOMP\tFORMULA\n-// Inequalities for Input and Output Fluxes are generated automatically\n-\t\t1\t<=\tpyk\n-\t\t0.0001\t<=\tedd\n-\t\t0.0001\t<=\tgnd\n-\t\t0.0001\t<=\tzwf\n-\t\t0.0001\t<=\tppc\n-\t\t0.0001\t<=\tmae\n-//\t\t2\t>=\tCO2upt // 2010-08-18 too high value makes jacobian rank deficient\n-\tXCH\n-\t\tVALUE\tCOMP\tFORMULA\n-// Inequalities for Input and Output Fluxes are generated automatically\n-\n-\n-FLUX_MEASUREMENTS\n-\tFLUX_NAME\tVALUE\tDEVIATION\t//\t\tVal\tDev\n-\tout_Ac\t0.213\t0.0001\n-\n-LABEL_INPUT\n-\tMETA_NAME\tISOTOPOMER\tVALUE\n-\n-\tGluc_U\t#111111\t1\n-\t\t#000000\t0.\n-\tGluc_1\t#100000\t1.\n-\t\t#000000\t0.\n-//\tCO2_ext\t#0\t0.989\n-//\t\t#1\t0.011\n-\n-//\tFTHF_0\t#0\t1\n-//\tFTHF_1\t#1\t1\n-\n-\n-LABEL_MEASUREMENTS\n-\tMETA_NAME\tCUM_GROUP\tVALUE\tDEVIATION\tCUM_CONSTRAINTS\n-\t\t\t\t\t\t\t\t\t\t\t// Example\n-\n-PEAK_MEASUREMENTS\n-\tMETA_NAME\tPEAK_NO\tVALUE_S\tVALUE_D-\tVALUE_D+\tVALUE_DD\tVALUE_T\tDEVIATION_S\tDEVIATION_D-\tDEVIATION_D+\tDEVIATION_DD/T\n-\n-\n-MASS_SPECTROMETRY\n-\tMETA_NAME\tFRAGMENT\tWEIGHT\tVALUE\tDEVIATION\n-\n-// Deviation fixee a 0.02\t\t\t\t// correction inoc 0.062\n-\n-\n-\n-\tSuc\t1,2,3,4\t1\t0.371605319\t0.01\n-\t\t\t2\t0.360829749\t0.01\n-\t\t\t3\t0.208425325\t0.01\n-\t\t\t4\t0.059139607\t0.01\n-//\tMal\t1,2,3,4\t0\t0.164619329483\t0.02\n-//\t\t\t1\t0.110072868518\t0.02\n-//\t\t\t2\t0.637801316225333\t0.02\n-//\t\t\t3\t0.0863461044204333\t0.02\n-//\t\t\t4\t0.00116038135315367\t0.02\n-\tICit\t1,2,3,4,5,6\t0\t0.131864539419667\t0.02\n-\t\t\t1\t0.225857638569\t0.02\n-\t\t\t2\t0.256421170949333\t0.02\n-\t\t\t3\t0.209230210478667\t0.02\n-\t\t\t4\t0.116863585449667\t0.02\n-\t\t\t5\t0.0457727744643333\t0.02\n-\t\t\t6\t0.0139900806697867\t0.02\n-\tPEP\t1,2,3\t0\t0.421359839367667\t0.01\n-\t\t\t1\t0.358998301162333\t0.01\n-\t\t\t2\t0.0348521859365667\t0.01\n-\t\t\t3\t0.184789673534\t0.01\n-\tPGA\t1,2,3\t0\t0.434335785072667\t0.01\n-\t\t\t1\t0.352829683224667\t0.01\n-\t\t\t2\t0.0323479804176\t0.01\n-\t\t\t3\t0.180486551285333\t0.01\n-\tFruBP\t1,2,3,4,5,6\t0\t0.0738121029259333\t0.01\n-\t\t\t1\t0.454450017158667\t0.01\n-\t\t\t2\t0.160823529969333\t0.01\n-\t\t\t3\t0.0944468077710667\t0.01\n-\t\t\t4\t0.105281338489667\t0.01\n-\t\t\t5\t0.0155016033633\t0.01\n-\t\t\t6\t0.0956846003217333\t0.01\n-\tGlc6P\t1,2,3,4,5,6\t0\t0.0160587173349\t0.01\n-\t\t\t1\t0.673510772480667\t0.01\n-\t\t\t2\t0.0930110047641\t0.01\n-\t\t\t3\t0.0280359937297\t0.01\n-\t\t\t4\t0.0397315614067667\t0.01\n-\t\t\t5\t0.0145524520950667\t0.01\n-\t\t\t6\t0.135099498189\t0.01\n-\tFru6P\t1,2,3,4,5,6\t0\t0.0235029951295\t0.01\n-\t\t\t1\t0.624253565357667\t0.01\n-\t\t\t2\t0.113068441282333\t0.01\n-\t\t\t3\t0.0456605631765\t0.01\n-\t\t\t4\t0.0516089447155667\t0.01\n-\t\t\t5\t0.0185881765378333\t0.01\n-\t\t\t6\t0.123317313800333\t0.01\n-\tRib5P\t1,2,3,4,5\t0\t0.341615670498667\t0.01\n-\t\t\t1\t0.25454117519\t0.01\n-\t\t\t2\t0.159027180368333\t0.01\n-\t\t\t3\t0.113789577528667\t0.01\n-\t\t\t4\t0.0615266612553333\t0.01\n-\t\t\t5\t0.0694997351590667\t0.01\n-\tGnt6P\t1,2,3,4,5,6\t0\t0.0249552273874\t0.01\n-\t\t\t1\t0.672556163913\t0.01\n-\t\t\t2\t0.0866890773125333\t0.01\n-\t\t\t3\t0.0313987199704333\t0.01\n-\t\t\t4\t0.0314691889898667\t0.01\n-\t\t\t5\t0.0138168327362333\t0.01\n-\t\t\t6\t0.139114789690333\t0.01\n-//\tEry4P\t1,2,3,4\t0\t0.178453461108\t0.01\n-//\t\t\t1\t0.412398433968333\t0.01\n-//\t\t\t2\t0.273694508221667\t0.01\n-//\t\t\t3\t0.116142498670667\t0.01\n-//\t\t\t4\t0.0193110980315\t0.01\n-\n-OPTIONS\n-\tOPT_NAME\tOPT_VALUE\n-\t//MATLAB_FOR_FLUX_EQ_CONSTR_MATR\t1\n-\t//optctrl_history\t1 // nlsic\n-\t//optctrl_trace\t3 // BFGS\n-\t//optctrl_reltol\t1.e-10 // BFGS\n-\t//optctrl_maxit\t1000 // BFGS\n-\tcommandArgs\t--TIMEIT\n-\tposttreat_R\tplot_smeas.R\n"
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diff -r 4e3d4318113b -r 57f199aa07e4 test-data/e_coli.log
--- a/test-data/e_coli.log Wed Sep 13 19:52:44 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -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
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diff -r 4e3d4318113b -r 57f199aa07e4 test-data/e_coli.zip
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Binary file test-data/e_coli.zip has changed
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diff -r 4e3d4318113b -r 57f199aa07e4 test-data/e_coli_1-Glc_exact.ftbl
--- 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
b
b"@@ -1,713 +0,0 @@\n-PROJECT\n-\tNAME\tVERSION\tFORMAT\tDATE\tCOMMENT\n-\tK12_MG1655.ftbl\t1\t\t101109\tmodele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees\n-\n-NETWORK\n-\tFLUX_NAME\tEDUCT_1\tEDUCT_2\tPRODUCT_1\tPRODUCT_2\n-\n-// Glycolyse.\n-// PPP\n-// TCA\n-// voies anaplerotiques: pepc. enz malique\n-// voie glyoxylate\n-// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre)\n-// saisie differentielle des substrats marques\n-\n-\n-// Uptake substrats\n-\n-\tGlucupt\tGluc\t\tGlc6P\n-\t\t#ABCDEF\t\t#ABCDEF\t\n-//\tCO2upt\tCO2_ext\t\tCO2\t\t// entree de CO2 non marque\n-//\t\t#A\t\t#A\t\t// ce flux est a laisser libre\n-\n-//\tFTHF0\tFTHF_0\t\tFTHF\t\t// prise en charge de FTHF non marque\n-//\t\t#A\t\t#A\n-\n-//\tFTHF1\tFTHF_1\t\tFTHF\t\t// prise en charge de FTHF marque\n-//\t\t#a\t\t#a\n-\n-\n-// Embden Meyerhof Parnas Pathway\n-\n-\tpgi\tGlc6P\t\tFru6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tpfk\tFru6P\t\tFruBP\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tald\tFruBP\t\tGA3P\tGA3P\n-\t\t#ABCDEF\t\t#CBA\t#DEF\n-\n-//\ttpi\tDHAP\t\tGA3P\n-//\t\t#ABC\t\t#CBA\n-\n-\tpgk\tGA3P\t\tPGA\n-\t\t#ABC\t\t#ABC\n-\n-\teno\tPGA\t\tPEP\n-\t\t#ABC\t\t#ABC\n-\n-\tpyk\tPEP\t\tPyr\n-\t\t#ABC\t\t#ABC\n-\n-\n-// Methylglyoxal Pathway\n-\n-//\tmgs\tDHAP\t\tPyr\n-//\t\t#ABC\t\t#ABC\n-\n-\n-// Pentose Phosphate Pathway\n-\n-\tzwf\tGlc6P\t\tGnt6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tgnd\tGnt6P\t\tCO2\tRib5P\n-\t\t#ABCDEF\t\t#A\t#BCDEF\n-\n-\tedd\tGnt6P\t\tPyr\tGA3P\n-\t\t#ABCDEF\t\t#ABC\t#DEF\n-\n-//\tta\tEry4P\tFru6P\tGA3P\tSed7P\n-//\t\t#ABCD\t#abcdef\t#def\t#abcABCD\n-\n-//\ttk1\tGA3P\tSed7P\tRib5P\tRib5P\n-//\t\t#ABC\t#abcdefg\t#abABC\t#cdefg\n-\n-//\ttk2\tGA3P\tFru6P\tRib5P\tEry4P\n-//\t\t#ABC\t#abcdef\t#abABC\t#cdef\n-\n-\tta\tGA3P\tSed7P\tEry4P\tFru6P\n-\t\t#ABC\t#abcdefg\t#defg\t#abcABC\n-\n-\ttk1\tRib5P\tRib5P\tGA3P\tSed7P\n-\t\t#ABCDE\t#abcde\t#CDE\t#ABabcde\n-\n-\ttk2\tRib5P\tEry4P\tGA3P\tFru6P\n-\t\t#ABCDE\t#abcd\t#CDE\t#ABabcd\n-\n-\n-// Tricarboxylic Acid