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changeset 1:a9e9eb8a392c draft

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Uploaded
author tduigou
date Mon, 15 Nov 2021 13:20:34 +0000
parents 37185c8a8f46
children a38e9f95d155
files rpbasicdesign/rpbasicdesign.xml rpbasicdesign/test-data/BASIC_construct_A1.xml rpbasicdesign/test-data/BASIC_construct_A2.xml rpbasicdesign/test-data/BASIC_construct_A3.xml rpbasicdesign/test-data/BASIC_construct_B1.xml rpbasicdesign/test-data/BASIC_construct_C1.xml rpbasicdesign/test-data/constructs.csv rpbasicdesign/test-data/lycopene_CrtEBI_from_selenzy.xml rpbasicdesign/test-data/muconate_example.xml rpbasicdesign/test-data/user_parts_plate.csv
diffstat 10 files changed, 1360 insertions(+), 1738 deletions(-) [+]
line wrap: on
line diff
--- a/rpbasicdesign/rpbasicdesign.xml	Tue Oct 12 15:24:00 2021 +0000
+++ b/rpbasicdesign/rpbasicdesign.xml	Mon Nov 15 13:20:34 2021 +0000
@@ -1,7 +1,7 @@
-<tool id="rpbasicdesign" name="BasicDesign" version="0.3.1">
+<tool id="rpbasicdesign" name="BasicDesign" version="0.3.4">
     <description>Build DNA-BOT input files from rpSBML</description>
     <requirements>
-        <requirement type="package" version="0.3.1">rpbasicdesign</requirement>
+        <requirement type="package" version="0.3.4">rpbasicdesign</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         python -m rpbasicdesign.cli
@@ -34,73 +34,70 @@
         </section>
     </inputs>
     <outputs>
-        <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name}: constructs" />
-        <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name}: User parts plate"/>
-        <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name}: Biolegio plate"/>
-        <collection name="sbol_dir" type="list" label="${tool.name}: SBOL constructs">
+        <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} - ${rpsbml_file.name}: constructs" />
+        <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} - ${rpsbml_file.name}: User parts plate"/>
+        <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} - ${rpsbml_file.name}: Biolegio plate"/>
+        <collection name="sbol_dir" type="list" label="${tool.name} - ${rpsbml_file.name}: SBOL constructs">
             <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" />
         </collection>
     </outputs>
     <tests>
         <test>
         <!-- test 1: check if identical outputs are produced -->
-        <param name="rpsbml_file" value="muconate_example.xml" />
+        <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" />
         <param name="sample_size" value="3" />
         <output name="Constructs" file="constructs.csv" ftype="csv" compare="diff"/>
         <output name="User parts plate" file="user_parts_plate.csv" ftype="csv" compare="diff"/>
         <output name="Biolegio plate" file="biolegio_plate.csv" ftype="csv" compare="diff"/>
         <output_collection name="sbol_dir" type="list">
             <discovered_dataset designation="BASIC_construct_A1" ftype="xml" file="BASIC_construct_A1.xml"/>
-            <discovered_dataset designation="BASIC_construct_A2" ftype="xml" file="BASIC_construct_A2.xml"/>
-            <discovered_dataset designation="BASIC_construct_A3" ftype="xml" file="BASIC_construct_A3.xml"/>
+            <discovered_dataset designation="BASIC_construct_B1" ftype="xml" file="BASIC_construct_B1.xml"/>
+            <discovered_dataset designation="BASIC_construct_C1" ftype="xml" file="BASIC_construct_C1.xml"/>
         </output_collection>
         </test>
     </tests>
     <help><![CDATA[
-        usage: python -m rpbasicdesign.cli [-h] --rpsbml_file RPSBML_FILE
-
-                             [--parts_files PARTS_FILES [PARTS_FILES ...]]
-
-                             [--lms_id LMS_ID]
-                             [--lmp_id LMP_ID] [--backbone_id BACKBONE_ID]
-                             [--sample_size SAMPLE_SIZE]
-                             [--cds_permutation CDS_PERMUTATION]
-                             [--o_dnabot_dir O_DNABOT_DIR]
-                             [--o_sbol_dir O_SBOL_DIR]
+rpbasicdesign
+================
 
 Convert rpSBML enzyme info in to BASIC construct. UniProt IDs corresponding
-enzyme variants are extracted from rpSBMl files. Promoters and RBSs are
-randomly chosen from a default list. CDSs, in other words gene variants, of
-enzymes are randomly chosen from amongst the UniProt IDs extracted. Constructs
-generated can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as
-SBOL files.
+enzyme variants are extracted rpSBMl files. Promoters and RBSs are randomly
+chosen from a default list. CDSs, in other words gene variants, of enzymes are
+randomly chosen from amongst the UniProt IDs extracted. Constructs generated
+can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as SBOL
+files.
 
-optional arguments:
-  -h, --help            show this help message and exit
-  --rpsbml_file RPSBML_FILE
-                        rpSBML file from which enzymes UniProt IDs will be
-                        collected
+Input
+-----
 
-  --parts_files PARTS_FILES [PARTS_FILES ...]
-                        List of files providing available linkers and user
-                        parts (backbone, promoters, ...) for constructs.
+Required:
+
+* **rpsbml_file**\ : (string) rpSBML file from which enzymes UniProt IDs will be collected.
+
+Advanced options:
 
-  --lms_id LMS_ID       part ID to be used as the LMS methylated linker
-  --lmp_id LMP_ID       part ID to be used as the LMP methylated linker
-  --backbone_id BACKBONE_ID
-                        part ID to be used as the backbone
-  --sample_size SAMPLE_SIZE
-                        Number of construct to generate.
-  --cds_permutation CDS_PERMUTATION
-                        Whether all combinations of CDS permutation should be built Default: true
-  --o_dnabot_dir O_DNABOT_DIR
-                        Output folder to write construct and plate files.
-                        It will be created if it does not exist yet. Existing
-                        files will be overwritten. Default: out/dnabot_in
-  --o_sbol_dir O_SBOL_DIR
-                        Output folder to write SBOL depictions of constructs.
-                        It will be created if it does not exist yet. Existing
-                        files will be overwritten. Default: out/sbol_export
+* **parts_files**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, user_parts.csv]
+* **lms_id**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS.
+* **lmp_id**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP.
+* **backbone_id**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1.
+* **sample_size**\ : (int) Number of construct to generate.Default: 3.
+* **cds_permutation**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true.
+
+Output
+------
+
+* **o_dnabot_dir**\ : (string) Output folder to write construct and plate files. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/dnabot_in.
