Mercurial > repos > ggricourt > data_manager_bigg

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bigg_model_sbml_fetcher.py	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,62 @@
+import argparse
+import json
+import os
+import sys
+try:
+    # For Python 3.0 and later
+    from urllib.request import Request, urlopen
+except ImportError:
+    # Fall back to Python 2 imports
+    from urllib2 import Request, urlopen
+
+
+def url_download(url, workdir):
+    file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url)))
+    src = None
+    dst = None
+    try:
+        req = Request(url)
+        src = urlopen(req)
+        with open(file_path, 'wb') as dst:
+            while True:
+                chunk = src.read(2**10)
+                if chunk:
+                    dst.write(chunk)
+                else:
+                    break
+    except Exception as e:
+        sys.exit(str(e))
+    finally:
+        if src:
+            src.close()
+    return file_path
+
+
+def download(model_id, out_file):
+
+    with open(out_file) as fh:
+        params = json.load(fh)
+
+    workdir = params['output_data'][0]['extra_files_path']
+    os.makedirs(workdir)
+    file_path = url_download('http://bigg.ucsd.edu/static/models/%s.xml' % (model_id,), workdir)
+    entry_name = os.path.basename(file_path)
+
+    data_manager_json = {"data_tables": {}}
+    data_manager_entry = {}
+    data_manager_entry['value'] = model_id
+    data_manager_entry['name'] = entry_name
+    data_manager_entry['path'] = file_path
+
+    with open(out_file, 'w') as fh:
+        json.dump(data_manager_json, fh, sort_keys=True)
+
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('--model-id', help='Model id')
+parser.add_argument('--out-file', help='JSON output file')
+
+args = parser.parse_args()
+
+download(args.model_id, args.out_file)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bigg_model_sbml_fetcher.xml	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,38 @@
+<tool id="model_sbml_fetcher" name="Bigg SBML data manager" tool_type="manage_data" profile="18.09" version="0.0.1">
+    <description>Get an SBML model (BiGG)</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/bigg_model_sbml_fetcher.py'
+        --model-id '$model_id'
+        --out-file '$out_file'
+    ]]></command>
+    <inputs>
+        <param name="model_id" type="text" label="Model Id"/>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help><![CDATA[
+Pick SBML Model
+=================
+
+Download the selected SBML model fromg BiGG database.
+
+
+Version
+----------
+0.0.1
+
+License
+-------
+
+`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
+
+    ]]></help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/model_sbml_fetcher.py	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,62 @@
+import argparse
+import json
+import os
+import sys
+try:
+    # For Python 3.0 and later
+    from urllib.request import Request, urlopen
+except ImportError:
+    # Fall back to Python 2 imports
+    from urllib2 import Request, urlopen
+
+
+def url_download(url, workdir):
+    file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url)))
+    src = None
+    dst = None
+    try:
+        req = Request(url)
+        src = urlopen(req)
+        with open(file_path, 'wb') as dst:
+            while True:
+                chunk = src.read(2**10)
+                if chunk:
+                    dst.write(chunk)
+                else:
+                    break
+    except Exception as e:
+        sys.exit(str(e))
+    finally:
+        if src:
+            src.close()
+    return file_path
+
+
+def download(model_id, out_file):
+
+    with open(out_file) as fh:
+        params = json.load(fh)
+
+    workdir = params['output_data'][0]['extra_files_path']
+    os.makedirs(workdir)
+    file_path = url_download('http://bigg.ucsd.edu/static/models/%s.xml.gz' % (model_id,), workdir)
+    entry_name = os.path.basename(file_path)
+
+    data_manager_json = {"data_tables": {}}
+    data_manager_entry = {}
+    data_manager_entry['id'] = model_id
+    data_manager_entry['name'] = entry_name
+    data_manager_entry['path'] = file_path
+
+    with open(out_file, 'w') as fh:
+        json.dump(data_manager_json, fh, sort_keys=True)
+
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('--model-id', help='Model id')
+parser.add_argument('--out-file', help='JSON output file')
+
+args = parser.parse_args()
+
+download(args.model_id, args.out_file)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/model_sbml_fetcher.xml	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,38 @@
+<tool id="model_sbml_fetcher" name="Bigg SBML data manager" tool_type="manage_data" profile="18.09" version="0.0.1">
+    <description>Get an SBML model (BiGG)</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/model_sbml_fetcher.py'
+        --model-id '$model_id'
+        --out-file '$out_file'
+    ]]></command>
+    <inputs>
+        <param name="model_id" type="text" label="Model Id"/>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help><![CDATA[
+Pick SBML Model
+=================
+
+Download the selected SBML model fromg BiGG database.
+
+
+Version
+----------
+0.0.1
+
+License
+-------
+
+`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
+
+    ]]></help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/bigg_model_sbml_fetcher.xml" id="bigg_model_sbml_fetcher">
+        <data_table name="bigg_model_sbml">
+            <output>
+                <column name="value" />
+                <column name="name" />
+                <column name="path" output_ref="out_file">
+                    <move type="file" relativize_symlinks="True">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bigg/model/${name}.xml</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/bigg/model/${name}.xml</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigg_model_sbml.json	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"model_sbml": {"value": "iAF1260", "name": "Escherichia coli str. K-12 substr. MG1655 (iAF1260)", "path": "bigg/model/iAF1260.xml"}}}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigg_model_sbml.loc	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,12 @@
+#This file has the format (white space characters are TAB characters):
+#
+#<model_id>  <organism>     <file_path>
+#
+#So, model_smbl.loc could look something like this:
+#
+#e_coli_core		Escherichia coli str. K-12 substr. MG1655	e_coli_core.xml
+#
+#Your model_sbml.loc file should contain an entry for each individual
+#sbml file.
+#
+e_coli_core		Escherichia coli str. K-12 substr. MG1655	${__HERE__}/e_coli_core.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/e_coli_core.xml	Wed Feb 23 14:33:49 2022 +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 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_glu__L_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="L-Glutamate" metaid="M_glu__L_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="-1" fbc:chemicalFormula="C5H8NO4">
+        <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_glu__L_c">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/glu__L"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:Glutamates"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:76051"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:21301"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:29985"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42825"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:29987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18237"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:24314"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16015"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13107"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:5431"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:21304"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:6224"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:14321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:29988"/>
+                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00148"/>
+                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB60475"/>
+                  <rdf:li rdf:resource="http://identifiers.org/inchi_key/WHUUTDBJXJRKMK-VKHMYHEASA-M"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00025"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00302"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D00007"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D04341"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM89557"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.compound/428614"/>
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+          <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1723"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRUVFORMLY-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00157"/>
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+        <listOfReactants>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29941"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29940"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29942"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05312"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09833"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09811"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09723"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09120"/>
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+          <speciesReference species="M_pi_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2987"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3493"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-71707"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25291"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25293"/>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0356"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1478"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1241"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08033"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08032"/>
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+        <listOfProducts>
+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_actp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
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+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3115"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2296"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1849"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00251"/>
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+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3956"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACONITATEDEHYDR-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95386"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10228"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00974"/>
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+          <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_acon_C_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0118"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1276"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_icit_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0118"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1276"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1702"/>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0474"/>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0726"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0727"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08173"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10042"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
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+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b3736"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3737"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3738"/>
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+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b3731"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3732"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3733"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3734"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3735"/>
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+        <listOfProducts>
+          <speciesReference species="M_etoh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29188"/>
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+        <listOfProducts>
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+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0722"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0723"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0724"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0729"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1603"/>
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+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2465"/>
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+          <speciesReference species="M_ac_e" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mal__L_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-225"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-224"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101367"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13793"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10967"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08868"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mal__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_nh4_e" fast="false" reversible="true" name="Ammonia exchange" metaid="R_EX_nh4_e" sboTerm="SBO:0000627" 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_EX_nh4_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_nh4_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-206"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9615"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-544"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101950"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-444416"/>
+                  <rdf:li 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>
+      </reaction>
+      <reaction id="R_EX_o2_e" fast="false" reversible="true" name="O2 exchange" metaid="R_EX_o2_e" sboTerm="SBO:0000627" 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_EX_o2_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_o2_e"/>
+                  <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>
+      </reaction>
+      <reaction id="R_EX_pi_e" fast="false" reversible="true" name="Phosphate exchange" metaid="R_EX_pi_e" sboTerm="SBO:0000627" 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_EX_pi_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pi_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-470"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32824"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32826"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32825"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32823"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/10985"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10838"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09722"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09121"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13178"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pi_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_pyr_e" fast="false" reversible="false" name="Pyruvate exchange" metaid="R_EX_pyr_e" sboTerm="SBO:0000627" 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_EX_pyr_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pyr_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-506"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-570"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103384"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12168"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10929"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09218"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pyr_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_succ_e" fast="false" reversible="false" name="Succinate exchange" metaid="R_EX_succ_e" sboTerm="SBO:0000627" 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_EX_succ_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_succ_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-552"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104619"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10952"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09271"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_succ_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_FBA" fast="false" reversible="true" name="Fructose-bisphosphate aldolase" metaid="R_FBA" 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_FBA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FBA"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.13"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01068"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99459"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14729"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14732"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14731"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14730"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1338"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00786"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2097"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1773"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2925"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FBP" fast="false" reversible="false" name="Fructose-bisphosphatase" metaid="R_FBP" 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_FBP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FBP"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.11"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99465"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11067"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11065"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11066"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11064"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2084"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3925"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4232"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FORt2" fast="false" reversible="false" name="Formate transport in via proton symport" metaid="R_FORt2" 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_FORt2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FORt2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99621"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08524"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05559"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_for_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0904"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2492"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FORt" fast="false" reversible="true" name="Formate transport via diffusion" metaid="R_FORt" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_0_bound" 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_FORt">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FORt"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99620"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6803255"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29681"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29680"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29679"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12483"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09754"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08525"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08526"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_for_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0904"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2492"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FRD7" fast="false" reversible="false" name="Fumarate reductase" metaid="R_FRD7" 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_FRD7">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRD7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99641"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29190"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29189"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29187"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29188"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09272"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4151"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4152"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4153"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4154"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FRUpts2" fast="false" reversible="false" name="Fructose transport via PEP:Pyr PTS (f6p generating)" metaid="R_FRUpts2" 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_FRUpts2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRUpts2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99662"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fru_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0810"/>
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+                  <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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/model_sbml.json	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"bigg_sbml": {"id": "iAF1260", "name": "Escherichia coli str. K-12 substr. MG1655 (iAF1260)", "path": "bigg/model/iAF1260.xml"}}}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/model_sbml.loc.sample	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,3 @@
+## Bigg SBML files
+#Value	Name	Path
+#iAF1260	Escherichia coli str. K-12 substr. MG1655 (iAF1260)	bigg/model/iAF1260.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,8 @@
+<tables>
+    <!-- Location of sbml models -->
+    <table name="bigg_model_sbml" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/bigg_model_sbml.loc" />
+    </table>
+</tables>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of sbml models -->
+    <table name="bigg_model_sbml" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/bigg_model_sbml.loc" />
+    </table>
+</tables>