Cycle\n-\n-\tpdh\tPyr\t\tAcCoA\tCO2\n-\t\t#ABC\t\t#BC\t#A\n-\n-\tcitsynth\tAcCoA\tOAA\tICit\n-\t\t#AB\t#abcd\t#dcbaBA\n-\n-\tidh\tICit\t\tAKG\tCO2\n-\t\t#ABCDEF\t\t#ABCEF\t#D\n-\n-\takgdh\tAKG\t\tSuc\tCO2\n-\t\t#ABCDE\t\t#BCDE\t#A\n-\n-\tfum_a\tSuc\t\tMal\n-\t\t#ABCD\t\t#ABCD\n-\n-\tfum_b\tSuc\t\tMal\n-\t\t#ABCD\t\t#DCBA\n-\n-\tmaldh\tMal\t\tOAA\n-\t\t#ABCD\t\t#ABCD\n-\n-\n-// Glyoxylate Shunt\n-\n-//\tgs1\tICit\t\tGlyOx\tSuc\n-//\t\t#ABCDEF\t\t#AB\t#DCEF\n-\n-//\tgs2\tGlyOx\tAcCoA\tOAA\n-//\t\t#AB\t#ab\t#ABba\n-\n-\n-// Anaplerotic Reactions\n-\n-\tppc\tPEP\tCO2\tOAA\t\t\t// PEPcarboxylase\n-\t\t#ABC\t#a\t#ABCa\n-\n-\tmae\tMal\t\tPyr\tCO2\t\t// enzyme malique\n-\t\t#ABCD\t\t#ABC\t#D\n-\n-//\tpck\tOAA\t\tPEP\tCO2\t\t// PEP carboxykinase\n-//\t\t#ABCD\t\t#ABC\t#D\n-\n-\n-// Biosynthetic Pathways\n-\n-\t// Glucose-6-Phosphate Family\n-\n-\tbs_glc6P\tGlc6P\t\tBM_Glc6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\t// Fructose-6-Phosphate Family\n-\n-\tbs_fru6P\tFru6P\t\tBM_Fru6P\t\t// sortie de Fru6P pour biomasse\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\t// Phosphoglycerate Family\n-\n-\tbs_pga\tPGA\t\tBM_PGA\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga_aux\tBM_PGA\t\tPGA_Aux\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga1\tBM_PGA\t\tSer\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga1_aux\tSer\t\tSer_Aux\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga2\tSer\t\tCys\t\t\t// ce flux sert de sortie pour PGA hors formation de Gly\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga2_aux\tCys\t\tCys_Aux\t\t\t// ce flux sert de sortie pour PGA hors formation de Gly\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga3\tSer\t\tGly\tFTHF\t\t// formation de gly pour biomasse\n-\t\t#ABC\t\t#AB\t#C\t\t// ce flux est reversible\n-\n-\tbs_pga3_aux\tGly\t\tGly_Aux\t\t// pour conserver Gly comme metabolite intracellulaire\n-\t\t#AB\t\t#AB\n-\n-\t// TrioseP Family\n-\n-\tbs_DHAP\tGA3P\t\tGlp\t\t\t// formation glycerolP pour lipides\n-\t\t#ABC\t\t#ABC\n-\n-\t// Pyruvate Family\n-\n-\tbs_pyr\tPyr\t\tBM_Pyr\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr1\tBM_Pyr\t\tAla\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr1_aux\tAla\t\tAla_Aux\t\t// pour conserver Ala comme metabolite intracellulaire\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr2\tBM_Pyr\tBM_Pyr\tAKV\tCO2\t\t// AKV et Val ont le meme squelette C\n-\t\t#ABC\t#abc\t#ABbcC\t#a\t\t// cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val\n-\n-\tbs_pyr4\tAKV\t\tVal\t\t// permet de tenir compte de la sortie de Val\n-\t\t#ABCDE\t\t#ABCDE\n-\n-\tbs_pyr4_aux\tVal\t\tVal_Aux\t\t// permet de tenir compte de la sortie de Val\n-\t\t#ABCDE\t\t#ABCDE\n-\n-\tbs_pyr3\tAKV\tBM_AcCoA\tLeu\tCO2\n-\t\t#ABCDE\t#ab\t#abBCDE\t#A\n-\n-\tbs_pyr3_aux\tLeu\t\tLeu_Aux\t\t// pour conserver Leu comme metabolite intracellulaire\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\n"..b"\t0\n-\t\tbs_akg2\tD\n-\t\tbs_akg3\tD\n-\t\tbs_akg4\tC\t0\n-\t\tbs_akg4_aux\tD\n-\t\tbs_oaa\tC\t0\n-\t\tbs_oaa1\tC\t0\t\t// sortie d'OAA autres que Met\n-\t\tbs_oaa1_aux\tD\t\t// sortie d'OAA autres que Met\n-\t\tbs_oaa2\tC\t0\t\t// synthese de Met\n-\t\tbs_oaa2_aux\tD\t\t// sortie de Met\n-\t\tbs_oaa3a\tC\t0\n-\t\tbs_oaa3b\tC\t0\n-\t\tbs_oaa3_aux\tD\n-\t\tbs_oaa4\tD\n-\t\tbs_oaa5\tC\t0\n-\t\tbs_oaa5_aux\tD\n-\t\tbs_oaa6\tC\t0\n-\t\tbs_oaa6_aux\tD\n-\t\tbs_oaa7\tC\t0\n-\t\tbs_oaa7_aux\tD\n-\n-\t\t// Flux de sortie\n-\n-\t\tout_co2\tD\t\t\t// sortie de CO2\n-\t\tout_Ac\tD\t\t\t// sortie d'acetate\n-\t\tout_FTHF\tD\t\t// sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF\n-\n-\n-EQUALITIES\n-\tNET\n-\t\tVALUE\tFORMULA\n-\n-\t\t0\tfum_a-fum_b\t\t// scrambling reaction\n-\t\t0\tbs_oaa3a-bs_oaa3b\n-\t\t0\tbs_pep3a-bs_pep3b\n-\t\t0\tbs_pep4a-bs_pep4b\n-\n-\tXCH\n-\t\tVALUE\tFORMULA\n-\n-\t\t0\tfum_a-fum_b\n-\n-INEQUALITIES\n-\tNET\n-\t\tVALUE\tCOMP\tFORMULA\n-// Inequalities for Input and Output Fluxes are generated automatically\n-\t\t1\t<=\tpyk\n-\t\t0.0001\t<=\tedd\n-\t\t0.0001\t<=\tgnd\n-\t\t0.0001\t<=\tzwf\n-\t\t0.0001\t<=\tppc\n-\t\t0.0001\t<=\tmae\n-//\t\t2\t>=\tCO2upt // 2010-08-18 too high value makes jacobian rank deficient\n-\tXCH\n-\t\tVALUE\tCOMP\tFORMULA\n-// Inequalities for Input and Output Fluxes are generated automatically\n-\n-\n-FLUX_MEASUREMENTS\n-\tFLUX_NAME\tVALUE\tDEVIATION\t//\t\tVal\tDev\n-\tout_Ac\t0.213\t0.0001\n-\n-LABEL_INPUT\n-\tMETA_NAME\tISOTOPOMER\tVALUE\n-\n-\tGluc\t#100000\t0.8\n-\t\t#000000\t0.2\n-//\tCO2_ext\t#0\t0.989\n-//\t\t#1\t0.011\n-\n-//\tFTHF_0\t#0\t1\n-//\tFTHF_1\t#1\t1\n-\n-\n-LABEL_MEASUREMENTS\n-\tMETA_NAME\tCUM_GROUP\tVALUE\tDEVIATION\tCUM_CONSTRAINTS\n-\t\t\t\t\t\t\t\t\t\t\t// Example\n-\n-PEAK_MEASUREMENTS\n-\tMETA_NAME\tPEAK_NO\tVALUE_S\tVALUE_D-\tVALUE_D+\tVALUE_DD\tVALUE_T\tDEVIATION_S\tDEVIATION_D-\tDEVIATION_D+\tDEVIATION_DD/T\n-\n-\n-MASS_SPECTROMETRY\n-\tMETA_NAME\tFRAGMENT\tWEIGHT\tVALUE\tDEVIATION\n-\n-// Deviation fixee a 0.02\t\t\t\t// correction inoc 0.062\n-\n-\n-\n-\tSuc\t1,2,3,4\t1\t0.371605319\t0.01\n-\t\t\t2\t0.360829749\t0.01\n-\t\t\t3\t0.208425325\t0.01\n-\t\t\t4\t0.059139607\t0.01\n-//\tMal\t1,2,3,4\t0\t0.164619329483\t0.02\n-//\t\t\t1\t0.110072868518\t0.02\n-//\t\t\t2\t0.637801316225333\t0.02\n-//\t\t\t3\t0.0863461044204333\t0.02\n-//\t\t\t4\t0.00116038135315367\t0.02\n-\tICit\t1,2,3,4,5,6\t0\t0.131864539419667\t0.02\n-\t\t\t1\t0.225857638569\t0.02\n-\t\t\t2\t0.256421170949333\t0.02\n-\t\t\t3\t0.209230210478667\t0.02\n-\t\t\t4\t0.116863585449667\t0.02\n-\t\t\t5\t0.0457727744643333\t0.02\n-\t\t\t6\t0.0139900806697867\t0.02\n-\tPEP\t1,2,3\t0\t0.421359839367667\t0.01\n-\t\t\t1\t0.358998301162333\t0.01\n-\t\t\t2\t0.0348521859365667\t0.01\n-\t\t\t3\t0.184789673534\t0.01\n-\tPGA\t1,2,3\t0\t0.434335785072667\t0.01\n-\t\t\t1\t0.352829683224667\t0.01\n-\t\t\t2\t0.0323479804176\t0.01\n-\t\t\t3\t0.180486551285333\t0.01\n-\tFruBP\t1,2,3,4,5,6\t0\t0.0738121029259333\t0.01\n-\t\t\t1\t0.454450017158667\t0.01\n-\t\t\t2\t0.160823529969333\t0.01\n-\t\t\t3\t0.0944468077710667\t0.01\n-\t\t\t4\t0.105281338489667\t0.01\n-\t\t\t5\t0.0155016033633\t0.01\n-\t\t\t6\t0.0956846003217333\t0.01\n-\tGlc6P\t1,2,3,4,5,6\t0\t0.0160587173349\t0.01\n-\t\t\t1\t0.673510772480667\t0.01\n-\t\t\t2\t0.0930110047641\t0.01\n-\t\t\t3\t0.0280359937297\t0.01\n-\t\t\t4\t0.0397315614067667\t0.01\n-\t\t\t5\t0.0145524520950667\t0.01\n-\t\t\t6\t0.135099498189\t0.01\n-\tFru6P\t1,2,3,4,5,6\t0\t0.0235029951295\t0.01\n-\t\t\t1\t0.624253565357667\t0.01\n-\t\t\t2\t0.113068441282333\t0.01\n-\t\t\t3\t0.0456605631765\t0.01\n-\t\t\t4\t0.0516089447155667\t0.01\n-\t\t\t5\t0.0185881765378333\t0.01\n-\t\t\t6\t0.123317313800333\t0.01\n-\tRib5P\t1,2,3,4,5\t0\t0.341615670498667\t0.01\n-\t\t\t1\t0.25454117519\t0.01\n-\t\t\t2\t0.159027180368333\t0.01\n-\t\t\t3\t0.113789577528667\t0.01\n-\t\t\t4\t0.0615266612553333\t0.01\n-\t\t\t5\t0.0694997351590667\t0.01\n-\tGnt6P\t1,2,3,4,5,6\t0\t0.0249552273874\t0.01\n-\t\t\t1\t0.672556163913\t0.01\n-\t\t\t2\t0.0866890773125333\t0.01\n-\t\t\t3\t0.0313987199704333\t0.01\n-\t\t\t4\t0.0314691889898667\t0.01\n-\t\t\t5\t0.0138168327362333\t0.01\n-\t\t\t6\t0.139114789690333\t0.01\n-//\tEry4P\t1,2,3,4\t0\t0.178453461108\t0.01\n-//\t\t\t1\t0.412398433968333\t0.01\n-//\t\t\t2\t0.273694508221667\t0.01\n-//\t\t\t3\t0.116142498670667\t0.01\n-//\t\t\t4\t0.0193110980315\t0.01\n-\n-OPTIONS\n-\tOPT_NAME\tOPT_VALUE\n-\tMATLAB_FOR_FLUX_EQ_CONSTR_MATR\t1\n-\t//optctrl_history\t1 // nlsic\n-\t//optctrl_trace\t3 // BFGS\n-\t//optctrl_reltol\t1.e-10 // BFGS\n-\t//optctrl_maxit\t1000 // BFGS\n-\tposttreat_R\tplot_smeas.R\n-\tprl_exp\te_coli_U-Glc_exact.ftbl\n-\tcommandArgs\t--TIMEIT --noscale\n-\n"
