Mercurial > repos > tduigou > get_sbml_model
changeset 6:9b5947d48192 draft
planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 87a863d4074543870caef1116b8e9be58005dcdd
| author | tduigou |
|---|---|
| date | Mon, 28 Aug 2023 14:24:48 +0000 |
| parents | 80c32f0cb716 |
| children | 8dc4d3964ab5 |
| files | get_sbml_model.xml test-data/e_coli_core.xml |
| diffstat | 2 files changed, 9992 insertions(+), 64 deletions(-) [+] |
line wrap: on
line diff
--- a/get_sbml_model.xml Tue May 30 21:03:04 2023 +0000 +++ b/get_sbml_model.xml Mon Aug 28 14:24:48 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT"> +<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.4" profile="21.09" license="MIT"> <description>Get an SBML model (BiGG)</description> <requirements> <requirement type="package" version="7.81.0">curl</requirement> @@ -7,87 +7,117 @@ <requirement type="package" version="2.29">requests</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz' - | gunzip > '$model'; + #if str($cond_src.from_src) == 'from_bigg' + curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' && + #else + cp '${cond_src.input_file}' '$model' && + #end if python '$__tool_directory__/'get_infos.py '$model' - --hostid '$input' + --hostid '${cond_src.hostid}' --comp '$compartments' --biomass '$biomass' --taxid '$taxid' ]]></command> <inputs> - <param name="input" type="select" label="Strain"> - <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option> - <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option> - <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option> - <option value="iCN900">Clostridioides difficile 630 (iCN900)</option> - <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option> - <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option> - <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option> - <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option> - <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option> - <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option> - <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option> - <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option> - <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option> - <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option> - <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option> - <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option> - <option value="Recon3D">Homo sapiens (Recon3D)</option> - <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option> - <option value="RECON1">Homo sapiens (RECON1)</option> - <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option> - <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option> - <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option> - <option value="iMM1415">Mus musculus (iMM1415)</option> - <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option> - <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option> - <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option> - <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option> - <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option> - <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option> - <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option> - <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option> - <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option> - <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option> - <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option> - <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option> - <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option> - <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option> - <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option> - <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option> - <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option> - <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option> - <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option> - <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option> - <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option> - <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option> - <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option> - <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option> - </param> + <conditional name="cond_src"> + <param name="from_src" type="select" label="Select source"> + <option value="from_bigg" selected="True">Download model from BiGG</option> + <option value="from_history">Select file from the History</option> + </param> + <when value="from_history"> + <param name="hostid" type="text" help="ID of the model"> + <validator type="empty_field" message="An ID is required"/> + </param> + <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/> + </when> + <when value="from_bigg"> + <param name="hostid" type="select" label="Strain"> + <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option> + <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option> + <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option> + <option value="iCN900">Clostridioides difficile 630 (iCN900)</option> + <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option> + <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option> + <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option> + <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option> + <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option> + <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option> + <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option> + <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option> + <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option> + <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option> + <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option> + <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option> + <option value="Recon3D">Homo sapiens (Recon3D)</option> + <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option> + <option value="RECON1">Homo sapiens (RECON1)</option> + <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option> + <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option> + <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option> + <option value="iMM1415">Mus musculus (iMM1415)</option> + <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option> + <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option> + <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option> + <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option> + <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option> + <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option> + <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option> + <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option> + <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option> + <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option> + <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option> + <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option> + <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option> + <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option> + <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option> + <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option> + <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option> + <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option> + <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option> + <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option> + <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option> + <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option> + <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option> + <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option> + </param> + </when> + </conditional> </inputs> <outputs> - <data name="model" format="sbml" label="${input}" /> - <data name="taxid" format="tsv" label="${input} (taxon id)" /> - <data name="compartments" format="tsv" label="${input} (compartments)" /> - <data name="biomass" format="tsv" label="${input} (biomass reactions)" /> + <data name="model" format="sbml" label="${cond_src.hostid}" /> + <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" /> + <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" /> + <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" /> </outputs> <tests> <test> - <!-- test 1: check if identical outputs are produced with iML1515 model input --> - <param name="input" value="iML1515" /> - <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/> - <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e"/> - <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/> - <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/> + <conditional name="cond_src"> + <param name="from_src" value="from_bigg" /> + <param name="hostid" value="iML1515" /> + </conditional> + <output name="model" md5="9bf81d20cab5476700697ded95b716d1" /> + <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" /> + <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" /> + <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" /> </test> + <test> + <conditional name="cond_src"> + <param name="from_src" value="from_history" /> + <param name="hostid" value="e_coli_core" /> + <param name="input_file" value="e_coli_core.xml" /> + </conditional> + <output name="model" md5="4574760460afe9e1b3388dc15f354706" /> + <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" /> + <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" /> + <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" /> + </test> </tests> <help><![CDATA[ Pick SBML Model ================= -Download the selected SBML model fromg BiGG database. +Download the selected SBML model fromg BiGG database or get statistics from local SBML model. ]]></help> <creator> <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli_core.xml Mon Aug 28 14:24:48 2023 +0000 @@ -0,0 +1,9898 @@ +<?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="e_coli_core"> + <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_Ecoli_core_w_GAM" fbc:coefficient="1"/> + </fbc:listOfFluxObjectives> + </fbc:objective> + </fbc:listOfObjectives> + <listOfParameters> + <parameter value="-1000" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> + <parameter value="1000" 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_lower_bound" value="8.39" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/> + <parameter id="R_EX_glc__D_e_lower_bound" value="-10" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/> + </listOfParameters> + <listOfCompartments> + <compartment id="e" name="extracellular space" constant="true"/> + <compartment id="c" name="cytosol" constant="true"/> + </listOfCompartments> + <listOfSpecies> + <species id="M_glc__D_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="D-Glucose" metaid="M_glc__D_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="C6H12O6"> + <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="#M_glc__D_e"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/glc__D"/> + <rdf:li rdf:resource="http://identifiers.org/biocyc/META:Glucopyranose"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:12965"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:20999"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:4167"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:17634"/> + <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00122"/> + <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB06564"/> + <rdf:li rdf:resource="http://identifiers.org/inchi_key/WQZGKKKJIJFFOK-GASJEMHNSA-N"/> + <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00031"/> + <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D00009"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM41"/> + <rdf:li rdf:resource="http://identifiers.org/sabiork/1406"/> + <rdf:li rdf:resource="http://identifiers.org/sabiork/1407"/> + <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd26821"/> + <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00027"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </sbml:annotation> + </species> + <species id="M_gln__L_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="L-Glutamine" metaid="M_gln__L_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="0" fbc:chemicalFormula="C5H10N2O3"> + <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="#M_gln__L_c"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/gln__L"/> + <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLN"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42943"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42899"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32679"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32678"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:58359"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:28300"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42812"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13110"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18050"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32666"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:6227"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32665"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:21308"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42814"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:5432"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:24316"/> + <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00641"/> + <rdf:li rdf:resource="http://identifiers.org/inchi_key/ZDXPYRJPNDTMRX-VKHMYHEASA-N"/> + <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00064"/> + <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00303"/> + <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D00015"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM37"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.compound/113522"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.compound/212615"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.compound/29472"/> + <rdf:li rdf:resource="http://identifiers.org/sabiork/2011"/> + <rdf:li rdf:resource="http://identifiers.org/sabiork/74"/> + <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00253"/> + <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00053"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </sbml:annotation> + </species> + <species id="M_gln__L_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="L-Glutamine" metaid="M_gln__L_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="C5H10N2O3"> + <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="#M_gln__L_e"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/gln__L"/> + <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLN"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42943"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42899"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32679"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32678"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:58359"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:28300"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42812"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13110"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18050"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32666"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:6227"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32665"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:21308"/> + <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42814"/> + <rdf:li 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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_ME2"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ME2"/> + <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALIC-NADP-RXN"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.40"/> + <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00216"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101443"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/18255"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/18256"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/18254"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/18253"/> + <rdf:li 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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_NADH16"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADH16"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.5.3"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101864"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08972"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </sbml:annotation> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_e" 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reversible="false" name="NAD transhydrogenase" metaid="R_NADTRHD" 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_NADTRHD"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADTRHD"/> + <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRNUTRANSHYDROGEN-RXN"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.3"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.2"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.1"/> + <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00112"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101898"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/11692"/> 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rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-444416"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-444416"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-444416"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-444416"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-444416"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-444416"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-444416"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-444416"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-444416"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-444416"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-444416"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-444416"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/28749"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/28748"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/28750"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/28747"/> + <rdf:li rdf:resource="http://identifiers.org/sabiork/11683"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13364"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09835"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05466"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08987"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08986"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09736"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </sbml:annotation> + <listOfReactants> + <speciesReference species="M_nh4_e" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_s0001"/> + <fbc:geneProductRef fbc:geneProduct="G_b0451"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_O2t" fast="false" reversible="true" name="O2 transport diffusion " metaid="R_O2t" 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_O2t"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O2t"/> + <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-474"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102090"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09641"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05468"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09031"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09032"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09734"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </sbml:annotation> + <listOfReactants> + <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_s0001"/> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_PDH" fast="false" reversible="false" name="Pyruvate dehydrogenase" metaid="R_PDH" 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_PDH"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PDH"/> + <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRUVDEH-RXN"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.1.4"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.51"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.4.1"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.12"/> + <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00209"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102425"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373177"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-71397"/> + <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-71397"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/28043"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/28045"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/28044"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/28042"/> + <rdf:li rdf:resource="http://identifiers.org/sabiork/523"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00154"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </sbml:annotation> + <listOfReactants> + <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_b0114"/> + <fbc:geneProductRef fbc:geneProduct="G_b0115"/> + <fbc:geneProductRef fbc:geneProduct="G_b0116"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + </listOfReactions> + </model> +</sbml>