Mercurial > repos > ggricourt > rp_fba_analysis
changeset 1:9142d12aa3a9 draft
"planemo upload for repository https://github.com/brsynth/rpFbaAnalysis commit ee9dd570c679d19cb4cdd54cc7414f64ca4cd07d"
| author | ggricourt |
|---|---|
| date | Fri, 11 Feb 2022 16:10:33 +0000 |
| parents | 33464679bbe5 |
| children | 7f6f0555dad8 |
| files | README README.md config/job_conf.xml config/tool_conf.xml test-data/iAF1260.xml test-data/iAF1260.xml.gz wrap.xml |
| diffstat | 7 files changed, 40 insertions(+), 150414 deletions(-) [+] |
line wrap: on
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Fri Feb 11 16:10:33 2022 +0000 @@ -0,0 +1,36 @@ +# rpFbaAnalysis -- Run OptGene, OptKnock with an heterologous pathway + +The open-source software package rpFbaAnalysis is available here : https://github.com/brsynth/rptools/tree/master/rptools/rpFbaAnalysis + +## How to run rpFbaAnalysis wrapper tests + +In order to execute tests on rpFbaAnalysis wrapper, you need to: + + - Connect to your galaxy instance in interactive mode: + + ```bash + docker exec -it -u root galaxy_galaxy_1 bash + ``` + - Copy all the contents of `test-data` folder into your own test-data directory which is located in your local galaxy instance : `/galaxy/test-data`. It contains all the input files and expected output files needed for the tests. + + - Install Planemo: + You can see here the documentation for Planemo Installation : https://planemo.readthedocs.io/en/latest/installation.html + Note that they recommand to install Planemo by setting up a virtual environment: + + ```bash + python3 -m venv planemo + . planemo/bin/activate + pip install -U planemo + ``` + + Upgrade pip if needed. + + - run the tests: + + ```bash + planemo test --conda_channels conda-forge --conda_debug tools/BRSynthTools/rpFbaAnalysis/wrap.xml + ``` + + IMPORTANT: Maybe you will need to remove CONDA from your PATH for the command `planemo test` to run correctly. To do that, you can edit this file `~/.bashrc`, comment this line `PATH="/root/anaconda3/bin:$PATH"` and save changes. + + Planemo will output an html test summary `tool_test_output.html`.
--- a/README.md Thu Feb 10 12:04:05 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -# rpFbaAnalysis -- Run OptGene, OptKnock with an heterologous pathway - -The open-source software package rpFbaAnalysis is available here : https://github.com/brsynth/rptools/tree/master/rptools/rpFbaAnalysis - -## How to run rpFbaAnalysis wrapper tests - -In order to execute tests on rpFbaAnalysis wrapper, you need to: - - - Connect to your galaxy instance in interactive mode: - - ```bash - docker exec -it -u root galaxy_galaxy_1 bash - ``` - - Copy all the contents of `test-data` folder into your own test-data directory which is located in your local galaxy instance : `/galaxy/test-data`. It contains all the input files and expected output files needed for the tests. - - - Install Planemo: - You can see here the documentation for Planemo Installation : https://planemo.readthedocs.io/en/latest/installation.html - Note that they recommand to install Planemo by setting up a virtual environment: - - ```bash - python3 -m venv planemo - . planemo/bin/activate - pip install -U planemo - ``` - - Upgrade pip if needed. - - - run the tests: - - ```bash - planemo test --conda_channels conda-forge --conda_debug tools/BRSynthTools/rpFbaAnalysis/wrap.xml - ``` - - IMPORTANT: Maybe you will need to remove CONDA from your PATH for the command `planemo test` to run correctly. To do that, you can edit this file `~/.bashrc`, comment this line `PATH="/root/anaconda3/bin:$PATH"` and save changes. - - Planemo will output an html test summary `tool_test_output.html`.