b
diff -r 4e3d4318113b -r 57f199aa07e4 test-data/e_coli_1-Glc_exact.log
--- 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
b
@@ -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
b
diff -r 4e3d4318113b -r 57f199aa07e4 test-data/e_coli_U-Glc_exact.ftbl
--- 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
b
b"@@ -1,711 +0,0 @@\n-PROJECT\n-\tNAME\tVERSION\tFORMAT\tDATE\tCOMMENT\n-\tK12_MG1655.ftbl\t1\t\t101109\tmodele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees\n-\n-NETWORK\n-\tFLUX_NAME\tEDUCT_1\tEDUCT_2\tPRODUCT_1\tPRODUCT_2\n-\n-// Glycolyse.\n-// PPP\n-// TCA\n-// voies anaplerotiques: pepc. enz malique\n-// voie glyoxylate\n-// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre)\n-// saisie differentielle des substrats marques\n-\n-\n-// Uptake substrats\n-\n-\tGlucupt\tGluc\t\tGlc6P\n-\t\t#ABCDEF\t\t#ABCDEF\t\n-//\tCO2upt\tCO2_ext\t\tCO2\t\t// entree de CO2 non marque\n-//\t\t#A\t\t#A\t\t// ce flux est a laisser libre\n-\n-//\tFTHF0\tFTHF_0\t\tFTHF\t\t// prise en charge de FTHF non marque\n-//\t\t#A\t\t#A\n-\n-//\tFTHF1\tFTHF_1\t\tFTHF\t\t// prise en charge de FTHF marque\n-//\t\t#a\t\t#a\n-\n-\n-// Embden Meyerhof Parnas Pathway\n-\n-\tpgi\tGlc6P\t\tFru6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tpfk\tFru6P\t\tFruBP\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tald\tFruBP\t\tGA3P\tGA3P\n-\t\t#ABCDEF\t\t#CBA\t#DEF\n-\n-//\ttpi\tDHAP\t\tGA3P\n-//\t\t#ABC\t\t#CBA\n-\n-\tpgk\tGA3P\t\tPGA\n-\t\t#ABC\t\t#ABC\n-\n-\teno\tPGA\t\tPEP\n-\t\t#ABC\t\t#ABC\n-\n-\tpyk\tPEP\t\tPyr\n-\t\t#ABC\t\t#ABC\n-\n-\n-// Methylglyoxal Pathway\n-\n-//\tmgs\tDHAP\t\tPyr\n-//\t\t#ABC\t\t#ABC\n-\n-\n-// Pentose Phosphate Pathway\n-\n-\tzwf\tGlc6P\t\tGnt6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tgnd\tGnt6P\t\tCO2\tRib5P\n-\t\t#ABCDEF\t\t#A\t#BCDEF\n-\n-\tedd\tGnt6P\t\tPyr\tGA3P\n-\t\t#ABCDEF\t\t#ABC\t#DEF\n-\n-//\tta\tEry4P\tFru6P\tGA3P\tSed7P\n-//\t\t#ABCD\t#abcdef\t#def\t#abcABCD\n-\n-//\ttk1\tGA3P\tSed7P\tRib5P\tRib5P\n-//\t\t#ABC\t#abcdefg\t#abABC\t#cdefg\n-\n-//\ttk2\tGA3P\tFru6P\tRib5P\tEry4P\n-//\t\t#ABC\t#abcdef\t#abABC\t#cdef\n-\n-\tta\tGA3P\tSed7P\tEry4P\tFru6P\n-\t\t#ABC\t#abcdefg\t#defg\t#abcABC\n-\n-\ttk1\tRib5P\tRib5P\tGA3P\tSed7P\n-\t\t#ABCDE\t#abcde\t#CDE\t#ABabcde\n-\n-\ttk2\tRib5P\tEry4P\tGA3P\tFru6P\n-\t\t#ABCDE\t#abcd\t#CDE\t#ABabcd\n-\n-\n-// Tricarboxylic Acid Cycle\n-\n-\tpdh\tPyr\t\tAcCoA\tCO2\n-\t\t#ABC\t\t#BC\t#A\n-\n-\tcitsynth\tAcCoA\tOAA\tICit\n-\t\t#AB\t#abcd\t#dcbaBA\n-\n-\tidh\tICit\t\tAKG\tCO2\n-\t\t#ABCDEF\t\t#ABCEF\t#D\n-\n-\takgdh\tAKG\t\tSuc\tCO2\n-\t\t#ABCDE\t\t#BCDE\t#A\n-\n-\tfum_a\tSuc\t\tMal\n-\t\t#ABCD\t\t#ABCD\n-\n-\tfum_b\tSuc\t\tMal\n-\t\t#ABCD\t\t#DCBA\n-\n-\tmaldh\tMal\t\tOAA\n-\t\t#ABCD\t\t#ABCD\n-\n-\n-// Glyoxylate Shunt\n-\n-//\tgs1\tICit\t\tGlyOx\tSuc\n-//\t\t#ABCDEF\t\t#AB\t#DCEF\n-\n-//\tgs2\tGlyOx\tAcCoA\tOAA\n-//\t\t#AB\t#ab\t#ABba\n-\n-\n-// Anaplerotic Reactions\n-\n-\tppc\tPEP\tCO2\tOAA\t\t\t// PEPcarboxylase\n-\t\t#ABC\t#a\t#ABCa\n-\n-\tmae\tMal\t\tPyr\tCO2\t\t// enzyme malique\n-\t\t#ABCD\t\t#ABC\t#D\n-\n-//\tpck\tOAA\t\tPEP\tCO2\t\t// PEP carboxykinase\n-//\t\t#ABCD\t\t#ABC\t#D\n-\n-\n-// Biosynthetic Pathways\n-\n-\t// Glucose-6-Phosphate Family\n-\n-\tbs_glc6P\tGlc6P\t\tBM_Glc6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\t// Fructose-6-Phosphate Family\n-\n-\tbs_fru6P\tFru6P\t\tBM_Fru6P\t\t// sortie de Fru6P pour biomasse\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\t// Phosphoglycerate Family\n-\n-\tbs_pga\tPGA\t\tBM_PGA\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga_aux\tBM_PGA\t\tPGA_Aux\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga1\tBM_PGA\t\tSer\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga1_aux\tSer\t\tSer_Aux\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga2\tSer\t\tCys\t\t\t// ce flux sert de sortie pour PGA hors formation de Gly\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga2_aux\tCys\t\tCys_Aux\t\t\t// ce flux sert de sortie pour PGA hors formation de Gly\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga3\tSer\t\tGly\tFTHF\t\t// formation de gly pour biomasse\n-\t\t#ABC\t\t#AB\t#C\t\t// ce flux est reversible\n-\n-\tbs_pga3_aux\tGly\t\tGly_Aux\t\t// pour conserver Gly comme metabolite intracellulaire\n-\t\t#AB\t\t#AB\n-\n-\t// TrioseP Family\n-\n-\tbs_DHAP\tGA3P\t\tGlp\t\t\t// formation glycerolP pour lipides\n-\t\t#ABC\t\t#ABC\n-\n-\t// Pyruvate Family\n-\n-\tbs_pyr\tPyr\t\tBM_Pyr\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr1\tBM_Pyr\t\tAla\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr1_aux\tAla\t\tAla_Aux\t\t// pour conserver Ala comme metabolite intracellulaire\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr2\tBM_Pyr\tBM_Pyr\tAKV\tCO2\t\t// AKV et Val ont le meme squelette C\n-\t\t#ABC\t#abc\t#ABbcC\t#a\t\t// cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val\n-\n-\tbs_pyr4\tAKV\t\tVal\t\t// permet de tenir compte de la sortie de Val\n-\t\t#ABCDE\t\t#ABCDE\n-\n-\tbs_pyr4_aux\tVal\t\tVal_Aux\t\t// permet de tenir compte de la sortie de Val\n-\t\t#ABCDE\t\t#ABCDE\n-\n-\tbs_pyr3\tAKV\tBM_AcCoA\tLeu\tCO2\n-\t\t#ABCDE\t#ab\t#abBCDE\t#A\n-\n-\tbs_pyr3_aux\tLeu\t\tLeu_Aux\t\t// pour conserver Leu comme metabolite intracellulaire\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\n"..b"p6_aux\tD\n-\t\tbs_pep7\tC\t0\n-\t\tbs_akg\tC\t0\t\t// sortie d'AKG\n-\t\tbs_akg1\tC\t0\n-\t\tbs_akg2\tD\n-\t\tbs_akg3\tD\n-\t\tbs_akg4\tC\t0\n-\t\tbs_akg4_aux\tD\n-\t\tbs_oaa\tC\t0\n-\t\tbs_oaa1\tC\t0\t\t// sortie d'OAA autres que Met\n-\t\tbs_oaa1_aux\tD\t\t// sortie d'OAA autres que Met\n-\t\tbs_oaa2\tC\t0\t\t// synthese de Met\n-\t\tbs_oaa2_aux\tD\t\t// sortie de Met\n-\t\tbs_oaa3a\tC\t0\n-\t\tbs_oaa3b\tC\t0\n-\t\tbs_oaa3_aux\tD\n-\t\tbs_oaa4\tD\n-\t\tbs_oaa5\tC\t0\n-\t\tbs_oaa5_aux\tD\n-\t\tbs_oaa6\tC\t0\n-\t\tbs_oaa6_aux\tD\n-\t\tbs_oaa7\tC\t0\n-\t\tbs_oaa7_aux\tD\n-\n-\t\t// Flux de sortie\n-\n-\t\tout_co2\tD\t\t\t// sortie de CO2\n-\t\tout_Ac\tD\t\t\t// sortie d'acetate\n-\t\tout_FTHF\tD\t\t// sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF\n-\n-\n-EQUALITIES\n-\tNET\n-\t\tVALUE\tFORMULA\n-\n-\t\t0\tfum_a-fum_b\t\t// scrambling reaction\n-\t\t0\tbs_oaa3a-bs_oaa3b\n-\t\t0\tbs_pep3a-bs_pep3b\n-\t\t0\tbs_pep4a-bs_pep4b\n-\n-\tXCH\n-\t\tVALUE\tFORMULA\n-\n-\t\t0\tfum_a-fum_b\n-\n-INEQUALITIES\n-\tNET\n-\t\tVALUE\tCOMP\tFORMULA\n-// Inequalities for Input and Output Fluxes are generated automatically\n-\t\t1\t<=\tpyk\n-\t\t0.0001\t<=\tedd\n-\t\t0.0001\t<=\tgnd\n-\t\t0.0001\t<=\tzwf\n-\t\t0.0001\t<=\tppc\n-\t\t0.0001\t<=\tmae\n-//\t\t2\t>=\tCO2upt // 2010-08-18 too high value makes jacobian rank deficient\n-\tXCH\n-\t\tVALUE\tCOMP\tFORMULA\n-// Inequalities for Input and Output Fluxes are generated automatically\n-\n-\n-FLUX_MEASUREMENTS\n-\tFLUX_NAME\tVALUE\tDEVIATION\t//\t\tVal\tDev\n-\tout_Ac\t0.213\t0.0001\n-\n-LABEL_INPUT\n-\tMETA_NAME\tISOTOPOMER\tVALUE\n-\n-\tGluc\t#111111\t0.2\n-\t\t#000000\t0.8\n-//\tCO2_ext\t#0\t0.989\n-//\t\t#1\t0.011\n-\n-//\tFTHF_0\t#0\t1\n-//\tFTHF_1\t#1\t1\n-\n-\n-LABEL_MEASUREMENTS\n-\tMETA_NAME\tCUM_GROUP\tVALUE\tDEVIATION\tCUM_CONSTRAINTS\n-\t\t\t\t\t\t\t\t\t\t\t// Example\n-\n-PEAK_MEASUREMENTS\n-\tMETA_NAME\tPEAK_NO\tVALUE_S\tVALUE_D-\tVALUE_D+\tVALUE_DD\tVALUE_T\tDEVIATION_S\tDEVIATION_D-\tDEVIATION_D+\tDEVIATION_DD/T\n-\n-\n-MASS_SPECTROMETRY\n-\tMETA_NAME\tFRAGMENT\tWEIGHT\tVALUE\tDEVIATION\n-\n-// Deviation fixee a 0.02\t\t\t\t// correction inoc 0.062\n-\n-\n-\n-\tSuc\t1,2,3,4\t1\t0.371605319\t0.01\n-\t\t\t2\t0.360829749\t0.01\n-\t\t\t3\t0.208425325\t0.01\n-\t\t\t4\t0.059139607\t0.01\n-//\tMal\t1,2,3,4\t0\t0.164619329483\t0.02\n-//\t\t\t1\t0.110072868518\t0.02\n-//\t\t\t2\t0.637801316225333\t0.02\n-//\t\t\t3\t0.0863461044204333\t0.02\n-//\t\t\t4\t0.00116038135315367\t0.02\n-\tICit\t1,2,3,4,5,6\t0\t0.131864539419667\t0.02\n-\t\t\t1\t0.225857638569\t0.02\n-\t\t\t2\t0.256421170949333\t0.02\n-\t\t\t3\t0.209230210478667\t0.02\n-\t\t\t4\t0.116863585449667\t0.02\n-\t\t\t5\t0.0457727744643333\t0.02\n-\t\t\t6\t0.0139900806697867\t0.02\n-\tPEP\t1,2,3\t0\t0.421359839367667\t0.01\n-\t\t\t1\t0.358998301162333\t0.01\n-\t\t\t2\t0.0348521859365667\t0.01\n-\t\t\t3\t0.184789673534\t0.01\n-\tPGA\t1,2,3\t0\t0.434335785072667\t0.01\n-\t\t\t1\t0.352829683224667\t0.01\n-\t\t\t2\t0.0323479804176\t0.01\n-\t\t\t3\t0.180486551285333\t0.01\n-\tFruBP\t1,2,3,4,5,6\t0\t0.0738121029259333\t0.01\n-\t\t\t1\t0.454450017158667\t0.01\n-\t\t\t2\t0.160823529969333\t0.01\n-\t\t\t3\t0.0944468077710667\t0.01\n-\t\t\t4\t0.105281338489667\t0.01\n-\t\t\t5\t0.0155016033633\t0.01\n-\t\t\t6\t0.0956846003217333\t0.01\n-\tGlc6P\t1,2,3,4,5,6\t0\t0.0160587173349\t0.01\n-\t\t\t1\t0.673510772480667\t0.01\n-\t\t\t2\t0.0930110047641\t0.01\n-\t\t\t3\t0.0280359937297\t0.01\n-\t\t\t4\t0.0397315614067667\t0.01\n-\t\t\t5\t0.0145524520950667\t0.01\n-\t\t\t6\t0.135099498189\t0.01\n-\tFru6P\t1,2,3,4,5,6\t0\t0.0235029951295\t0.01\n-\t\t\t1\t0.624253565357667\t0.01\n-\t\t\t2\t0.113068441282333\t0.01\n-\t\t\t3\t0.0456605631765\t0.01\n-\t\t\t4\t0.0516089447155667\t0.01\n-\t\t\t5\t0.0185881765378333\t0.01\n-\t\t\t6\t0.123317313800333\t0.01\n-\tRib5P\t1,2,3,4,5\t0\t0.341615670498667\t0.01\n-\t\t\t1\t0.25454117519\t0.01\n-\t\t\t2\t0.159027180368333\t0.01\n-\t\t\t3\t0.113789577528667\t0.01\n-\t\t\t4\t0.0615266612553333\t0.01\n-\t\t\t5\t0.0694997351590667\t0.01\n-\tGnt6P\t1,2,3,4,5,6\t0\t0.0249552273874\t0.01\n-\t\t\t1\t0.672556163913\t0.01\n-\t\t\t2\t0.0866890773125333\t0.01\n-\t\t\t3\t0.0313987199704333\t0.01\n-\t\t\t4\t0.0314691889898667\t0.01\n-\t\t\t5\t0.0138168327362333\t0.01\n-\t\t\t6\t0.139114789690333\t0.01\n-//\tEry4P\t1,2,3,4\t0\t0.178453461108\t0.01\n-//\t\t\t1\t0.412398433968333\t0.01\n-//\t\t\t2\t0.273694508221667\t0.01\n-//\t\t\t3\t0.116142498670667\t0.01\n-//\t\t\t4\t0.0193110980315\t0.01\n-\n-OPTIONS\n-\tOPT_NAME\tOPT_VALUE\n-\tMATLAB_FOR_FLUX_EQ_CONSTR_MATR\t1\n-\t//optctrl_history\t1 // nlsic\n-\t//optctrl_trace\t3 // BFGS\n-\t//optctrl_reltol\t1.e-10 // BFGS\n-\t//optctrl_maxit\t1000 // BFGS\n-\tposttreat_R\tplot_smeas.R\n-\n"
b
diff -r 4e3d4318113b -r 57f199aa07e4 test-data/e_coli_growth.ftbl
--- 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
b
b"@@ -1,822 +0,0 @@\n-PROJECT\n-\tNAME\tVERSION\tFORMAT\tDATE\tCOMMENT\n-\tNissle.ftbl\t1\t\t100910\tmodele E coli Nissle WT avec voies centrales completes et voies biomasse\n-\tNissle.ftbl\t2\t\t121025\tgrowth fluxes+pooled penthoses\n-\tNissle.ftbl\t3\t\t121123\tconcentration measurements\n-\n-NETWORK\n-\tFLUX_NAME\tEDUCT_1\tEDUCT_2\tPRODUCT_1\tPRODUCT_2\n-\n-// Glycolyse.\n-// PPP\n-// TCA\n-// voies anaplerotiques: pepc. enz malique\n-// voie glyoxylate\n-// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre)\n-// saisie differentielle des substrats marques\n-\n-\n-// Uptake substrats\n-\n-\tGlucupt_1\tGluc_1\t\tGlc\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tGlucupt_U\tGluc_U\t\tGlc\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tGlucupt\tGlc\t\tGlc6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tCO2upt\tCO2_ext\t\tCO2\t\t// entree de CO2 non marque\n-\t\t#A\t\t#A\t\t// ce flux est a laisser libre\n-\n-//\tFTHF0\tFTHF_0\t\tFTHF\t\t// prise en charge de FTHF non marque\n-//\t\t#A\t\t#A\n-\n-//\tFTHF1\tFTHF_1\t\tFTHF\t\t// prise en charge de FTHF marque\n-//\t\t#a\t\t#a\n-\n-\n-// Embden Meyerhof Parnas Pathway\n-\n-\tpgi\tGlc6P\t\tFru6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tpfk\tFru6P\t\tFruBP\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tald\tFruBP\t\tGA3P\tGA3P\n-\t\t#ABCDEF\t\t#CBA\t#DEF\n-\n-//\ttpi\tDHAP\t\tGA3P\n-//\t\t#ABC\t\t#CBA\n-\n-\tpgk\tGA3P\t\tPGA\n-\t\t#ABC\t\t#ABC\n-\n-\teno\tPGA\t\tPEP\n-\t\t#ABC\t\t#ABC\n-\n-\tpyk\tPEP\t\tPyr\n-\t\t#ABC\t\t#ABC\n-\n-\n-// Methylglyoxal Pathway\n-\n-//\tmgs\tDHAP\t\tPyr\n-//\t\t#ABC\t\t#ABC\n-\n-\n-// Pentose Phosphate Pathway\n-\n-\tzwf\tGlc6P\t\tGnt6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tgnd\tGnt6P\t\tCO2 \tRub5P\n-\t\t#ABCDEF\t\t#A\t#BCDEF\n-\n-\trib\tRub5P\t\tRib5P\n-\t\t#ABCDE\t\t#ABCDE\n-\n-\txul\tRub5P\t\tXul5P\n-\t\t#ABCDE\t\t#ABCDE\n-\n-\tedd\tGnt6P\t\tPyr\tGA3P\n-\t\t#ABCDEF\t\t#ABC\t#DEF\n-\n-//\tta\tGA3P\tSed7P\tEry4P\tFru6P\n-//\t\t#ABC\t#abcdefg\t#defg\t#abcABC\n-\n-//\ttk1\tRib5P\tRib5P\tGA3P\tSed7P\n-//\t\t#ABCDE\t#abcde\t#CDE\t#ABabcde\n-\n-//\ttk2\tRib5P\tEry4P\tGA3P\tFru6P\n-//\t\t#ABCDE\t#abcd\t#CDE\t#ABabcd\n-\n-\tHR1\tGA3P\tE2\tXul5P\n-\t\t#CDE\t#AB\t#ABCDE\n-\n-\tHR2\tFru6P\t\tEry4P\tE2\n-\t\t#ABCDEF\t\t#CDEF\t#AB\n-\n-\tHR3\tFru6P\t\tGA3P\tE3\n-\t\t#ABCDEF\t\t#DEF\t#ABC\n-\n-\tHR4\tSed7P\t\tRib5P\tE2\n-\t\t#abABCDE\t\t#ABCDE\t#ab\n-\n-\tHR5\tEry4P\tE3\tSed7P\n-\t\t#ABCD\t#abc\t#abcABCD\n-\n-\n-// Tricarboxylic Acid Cycle\n-\n-\tpdh\tPyr\t\tAcCoA\tCO2\n-\t\t#ABC\t\t#BC\t#A\n-\n-\tcitsynth\tAcCoA\tOAA\tCit\n-\t\t#AB\t#abcd\t#dcbaBA\n-\n-\tidh\tCit\t\tAKG\tCO2\n-\t\t#ABCDEF\t\t#ABCEF\t#D\n-\n-\takgdh\tAKG\t\tSuc\tCO2\n-\t\t#ABCDE\t\t#BCDE\t#A\n-\n-\tfum_a\tSuc\t\tMal\n-\t\t#ABCD\t\t#ABCD\n-\n-\tfum_b\tSuc\t\tMal\n-\t\t#ABCD\t\t#DCBA\n-\n-\tmaldh\tMal\t\tOAA\n-\t\t#ABCD\t\t#ABCD\n-\n-\n-// Glyoxylate Shunt\n-\n-//\tgs1\tCit\t\tGlyOx\tSuc\n-//\t\t#ABCDEF\t\t#AB\t#DCEF\n-\n-//\tgs2\tGlyOx\tAcCoA\tOAA\n-//\t\t#AB\t#ab\t#ABba\n-\n-\n-// Anaplerotic Reactions\n-\n-\tppc\tPEP\tCO2\tOAA\t\t\t// PEPcarboxylase\n-\t\t#ABC\t#a\t#ABCa\n-\n-//\tmae\tMal\t\tPyr\tCO2\t\t// enzyme malique\n-//\t\t#ABCD\t\t#ABC\t#D\n-\n-//\tpck\tOAA\t\tPEP\tCO2\t\t// PEP carboxykinase\n-//\t\t#ABCD\t\t#ABC\t#D\n-\n-\n-// Biosynthetic Pathways\n-\n-\t// Glucose-6-Phosphate Family\n-\n-\tbs_glc6P\tGlc6P\t\tBM_Glc6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\t// Fructose-6-Phosphate Family\n-\n-\tbs_fru6P\tFru6P\t\tBM_Fru6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\t// Phosphoglycerate Family\n-\n-\tbs_pga\tPGA\t\tBM_PGA\n-\t\t#ABC\t\t#ABC\n-\n-//\tbs_pga_aux\tBM_PGA\t\tPGA_Aux\n-//\t\t#ABC\t\t#ABC\n-\n-//\tbs_pga1\tBM_PGA\t\tSer\n-//\t\t#ABC\t\t#ABC\n-\n-//\tbs_pga1_aux\tSer\t\tSer_Aux\n-//\t\t#ABC\t\t#ABC\n-\n-//\tbs_pga2\tSer\t\tCys\n-//\t\t#ABC\t\t#ABC\n-\n-//\tbs_pga2_aux\tCys\t\tCys_Aux\n-//\t\t#ABC\t\t#ABC\n-\n-//\tbs_pga3\tSer\t\tGly\tFTHF\n-//\t\t#ABC\t\t#AB\t#C\n-\n-//\tbs_pga3_aux\tGly\t\tGly_Aux\n-//\t\t#AB\t\t#AB\n-\n-\t// TrioseP Family\n-\n-\tbs_DHAP\tGA3P\t\tGlp\n-\t\t#ABC\t\t#ABC\n-\n-\t// Pyruvate Family\n-\n-\tbs_pyr\tPyr\t\tBM_Pyr\n-\t\t#ABC\t\t#ABC\n-\n-//\tbs_pyr1\tBM_Pyr\t\tAla\n-//\t\t#ABC\t\t#ABC\n-\n-//\tbs_pyr1_aux\tAla\t\tAla_Aux\n-//\t\t#ABC\t\t#ABC\n-\n-//\tbs_pyr2\tBM_Pyr\tBM_Pyr\tAKV\tCO2\n-//\t\t#ABC\t#abc\t#ABbcC\t#a\n-\n-//\tbs_pyr4\tAKV\t\tVal\n-//\t\t#ABCDE\t\t#ABCDE\n-\n-//\tbs_pyr4_aux\tVal\t\tVal_Aux\n-//\t\t#ABCDE\t\t#ABCDE\n-\n-//\tbs_pyr3\tAKV\tBM_AcCoA\tLeu\tCO2\n-//\t\t#ABCDE\t#ab\t#abBCDE\t#A\n-\n-//\tbs_pyr3_aux\tLeu\t\tLeu_Aux\n-//\t\t#ABCDEF\t\t#ABCDEF\n-\n-\t// Erythrose-4-Phosphate Family\n-\n-\tbs_e4p\tEry4P\t\tBM_Ery4P\n-\t\t#ABCD\t\t#ABCD\n-\n-//\tbs_e4p_aux\tBM_Ery4P\t\tEry4P_aux\n-//\t\t#ABCD\t\t#ABCD\n-\n-\t// Ribose-5-Phosphate Family\n-\n-\tbs_rib5P\tRib5P\t\tBM_Rib5P\n-\t\t#ABCDE\t\t#ABCDE\n-\n-//\tbs_rib5P1\tBM_Rib5P\tFTHF\tHis\n-//\t\t#ABCDE\t#a\t#EDCBAa\n-\n-//\tbs_rib5P"..b'/10.7\t1.e-2\n-\tRub5P+Rib5P+Xul5P\t1.66034545348219*1.e-3/10.7\t1.e-2\n-\n-MASS_SPECTROMETRY\n-\tMETA_NAME\tFRAGMENT\tWEIGHT\tVALUE\tDEVIATION\n-\tMal\t1,2,3,4\t1\t0.587391867374382\t0.0493159626907812\n-\t\t\t2\t0.216493214407424\t0.0306546571894417\n-\t\t\t3\t0.159494782909672\t0.03\n-\t\t\t4\t0.0366201353085213\t0.03\n-\tPEP\t1,2,3\t0\t0.462166666666667\t0.01\n-\t\t\t1\t0.340003333333333\t0.01\n-\t\t\t2\t0.0273166666666667\t0.01\n-\t\t\t3\t0.170513333333333\t0.01\n-\tPGA\t1,2,3\t0\t0.447066666666667\t0.0180848260520618\n-\t\t\t1\t0.34127\t0.018075350619006\n-\t\t\t2\t0.02441\t0.01\n-\t\t\t3\t0.187253333333333\t0.01\n-\tGnt6P\t1,2,3,4,5,6\t0\t0.0195533333333333\t0.01\n-\t\t\t1\t0.72562\t0.0120547874307264\n-\t\t\t2\t0.0571233333333333\t0.01\n-\t\t\t3\t0.0135033333333333\t0.01\n-\t\t\t4\t0.01331\t0.01\n-\t\t\t5\t0.0131033333333333\t0.01\n-\t\t\t6\t0.157793333333333\t0.01\n-\tSed7P\t1,2,3,4,5,6,7\t0\t0.272433333333333\t0.0122309539012022\n-\t\t\t1\t0.23752\t0.01\n-\t\t\t2\t0.180446666666667\t0.01\n-\t\t\t3\t0.12744\t0.01\n-\t\t\t4\t0.06321\t0.01\n-\t\t\t5\t0.0839233333333333\t0.01\n-\t\t\t6\t0.01751\t0.01\n-\t\t\t7\t0.0175266666666667\t0.01\n-\tFruBP\t1,2,3,4,5,6\t0\t0.0853733333333333\t0.02\n-\t\t\t1\t0.482283333333333\t0.02\n-\t\t\t2\t0.140086666666667\t0.02\n-\t\t\t3\t0.0953466666666667\t0.02\n-\t\t\t4\t0.09712\t0.02\n-\t\t\t5\t0.0120166666666667\t0.02\n-\t\t\t6\t0.0877666666666667\t0.02\n-\tRib5P+Xul5P+Rub5P\t1,2,3,4,5\t0\t0.433956666666667\t0.0115292555411585\n-\t\t\t1\t0.215956666666667\t0.01\n-\t\t\t2\t0.09658\t0.01\n-\t\t\t3\t0.129033333333333\t0.01\n-\t\t\t4\t0.0272733333333333\t0.01\n-\t\t\t5\t0.0971933333333333\t0.01\n-\tGlc6P\t1,2,3,4,5,6\t0\t0.0167633333333333\t0.01\n-\t\t\t1\t0.716826666666667\t0.01\n-\t\t\t2\t0.0578233333333333\t0.01\n-\t\t\t3\t0.0122433333333333\t0.01\n-\t\t\t4\t0.01151\t0.01\n-\t\t\t5\t0.01089\t0.01\n-\t\t\t6\t0.173946666666667\t0.01\n-\tFru6P\t1,2,3,4,5,6\t0\t0.04716\t0.01\n-\t\t\t1\t0.623343333333333\t0.0106878170518274\n-\t\t\t2\t0.0820266666666667\t0.01\n-\t\t\t3\t0.03604\t0.01\n-\t\t\t4\t0.0315766666666667\t0.01\n-\t\t\t5\t0.0149133333333333\t0.01\n-\t\t\t6\t0.164943333333333\t0.0111688555068697\n-\n-\tCit\t1,2,3,4,5,6\t1\t0.322208057034832\t0.03\n-\t\t\t2\t0.288291305558056\t0.03\n-\t\t\t3\t0.212855540659154\t0.03\n-\t\t\t4\t0.117626468347467\t0.03\n-\t\t\t5\t0.0484839619377435\t0.03\n-\t\t\t6\t0.0105346664627478\t0.03\n-\n-OPTIONS\n-\tOPT_NAME\tOPT_VALUE\n-\tMATLAB_FOR_FLUX_EQ_CONSTR_MATR\t1\n-\tinclude_growth_flux\t1\n-\tmu\t0.8\n-\toptctrl_maxit\t50\n-\tcommandArgs\t--TIMEIT\n-\t//optctrl_btdesc\t0.1\n-\tposttreat_R\tplot_smeas.R\n-METABOLITE_POOLS\n-\tMETA_NAME\tMETA_SIZE\t// size is in units of metab_scale option defined before\n-\t// source: p.millard 2010/12/03 Nissle_Glc_conc.xlsx sent by email\n-\t//Fum\t-2.47158569399681*1.e-3/10.7\n-\tSuc\t-15.8893144279264*1.e-3/10.7\n-\tMal\t-6.47828321758155*1.e-3/10.7\n-\tPEP\t-0.588638938013844*1.e-3/10.7\n-\t//Aco\t-0.871035781090548*1.e-3/10.7\n-\tPGA\t-5.35922289028553*1.e-3/10.7\n-\tCit\t-17.4452511107891*1.e-3/10.7\n-\t//1-3diPG\t-7.31670971749174*1.e-3/10.7\n-\tGnt6P\t-1.54945619497337*1.e-3/10.7\n-\t//Sed7P\t-11.5512490274248*1.e-3/10.7 conc\n-\t//PRPP\t-2.74943425027474*1.e-3/10.7\n-\t//CMP\t-0.433742769835568*1.e-3/10.7\n-\t//UMP\t-4.69421895911195*1.e-3/10.7\n-\t//cAMP\t-0.109838817225867*1.e-3/10.7\n-\tFruBP\t-5.27278870110121*1.e-3/10.7\n-\t//AMP\t-0.801372321192278*1.e-3/10.7\n-\t//GMP\t-0.394103922207334*1.e-3/10.7\n-\t//dCDP\t-4.41071909173208*1.e-3/10.7\n-\t//CDP\t-0.204009683016196*1.e-3/10.7\n-\t//UDP\t-0.528949008341637*1.e-3/10.7\n-\t//ADP\t-2.0246124170601*1.e-3/10.7\n-\t//GDP\t-1.02724694822302*1.e-3/10.7\n-\t//CTP\t-1.39055711133101*1.e-3/10.7\n-\t//UTP\t-1.73433655893259*1.e-3/10.7\n-\t//ATP\t-6.32820169657847*1.e-3/10.7\n-\t//UDP-Glc\t-9.93608536663137*1.e-3/10.7 conc\n-\t//ADP-Glc\t-0*1.e-3/10.7\n-\t//GDP-Man\t-5.52555199979534*1.e-3/10.7\n-\t//G1P\t-72.1756241692542*1.e-3/10.7 conc\n-\t//F1P\t-0.0942291270750201*1.e-3/10.7\n-\tFru6P\t-1.07071770798187*1.e-3/10.7\n-\tGlc6P\t-5.24845556085526*1.e-3/10.7\n-\t//M6P\t-0.642830603277483*1.e-3/10.7\n-\t//Rib1P\t-0.0558080128279041*1.e-3/10.7\n-\tRub5P\t-1.66034545348219/3*1.e-3/10.7\n-//\tRib5P\t-1.66034545348219/3*1.e-3/10.7\n-\tRib5P\t1.e-7\t// fixed arbitrary low\n-\tXul5P\t-4*1.66034545348219/3*1.e-3/10.7\n-\t//dADP\t-5.86959266616353*1.e-3/10.7 conc\n-\t//dATP\t-13.1542008577561*1.e-3/10.7 conc\n-\t//dTDP\t-9.52423600696743*1.e-3/10.7 conc\n-\t//dTTP\t-19.9757914243397*1.e-3/10.7 conc\n'
