# HG changeset patch
# User iuc
# Date 1648645531 0
# Node ID cdd6a526bdcf1d8ccfdbaf6a61b79fcf9dc44b1f

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign commit bdac148247c9c3d3da3420220d006e723c718277"

diff -r 000000000000 -r cdd6a526bdcf rpbasicdesign.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign.xml	Wed Mar 30 13:05:31 2022 +0000
@@ -0,0 +1,172 @@
+<tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="21.09">
+    <description>Build DNA-BOT input files from rpSBML</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m rpbasicdesign.cli
+        --rpsbml_file '$rpsbml_file'
+        #if $adv.parts_files
+            #set files = '" "'.join([str($file) for $file in $adv.parts_files])
+            --parts_files "${files}"
+        #end if
+        --lms_id '$adv.lms_id'
+        --lmp_id '$adv.lmp_id'
+        --backbone_id '$backbone_id'
+        --sample_size '$sample_size'
+        $adv.cds_permutation
+        --o_dnabot_dir 'out/dnabot_in'
+        $adv.sbol_output
+        --max_enz_per_rxn $adv.max_enz_per_rxn
+    ]]></command>
+    <inputs>
+        <param name="rpsbml_file" type="data" format="sbml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/>
+        <param argument="--backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" help="Part ID to be used as the backbone.">
+            <sanitizer invalid_char="">
+                <valid initial="string.letters,string.digits">
+                    <add value=":" />
+                    <add value="." />
+                    <add value="-" />
+                    <add value="_" />
+                </valid>
+            </sanitizer>
+            <validator type="empty_field" message="Backbone ID is required"/>
+        </param>
+        <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Sample size" help="Number of constructs to generate."/>
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" help="List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: Standard Biolegio Parts (BBP-18500)" />
+            <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." >
+                <sanitizer invalid_char="">
+                    <valid initial="string.letters,string.digits">
+                        <add value=":" />
+                        <add value="-" />
+                        <add value="_" />
+                        <add value="." />
+                    </valid>
+                </sanitizer>
+                <validator type="empty_field" message="LMS ID is required"/>
+            </param>
+            <param argument="--lmp_id" type="text" value="LMP" label="LMP part ID" help="Part ID to be used as the LMP methylated linker.">
+                <sanitizer invalid_char="">
+                    <valid initial="string.letters,string.digits">
+                        <add value=":" />
+                        <add value="-" />
+                        <add value="_" />
+                        <add value="." />
+                    </valid>
+                </sanitizer>
+                <validator type="empty_field" message="LMP ID is required"/>
+            </param>
+            <param argument="--cds_permutation" type="boolean" truevalue="--cds_permutation true" falsevalue="--cds_permutation false" checked="true" label="Perform CDS permutation?" help="Whether all combinations of CDS permutation should be built." />
+            <param argument="--sbol_output" type="boolean" checked="false" truevalue="--o_sbol_dir out/sbol_export" falsevalue="" label="Output SBOL results?" help="Whether SBOL (Synthetic Biology Open Language) depictions of constructs should be outputted" />
+            <param argument="--max_enz_per_rxn" type="integer" value="1" min="1" max="99" label="Maximum number of enyzme to consider per reaction." help="Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} on ${rpsbml_file.name}: constructs" />
+        <data name="User_parts_plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} on ${rpsbml_file.name}: User parts plate"/>
+        <data name="Biolegio_plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} on ${rpsbml_file.name}: Biolegio plate"/>
+        <collection name="sbol_dir" type="list" label="${tool.name} on ${rpsbml_file.name}: SBOL constructs">
+            <filter> adv['sbol_output'] </filter>
+            <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" />
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="4">
+            <!-- test 1: check if identical outputs are produced (Lycopene input)-->
+            <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" />
+            <param name="sample_size" value="3" />
+            <output name="Constructs" file="constructs_lycopene.csv" ftype="csv" compare="diff">
+                <assert_contents>
+                    <has_n_lines n="4"/>
+                </assert_contents>
+            </output>
+            <output name="User_parts_plate" file="user_parts_plate_lycopene.csv" ftype="csv" compare="diff"/>
+            <output name="Biolegio_plate" file="biolegio_plate_lycopene.csv" ftype="csv" compare="diff"/>
+            <param name="sbol_output" value="true" />
+            <output_collection name="sbol_dir" type="list" count="3">
+                <element name="BASIC_construct_A1">
+                    <assert_contents>
+                        <is_valid_xml />
+                        <has_text text="BASIC_construct_A1" />
+                        <has_n_lines n="339" />
+                    </assert_contents>
+                </element>
+                <element name="BASIC_construct_B1">
+                    <assert_contents>
+                        <is_valid_xml />
+                        <has_text text="BASIC_construct_B1" />
+                        <has_n_lines n="339" />
+                    </assert_contents>
+                </element>
+                <element name="BASIC_construct_C1">
+                    <assert_contents>
+                        <is_valid_xml />
+                        <has_text text="BASIC_construct_C1" />
+                        <has_n_lines n="339" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="3">
+            <!-- test 2: check if identical outputs are produced (Muconate input)-->
+            <param name="rpsbml_file" value="muconate_example.xml" />
+            <param name="sample_size" value="88" />
+            <output name="Constructs" file="constructs_muconate.csv" ftype="csv" compare="diff">
+                <assert_contents>
+                    <has_n_lines n="89"/>
+                </assert_contents>
+            </output>
+            <output name="User_parts_plate" file="user_parts_plate_muconate.csv" ftype="csv" compare="diff"/>
+            <output name="Biolegio_plate" file="biolegio_plate_muconate.csv" ftype="csv" compare="diff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+rpbasicdesign
+================
+
+rpbasicdesign extracts enzyme IDs from rpSBML (System Biology Markup Language) files containing additionnal annotations (e.g. reaction rules ID) and produced by the RP (RetroPath) suite available in `SynBioCAD Galaxy platform <https://galaxy-synbiocad.org/>`_, to generate genetic constructs compliant with the BASIC (Biopart Assembly Standard for Idempotent Cloning) assembly approach. CSV files produced are ready to be used with DNA-Bot to generate instructions for automated build of the genetic constructs using OpenTrons liquid handling robots.
+
+Input
+-----
+
+Required:
+
+* **rpSBML file**\ : rpSBML file from which enzymes UniProt IDs will be collected.
+
+Advanced options:
+
+* **Linkers and user parts**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: ( `Standard Biolegio Parts <https://www.biolegio.com/>`_: BBP-18500).
+* **LMS part ID**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS.
+* **LMP part ID**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP.
+* **Backbone part ID**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1.
+* **Sample size**\ : (int) Number of constructs to generate. Default: 88.
+* **Perform CDS permutation?**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true.
+* **Maximum number of enyzme to consider per reaction**\ : (int) Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept. (Default: 1). 
+
+Output
+------
+
+* **constructs**\ : CSV construct file listing the constructs to be built.
+* **User parts plate**\ : CSV file listing the DNA parts to be included into each construct.
+* **Biolegio plate**\ : CSV file listing the plate coordinates of the BASIC linkers.
+* **SBOL constructs**\ : (optional) one SBOL (Synthetic Biology Open Language) file is produced for each construct generated in XML format. 
+
+Project Links
+------------------
+
+* `GitHub <https://github.com/brsynth/rpbasicdesign>`_
+
+License
+-------
+
+* `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/synbio/ysaa010</citation>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r cdd6a526bdcf test-data/biolegio_plate_lycopene.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biolegio_plate_lycopene.csv	Wed Mar 30 13:05:31 2022 +0000
@@ -0,0 +1,83 @@
+Part/linker,Well,Part concentration (ng/uL)
+L1-S,A1,
+L1-P,B1,
+L2-S,A2,
+L2-P,B2,
+L3-S,A3,
+L3-P,B3,
+L4-S,A4,
+L4-P,B4,
+L5-S,A5,
+L5-P,B5,
+L6-S,A6,
+L6-P,B6,
+LMP-S,A7,
+LMP-P,B7,
+LMS-S,A8,
+LMS-P,B8,
+U1-S,C1,
+U2-S,C2,
+U3-S,C3,
+U1-RBS1-P,C4,
+U1-RBS2-P,C5,
+U1-RBS3-P,C6,
+U1-A01-P,D1,
+U1-A02-P,D2,
+U1-A03-P,D3,
+U1-A04-P,D4,
+U1-A05-P,D5,
+U1-A06-P,D6,
+U1-A07-P,D7,
+U1-A08-P,D8,
+U1-A09-P,D9,
+U1-A10-P,D10,
+U1-A11-P,D11
+U1-A12-P,D12,
+U2-RBS1-P,C7,
+U2-RBS2-P,C8,
+U2-RBS3-P,C9,
+U2-A01-P,E1,
+U2-A02-P,E2,
+U2-A03-P,E3,
+U2-A04-P,E4,
+U2-A05-P,E5,
+U2-A06-P,E6,
+U2-A07-P,E7,
+U2-A08-P,E8,
+U2-A09-P,E9,
+U2-A10-P,E10,
+U2-A11-P,E11
+U2-A12-P,E12,
+U3-RBS1-P,C10,
+U3-RBS2-P,C11,
+U3-RBS3-P,C12,
+U3-A01-P,F1,
+U3-A02-P,F2,
+U3-A03-P,F3,
+U3-A04-P,F4,
+U3-A05-P,F5,
+U3-A06-P,F6,
+U3-A07-P,F7,
+U3-A08-P,F8,
+U3-A09-P,F9,
+U3-A10-P,F10,
+U3-A11-P,F11
+U3-A12-P,F12,
+U1-AM12-P,A10,
+U1-AM24-P,B10,
+U2-AM12-P,A11,
+U2-AM24-P,B11,
+U3-AM12-P,A12,
+U3-AM24-P,B12,
+LF1-S,A9,
+LF1-P,B9,
+LF2-S,G1,
+LF2-P,H1,
+LF3-S,G2,
+LF3-P,H2,
+LF4-S,G3,
+LF4-P,H3,
+LF5-S,G4,
+LF5-P,H4,
+LF6-S,G5,
+LF6-P,H5,
\ No newline at end of file
diff -r 000000000000 -r cdd6a526bdcf test-data/biolegio_plate_muconate.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biolegio_plate_muconate.csv	Wed Mar 30 13:05:31 2022 +0000
@@ -0,0 +1,83 @@
+Part/linker,Well,Part concentration (ng/uL)
+L1-S,A1,
+L1-P,B1,
+L2-S,A2,
+L2-P,B2,
+L3-S,A3,
+L3-P,B3,
+L4-S,A4,
+L4-P,B4,
+L5-S,A5,
+L5-P,B5,
+L6-S,A6,
+L6-P,B6,
+LMP-S,A7,
+LMP-P,B7,
+LMS-S,A8,
+LMS-P,B8,
+U1-S,C1,
+U2-S,C2,
+U3-S,C3,
+U1-RBS1-P,C4,
+U1-RBS2-P,C5,
+U1-RBS3-P,C6,
+U1-A01-P,D1,
+U1-A02-P,D2,
+U1-A03-P,D3,
+U1-A04-P,D4,
+U1-A05-P,D5,
+U1-A06-P,D6,
+U1-A07-P,D7,
+U1-A08-P,D8,
+U1-A09-P,D9,
+U1-A10-P,D10,
+U1-A11-P,D11
+U1-A12-P,D12,
+U2-RBS1-P,C7,
+U2-RBS2-P,C8,
+U2-RBS3-P,C9,
+U2-A01-P,E1,
+U2-A02-P,E2,
+U2-A03-P,E3,
+U2-A04-P,E4,
+U2-A05-P,E5,
+U2-A06-P,E6,
+U2-A07-P,E7,
+U2-A08-P,E8,
+U2-A09-P,E9,
+U2-A10-P,E10,
+U2-A11-P,E11
+U2-A12-P,E12,
+U3-RBS1-P,C10,
+U3-RBS2-P,C11,
+U3-RBS3-P,C12,
+U3-A01-P,F1,
+U3-A02-P,F2,
+U3-A03-P,F3,
+U3-A04-P,F4,
+U3-A05-P,F5,
+U3-A06-P,F6,
+U3-A07-P,F7,
+U3-A08-P,F8,
+U3-A09-P,F9,
+U3-A10-P,F10,
+U3-A11-P,F11
+U3-A12-P,F12,
+U1-AM12-P,A10,
+U1-AM24-P,B10,
+U2-AM12-P,A11,
+U2-AM24-P,B11,
+U3-AM12-P,A12,
+U3-AM24-P,B12,
+LF1-S,A9,
+LF1-P,B9,
+LF2-S,G1,
+LF2-P,H1,
+LF3-S,G2,
+LF3-P,H2,
+LF4-S,G3,
+LF4-P,H3,
+LF5-S,G4,
+LF5-P,H4,
+LF6-S,G5,
+LF6-P,H5,
\ No newline at end of file
diff -r 000000000000 -r cdd6a526bdcf test-data/constructs_lycopene.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/constructs_lycopene.csv	Wed Mar 30 13:05:31 2022 +0000
@@ -0,0 +1,4 @@
+Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10
+A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,,
+B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,,
+C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,P21684,U3-RBS2,P21685,U2-RBS2,P21683,,,,,,,,,,
diff -r 000000000000 -r cdd6a526bdcf test-data/constructs_muconate.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/constructs_muconate.csv	Wed Mar 30 13:05:31 2022 +0000
@@ -0,0 +1,89 @@
+Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10
+A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS2,O33948,U1-RBS2,O85675,,,,,,,,,,,,
+B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,O85675,U2-RBS2,O33948,,,,,,,,,,,,
+C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,,
+D1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,,
+E1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS1,O33948,U1-RBS3,O85675,,,,,,,,,,,,
+F1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS2,O85675,U2-RBS3,O33948,,,,,,,,,,,,
+G1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,,
+H1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS1,O33948,U1-RBS3,O85675,,,,,,,,,,,,
+A2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS2,O33948,U1-RBS3,O85675,,,,,,,,,,,,
+B2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS3,O33948,U1-RBS2,O85675,,,,,,,,,,,,
+C2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,,
+D2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U1-RBS1,O85675,U2-RBS1,O33948,,,,,,,,,,,,
+E2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,O85675,U2-RBS3,O33948,,,,,,,,,,,,
+F2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS2,O33948,U1-RBS3,O85675,,,,,,,,,,,,
+G2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS2,O85675,U2-RBS2,O33948,,,,,,,,,,,,
+H2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS2,O33948,U1-RBS2,O85675,,,,,,,,,,,,
+A3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS3,O33948,U1-RBS2,O85675,,,,,,,,,,,,
+B3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U1-RBS2,O85675,U2-RBS3,O33948,,,,,,,,,,,,
+C3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,O85675,U2-RBS3,O33948,,,,,,,,,,,,
+D3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS1,O33948,U1-RBS2,O85675,,,,,,,,,,,,
+E3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,,
+F3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,,
+G3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS3,O85675,U2-RBS1,O33948,,,,,,,,,,,,
+H3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,,
+A4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS3,O85675,U2-RBS2,O33948,,,,,,,,,,,,
+B4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,O85675,U2-RBS1,O33948,,,,,,,,,,,,
+C4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS1,O85675,U2-RBS2,O33948,,,,,,,,,,,,
+D4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U1-RBS2,O85675,U2-RBS2,O33948,,,,,,,,,,,,
+E4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,O85675,U2-RBS2,O33948,,,,,,,,,,,,
+F4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,,
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diff -r 000000000000 -r cdd6a526bdcf test-data/lycopene_CrtEBI_from_selenzy.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lycopene_CrtEBI_from_selenzy.xml	Wed Mar 30 13:05:31 2022 +0000
@@ -0,0 +1,393 @@
+<?xml version="1.0" encoding="UTF-8"?>
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+  <model metaid="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
+    <listOfCompartments>
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
+                  <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
+                </rdf:Bag>
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+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
+                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="MNXM83" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
+                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999_0" value="999999" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0_0" value="0" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_999999_0">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21684"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.29"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H].[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]&gt;&gt;[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H].O=P(O)(O)OP(=O)(O)O.O=P(O)(O)OP(=O)(O)O.O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:rp2_transfo_id value="TRS_0_2_363"/>
+                <brsynth:rule_ids>
+                  <brsynth:RR-02-90bcfd187709eb1b-16-F/>
+                </brsynth:rule_ids>
+                <brsynth:tmpl_rxn_ids>
+                  <brsynth:MNXR132232/>
+                </brsynth:tmpl_rxn_ids>
+                <brsynth:rule_score value="0.5869134225065102"/>
+                <brsynth:idx_in_path value="1"/>
+                <brsynth:selenzy_P21684>
+                  <brsynth:score value="85.958"/>
+                  <brsynth:target_ID value="553"/>
+                </brsynth:selenzy_P21684>
+                <brsynth:selenzy_P21683>
+                  <brsynth:score value="48.927"/>
+                  <brsynth:target_ID value="553"/>
+                </brsynth:selenzy_P21683>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="MNXM132" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM83" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM11" stoichiometry="3" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_999999_0">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21684"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.32"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.99"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.96"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]&gt;&gt;[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H].O=P(O)(O)OP(=O)(O)O.O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:rp2_transfo_id value="TRS_0_1_9"/>
+                <brsynth:rule_ids>
+                  <brsynth:RR-02-b25156a335e3e30f-16-F/>
+                </brsynth:rule_ids>
+                <brsynth:tmpl_rxn_ids>
+                  <brsynth:MNXR111250/>
+                  <brsynth:MNXR111499/>
+                  <brsynth:MNXR113543/>
+                  <brsynth:MNXR118024/>
+                  <brsynth:MNXR139549/>
+                </brsynth:tmpl_rxn_ids>
+                <brsynth:rule_score value="0.5683242688496836"/>
+                <brsynth:idx_in_path value="2"/>
+                <brsynth:selenzy_P21683>
+                  <brsynth:score value="91.9"/>
+                  <brsynth:target_ID value="553"/>
+                </brsynth:selenzy_P21683>
+                <brsynth:selenzy_P21684>
+                  <brsynth:score value="74.885"/>
+                  <brsynth:target_ID value="553"/>
+                </brsynth:selenzy_P21684>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_999999_0">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21685"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.31"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]&gt;&gt;[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:rp2_transfo_id value="TRS_0_0_1"/>
+                <brsynth:rule_ids>
+                  <brsynth:RR-02-bdf7d8715e2e4d93-16-F/>
+                </brsynth:rule_ids>
+                <brsynth:tmpl_rxn_ids>
+                  <brsynth:MNXR113128/>
+                </brsynth:tmpl_rxn_ids>
+                <brsynth:rule_score value="0.7486085128675456"/>
+                <brsynth:idx_in_path value="3"/>
+                <brsynth:selenzy_P21685>
+                  <brsynth:score value="81.82"/>
+                  <brsynth:target_ID value="553"/>
+                </brsynth:selenzy_P21685>
+                <brsynth:selenzy_P21683>
+                  <brsynth:score value="63.183"/>
+                  <brsynth:target_ID value="553"/>
+                </brsynth:selenzy_P21683>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM8975" stoichiometry="4" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="MNXM24" stoichiometry="4" constant="true"/>
+          <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+    </listOfReactions>
+    <groups:listOfGroups>
+      <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:global_score value="-1"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="rxn_1"/>
+          <groups:member groups:idRef="rxn_2"/>
+          <groups:member groups:idRef="rxn_3"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="CMPD_0000000003"/>
+          <groups:member groups:idRef="CMPD_0000000001"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="CMPD_0000000001"/>
+          <groups:member groups:idRef="MNXM132"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
+          <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="MNXM83"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM8975"/>
+          <groups:member groups:idRef="MNXM24"/>
+          <groups:member groups:idRef="MNXM11"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
+          <groups:member groups:idRef="MNXM132"/>
+          <groups:member groups:idRef="MNXM11"/>
+        </groups:listOfMembers>
+      </groups:group>
+    </groups:listOfGroups>
+  </model>
+</sbml>
diff -r 000000000000 -r cdd6a526bdcf test-data/muconate_example.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/muconate_example.xml	Wed Mar 30 13:05:31 2022 +0000
@@ -0,0 +1,5328 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false">
+  <model metaid="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
+    <listOfCompartments>
+      <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
+                  <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </annotation>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species metaid="_4a3e4e32a6db24e5ddaa18997f93519c4ef1c0172e96160cd56ad49ecf025995" id="MNXM5" name="MNXM5" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_4a3e4e32a6db24e5ddaa18997f93519c4ef1c0172e96160cd56ad49ecf025995">
+              <bqbiol:is>
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+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="N=C(O)c1ccc[n+](C2OC(COP(=O)(O)OP(=O)(O)OCC3OC(n4cnc5c(N)ncnc54)C(OP(=O)(O)O)C3O)C(O)C2O)c1"/>
+                <brsynth:inchi value="InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/p+1"/>
+                <brsynth:inchikey value="XJLXINKUBYWONI-UHFFFAOYSA-O"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
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+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
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+            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]Oc1c([H])c([H])c([H])c([H])c1O[H]"/>
+                <brsynth:inchi value="InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H"/>
+                <brsynth:inchikey value="YCIMNLLNPGFGHC-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="c18fc797adf5be2d9c14427deceaaecd152233bfd9b8c8ef9627274f3b2ee5da" id="MNXM4" name="MNXM4" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#c18fc797adf5be2d9c14427deceaaecd152233bfd9b8c8ef9627274f3b2ee5da">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#c18fc797adf5be2d9c14427deceaaecd152233bfd9b8c8ef9627274f3b2ee5da">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="O=O"/>
+                <brsynth:inchi value="InChI=1S/O2/c1-2"/>
+                <brsynth:inchikey value="MYMOFIZGZYHOMD-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_412740f4df65e5c27b3cb3342d9c78e498c4f5c7ed5c08bfd1e7bef604d5e466" id="MNXM188" name="MNXM188" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_412740f4df65e5c27b3cb3342d9c78e498c4f5c7ed5c08bfd1e7bef604d5e466">
+              <bqbiol:is>
+                <rdf:Bag/>
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+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_412740f4df65e5c27b3cb3342d9c78e498c4f5c7ed5c08bfd1e7bef604d5e466">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OC(=O)c1c([H])c([H])c([H])c([H])c1N([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C7H7NO2/c8-6-4-2-1-3-5(6)7(9)10/h1-4H,8H2,(H,9,10)"/>
+                <brsynth:inchikey value="RWZYAGGXGHYGMB-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <bqbiol:is>
+                <rdf:Bag/>
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+            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]"/>
+                <brsynth:inchi value="InChI=1S/C6H6O4/c7-5(8)3-1-2-4-6(9)10/h1-4H,(H,7,8)(H,9,10)"/>
+                <brsynth:inchikey value="TXXHDPDFNKHHGW-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb" id="MNXM6" name="MNXM6" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)"/>
+                <brsynth:inchikey value="ACFIXJIJDZMPPO-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
+              <bqbiol:is>
+                <rdf:Bag/>
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+            <rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H+]"/>
+                <brsynth:inchi value="InChI=1S/p+1"/>
+                <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
+              <bqbiol:is>
+                <rdf:Bag/>
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+            <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="O=C=O"/>
+                <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/>
+                <brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
+              <bqbiol:is>
+                <rdf:Bag/>
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+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="N"/>
+                <brsynth:inchi value="InChI=1S/H3N/h1H3"/>
+                <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999_0" value="999999" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0_0" value="0" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_999999_0">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P08684"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8HZ69"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P78329"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9HBI6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A1Z746"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P05181"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O60774"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8HZ70"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q7YS44"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8VHG0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8SPQ7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q5REK0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q28505"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q01740"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P97872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9Y2Z9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q99518"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8K2I3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P97501"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P50285"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P49326"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P31513"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P31512"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8K0C4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q5RE72"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q4R8S6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q16850"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8K4B7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q6IRI9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9EQ76"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8K4C0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P36365"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q64654"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q6GUQ4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q05421"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P33266"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8HYJ9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q4PJW3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q91WN4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O15229"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P51581"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P05182"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q95LA2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q95LA1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P49109"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P36366"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P49328"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O88867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O18963"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P36367"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q04799"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P32417"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P17636"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P17635"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P16549"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q7Q6A7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O46420"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9MZY0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q945B7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q1RLY6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q86PM2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P79383"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P08682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8S7V0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q2Q094"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q2Q093"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9MZS9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8S7E1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A4ZKM5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q5EFU4"/>
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+                <brsynth:selenzy_Q93099>
+                  <brsynth:score value="18.633"/>
+                  <brsynth:target_ID value="9606"/>
+                </brsynth:selenzy_Q93099>
+                <brsynth:selenzy_P51581>
+                  <brsynth:score value="18.551"/>
+                  <brsynth:target_ID value="10036"/>
+                </brsynth:selenzy_P51581>
+                <brsynth:selenzy_Q5RF05>
+                  <brsynth:score value="18.533"/>
+                  <brsynth:target_ID value="9601"/>
+                </brsynth:selenzy_Q5RF05>
+                <brsynth:selenzy_P21396>
+                  <brsynth:score value="18.478"/>
+                  <brsynth:target_ID value="10116"/>
+                </brsynth:selenzy_P21396>
+                <brsynth:selenzy_C0HJM0>
+                  <brsynth:score value="17.738"/>
+                  <brsynth:target_ID value="128967"/>
+                </brsynth:selenzy_C0HJM0>
+                <brsynth:selenzy_O44249>
+                  <brsynth:score value="17.738"/>
+                  <brsynth:target_ID value="7130"/>
+                </brsynth:selenzy_O44249>
+                <brsynth:selenzy_P11344>
+                  <brsynth:score value="17.738"/>
+                  <brsynth:target_ID value="10090"/>
+                </brsynth:selenzy_P11344>
+                <brsynth:selenzy_P14679>
+                  <brsynth:score value="17.738"/>
+                  <brsynth:target_ID value="9606"/>
+                </brsynth:selenzy_P14679>
+                <brsynth:selenzy_Q25519>
+                  <brsynth:score value="17.738"/>
+                  <brsynth:target_ID value="7130"/>
+                </brsynth:selenzy_Q25519>
+                <brsynth:selenzy_P05181>
+                  <brsynth:score value="17.651"/>
+                  <brsynth:target_ID value="9606"/>
+                </brsynth:selenzy_P05181>
+                <brsynth:selenzy_P33266>
+                  <brsynth:score value="17.551"/>
+                  <brsynth:target_ID value="9541"/>
+                </brsynth:selenzy_P33266>
+                <brsynth:selenzy_Q05421>
+                  <brsynth:score value="17.551"/>
+                  <brsynth:target_ID value="10090"/>
+                </brsynth:selenzy_Q05421>
+                <brsynth:selenzy_Q6GUQ4>
+                  <brsynth:score value="17.551"/>
+                  <brsynth:target_ID value="9544"/>
+                </brsynth:selenzy_Q6GUQ4>
+                <brsynth:selenzy_P35354>
+                  <brsynth:score value="17.509"/>
+                  <brsynth:target_ID value="9606"/>
+                </brsynth:selenzy_P35354>
+                <brsynth:selenzy_Q06278>
+                  <brsynth:score value="17.41"/>
+                  <brsynth:target_ID value="9606"/>
+                </brsynth:selenzy_Q06278>
+                <brsynth:selenzy_Q86B61>
+                  <brsynth:score value="16.553"/>
+                  <brsynth:target_ID value="7227"/>
+                </brsynth:selenzy_Q86B61>
+                <brsynth:selenzy_Q9BDE0>
+                  <brsynth:score value="16.538"/>
+                  <brsynth:target_ID value="9595"/>
+                </brsynth:selenzy_Q9BDE0>
+                <brsynth:selenzy_P55024>
+                  <brsynth:score value="15.638"/>
+                  <brsynth:target_ID value="9031"/>
+                </brsynth:selenzy_P55024>
+                <brsynth:selenzy_Q9VKJ0>
+                  <brsynth:score value="15.633"/>
+                  <brsynth:target_ID value="7227"/>
+                </brsynth:selenzy_Q9VKJ0>
+                <brsynth:selenzy_Q08410>
+                  <brsynth:score value="15.538"/>
+                  <brsynth:target_ID value="93934"/>
+                </brsynth:selenzy_Q08410>
+                <brsynth:selenzy_Q9V521>
+                  <brsynth:score value="14.738"/>
+                  <brsynth:target_ID value="7227"/>
+                </brsynth:selenzy_Q9V521>
+                <brsynth:selenzy_Q9W1V6>
+                  <brsynth:score value="14.738"/>
+                  <brsynth:target_ID value="7227"/>
+                </brsynth:selenzy_Q9W1V6>
+                <brsynth:selenzy_P55025>
+                  <brsynth:score value="14.638"/>
+                  <brsynth:target_ID value="8090"/>
+                </brsynth:selenzy_P55025>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM4" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="MNXM1" stoichiometry="2" constant="true"/>
+          <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+    </listOfReactions>
+    <groups:listOfGroups>
+      <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:global_score value="-1"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="rxn_1"/>
+          <groups:member groups:idRef="rxn_2"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="CMPD_0000000003"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="CMPD_0000000003"/>
+          <groups:member groups:idRef="MNXM4"/>
+          <groups:member groups:idRef="MNXM188"/>
+          <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="MNXM6"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM15"/>
+          <groups:member groups:idRef="MNXM1"/>
+          <groups:member groups:idRef="MNXM5"/>
+          <groups:member groups:idRef="MNXM13"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM5"/>
+          <groups:member groups:idRef="MNXM4"/>
+          <groups:member groups:idRef="MNXM188"/>
+          <groups:member groups:idRef="MNXM1"/>
+          <groups:member groups:idRef="MNXM6"/>
+          <groups:member groups:idRef="MNXM13"/>
+          <groups:member groups:idRef="MNXM15"/>
+        </groups:listOfMembers>
+      </groups:group>
+    </groups:listOfGroups>
+  </model>
+</sbml>
diff -r 000000000000 -r cdd6a526bdcf test-data/user_parts_plate_lycopene.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/user_parts_plate_lycopene.csv	Wed Mar 30 13:05:31 2022 +0000
@@ -0,0 +1,7 @@
+Part/linker,Well,Part concentration (ng/uL)
+BASIC_SEVA_37_CmR-p15A.1,A1,
+P21683,B1,
+P21684,C1,
+P21685,D1,
+PJ23101_BASIC,E1,
+PJ23119_BASIC,F1,
diff -r 000000000000 -r cdd6a526bdcf test-data/user_parts_plate_muconate.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/user_parts_plate_muconate.csv	Wed Mar 30 13:05:31 2022 +0000
@@ -0,0 +1,9 @@
+Part/linker,Well,Part concentration (ng/uL)
+BASIC_SEVA_37_CmR-p15A.1,A1,
+O33948,B1,
+O85675,C1,
+PJ23101_BASIC,D1,
+PJ23104_BASIC,E1,
+PJ23108_BASIC,F1,
+PJ23111_BASIC,G1,
+PJ23119_BASIC,H1,