+* **o_sbol_dir**\ : (string) Output folder to write SBOL depictions of constructs. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/sbol_export.
+
+Project Links
+------------------
+
+* `GitHub <https://github.com/brsynth/rpbasicdesign>`_
+
+License
+-------
+
+* `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_
 
     ]]></help>
     <citations>
--- a/rpbasicdesign/test-data/BASIC_construct_A1.xml	Tue Oct 12 15:24:00 2021 +0000
+++ b/rpbasicdesign/test-data/BASIC_construct_A1.xml	Mon Nov 15 13:20:34 2021 +0000
@@ -1,339 +1,339 @@
 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#">
   <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1">
     <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/>
+    <sbol:version>1</sbol:version>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
     <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/>
     <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>
-    <sbol:version>1</sbol:version>
     <sbol:displayId>LMS</sbol:displayId>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
   </sbol:ComponentDefinition>
   <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1">
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
     <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/>
-    <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>
     <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/>
     <sbol:version>1</sbol:version>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>
+    <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>
   </sbol:ComponentDefinition>
   <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1">
     <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>
+    <sbol:displayId>LMP</sbol:displayId>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>
     <sbol:version>1</sbol:version>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>
     <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>
-    <sbol:displayId>LMP</sbol:displayId>
   </sbol:ComponentDefinition>
   <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23119_BASIC/1">
+    <sbol:version>1</sbol:version>
     <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:displayId>PJ23119_BASIC</sbol:displayId>
     <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23119_BASIC/1"/>
     <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:version>1</sbol:version>
-    <sbol:displayId>PJ23119_BASIC</sbol:displayId>
   </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS3/1">
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS3"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS3/1"/>
-    <sbol:version>1</sbol:version>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1">
+    <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/>
     <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
-    <sbol:displayId>U3_RBS3</sbol:displayId>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P31019/1">
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P31019"/>
-    <sbol:displayId>P31019</sbol:displayId>
-    <sbol:version>1</sbol:version>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/P31019/1"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS3/1">
-    <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS3/1"/>
-    <sbol:displayId>U2_RBS3</sbol:displayId>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS3"/>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/Q84BZ3/1">
-    <sbol:sequence rdf:resource="https://localhost/Sequence/Q84BZ3/1"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/Q84BZ3"/>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
-    <sbol:displayId>Q84BZ3</sbol:displayId>
+    <sbol:displayId>U1_RBS1</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/>
     <sbol:version>1</sbol:version>
     <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
   </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS2/1">
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS2"/>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1">
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/>
     <sbol:version>1</sbol:version>
-    <sbol:displayId>U1_RBS2</sbol:displayId>
     <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS2/1"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/>
+    <sbol:displayId>P21684</sbol:displayId>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1">
+    <sbol:displayId>U2_RBS1</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/>
+    <sbol:version>1</sbol:version>
     <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/>
   </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/Q8FB35/1">
-    <sbol:sequence rdf:resource="https://localhost/Sequence/Q8FB35/1"/>
-    <sbol:displayId>Q8FB35</sbol:displayId>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21683/1">
+    <sbol:displayId>P21683</sbol:displayId>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21683"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/P21683/1"/>
     <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/>
     <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/Q8FB35"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/>
+    <sbol:displayId>U3_RBS2</sbol:displayId>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21685/1">
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21685"/>
+    <sbol:displayId>P21685</sbol:displayId>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/P21685/1"/>
+    <sbol:version>1</sbol:version>
   </sbol:ComponentDefinition>
   <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/1">
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_7/1">
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_7"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:displayId>constraint_7</sbol:displayId>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/Q84BZ3_0/1"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS2_0/1"/>
-        <sbol:version>1</sbol:version>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_1/1">
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:displayId>constraint_1</sbol:displayId>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_1"/>
-        <sbol:version>1</sbol:version>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
     <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/Q8FB35_0/1">
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/Q8FB35_0"/>
-        <sbol:displayId>Q8FB35_0</sbol:displayId>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/Q8FB35/1"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_6/1">
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:displayId>constraint_6</sbol:displayId>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_6"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/Q84BZ3_0/1"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS3_0/1"/>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1">
+        <sbol:displayId>U3_RBS2_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS2/1"/>
         <sbol:version>1</sbol:version>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_8/1">
-        <sbol:displayId>constraint_8</sbol:displayId>
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_8"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/Q8FB35_0/1"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS2_0/1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_4/1">
-        <sbol:displayId>constraint_4</sbol:displayId>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_4"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS3_0/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P31019_0/1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/Q84BZ3_0/1">
-        <sbol:displayId>Q84BZ3_0</sbol:displayId>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/Q84BZ3/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/Q84BZ3_0"/>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1">
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>PJ23119_BASIC_0</sbol:displayId>
         <sbol:access rdf:resource="http://sbols.org/v2#public"/>
       </sbol:Component>
     </sbol:component>
     <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_0/1">
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_0"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0/1"/>
-        <sbol:displayId>constraint_0</sbol:displayId>
-        <sbol:version>1</sbol:version>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS3_0/1">
-        <sbol:displayId>U2_RBS3_0</sbol:displayId>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_5/1">
         <sbol:version>1</sbol:version>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS3/1"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS3_0"/>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1"/>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS3_0/1">
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS3/1"/>
-        <sbol:displayId>U3_RBS3_0</sbol:displayId>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS3_0"/>
-        <sbol:version>1</sbol:version>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_3/1">
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1"/>
+        <sbol:displayId>constraint_5</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_5"/>
         <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_3"/>
-        <sbol:displayId>constraint_3</sbol:displayId>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS3_0/1"/>
-        <sbol:version>1</sbol:version>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1"/>
       </sbol:SequenceConstraint>
     </sbol:sequenceConstraint>
     <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_2/1">
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"/>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_7/1">
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"/>
+        <sbol:displayId>constraint_7</sbol:displayId>
         <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"/>
-        <sbol:displayId>constraint_2</sbol:displayId>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_2"/>
         <sbol:version>1</sbol:version>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_7"/>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1"/>
       </sbol:SequenceConstraint>
     </sbol:sequenceConstraint>
+    <sbol:version>1</sbol:version>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1">