b
diff -r 4e3d4318113b -r 57f199aa07e4 test-data/e_coli_growth.log
--- 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
b
@@ -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
b
diff -r 4e3d4318113b -r 57f199aa07e4 test-data/e_coli_i.ftbl
--- 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
b
b"@@ -1,789 +0,0 @@\n-PROJECT\n-\tNAME\tVERSION\tFORMAT\tDATE\tCOMMENT\n-\tK12_MG1655.ftbl\t1\t\t101109\tmodele E coli K12 MG1655 WT avec voies centrales completes et voies biomasse simplifiees\n-\n-NETWORK\n-\tFLUX_NAME\tEDUCT_1\tEDUCT_2\tPRODUCT_1\tPRODUCT_2\n-\n-// Glycolyse.\n-// PPP\n-// TCA\n-// voies anaplerotiques: pepc. enz malique\n-// voie glyoxylate\n-// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre)\n-// saisie differentielle des substrats marques\n-\n-\n-// Uptake substrats\n-\n-\tGlucupt_1\tGluc_1\t\tGlc6P\t\t// fehlt bei wolfgang\n-\t\t#ABCDEF\t\t#ABCDEF\t\t// fehlt bei wolfgang\n-\n-\tGlucupt_U\tGluc_U\t\tGlc6P\t\t// fehlt bei wolfgang\n-\t\t#ABCDEF\t\t#ABCDEF\t\t// fehlt bei wolfgang\n-\n-//\tCO2upt\tCO2_ext\t\tCO2\t\t// entree de CO2 non marque\n-//\t\t#A\t\t#A\t\t// ce flux est a laisser libre\n-\n-//\tFTHF0\tFTHF_0\t\tFTHF\t\t// prise en charge de FTHF non marque\n-//\t\t#A\t\t#A\n-\n-//\tFTHF1\tFTHF_1\t\tFTHF\t\t// prise en charge de FTHF marque\n-//\t\t#a\t\t#a\n-\n-\n-// Embden Meyerhof Parnas Pathway\n-\n-\tpgi\tGlc6P\t\tFru6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tpfk\tFru6P\t\tFruBP\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tald\tFruBP\t\tGA3P\tGA3P\n-\t\t#ABCDEF\t\t#CBA\t#DEF\n-\n-//\ttpi\tDHAP\t\tGA3P\n-//\t\t#ABC\t\t#CBA\n-\n-\tpgk\tGA3P\t\tPGA\n-\t\t#ABC\t\t#ABC\n-\n-\teno\tPGA\t\tPEP\n-\t\t#ABC\t\t#ABC\n-\n-\tpyk\tPEP\t\tPyr\n-\t\t#ABC\t\t#ABC\n-\n-\n-// Methylglyoxal Pathway\n-\n-//\tmgs\tDHAP\t\tPyr\n-//\t\t#ABC\t\t#ABC\n-\n-\n-// Pentose Phosphate Pathway\n-\n-\tzwf\tGlc6P\t\tGnt6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\tgnd\tGnt6P\t\tCO2\tRib5P\n-\t\t#ABCDEF\t\t#A\t#BCDEF\n-\n-\tedd\tGnt6P\t\tPyr\tGA3P\n-\t\t#ABCDEF\t\t#ABC\t#DEF\n-\n-//\tta\tEry4P\tFru6P\tGA3P\tSed7P\n-//\t\t#ABCD\t#abcdef\t#def\t#abcABCD\n-\n-//\ttk1\tGA3P\tSed7P\tRib5P\tRib5P\n-//\t\t#ABC\t#abcdefg\t#abABC\t#cdefg\n-\n-//\ttk2\tGA3P\tFru6P\tRib5P\tEry4P\n-//\t\t#ABC\t#abcdef\t#abABC\t#cdef\n-\n-\tta\tGA3P\tSed7P\tEry4P\tFru6P\n-\t\t#ABC\t#abcdefg\t#defg\t#abcABC\n-\n-\ttk1\tRib5P\tRib5P\tGA3P\tSed7P\n-\t\t#ABCDE\t#abcde\t#CDE\t#ABabcde\n-\n-\ttk2\tRib5P\tEry4P\tGA3P\tFru6P\n-\t\t#ABCDE\t#abcd\t#CDE\t#ABabcd\n-\n-\n-// Tricarboxylic Acid Cycle\n-\n-\tpdh\tPyr\t\tAcCoA\tCO2\n-\t\t#ABC\t\t#BC\t#A\n-\n-\tcitsynth\tAcCoA\tOAA\tICit\n-\t\t#AB\t#abcd\t#dcbaBA\n-\n-\tidh\tICit\t\tAKG\tCO2\n-\t\t#ABCDEF\t\t#ABCEF\t#D\n-\n-\takgdh\tAKG\t\tSuc\tCO2\n-\t\t#ABCDE\t\t#BCDE\t#A\n-\n-\tfum_a\tSuc\t\tMal\n-\t\t#ABCD\t\t#ABCD\n-\n-\tfum_b\tSuc\t\tMal\n-\t\t#ABCD\t\t#DCBA\n-\n-\tmaldh\tMal\t\tOAA\n-\t\t#ABCD\t\t#ABCD\n-\n-\n-// Glyoxylate Shunt\n-\n-//\tgs1\tICit\t\tGlyOx\tSuc\n-//\t\t#ABCDEF\t\t#AB\t#DCEF\n-\n-//\tgs2\tGlyOx\tAcCoA\tOAA\n-//\t\t#AB\t#ab\t#ABba\n-\n-\n-// Anaplerotic Reactions\n-\n-\tppc\tPEP\tCO2\tOAA\t\t\t// PEPcarboxylase\n-\t\t#ABC\t#a\t#ABCa\n-\n-\tmae\tMal\t\tPyr\tCO2\t\t// enzyme malique\n-\t\t#ABCD\t\t#ABC\t#D\n-\n-//\tpck\tOAA\t\tPEP\tCO2\t\t// PEP carboxykinase\n-//\t\t#ABCD\t\t#ABC\t#D\n-\n-\n-// Biosynthetic Pathways\n-\n-\t// Glucose-6-Phosphate Family\n-\n-\tbs_glc6P\tGlc6P\t\tBM_Glc6P\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\t// Fructose-6-Phosphate Family\n-\n-\tbs_fru6P\tFru6P\t\tBM_Fru6P\t\t// sortie de Fru6P pour biomasse\n-\t\t#ABCDEF\t\t#ABCDEF\n-\n-\t// Phosphoglycerate Family\n-\n-\tbs_pga\tPGA\t\tBM_PGA\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga_aux\tBM_PGA\t\tPGA_Aux\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga1\tBM_PGA\t\tSer\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga1_aux\tSer\t\tSer_Aux\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga2\tSer\t\tCys\t\t\t// ce flux sert de sortie pour PGA hors formation de Gly\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga2_aux\tCys\t\tCys_Aux\t\t\t// ce flux sert de sortie pour PGA hors formation de Gly\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pga3\tSer\t\tGly\tFTHF\t\t// formation de gly pour biomasse\n-\t\t#ABC\t\t#AB\t#C\t\t// ce flux est reversible\n-\n-\tbs_pga3_aux\tGly\t\tGly_Aux\t\t// pour conserver Gly comme metabolite intracellulaire\n-\t\t#AB\t\t#AB\n-\n-\t// TrioseP Family\n-\n-\tbs_DHAP\tGA3P\t\tGlp\t\t\t// formation glycerolP pour lipides\n-\t\t#ABC\t\t#ABC\n-\n-\t// Pyruvate Family\n-\n-\tbs_pyr\tPyr\t\tBM_Pyr\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr1\tBM_Pyr\t\tAla\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr1_aux\tAla\t\tAla_Aux\t\t// pour conserver Ala comme metabolite intracellulaire\n-\t\t#ABC\t\t#ABC\n-\n-\tbs_pyr2\tBM_Pyr\tBM_Pyr\tAKV\tCO2\t\t// AKV et Val ont le meme squelette C\n-\t\t#ABC\t#abc\t#ABbcC\t#a\t\t// cette reaction permet d'utiliser eventuellement les donnees obtenues sur Val\n-\n-\tbs_pyr4\tAKV\t\tVal\t\t// permet de tenir compte de la sortie de Val\n-\t\t#ABCDE\t\t#ABCDE\n-\n-\tbs_pyr4_aux\tVal\t\tVal_Aux\t\t// permet de tenir compte de la sortie de Val\n-\t\t#ABCDE\t\t#ABCDE\n-\n-\tbs_pyr3\tAKV\tBM_AcC"..b'matically\n-\t\t1\t<=\tpyk\n-\t\t0.0001\t<=\tedd\n-\t\t0.0001\t<=\tgnd\n-\t\t0.0001\t<=\tzwf\n-\t\t0.0001\t<=\tppc\n-\t\t0.0001\t<=\tmae\n-//\t\t2\t>=\tCO2upt // 2010-08-18 too high value makes jacobian rank deficient\n-\tXCH\n-\t\tVALUE\tCOMP\tFORMULA\n-// Inequalities for Input and Output Fluxes are generated automatically\n-\tMETAB\n-\t\tVALUE\tCOMP\tFORMULA\n-//\t\t1.2\t>=\tAKG\n-\n-\n-FLUX_MEASUREMENTS\n-\tFLUX_NAME\tVALUE\tDEVIATION\t//\t\tVal\tDev\n-\tout_Ac\t0.213\t0.0001\n-\n-LABEL_INPUT\n-\tMETA_NAME\tISOTOPOMER\tVALUE\n-\n-\tGluc_U\t#111111\t1\n-\t\t#000000\t0.\n-\tGluc_1\t#100000\t1.\n-\t\t#000000\t0.\n-//\tCO2_ext\t#0\t0.989\n-//\t\t#1\t0.011\n-\n-//\tFTHF_0\t#0\t1\n-//\tFTHF_1\t#1\t1\n-\n-\n-LABEL_MEASUREMENTS\n-\tMETA_NAME\tCUM_GROUP\tVALUE\tDEVIATION\tCUM_CONSTRAINTS\n-\t\t\t\t\t\t\t\t\t\t\t// Example\n-\n-PEAK_MEASUREMENTS\n-\tMETA_NAME\tPEAK_NO\tVALUE_S\tVALUE_D-\tVALUE_D+\tVALUE_DD\tVALUE_T\tDEVIATION_S\tDEVIATION_D-\tDEVIATION_D+\tDEVIATION_DD/T\n-\n-\n-MASS_SPECTROMETRY\n-\tMETA_NAME\tFRAGMENT\tWEIGHT\tVALUE\tDEVIATION\n-\n-// Deviation fixee a 0.02\t\t\t\t// correction inoc 0.062\n-\n-\n-\n-\tSuc\t1,2,3,4\t1\t0.371605319\t0.01\n-\t\t\t2\t0.360829749\t0.01\n-\t\t\t3\t0.208425325\t0.01\n-\t\t\t4\t0.059139607\t0.01\n-//\tMal\t1,2,3,4\t0\t0.164619329483\t0.02\n-//\t\t\t1\t0.110072868518\t0.02\n-//\t\t\t2\t0.637801316225333\t0.02\n-//\t\t\t3\t0.0863461044204333\t0.02\n-//\t\t\t4\t0.00116038135315367\t0.02\n-\tICit\t1,2,3,4,5,6\t0\t0.131864539419667\t0.02\n-\t\t\t1\t0.225857638569\t0.02\n-\t\t\t2\t0.256421170949333\t0.02\n-\t\t\t3\t0.209230210478667\t0.02\n-\t\t\t4\t0.116863585449667\t0.02\n-\t\t\t5\t0.0457727744643333\t0.02\n-\t\t\t6\t0.0139900806697867\t0.02\n-\tPEP\t1,2,3\t0\t0.421359839367667\t0.01\n-\t\t\t1\t0.358998301162333\t0.01\n-\t\t\t2\t0.0348521859365667\t0.01\n-\t\t\t3\t0.184789673534\t0.01\n-\tPGA\t1,2,3\t0\t0.434335785072667\t0.01\n-\t\t\t1\t0.352829683224667\t0.01\n-\t\t\t2\t0.0323479804176\t0.01\n-\t\t\t3\t0.180486551285333\t0.01\n-\tFruBP\t1,2,3,4,5,6\t0\t0.0738121029259333\t0.01\n-\t\t\t1\t0.454450017158667\t0.01\n-\t\t\t2\t0.160823529969333\t0.01\n-\t\t\t3\t0.0944468077710667\t0.01\n-\t\t\t4\t0.105281338489667\t0.01\n-\t\t\t5\t0.0155016033633\t0.01\n-\t\t\t6\t0.0956846003217333\t0.01\n-\tGlc6P\t1,2,3,4,5,6\t0\t0.0160587173349\t0.01\n-\t\t\t1\t0.673510772480667\t0.01\n-\t\t\t2\t0.0930110047641\t0.01\n-\t\t\t3\t0.0280359937297\t0.01\n-\t\t\t4\t0.0397315614067667\t0.01\n-\t\t\t5\t0.0145524520950667\t0.01\n-\t\t\t6\t0.135099498189\t0.01\n-\tFru6P\t1,2,3,4,5,6\t0\t0.0235029951295\t0.01\n-\t\t\t1\t0.624253565357667\t0.01\n-\t\t\t2\t0.113068441282333\t0.01\n-\t\t\t3\t0.0456605631765\t0.01\n-\t\t\t4\t0.0516089447155667\t0.01\n-\t\t\t5\t0.0185881765378333\t0.01\n-\t\t\t6\t0.123317313800333\t0.01\n-\tRib5P\t1,2,3,4,5\t0\t0.341615670498667\t0.01\n-\t\t\t1\t0.25454117519\t0.01\n-\t\t\t2\t0.159027180368333\t0.01\n-\t\t\t3\t0.113789577528667\t0.01\n-\t\t\t4\t0.0615266612553333\t0.01\n-\t\t\t5\t0.0694997351590667\t0.01\n-\tGnt6P\t1,2,3,4,5,6\t0\t0.0249552273874\t0.01\n-\t\t\t1\t0.672556163913\t0.01\n-\t\t\t2\t0.0866890773125333\t0.01\n-\t\t\t3\t0.0313987199704333\t0.01\n-\t\t\t4\t0.0314691889898667\t0.01\n-\t\t\t5\t0.0138168327362333\t0.01\n-\t\t\t6\t0.139114789690333\t0.01\n-//\tEry4P\t1,2,3,4\t0\t0.178453461108\t0.01\n-//\t\t\t1\t0.412398433968333\t0.01\n-//\t\t\t2\t0.273694508221667\t0.01\n-//\t\t\t3\t0.116142498670667\t0.01\n-//\t\t\t4\t0.0193110980315\t0.01\n-METABOLITE_POOLS\n-\tMETA_NAME\tMETA_SIZE\n-\tAKG\t-1\n-\tAKV\t1\n-\tAcCoA\t1\n-\tAla\t1\n-\tArg\t1\n-\tAsn\t1\n-\tAsp\t1\n-\tBM_AKG\t1\n-\tBM_AcCoA\t1\n-\tBM_Ery4P\t1\n-\tBM_OAA\t1\n-\tBM_PEP\t1\n-\tBM_PGA\t1\n-\tBM_Pyr\t1\n-\tBM_Rib5P\t1\n-\tCO2\t1\n-\tChor\t1\n-\tCys\t1\n-\tDAHP\t1\n-\tEry4P\t-1\n-\tFTHF\t1\n-\tFru6P\t-1\n-\tFruBP\t-1\n-\tGA3P\t-1\n-\tGlc6P\t1\n-\tGlu\t1\n-\tGly\t1\n-\tGnt6P\t-1\n-\tHis\t1\n-\tICit\t-1\n-\tIle\t1\n-\tLeu\t1\n-\tLys\t1\n-\tMal\t1\n-\tMet\t1\n-\tOAA\t-1\n-\tPEP\t-1\n-\tPGA\t-1\n-\tPhe\t1\n-\tPyr\t-1\n-\tPyrCO2\t1\n-\tRib5P\t-1\n-\tSed7P\t-1\n-\tSer\t1\n-\tSuc\t-1\n-\tThr\t1\n-\tTrp\t1\n-\tTyr\t1\n-\tVal\t1\n-METAB_MEASUREMENTS\n-\tMETA_NAME\tVALUE\tDEVIATION\n-\tFru6P\t0.4263681348074568\t0.01\n-\tGA3P\t0.469998855791378\t0.01\n-\tFruBP\t1.860001398406723\t0.01\n-\tPEP\t0.1099999780931608\t0.01\n-\tRib5P\t0.01933825682263468\t0.01\n-\tSed7P\t0.05727159999541005\t0.01\n-\n-OPTIONS\n-\tOPT_NAME\tOPT_VALUE\n-\tdt\t1\n-\tnsubdiv_dt\t4\n-\t//tmax\t10\n-\tfile_labcin\te_coli_msen.txt\n-\tcommandArgs\t--noscale --TIMEIT --time_order=2 --zc=0 --clowp 1.e-9\n-\toptctrl_errx\t1.e-3\n-\toptctrl_maxit\t50\n-\toptctrl_btmaxit\t16\n-\toptctrl_btstart\t1\n-\toptctrl_btfrac\t0.5\n-\t//optctrl_history\t1\n-\toptctrl_adaptbt\t1\n-\toptctrl_monotone\t1\n-\tposttreat_R\tplot_imass.R\n'
b
diff -r 4e3d4318113b -r 57f199aa07e4 test-data/e_coli_i.log
--- 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
b
@@ -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
b
diff -r 4e3d4318113b -r 57f199aa07e4 test-data/e_coli_msen.txt
--- 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
b
b'@@ -1,62 +0,0 @@\n-# simulated measurement with noise (e_coli_mse.txt+noise with sd from e_coli_ie.ftbl)\n-row_col\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10 # see if ignored\n-m:Rib5P:1,2,3,4,5:0:693\t0.8301287113482\t0.705273440788489\t0.630962344759146\t0.599912176047555\t0.573404157056382\t0.549013957980969\t0.544210331911793\t0.508277982602693\t0.499016033193777\t0.485286541644114\n-m:Rib5P:1,2,3,4,5:1:694\t0.139499223890491\t0.222339755290909\t0.243819119211992\t0.251856352480698\t0.277951849850555\t0.26624702204022\t0.253318961326116\t0.242251579900221\t0.257243898371434\t0.245894214016595\n-m:Rib5P:1,2,3,4,5:2:695\t0.0290070095454754\t0.0533324485991101\t0.0672401633923346\t0.0862872836178193\t0.0903657887685621\t0.111438208430907\t0.106264456513264\t0.127665879867143\t0.129695750051211\t0.143194872657798\n-m:Rib5P:1,2,3,4,5:3:696\t0.00160408414038381\t0.0229950078431453\t0.0242885112480173\t0.0236262011871506\t0.0384713977458625\t0.0395862886561061\t0.0399422126310299\t0.0434575340902056\t0.057575220004768\t0.053327058437221\n-m:Rib5P:1,2,3,4,5:4:697\t0.00284213879991028\t0.00136220262120975\t0.00945113487347922\t0.0262298815476012\t0.0339069314888829\t0.045111483933521\t0.0308238334730582\t0.0483697721397453\t0.0489364990171572\t0.056352033597862\n-m:Rib5P:1,2,3,4,5:5:698\t0.00381673478018765\t0.0136152393183676\t0.0187948292708048\t0.029237436783619\t0.0340531521955641\t0.0266101321627734\t0.0399368276378717\t0.046845505348588\t0.0373560862314168\t0.0462793762301527\n-\n-m:Glc6P:1,2,3,4,5,6:0:679\t0.493952162617383\t0.241788346718873\t0.129931016363475\t0.0728422136538586\t0.0555639355367493\t0.0401826943349669\t0.0314283807166068\t0.0372888457858936\t0.0241841875922507\t0.030958811289491\n-m:Glc6P:1,2,3,4,5,6:1:680\t0.404262494562378\t0.601528892652349\t0.673997202888538\t0.700284514239992\t0.714448890273421\t0.702861007777799\t0.685523754578573\t0.704662941393205\t0.68684504474593\t0.682856315908778\n-m:Glc6P:1,2,3,4,5,6:2:681\t-0.00971071210181876\t0.00551823887717201\t0.00739665415406503\t0.0281297328224873\t0.0374856512913617\t0.0452870902703815\t0.0460785142653824\t0.0814776167048646\t0.0659155729271299\t0.0785432369222522\n-m:Glc6P:1,2,3,4,5,6:3:682\t0.0174215229553926\t0.0170559578191188\t0.025304157357846\t0.0430017639175836\t0.0348874311624526\t0.0489484715084225\t0.0351411534788991\t0.0269856593772156\t0.0192927092252581\t0.0385779418075484\n-m:Glc6P:1,2,3,4,5,6:4:683\t0.0043659263104226\t0.00877723557364165\t0.00725821330054203\t0.0126022050427868\t0.0289095437215765\t0.0282667499900472\t0.0428080102047586\t0.02592897485848\t0.0333262720524978\t0.0333836437820453\n-m:Glc6P:1,2,3,4,5,6:5:684\t-0.00295242877114927\t0.0228561008765114\t0.00107949443140708\t0.00576924101393923\t0.00359462341126682\t-0.00291644895745689\t-0.000650092439870991\t-0.00722996134202132\t-0.0148852807485112\t0.00354062643070811\n-m:Glc6P:1,2,3,4,5,6:6:685\t0.0949417468382319\t0.129448731101592\t0.11756999828035\t0.116834010941517\t0.156652332757322\t0.142614492470288\t0.136775707360364\t0.142247844825291\t0.128888546346649\t0.132781514945108\n-\n-m:ICit:1,2,3,4,5,6:0:657\t0.964808884433423\t1.00382002410753\t0.976023042393462\t0.894194434705964\t0.766995156890106\t0.690445464992781\t0.63176893227039\t0.528124368350999\t0.442923129524696\t0.395459161361152\n-m:ICit:1,2,3,4,5,6:1:658\t0.0143600676195567\t0.0436548728034513\t0.0534942728405111\t0.0639987878375545\t0.134065776629187\t0.146919412024849\t0.227799495903936\t0.272494318035825\t0.294024445522389\t0.247190260186848\n-m:ICit:1,2,3,4,5,6:2:659\t0.0166297755006583\t-0.0125797291227997\t0.0127788142463291\t0.0221526869422438\t0.0870629846959751\t0.124622112755198\t0.0805533586113773\t0.124589240328517\t0.174587994783957\t0.20637931969854\n-m:ICit:1,2,3,4,5,6:3:660\t-0.0164071602748031\t-0.021607873341015\t0.0405857166794395\t0.0067533469595018\t0.00856287955464007\t0.032691842098317\t0.03648172445535\t0.0897097881203855\t0.0377806396555514\t0.108435276435524\n-m:ICit:1,2,3,4,5,6:4:661\t-0.0311946635661311\t0.0112912100867262\t-0.00328434976694734\t-0.0291273953557248\t0.00347615542802288\t0.0135048730050441\t0.0071339543400162\t0.004515912946923\t0.00749482343750274\t0.0493479770558265\n-m:ICit:1,2'..b'-0.00484695474256728\t0.0153408517532834\t0.0041592776106311\t-0.00430377880030445\t-0.00244362524377602\t0.0109534229782509\t0.0137604488833386\t0.00586316823546521\n-m:PGA:1,2,3:0:668\t0.971624233727786\t0.88105488804591\t0.813066699228851\t0.740599622946611\t0.655913445307991\t0.631749494323584\t0.576140697543343\t0.557971599084521\t0.51860388489637\t0.51803381029278\n-m:PGA:1,2,3:1:669\t0.00220541233021583\t0.0757210734343468\t0.12052269067551\t0.162191306191376\t0.223937545869529\t0.241442753352368\t0.258583425386211\t0.30259748123379\t0.315427978552718\t0.321801842964539\n-m:PGA:1,2,3:2:670\t-0.00600635453904946\t0.0103004820964093\t0.000507682594582335\t-0.012889899397529\t0.0102382227596737\t0.00870989588467711\t0.0150594342872339\t0.0101818907371649\t0.0215484107926831\t0.0184451709580988\n-m:PGA:1,2,3:3:671\t0.0222666463570966\t0.0396053154740378\t0.0652581947362937\t0.108004619157695\t0.110623893009565\t0.138973931054194\t0.131470119271174\t0.137869954971786\t0.136658102046298\t0.135855362678781\n-\n-m:FruBP:1,2,3,4,5,6:0:672\t0.915100660678142\t0.710538255628495\t0.539707264234807\t0.410485596290365\t0.316133497140404\t0.260353766957447\t0.203404008159282\t0.182459522045085\t0.164876978870191\t0.148857194981653\n-m:FruBP:1,2,3,4,5,6:1:673\t0.0678013467712298\t0.226304674965867\t0.336541856973518\t0.416051058082716\t0.464564802241236\t0.485336774391881\t0.490207230868459\t0.513759561323935\t0.497418644493142\t0.480282911481621\n-m:FruBP:1,2,3,4,5,6:2:674\t-0.00198367254664417\t0.0125753789563416\t0.00042629691833386\t0.0251359606878703\t0.0458213984942464\t0.0537112170700128\t0.0582455692688059\t0.0732956046933924\t0.0761912369338422\t0.0857605693669639\n-m:FruBP:1,2,3,4,5,6:3:675\t-0.000392113325137966\t0.0132767242245432\t0.0467756022636571\t0.0803441546018749\t0.0732686847392194\t0.100607368009337\t0.100554195366947\t0.0912022225582722\t0.102199914711651\t0.0936825194012971\n-m:FruBP:1,2,3,4,5,6:4:676\t-0.0120394479858482\t-0.00593961237618397\t-0.000971488795492516\t0.00796387425034388\t0.00873461737604841\t0.0545832171869149\t0.0565000883937298\t0.0405511217315538\t0.0519562886079823\t0.0725381260214016\n-m:FruBP:1,2,3,4,5,6:5:677\t-0.00525294722682946\t0.00537247522397268\t-0.00380859480830061\t0.00270832479079256\t-0.00087264218392774\t0.00494152714714406\t0.00135371023071657\t0.00927633370606465\t0.00936073842733687\t0.00788049093123055\n-m:FruBP:1,2,3,4,5,6:6:678\t0.00402818220901069\t0.035673399588083\t0.0542952441027104\t0.0750899278339439\t0.0689359253522637\t0.0907137663313326\t0.0662239468820011\t0.0837284613547794\t0.0741911443336369\t0.0691637252843734\n-\n-m:Fru6P:1,2,3,4,5,6:0:686\t0.543315183156242\t0.271442215154307\t0.15342041555599\t0.104226528529691\t0.0601207158756622\t0.0667835627698116\t0.032169592051183\t0.0444987186974436\t0.0312424656505585\t0.0371738310019649\n-m:Fru6P:1,2,3,4,5,6:1:687\t0.381498556157925\t0.566820512279315\t0.64753590777845\t0.669325655114947\t0.672155048267478\t0.658521355463491\t0.672620087099418\t0.658937533256872\t0.65065211800828\t0.629670055679612\n-m:Fru6P:1,2,3,4,5,6:2:688\t-0.0102984598677217\t0.00689221621662103\t0.0339321967612094\t0.0465421546157055\t0.0571543647969092\t0.0732789089821859\t0.0959460289039786\t0.0715783489999898\t0.0926230588187283\t0.0957791120020438\n-m:Fru6P:1,2,3,4,5,6:3:689\t0.0250657939547482\t0.023460916637709\t0.0473358002097497\t0.0321217800543612\t0.0458500181495104\t0.0259668014922916\t0.0305191527374548\t0.0469266856851943\t0.0580452840754031\t0.0385375322919084\n-m:Fru6P:1,2,3,4,5,6:4:690\t-0.00136306896214337\t0.0137397725510333\t0.0170177475023465\t0.0417372012671271\t0.0258510180458119\t0.0385973494576826\t0.0622003922899037\t0.0620209065758034\t0.0670552727027324\t0.0510832683047673\n-m:Fru6P:1,2,3,4,5,6:5:691\t0.0126114174874434\t0.0168366636261353\t0.00613625694852706\t0.00646155542199223\t0.00416011463957945\t-0.0185323336578468\t0.00502015745762575\t0.0152813542807671\t0.00415755701611636\t0.0088205581757464\n-m:Fru6P:1,2,3,4,5,6:6:692\t0.0772794502106592\t0.105015237675548\t0.105838420467053\t0.117576197845624\t0.106974963083314\t0.126498375256686\t0.113727482281553\t0.12301912138022\t0.114583839516509\t0.122447416359013\n'