--- a/config/job_conf.xml Thu Feb 10 12:04:05 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ - <tool id="rp_fba_analysis" destination="local" />
--- a/config/tool_conf.xml Thu Feb 10 12:04:05 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ - <section id="sbc-pa" name="SynBioCAD Pathway Analysis"> - <tool file="synbiocad-galaxy-wrappers/rpFbaAnalysis/wrap.xml" /> - </section>
--- a/test-data/iAF1260.xml Thu Feb 10 12:04:05 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,150370 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1" sboTerm="SBO:0000624" fbc:required="false"> - <model fbc:strict="true" id="iAF1260"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit kind="mole" scale="-3" multiplier="1" exponent="1"/> - <unit kind="gram" scale="0" multiplier="1" exponent="-1"/> - <unit kind="second" scale="0" multiplier="3600" exponent="-1"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <fbc:listOfObjectives fbc:activeObjective="obj"> - <fbc:objective fbc:id="obj" fbc:type="maximize"> - <fbc:listOfFluxObjectives> - <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ec_iAF1260_core_59p81M" fbc:coefficient="1"/> - </fbc:listOfFluxObjectives> - </fbc:objective> - </fbc:listOfObjectives> - <listOfParameters> - <parameter value="-999999" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> - <parameter value="999999" id="cobra_default_ub" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> - <parameter value="0" id="cobra_0_bound" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> - <parameter id="R_ATPM_upper_bound" value="8.39" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/> - <parameter id="R_ATPM_lower_bound" value="8.39" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/> - <parameter id="R_EX_cbl1_e_lower_bound" value="-0.01" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/> - <parameter id="R_EX_o2_e_lower_bound" value="-18.5" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/> - <parameter id="R_EX_glc__D_e_lower_bound" value="-8" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/> - </listOfParameters> - 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<reaction id="R_G3PGtex" fast="false" reversible="true" name="Glycerophoglycerol transport via diffusion (extracellular to periplasm)" metaid="R_G3PGtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_G3PGtex"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PGtex"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99886"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08562"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_g3pg_e" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> - 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</fbc:geneProductAssociation> - </reaction> - <reaction id="R_G3PItex" fast="false" reversible="true" name="Glycero-3-phospho-1-inositol transport via diffusion (extracellular to periplasm)" metaid="R_G3PItex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_G3PItex"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PItex"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99888"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/32918"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/32917"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/32916"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/32915"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13292"/> - 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</reaction> - <reaction id="R_GALTptspp" fast="false" reversible="false" name="Galactitol transport via PEP:Pyr PTS (periplasm)" metaid="R_GALTptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_GALTptspp"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALTptspp"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100018"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08586"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05567"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_galt_p" stoichiometry="1" constant="true"/> - <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> - 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<fbc:geneProductRef fbc:geneProduct="G_b3825"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_LPLIPAL2G181" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C18:1)" metaid="R_LPLIPAL2G181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_LPLIPAL2G181"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2G181"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101196"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_2agpg181_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - 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<rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.276"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06126"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101242"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/21596"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/21599"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/21598"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/21597"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04137"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_2amsa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b1539"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_LYSDC" fast="false" reversible="false" name="Lysine decarboxylase" metaid="R_LYSDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_LYSDC"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYSDC"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:LYSDECARBOX-RXN"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.18"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00462"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101256"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/22353"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/22354"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/22352"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/22355"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/899"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00322"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_15dap_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_b0186"/> - <fbc:geneProductRef fbc:geneProduct="G_b4131"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_LPLIPAL1G140pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C14:0) (periplasm)" metaid="R_LPLIPAL1G140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - 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<fbc:geneProductRef fbc:geneProduct="G_b0494"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_LPLIPAL1G141pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C14:1) (periplasm)" metaid="R_LPLIPAL1G141pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_LPLIPAL1G141pp"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1G141pp"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101157"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_1agpg141_p" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> - <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b0494"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_LPLIPAL1G160pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C16:0) (periplasm)" metaid="R_LPLIPAL1G160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_LPLIPAL1G160pp"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1G160pp"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101158"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_1agpg160_p" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> - <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b0494"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_LPLIPAL1G161pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C16:1) (periplasm)" metaid="R_LPLIPAL1G161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_LPLIPAL1G161pp"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1G161pp"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101159"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_1agpg161_p" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> - <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b0494"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_LPLIPAL1G180pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C18:0) (periplasm)" metaid="R_LPLIPAL1G180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_LPLIPAL1G180pp"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1G180pp"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101160"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_1agpg180_p" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> - 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<fbc:geneProductRef fbc:geneProduct="G_b2323"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_MALDDH" fast="false" reversible="false" name="Malate decarboxylating oxidoreductase (decarboxylating)" metaid="R_MALDDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_MALDDH"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALDDH"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:1.1.1.83-RXN"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.83"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00215"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101339"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18366"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18365"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18368"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18367"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/744"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00160"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_mal__D_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b1800"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_MALDt2_2pp" fast="false" reversible="false" name="D-Malate transport via proton symport (2 H) (periplasm)" metaid="R_MALDt2_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - 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<bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATE181"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101175"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_2agpe181_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pg181_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_apg181_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b3825"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_LPLIPAL2ATG120" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C12:0)" metaid="R_LPLIPAL2ATG120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_LPLIPAL2ATG120"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATG120"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101176"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_2agpg120_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pg120_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_apg120_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b3825"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_MALTATr" fast="false" reversible="true" name="Maltose