+        <sbol:version>1</sbol:version>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS1/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0"/>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:displayId>U1_RBS1_0</sbol:displayId>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1">
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0"/>
+        <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId>
+        <sbol:version>1</sbol:version>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1">
+        <sbol:version>1</sbol:version>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:displayId>P21684_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21684/1"/>
+      </sbol:Component>
+    </sbol:component>
     <sbol:component>
       <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0/1">
         <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0"/>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/>
         <sbol:displayId>LMS_0</sbol:displayId>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/>
-        <sbol:version>1</sbol:version>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_5/1">
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P31019_0/1"/>
-        <sbol:displayId>constraint_5</sbol:displayId>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_5"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS3_0/1"/>
         <sbol:version>1</sbol:version>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1">
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:displayId>LMP_0</sbol:displayId>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0"/>
-        <sbol:version>1</sbol:version>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:displayId>BASIC_construct_A1</sbol:displayId>
-    <sbol:version>1</sbol:version>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS2_0/1">
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS2/1"/>
-        <sbol:displayId>U1_RBS2_0</sbol:displayId>
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS2_0"/>
         <sbol:access rdf:resource="http://sbols.org/v2#public"/>
       </sbol:Component>
     </sbol:component>
     <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1">
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1">
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0"/>
+        <sbol:version>1</sbol:version>
+        <sbol:displayId>LMP_0</sbol:displayId>
         <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0"/>
-        <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId>
-        <sbol:version>1</sbol:version>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/>
       </sbol:Component>
     </sbol:component>
     <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P31019_0/1">
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P31019/1"/>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1">
         <sbol:version>1</sbol:version>
-        <sbol:displayId>P31019_0</sbol:displayId>
         <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P31019_0"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21683/1"/>
+        <sbol:displayId>P21683_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0"/>
       </sbol:Component>
     </sbol:component>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1"/>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_8/1">
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_8"/>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1"/>
+        <sbol:version>1</sbol:version>
+        <sbol:displayId>constraint_8</sbol:displayId>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_2/1">
+        <sbol:displayId>constraint_2</sbol:displayId>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"/>
+        <sbol:version>1</sbol:version>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_2"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
+    <sbol:displayId>BASIC_construct_A1</sbol:displayId>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_0/1">
+        <sbol:displayId>constraint_0</sbol:displayId>
+        <sbol:version>1</sbol:version>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_0"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_6/1">
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:displayId>constraint_6</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_6"/>
+        <sbol:version>1</sbol:version>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1">
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC/1"/>
+        <sbol:version>1</sbol:version>
+        <sbol:displayId>PJ23119_BASIC_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0"/>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1">
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS1/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0"/>
+        <sbol:version>1</sbol:version>
+        <sbol:displayId>U2_RBS1_0</sbol:displayId>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_3/1">
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1"/>
+        <sbol:version>1</sbol:version>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_3"/>
+        <sbol:displayId>constraint_3</sbol:displayId>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0/1">
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0"/>
+        <sbol:version>1</sbol:version>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:displayId>P21685_0</sbol:displayId>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21685/1"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_1/1">
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_1"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"/>
+        <sbol:displayId>constraint_1</sbol:displayId>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_4/1">
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_4"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:version>1</sbol:version>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1"/>
+        <sbol:displayId>constraint_4</sbol:displayId>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
   </sbol:ComponentDefinition>
   <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1">
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>
     <sbol:displayId>LMS</sbol:displayId>
-    <sbol:version>1</sbol:version>
     <sbol:elements></sbol:elements>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>
   </sbol:Sequence>
   <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1">
     <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>
     <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
     <sbol:elements></sbol:elements>
     <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>
   </sbol:Sequence>
   <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1">
     <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
     <sbol:version>1</sbol:version>
+    <sbol:displayId>LMP</sbol:displayId>
     <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/>
-    <sbol:displayId>LMP</sbol:displayId>
     <sbol:elements></sbol:elements>
   </sbol:Sequence>
   <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23119_BASIC/1">
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23119_BASIC"/>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:version>1</sbol:version>
-    <sbol:displayId>PJ23119_BASIC</sbol:displayId>
-    <sbol:elements></sbol:elements>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS3/1">
-    <sbol:displayId>U3_RBS3</sbol:displayId>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS3"/>
     <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
     <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23119_BASIC"/>
     <sbol:elements></sbol:elements>
+    <sbol:displayId>PJ23119_BASIC</sbol:displayId>
   </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/P31019/1">
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P31019"/>
-    <sbol:elements>atgc</sbol:elements>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:displayId>P31019</sbol:displayId>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS3/1">
-    <sbol:displayId>U2_RBS3</sbol:displayId>
-    <sbol:version>1</sbol:version>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1">
     <sbol:elements></sbol:elements>
     <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS3"/>
+    <sbol:displayId>U1_RBS1</sbol:displayId>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/>
   </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/Q84BZ3/1">
+  <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1">
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
     <sbol:elements>atgc</sbol:elements>
-    <sbol:displayId>Q84BZ3</sbol:displayId>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/>
+    <sbol:displayId>P21684</sbol:displayId>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1">
+    <sbol:displayId>U2_RBS1</sbol:displayId>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:elements></sbol:elements>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/>
     <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/Q84BZ3"/>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/>
     <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:displayId>P21683</sbol:displayId>
+    <sbol:elements>atgc</sbol:elements>
+    <sbol:version>1</sbol:version>
   </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS2/1">
+  <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1">
     <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
     <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/>
+    <sbol:displayId>U3_RBS2</sbol:displayId>
     <sbol:elements></sbol:elements>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS2"/>
-    <sbol:displayId>U1_RBS2</sbol:displayId>
   </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/Q8FB35/1">
+  <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/>
+    <sbol:elements>atgc</sbol:elements>
     <sbol:version>1</sbol:version>
+    <sbol:displayId>P21685</sbol:displayId>
     <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/Q8FB35"/>
-    <sbol:elements>atgc</sbol:elements>
-    <sbol:displayId>Q8FB35</sbol:displayId>
   </sbol:Sequence>
 </rdf:RDF>
--- a/rpbasicdesign/test-data/BASIC_construct_A2.xml	Tue Oct 12 15:24:00 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,339 +0,0 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#">
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1">
-    <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>
-    <sbol:version>1</sbol:version>
-    <sbol:displayId>LMS</sbol:displayId>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1">
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/>
-    <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/>
-    <sbol:version>1</sbol:version>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1">
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>
-    <sbol:version>1</sbol:version>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>
-    <sbol:displayId>LMP</sbol:displayId>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1">
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
-    <sbol:displayId>PJ23101_BASIC</sbol:displayId>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:version>1</sbol:version>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1">
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
-    <sbol:version>1</sbol:version>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/>
-    <sbol:displayId>U2_RBS1</sbol:displayId>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/O85674/1">
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/O85674"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:displayId>O85674</sbol:displayId>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/O85674/1"/>
-    <sbol:version>1</sbol:version>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1">
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
-    <sbol:displayId>U3_RBS2</sbol:displayId>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/>
-    <sbol:version>1</sbol:version>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/Q43984/1">
-    <sbol:sequence rdf:resource="https://localhost/Sequence/Q43984/1"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
-    <sbol:version>1</sbol:version>
-    <sbol:displayId>Q43984</sbol:displayId>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/Q43984"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS3/1">
-    <sbol:version>1</sbol:version>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS3/1"/>
-    <sbol:displayId>U1_RBS3</sbol:displayId>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS3"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/Q3KIF2/1">
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
-    <sbol:displayId>Q3KIF2</sbol:displayId>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/Q3KIF2/1"/>
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/Q3KIF2"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/1">
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2"/>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_3/1">
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/U2_RBS1_0/1"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_3"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/PJ23101_BASIC_0/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>constraint_3</sbol:displayId>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/U1_RBS3_0/1">
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS3/1"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/U1_RBS3_0"/>
-        <sbol:version>1</sbol:version>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:displayId>U1_RBS3_0</sbol:displayId>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/Q3KIF2_0/1">
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/Q3KIF2_0"/>
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>Q3KIF2_0</sbol:displayId>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/Q3KIF2/1"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/U2_RBS1_0/1">
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS1/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:displayId>U2_RBS1_0</sbol:displayId>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/U2_RBS1_0"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/BASIC_SEVA_37_CmR_p15A_1_0/1">
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/BASIC_SEVA_37_CmR_p15A_1_0"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/>
-        <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId>
-        <sbol:version>1</sbol:version>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_4/1">
-        <sbol:displayId>constraint_4</sbol:displayId>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_4"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/U2_RBS1_0/1"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/O85674_0/1"/>
-        <sbol:version>1</sbol:version>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_6/1">
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/U3_RBS2_0/1"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_6"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/Q43984_0/1"/>
-        <sbol:displayId>constraint_6</sbol:displayId>
-        <sbol:version>1</sbol:version>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/LMS_0/1">
-        <sbol:displayId>LMS_0</sbol:displayId>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/LMS_0"/>
-        <sbol:version>1</sbol:version>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_7/1">
-        <sbol:version>1</sbol:version>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/Q43984_0/1"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_7"/>
-        <sbol:displayId>constraint_7</sbol:displayId>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/U1_RBS3_0/1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/U3_RBS2_0/1">
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/U3_RBS2_0"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS2/1"/>
-        <sbol:displayId>U3_RBS2_0</sbol:displayId>
-        <sbol:version>1</sbol:version>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_0/1">
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_0"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:displayId>constraint_0</sbol:displayId>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/LMS_0/1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_1/1">
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/LMP_0/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>constraint_1</sbol:displayId>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/Q43984_0/1">
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/Q43984/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>Q43984_0</sbol:displayId>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/Q43984_0"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_2/1">
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_2"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/PJ23101_BASIC_0/1"/>
-        <sbol:displayId>constraint_2</sbol:displayId>
-        <sbol:version>1</sbol:version>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/LMP_0/1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:displayId>BASIC_construct_A2</sbol:displayId>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/PJ23101_BASIC_0/1">
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>PJ23101_BASIC_0</sbol:displayId>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/PJ23101_BASIC_0"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC/1"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_8/1">
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/U1_RBS3_0/1"/>
-        <sbol:displayId>constraint_8</sbol:displayId>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_8"/>
-        <sbol:version>1</sbol:version>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/Q3KIF2_0/1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/O85674_0/1">
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:displayId>O85674_0</sbol:displayId>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/O85674_0"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/O85674/1"/>
-        <sbol:version>1</sbol:version>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:version>1</sbol:version>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/LMP_0/1">
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>LMP_0</sbol:displayId>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/LMP_0"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_5/1">
-        <sbol:version>1</sbol:version>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/O85674_0/1"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/U3_RBS2_0/1"/>
-        <sbol:displayId>constraint_5</sbol:displayId>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A2/constraint_5"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-  </sbol:ComponentDefinition>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1">
-    <sbol:displayId>LMS</sbol:displayId>
-    <sbol:version>1</sbol:version>
-    <sbol:elements></sbol:elements>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1">
-    <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:elements></sbol:elements>
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1">
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/>
-    <sbol:displayId>LMP</sbol:displayId>
-    <sbol:elements></sbol:elements>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1">
-    <sbol:displayId>PJ23101_BASIC</sbol:displayId>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/>
-    <sbol:elements></sbol:elements>
-    <sbol:version>1</sbol:version>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1">
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/>
-    <sbol:version>1</sbol:version>
-    <sbol:displayId>U2_RBS1</sbol:displayId>
-    <sbol:elements></sbol:elements>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/O85674/1">
-    <sbol:elements>atgc</sbol:elements>
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/O85674"/>
-    <sbol:displayId>O85674</sbol:displayId>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1">
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/>
-    <sbol:displayId>U3_RBS2</sbol:displayId>
-    <sbol:elements></sbol:elements>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/Q43984/1">
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/Q43984"/>
-    <sbol:elements>atgc</sbol:elements>
-    <sbol:displayId>Q43984</sbol:displayId>
-    <sbol:version>1</sbol:version>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS3/1">
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS3"/>
-    <sbol:elements></sbol:elements>
-    <sbol:displayId>U1_RBS3</sbol:displayId>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/Q3KIF2/1">
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/Q3KIF2"/>
-    <sbol:displayId>Q3KIF2</sbol:displayId>
-    <sbol:elements>atgc</sbol:elements>
-  </sbol:Sequence>
-</rdf:RDF>
--- a/rpbasicdesign/test-data/BASIC_construct_A3.xml	Tue Oct 12 15:24:00 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,339 +0,0 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#">
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1">
-    <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>
-    <sbol:version>1</sbol:version>
-    <sbol:displayId>LMS</sbol:displayId>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1">
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/>
-    <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/>
-    <sbol:version>1</sbol:version>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1">
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>
-    <sbol:version>1</sbol:version>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>
-    <sbol:displayId>LMP</sbol:displayId>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1">
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
-    <sbol:displayId>PJ23101_BASIC</sbol:displayId>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:version>1</sbol:version>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS3/1">
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS3"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS3/1"/>
-    <sbol:version>1</sbol:version>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
-    <sbol:displayId>U3_RBS3</sbol:displayId>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P95607/1">
-    <sbol:displayId>P95607</sbol:displayId>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P95607"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:version>1</sbol:version>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/P95607/1"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS2/1">
-    <sbol:version>1</sbol:version>
-    <sbol:displayId>U2_RBS2</sbol:displayId>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS2/1"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS2"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P23262/1">
-    <sbol:sequence rdf:resource="https://localhost/Sequence/P23262/1"/>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P23262"/>
-    <sbol:displayId>P23262</sbol:displayId>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1">
-    <sbol:displayId>U1_RBS1</sbol:displayId>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/>
-    <sbol:version>1</sbol:version>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/Q5QUP2/1">
-    <sbol:version>1</sbol:version>
-    <sbol:displayId>Q5QUP2</sbol:displayId>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/Q5QUP2"/>
-    <sbol:sequence rdf:resource="https://localhost/Sequence/Q5QUP2/1"/>
-    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-  </sbol:ComponentDefinition>
-  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/1">
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/Q5QUP2_0/1">
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/Q5QUP2/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>Q5QUP2_0</sbol:displayId>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/Q5QUP2_0"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_8/1">
-        <sbol:displayId>constraint_8</sbol:displayId>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/Q5QUP2_0/1"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/U1_RBS1_0/1"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_8"/>
-        <sbol:version>1</sbol:version>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:version>1</sbol:version>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_1/1">
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/LMP_0/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>constraint_1</sbol:displayId>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_1"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_7/1">
-        <sbol:version>1</sbol:version>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/P23262_0/1"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_7"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/U1_RBS1_0/1"/>
-        <sbol:displayId>constraint_7</sbol:displayId>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_5/1">
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_5"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/U2_RBS2_0/1"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:displayId>constraint_5</sbol:displayId>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/P95607_0/1"/>
-        <sbol:version>1</sbol:version>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/LMS_0/1">
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/LMS_0"/>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:displayId>LMS_0</sbol:displayId>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/BASIC_SEVA_37_CmR_p15A_1_0/1">
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/BASIC_SEVA_37_CmR_p15A_1_0"/>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/>
-        <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId>
-        <sbol:version>1</sbol:version>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/P23262_0/1">
-        <sbol:displayId>P23262_0</sbol:displayId>
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/P23262_0"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P23262/1"/>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_3/1">
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/PJ23101_BASIC_0/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_3"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/U3_RBS3_0/1"/>
-        <sbol:displayId>constraint_3</sbol:displayId>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/U2_RBS2_0/1">
-        <sbol:displayId>U2_RBS2_0</sbol:displayId>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/U2_RBS2_0"/>
-        <sbol:version>1</sbol:version>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS2/1"/>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/U3_RBS3_0/1">
-        <sbol:displayId>U3_RBS3_0</sbol:displayId>
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/U3_RBS3_0"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS3/1"/>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/PJ23101_BASIC_0/1">
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>PJ23101_BASIC_0</sbol:displayId>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/PJ23101_BASIC_0"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_6/1">
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/P23262_0/1"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/U2_RBS2_0/1"/>
-        <sbol:displayId>constraint_6</sbol:displayId>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_6"/>
-        <sbol:version>1</sbol:version>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_4/1">
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>constraint_4</sbol:displayId>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_4"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/U3_RBS3_0/1"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/P95607_0/1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/U1_RBS1_0/1">
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/U1_RBS1_0"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS1/1"/>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:displayId>U1_RBS1_0</sbol:displayId>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
-    <sbol:displayId>BASIC_construct_A3</sbol:displayId>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_2/1">
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_2"/>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/PJ23101_BASIC_0/1"/>
-        <sbol:displayId>constraint_2</sbol:displayId>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/LMP_0/1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:sequenceConstraint>
-      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_0/1">
-        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/constraint_0"/>
-        <sbol:displayId>constraint_0</sbol:displayId>
-        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
-        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/LMS_0/1"/>
-      </sbol:SequenceConstraint>
-    </sbol:sequenceConstraint>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/LMP_0/1">
-        <sbol:version>1</sbol:version>
-        <sbol:displayId>LMP_0</sbol:displayId>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/LMP_0"/>
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:component>
-      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A3/P95607_0/1">
-        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P95607/1"/>
-        <sbol:version>1</sbol:version>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-        <sbol:displayId>P95607_0</sbol:displayId>
-        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3/P95607_0"/>
-      </sbol:Component>
-    </sbol:component>
-    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A3"/>
-  </sbol:ComponentDefinition>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1">
-    <sbol:displayId>LMS</sbol:displayId>
-    <sbol:version>1</sbol:version>
-    <sbol:elements></sbol:elements>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1">
-    <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:elements></sbol:elements>
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1">
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/>
-    <sbol:displayId>LMP</sbol:displayId>
-    <sbol:elements></sbol:elements>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1">
-    <sbol:displayId>PJ23101_BASIC</sbol:displayId>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/>
-    <sbol:elements></sbol:elements>
-    <sbol:version>1</sbol:version>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS3/1">
-    <sbol:displayId>U3_RBS3</sbol:displayId>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS3"/>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:version>1</sbol:version>
-    <sbol:elements></sbol:elements>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/P95607/1">
-    <sbol:version>1</sbol:version>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P95607"/>
-    <sbol:displayId>P95607</sbol:displayId>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:elements>atgc</sbol:elements>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS2/1">
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS2"/>
-    <sbol:version>1</sbol:version>
-    <sbol:displayId>U2_RBS2</sbol:displayId>
-    <sbol:elements></sbol:elements>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/P23262/1">
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P23262"/>
-    <sbol:displayId>P23262</sbol:displayId>
-    <sbol:elements>atgc</sbol:elements>
-    <sbol:version>1</sbol:version>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1">
-    <sbol:displayId>U1_RBS1</sbol:displayId>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:version>1</sbol:version>
-    <sbol:elements></sbol:elements>
-  </sbol:Sequence>
-  <sbol:Sequence rdf:about="https://localhost/Sequence/Q5QUP2/1">
-    <sbol:version>1</sbol:version>
-    <sbol:displayId>Q5QUP2</sbol:displayId>
-    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
-    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/Q5QUP2"/>
-    <sbol:elements>atgc</sbol:elements>
-  </sbol:Sequence>
-</rdf:RDF>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/BASIC_construct_B1.xml	Mon Nov 15 13:20:34 2021 +0000
@@ -0,0 +1,339 @@
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#">
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1">
+    <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/>
+    <sbol:version>1</sbol:version>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>
+    <sbol:displayId>LMS</sbol:displayId>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1">
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/>
+    <sbol:version>1</sbol:version>
+    <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1">
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>
+    <sbol:displayId>LMP</sbol:displayId>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1">
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:displayId>PJ23101_BASIC</sbol:displayId>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/>
+    <sbol:version>1</sbol:version>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS3/1">
+    <sbol:displayId>U1_RBS3</sbol:displayId>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:version>1</sbol:version>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS3/1"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS3"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1">
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/>
+    <sbol:version>1</sbol:version>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/>
+    <sbol:displayId>P21684</sbol:displayId>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1">
+    <sbol:displayId>U2_RBS1</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/>
+    <sbol:version>1</sbol:version>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21683/1">
+    <sbol:displayId>P21683</sbol:displayId>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21683"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/P21683/1"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/>
+    <sbol:version>1</sbol:version>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/>
+    <sbol:displayId>U3_RBS2</sbol:displayId>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21685/1">
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21685"/>
+    <sbol:displayId>P21685</sbol:displayId>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/P21685/1"/>
+    <sbol:version>1</sbol:version>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/1">
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_1/1">
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:version>1</sbol:version>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_1"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
+        <sbol:displayId>constraint_1</sbol:displayId>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0/1"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:displayId>P21684_0</sbol:displayId>
+        <sbol:version>1</sbol:version>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21684/1"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_7/1">
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_7"/>
+        <sbol:version>1</sbol:version>
+        <sbol:displayId>constraint_7</sbol:displayId>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0/1"/>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0/1">
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS1/1"/>
+        <sbol:version>1</sbol:version>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:displayId>U2_RBS1_0</sbol:displayId>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0/1">
+        <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0"/>
+        <sbol:version>1</sbol:version>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_3/1">
+        <sbol:displayId>constraint_3</sbol:displayId>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0/1"/>
+        <sbol:version>1</sbol:version>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_3"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_6/1">
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:displayId>constraint_6</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_6"/>
+        <sbol:version>1</sbol:version>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0/1"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0/1">
+        <sbol:displayId>U3_RBS2_0</sbol:displayId>
+        <sbol:version>1</sbol:version>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS2/1"/>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_4/1">
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:displayId>constraint_4</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_4"/>
+        <sbol:version>1</sbol:version>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0/1"/>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0/1"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0/1">
+        <sbol:version>1</sbol:version>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0"/>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS3/1"/>
+        <sbol:displayId>U1_RBS3_0</sbol:displayId>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1"/>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_5/1">
+        <sbol:displayId>constraint_5</sbol:displayId>
+        <sbol:version>1</sbol:version>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0/1"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_5"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0/1">
+        <sbol:version>1</sbol:version>
+        <sbol:displayId>LMP_0</sbol:displayId>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/LMS_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:version>1</sbol:version>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/>
+        <sbol:displayId>LMS_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMS_0"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:displayId>BASIC_construct_B1</sbol:displayId>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/P21685_0/1">
+        <sbol:displayId>P21685_0</sbol:displayId>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21685/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21685_0"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0/1">
+        <sbol:version>1</sbol:version>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0"/>
+        <sbol:displayId>PJ23101_BASIC_0</sbol:displayId>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_8/1">
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0/1"/>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21685_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:version>1</sbol:version>
+        <sbol:displayId>constraint_8</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_8"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:displayId>P21683_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21683/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_0/1">
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_0"/>
+        <sbol:version>1</sbol:version>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
+        <sbol:displayId>constraint_0</sbol:displayId>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMS_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:version>1</sbol:version>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_2/1">
+        <sbol:version>1</sbol:version>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0/1"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:displayId>constraint_2</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_2"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+  </sbol:ComponentDefinition>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1">
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>
+    <sbol:displayId>LMS</sbol:displayId>
+    <sbol:elements></sbol:elements>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1">
+    <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:elements></sbol:elements>
+    <sbol:version>1</sbol:version>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1">
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+    <sbol:displayId>LMP</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/>
+    <sbol:elements></sbol:elements>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/>
+    <sbol:displayId>PJ23101_BASIC</sbol:displayId>
+    <sbol:elements></sbol:elements>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS3/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS3"/>
+    <sbol:elements></sbol:elements>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+    <sbol:displayId>U1_RBS3</sbol:displayId>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1">
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:elements>atgc</sbol:elements>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/>
+    <sbol:displayId>P21684</sbol:displayId>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1">
+    <sbol:displayId>U2_RBS1</sbol:displayId>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:elements></sbol:elements>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/>
+    <sbol:version>1</sbol:version>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:displayId>P21683</sbol:displayId>
+    <sbol:elements>atgc</sbol:elements>
+    <sbol:version>1</sbol:version>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1">
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/>
+    <sbol:displayId>U3_RBS2</sbol:displayId>
+    <sbol:elements></sbol:elements>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/>
+    <sbol:elements>atgc</sbol:elements>
+    <sbol:version>1</sbol:version>
+    <sbol:displayId>P21685</sbol:displayId>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+  </sbol:Sequence>
+</rdf:RDF>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/BASIC_construct_C1.xml	Mon Nov 15 13:20:34 2021 +0000
@@ -0,0 +1,339 @@
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#">
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1">
+    <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/>
+    <sbol:version>1</sbol:version>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>
+    <sbol:displayId>LMS</sbol:displayId>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1">
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/>
+    <sbol:version>1</sbol:version>
+    <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1">
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>
+    <sbol:displayId>LMP</sbol:displayId>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1">
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:displayId>PJ23101_BASIC</sbol:displayId>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/>
+    <sbol:version>1</sbol:version>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1">
+    <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
+    <sbol:displayId>U1_RBS1</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/>
+    <sbol:version>1</sbol:version>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1">
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/>
+    <sbol:version>1</sbol:version>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/>
+    <sbol:displayId>P21684</sbol:displayId>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/>
+    <sbol:version>1</sbol:version>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/>
+    <sbol:displayId>U3_RBS2</sbol:displayId>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21685/1">
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21685"/>
+    <sbol:displayId>P21685</sbol:displayId>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/P21685/1"/>
+    <sbol:version>1</sbol:version>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS2/1">
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
+    <sbol:displayId>U2_RBS2</sbol:displayId>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS2/1"/>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS2"/>
+    <sbol:version>1</sbol:version>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21683/1">
+    <sbol:displayId>P21683</sbol:displayId>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21683"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:sequence rdf:resource="https://localhost/Sequence/P21683/1"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1"/>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0/1">
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21685/1"/>
+        <sbol:version>1</sbol:version>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0"/>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:displayId>P21685_0</sbol:displayId>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0/1">
+        <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0"/>
+        <sbol:version>1</sbol:version>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0/1">
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0"/>
+        <sbol:version>1</sbol:version>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21684/1"/>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:displayId>P21684_0</sbol:displayId>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:version>1</sbol:version>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_6/1">
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0/1"/>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:displayId>constraint_6</sbol:displayId>
+        <sbol:version>1</sbol:version>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_6"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_4/1">
+        <sbol:displayId>constraint_4</sbol:displayId>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_4"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:version>1</sbol:version>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0/1"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0/1">
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0"/>
+        <sbol:version>1</sbol:version>
+        <sbol:displayId>LMP_0</sbol:displayId>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/P21683_0/1">
+        <sbol:displayId>P21683_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21683_0"/>
+        <sbol:version>1</sbol:version>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21683/1"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0/1">
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS2/1"/>
+        <sbol:displayId>U2_RBS2_0</sbol:displayId>
+        <sbol:version>1</sbol:version>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_5/1">
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_5"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0/1"/>
+        <sbol:version>1</sbol:version>
+        <sbol:displayId>constraint_5</sbol:displayId>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_8/1">
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:displayId>constraint_8</sbol:displayId>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21683_0/1"/>
+        <sbol:version>1</sbol:version>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_8"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_2/1">
+        <sbol:displayId>constraint_2</sbol:displayId>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_2"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_3/1">
+        <sbol:version>1</sbol:version>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_3"/>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0/1"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0/1"/>
+        <sbol:displayId>constraint_3</sbol:displayId>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/LMS_0/1">
+        <sbol:displayId>LMS_0</sbol:displayId>
+        <sbol:version>1</sbol:version>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMS_0"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0/1">
+        <sbol:displayId>U1_RBS1_0</sbol:displayId>
+        <sbol:version>1</sbol:version>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS1/1"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_1/1">
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
+        <sbol:version>1</sbol:version>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0/1"/>
+        <sbol:displayId>constraint_1</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_1"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0/1">
+        <sbol:displayId>U3_RBS2_0</sbol:displayId>
+        <sbol:version>1</sbol:version>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS2/1"/>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0"/>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_7/1">
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_7"/>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0/1"/>
+        <sbol:displayId>constraint_7</sbol:displayId>
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:displayId>BASIC_construct_C1</sbol:displayId>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_0/1">
+        <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMS_0/1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:displayId>constraint_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_0"/>
+        <sbol:version>1</sbol:version>
+        <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0/1"/>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:component>
+      <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC/1"/>
+        <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0"/>
+        <sbol:displayId>PJ23101_BASIC_0</sbol:displayId>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+  </sbol:ComponentDefinition>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1">
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>
+    <sbol:displayId>LMS</sbol:displayId>
+    <sbol:elements></sbol:elements>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1">
+    <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:elements></sbol:elements>
+    <sbol:version>1</sbol:version>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1">
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+    <sbol:displayId>LMP</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/>
+    <sbol:elements></sbol:elements>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/>
+    <sbol:displayId>PJ23101_BASIC</sbol:displayId>
+    <sbol:elements></sbol:elements>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1">
+    <sbol:elements></sbol:elements>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:displayId>U1_RBS1</sbol:displayId>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1">
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:elements>atgc</sbol:elements>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/>
+    <sbol:displayId>P21684</sbol:displayId>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1">
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/>
+    <sbol:displayId>U3_RBS2</sbol:displayId>
+    <sbol:elements></sbol:elements>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/>
+    <sbol:elements>atgc</sbol:elements>
+    <sbol:version>1</sbol:version>
+    <sbol:displayId>P21685</sbol:displayId>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS2/1">
+    <sbol:displayId>U2_RBS2</sbol:displayId>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+    <sbol:elements></sbol:elements>
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS2"/>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1">
+    <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:displayId>P21683</sbol:displayId>
+    <sbol:elements>atgc</sbol:elements>
+    <sbol:version>1</sbol:version>
+  </sbol:Sequence>
+</rdf:RDF>
--- a/rpbasicdesign/test-data/constructs.csv	Tue Oct 12 15:24:00 2021 +0000
+++ b/rpbasicdesign/test-data/constructs.csv	Mon Nov 15 13:20:34 2021 +0000
@@ -1,4 +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,U3-RBS3,P31019,U2-RBS3,Q84BZ3,U1-RBS2,Q8FB35,,,,,,,,,,
-A2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS1,O85674,U3-RBS2,Q43984,U1-RBS3,Q3KIF2,,,,,,,,,,
-A3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U3-RBS3,P95607,U2-RBS2,P23262,U1-RBS1,Q5QUP2,,,,,,,,,,
+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,,,,,,,,,,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/lycopene_CrtEBI_from_selenzy.xml	Mon Nov 15 13:20:34 2021 +0000
@@ -0,0 +1,393 @@
+<?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="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
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+                <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
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+                <brsynth:inchikey value="CBIDRCWHNCKSTO-UHFFFAOYSA-N"/>
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+                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
+                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
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+      <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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+            <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
+              <bqbiol:is>
+                <rdf:Bag/>
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+            <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
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+        </annotation>
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+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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+                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
+                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
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+                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
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+    </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>
--- a/rpbasicdesign/test-data/muconate_example.xml	Tue Oct 12 15:24:00 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,762 +0,0 @@
-<?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="_18c8363b353eb1a7e07d55a06341eb4d95a6b814d979179b3ce92dbf96f781d1" id="RP_model_10_1" name="RetroPath_Pathway_10_1" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
-    <listOfUnitDefinitions>
-      <unitDefinition metaid="_226864b81a892b72349b14689476616d515915efae9ce2fdae39d3e2d35080b7" id="mmol_per_gDW_per_hr">
-        <listOfUnits>
-          <unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
-          <unit kind="gram" exponent="1" scale="0" multiplier="1"/>
-          <unit kind="second" exponent="1" scale="0" multiplier="3600"/>
-        </listOfUnits>
-      </unitDefinition>
-      <unitDefinition metaid="_51acbb7fb816c66b4d28658c5a27b3f2f82eb1a3128d2be53ea26ba2512c7988" id="kj_per_mol">
-        <listOfUnits>
-          <unit kind="joule" exponent="1" scale="3" multiplier="1"/>
-          <unit kind="mole" exponent="-1" scale="1" multiplier="1"/>
-        </listOfUnits>
-      </unitDefinition>
-    </listOfUnitDefinitions>
-    <listOfCompartments>
-      <compartment metaid="_0c32e77f2fb959353e7468bcfd34f77e3ccdf372ee7cbfb421adaa62487323c0" sboTerm="SBO:0000290" id="MNXC3" 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="#_0c32e77f2fb959353e7468bcfd34f77e3ccdf372ee7cbfb421adaa62487323c0">
-              <bqbiol:is>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
-                  <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
-                  <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
-                  <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
-                  <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
-                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
-                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
-                </rdf:Bag>
-              </bqbiol:is>
-            </rdf:Description>
-          </rdf:RDF>
-        </annotation>
-      </compartment>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species metaid="_7eabbfed5f4f0a7a6fcb6d4590d6ea021f0bee237a58f70a612c8d09a8605b26" id="CMPD_0000000007__64__MNXC3" name="CMPD_0000000007" compartment="MNXC3" 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="#_7eabbfed5f4f0a7a6fcb6d4590d6ea021f0bee237a58f70a612c8d09a8605b26">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_7eabbfed5f4f0a7a6fcb6d4590d6ea021f0bee237a58f70a612c8d09a8605b26">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003__64__MNXC3" name="CMPD_0000000003" compartment="MNXC3" 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>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
-            </rdf:BRSynth>
-          </rdf:RDF>
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-          <speciesReference species="MNXM23__64__MNXC3" stoichiometry="1" constant="true"/>
-        </listOfProducts>
-      </reaction>
-      <reaction metaid="_4644b875fd2f70367b26dd66a105776b25947b502d29cc4790c2d4b6c4691823" sboTerm="SBO:0000176" id="rxn_target" reversible="true" fast="false" fbc:lowerFluxBound="B_0" fbc:upperFluxBound="B_999999">
-        <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="#_4644b875fd2f70367b26dd66a105776b25947b502d29cc4790c2d4b6c4691823">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_4644b875fd2f70367b26dd66a105776b25947b502d29cc4790c2d4b6c4691823">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-        <listOfReactants>
-          <speciesReference species="TARGET_0000000001__64__MNXC3" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-      </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:path_id value="rp_10_1"/>
-                <brsynth:path_base_idx value="10"/>
-                <brsynth:path_variant_idx value="1"/>
-                <brsynth:fba_obj_biomass units="mmol_per_gDW_per_hr" value="0.7638744755010283"/>
-                <brsynth:fba_obj_fraction units="mmol_per_gDW_per_hr" value="1.3739918359668453"/>
-                <brsynth:norm_fba_obj_biomass value="0.15277489510020564"/>
-                <brsynth:norm_fba_obj_fraction value="0.27479836719336903"/>
-                <brsynth:norm_rule_score value="0.8077964843146969"/>
-                <brsynth:norm_steps value="0.8571428571428572"/>
-                <brsynth:global_score value="0.6454105564835534"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-        <groups:listOfMembers>
-          <groups:member groups:idRef="rxn_3"/>
-          <groups:member groups:idRef="rxn_2"/>
-          <groups:member groups:idRef="rxn_1"/>
-        </groups:listOfMembers>
-      </groups:group>
-      <groups:group metaid="_8366edb8c9a74861fcde55baa072956b5f045bc88d208eca37144993dcd70a0e" groups:id="central_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="#_8366edb8c9a74861fcde55baa072956b5f045bc88d208eca37144993dcd70a0e">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-        <groups:listOfMembers>
-          <groups:member groups:idRef="CMPD_0000000007__64__MNXC3"/>
-          <groups:member groups:idRef="CMPD_0000000003__64__MNXC3"/>
-          <groups:member groups:idRef="TARGET_0000000001__64__MNXC3"/>
-          <groups:member groups:idRef="MNXM337__64__MNXC3"/>
-          <groups:member groups:idRef="MNXM4__64__MNXC3"/>
-          <groups:member groups:idRef="MNXM10__64__MNXC3"/>
-        </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="MNXM337__64__MNXC3"/>
-          <groups:member groups:idRef="MNXM4__64__MNXC3"/>
-          <groups:member groups:idRef="MNXM10__64__MNXC3"/>
-        </groups:listOfMembers>
-      </groups:group>
-      <groups:group metaid="a0632962b19a6626a8e5b8b0699565bc2b66d7a8198f2028eccf4fd75d766e04" groups:id="ignored_species_for_FBA" 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="#a0632962b19a6626a8e5b8b0699565bc2b66d7a8198f2028eccf4fd75d766e04">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </groups:group>
-    </groups:listOfGroups>
-    <fbc:listOfObjectives fbc:activeObjective="obj_fraction">
-      <fbc:objective fbc:id="obj_biomass" fbc:type="maximize">
-        <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="#">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:flux_value units="mmol_per_gDW_per_hr" value="0.7638744755010283"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-        <fbc:listOfFluxObjectives>
-          <fbc:fluxObjective fbc:reaction="biomass" fbc:coefficient="1">
-            <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="#">
-                  <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                    <brsynth:flux_value units="mmol_per_gDW_per_hr" value="0.7638744755010283"/>
-                  </brsynth:brsynth>
-                </rdf:BRSynth>
-              </rdf:RDF>
-            </annotation>
-          </fbc:fluxObjective>
-        </fbc:listOfFluxObjectives>
-      </fbc:objective>
-      <fbc:objective fbc:id="obj_fraction" fbc:type="maximize">
-        <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="#">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:flux_value units="mmol_per_gDW_per_hr" value="1.3739918359668453"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-        <fbc:listOfFluxObjectives>
-          <fbc:fluxObjective metaid="_079444b36c016c3df7c493b212a17c85744da6f580d18d9405e9a78475b3b909" fbc:reaction="rxn_target" fbc:coefficient="1">
-            <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="#_079444b36c016c3df7c493b212a17c85744da6f580d18d9405e9a78475b3b909">
-                  <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                    <brsynth:flux_value units="mmol_per_gDW_per_hr" value="1.3739918359668453"/>
-                  </brsynth:brsynth>
-                </rdf:BRSynth>
-              </rdf:RDF>
-            </annotation>
-          </fbc:fluxObjective>
-        </fbc:listOfFluxObjectives>
-      </fbc:objective>
-    </fbc:listOfObjectives>
-  </model>
-</sbml>
--- a/rpbasicdesign/test-data/user_parts_plate.csv	Tue Oct 12 15:24:00 2021 +0000
+++ b/rpbasicdesign/test-data/user_parts_plate.csv	Mon Nov 15 13:20:34 2021 +0000
@@ -1,13 +1,7 @@
 Part/linker,Well,Part concentration (ng/uL)
 BASIC_SEVA_37_CmR-p15A.1,A1,
-O85674,A2,
-P23262,A3,
-P31019,A4,
-P95607,A5,
-PJ23101_BASIC,A6,
-PJ23119_BASIC,A7,
-Q3KIF2,A8,
-Q43984,A9,
-Q5QUP2,A10,
-Q84BZ3,A11,
-Q8FB35,A12,
+P21683,B1,
+P21684,C1,
+P21685,D1,
+PJ23101_BASIC,E1,
+PJ23119_BASIC,F1,