O-acetyltransferase" metaid="R_MALTATr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_MALTATr"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTATr"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALTACETYLTRAN-RXN"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.79"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01556"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06251"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101351"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01133"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_malt_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_acmalt_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b0459"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_LPLIPAL2ATG140" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C14:0)" metaid="R_LPLIPAL2ATG140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - 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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_NO3R1pp"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO3R1pp"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101986"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/29149#1"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/29148#1"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/29150#1"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/29147#1"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09001"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10120"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_no3_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> - 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<speciesReference species="M_no2_p" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_b2206"/> - <fbc:geneProductRef fbc:geneProduct="G_b2203"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_b2202"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_NO3R2pp" fast="false" reversible="false" name="Nitrate reductase (Menaquinol-8) (periplasm)" metaid="R_NO3R2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_NO3R2pp"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO3R2pp"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101988"/> - 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</listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_b1223"/> - <fbc:geneProductRef fbc:geneProduct="G_b1469"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_MLTG4" fast="false" reversible="false" name="Maltodextrin glucosidase (maltohexaose)" metaid="R_MLTG4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_MLTG4"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTG4"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14282"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.20"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101622"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08935"/> - 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<bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTG5"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14283"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.20"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101623"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08936"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_malthp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b0403"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_MLTGY1pp" fast="false" reversible="false" name="Murein lytic transglycosylase (murein4p4p) (periplasm)" metaid="R_MLTGY1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_MLTGY1pp"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTGY1pp"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143245"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08937"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_murein4p4p_p" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_anhgm4p_p" stoichiometry="2" constant="true"/> - 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<rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UM4PL"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143441"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09360"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_LalaDgluMdapDala_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_uamr_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_um4p_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b4233"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_UMPK" fast="false" reversible="true" name="UMP kinase" metaid="R_UMPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_UMPK"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UMPK"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12002"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.4"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.22"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.14"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00158"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105118"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/24400"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/24402"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/24401"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/24403"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/201"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00119"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_b0171"/> - <fbc:geneProductRef fbc:geneProduct="G_b0910"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_UMPtex" fast="false" reversible="true" name="UMP transport via diffusion (extracellular to periplasm)" metaid="R_UMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_UMPtex"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UMPtex"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105127"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/27927"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/27929"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/27926"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/27928"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09808"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09361"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_ump_e" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_b2215"/> - <fbc:geneProductRef fbc:geneProduct="G_b0241"/> - <fbc:geneProductRef fbc:geneProduct="G_b0929"/> - <fbc:geneProductRef fbc:geneProduct="G_b1377"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_UNK3" fast="false" reversible="false" name="2-keto-4-methylthiobutyrate transamination" metaid="R_UNK3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_UNK3"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UNK3"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14147"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.57"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.5"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07396"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95923"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/25799"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/25797"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/25796"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/25798"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05108"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_2kmb_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction id="R_UPLA4FNF" fast="false" reversible="false" name="Undecaprenyl phosphate-L-Ara4FN formylase" metaid="R_UPLA4FNF" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_UPLA4FNF"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UPLA4FNF"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105132"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09363"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_uLa4fn_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_uLa4n_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction id="R_UPLA4FNT" fast="false" reversible="false" name="Undecaprenyl phosphate-L-Ara4FN transferase" metaid="R_UPLA4FNT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_UPLA4FNT"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UPLA4FNT"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105133"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_udcpp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_udpLa4fn_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_uLa4fn_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b2254"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_UPP3MT" fast="false" reversible="false" name="Uroporphyrinogen methyltransferase" metaid="R_UPP3MT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_UPP3MT"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UPP3MT"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-13403"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.107"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03194"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105137"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/32462"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/32461"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/32459"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/32460"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02287"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_amet_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_uppg3_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ahcys_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_dscl_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_b3368"/> - <fbc:geneProductRef fbc:geneProduct="G_b3803"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_UPP3S" fast="false" reversible="false" name="Uroporphyrinogen-III synthase" metaid="R_UPP3S" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_UPP3S"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UPP3S"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UROGENIIISYN-RXN"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.75"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03165"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105139"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-421482"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-189488"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-189488"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18966"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18968"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18965"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18967"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02264"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_hmbil_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_uppg3_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b3804"/> - </fbc:geneProductAssociation> - </reaction> - </listOfReactions> - </model> -</sbml>
--- a/wrap.xml Thu Feb 10 12:04:05 2022 +0000 +++ b/wrap.xml Fri Feb 11 16:10:33 2022 +0000 @@ -1,7 +1,7 @@ -<tool id="rpfa" name="rpFbaAnalysis" version="@TOOL_VERSION@" profile="19.09"> - <description>rpFbaAnalysis: run OptGene, OptKnock with an heterologous pathway</description> +<tool id="rp_fba_analysis" name="rpFbaAnalysis" version="@TOOL_VERSION@" profile="19.09"> + <description>Run OptGene, OptKnock with an heterologous pathway</description> <macros> - <token name="@TOOL_VERSION@">1.0.0</token> + <token name="@TOOL_VERSION@">1.0.1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">rpfa</requirement> @@ -65,7 +65,7 @@ <tests> <test> <!-- test 1: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718) --> - <param name="model" value="iAF1260.xml" /> + <param name="model" value="iAF1260.xml.gz" /> <param name="pathway" value="butanol.xml" /> <param name="medium" value="butanol.csv" /> <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />