Mercurial > repos > tduigou > rpbasicdesign
changeset 2:8a087d7546b8 draft
"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
| author | tduigou |
|---|---|
| date | Mon, 28 Mar 2022 14:16:59 +0000 |
| parents | de9f53630349 |
| children | e4821c820f7c |
| files | rpbasicdesign.xml test-data/BASIC_construct_A1.xml test-data/BASIC_construct_B1.xml test-data/BASIC_construct_C1.xml test-data/biolegio_plate.csv test-data/biolegio_plate_lycopene.csv test-data/biolegio_plate_muconate.csv test-data/constructs.csv test-data/constructs_lycopene.csv test-data/constructs_muconate.csv test-data/muconate_example.xml test-data/user_parts_plate.csv test-data/user_parts_plate_lycopene.csv test-data/user_parts_plate_muconate.csv |
| diffstat | 14 files changed, 5707 insertions(+), 1160 deletions(-) [+] |
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--- a/rpbasicdesign.xml Wed Dec 15 15:10:43 2021 +0000 +++ b/rpbasicdesign.xml Mon Mar 28 14:16:59 2022 +0000 @@ -1,7 +1,10 @@ -<tool id="rpbasicdesign" name="BasicDesign" version="0.3.4"> +<tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="19.09"> <description>Build DNA-BOT input files from rpSBML</description> + <macros> + <token name="@TOOL_VERSION@">1.0.1</token> + </macros> <requirements> - <requirement type="package" version="0.3.4">rpbasicdesign</requirement> + <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python -m rpbasicdesign.cli @@ -14,46 +17,112 @@ --lmp_id '$adv.lmp_id' --backbone_id '$backbone_id' --sample_size '$sample_size' - #if str($adv.cds_permutation) == "true" - --cds_permutation true - #else - --cds_permutation false - #end if + $adv.cds_permutation --o_dnabot_dir 'out/dnabot_in' - --o_sbol_dir 'out/sbol_export' + $adv.sbol_output + --max_enz_per_rxn $adv.max_enz_per_rxn ]]></command> <inputs> - <param name="rpsbml_file" type="data" format="xml" label="rpSBML file"/> - <param name="backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" /> - <param name="sample_size" type="integer" value="88" label="Number of constructs to generate" /> + <param name="rpsbml_file" type="data" format="xml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/> + <param argument="--backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" help="Part ID to be used as the backbone."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value=":" /> + <add value="." /> + <add value="-" /> + <add value="_" /> + </valid> + </sanitizer> + <validator type="empty_field" message="Backbone ID is required"/> + <validator type="regex">[0-9a-zA-Z_:-]+</validator> + </param> + <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Number of constructs to generate" help="Number of construct to generate."/> <section name="adv" title="Advanced Options" expanded="false"> - <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" /> - <param name="lms_id" type="text" value="LMS" label="LMS part ID" /> - <param name="lmp_id" type="text" value="LMP" label="LMP part ID" /> - <param name="cds_permutation" type="boolean" label="Perform CDS permutation?" checked="true" /> + <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" help="List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: Standard Biolegio Parts" /> + <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." > + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value=":" /> + <add value="-" /> + <add value="_" /> + <add value="." /> + </valid> + </sanitizer> + <validator type="empty_field" message="LMS ID is required"/> + </param> + <param argument="--lmp_id" type="text" value="LMP" label="LMP part ID" help="Part ID to be used as the LMP methylated linker."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value=":" /> + <add value="-" /> + <add value="_" /> + <add value="." /> + </valid> + </sanitizer> + <validator type="empty_field" message="LMP ID is required"/> + </param> + <param argument="--cds_permutation" type="boolean" truevalue="--cds_permutation true" falsevalue="--cds_permutation false" checked="true" label="Perform CDS permutation?" help="Whether all combinations of CDS permutation should be built." /> + <param argument="--sbol_output" type="boolean" checked="false" truevalue="--o_sbol_dir out/sbol_export" falsevalue="" label="Output SBOL results?" help="Output folder to write SBOL depictions of constructs." /> + <param argument="--max_enz_per_rxn" type="integer" value="1" min="1" max="99" label="Maximum number of enyzme to consider per reaction." help="Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept."/> </section> </inputs> <outputs> - <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} - ${rpsbml_file.name}: constructs" /> - <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${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} - ${rpsbml_file.name}: SBOL constructs"> + <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} on ${rpsbml_file.name}: constructs" /> + <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} on ${rpsbml_file.name}: User parts plate"/> + <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} on ${rpsbml_file.name}: Biolegio plate"/> + <collection name="sbol_dir" type="list" label="${tool.name} on ${rpsbml_file.name}: SBOL constructs"> + <filter> adv['sbol_output'] </filter> <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" /> </collection> </outputs> <tests> <test> - <!-- test 1: check if identical outputs are produced --> - <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"> - <element name="BASIC_construct_A1" ftype="xml" value="BASIC_construct_A1.xml" sort="true"/> - <element name="BASIC_construct_B1" ftype="xml" value="BASIC_construct_B1.xml" sort="true"/> - <element name="BASIC_construct_C1" ftype="xml" value="BASIC_construct_C1.xml" sort="true"/> - </output_collection> + <!-- test 1: check if identical outputs are produced (Lycopene input)--> + <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" /> + <param name="sample_size" value="3" /> + <output name="Constructs" file="constructs_lycopene.csv" ftype="csv" compare="diff"> + <assert_contents> + <has_n_lines n="4"/> + </assert_contents> + </output> + <output name="User parts plate" file="user_parts_plate_lycopene.csv" ftype="csv" compare="diff"/> + <output name="Biolegio plate" file="biolegio_plate_lycopene.csv" ftype="csv" compare="diff"/> + <param name="sbol_output" value="--o_sbol_dir out/sbol_export" /> + <output_collection name="sbol_dir" type="list" count="3"> + <element name="BASIC_construct_A1"> + <assert_contents> + <is_valid_xml /> + <has_text text="BASIC_construct_A1" /> + <has_n_lines n="339" /> + </assert_contents> + </element> + <element name="BASIC_construct_B1"> + <assert_contents> + <is_valid_xml /> + <has_text text="BASIC_construct_B1" /> + <has_n_lines n="339" /> + </assert_contents> + </element> + <element name="BASIC_construct_C1"> + <assert_contents> + <is_valid_xml /> + <has_text text="BASIC_construct_C1" /> + <has_n_lines n="339" /> + </assert_contents> + </element> + </output_collection> + </test> + <test> + <!-- test 2: check if identical outputs are produced (Muconate input)--> + <param name="rpsbml_file" value="muconate_example.xml" /> + <param name="sample_size" value="88" /> + <output name="Constructs" file="constructs_muconate.csv" ftype="csv" compare="diff"> + <assert_contents> + <has_n_lines n="89"/> + </assert_contents> + </output> + <output name="User parts plate" file="user_parts_plate_muconate.csv" ftype="csv" compare="diff"/> + <output name="Biolegio plate" file="biolegio_plate_muconate.csv" ftype="csv" compare="diff"/> </test> </tests> <help><![CDATA[ @@ -76,18 +145,19 @@ Advanced options: -* **parts_files**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, user_parts.csv] +* **parts_files**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, data/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. +* **sample_size**\ : (int) Number of construct to generate. Default: 88. * **cds_permutation**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. +* **max_enz_per_rxn**\ : (integer) Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept. (Default: 1). Output ------ * **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. +* **o_sbol_dir**\ : (string) Output folder to write SBOL depictions of constructs. Existing files will be overwritten. Default: not output. Project Links ------------------ @@ -101,21 +171,6 @@ ]]></help> <citations> - <citation type="bibtex"> - @article{10.1093/synbio/ysaa010, - author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S}, - title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology}, - journal = {Synthetic Biology}, - volume = {5}, - number = {1}, - year = {2020}, - month = {07}, - issn = {2397-7000}, - doi = {10.1093/synbio/ysaa010}, - url = {https://doi.org/10.1093/synbio/ysaa010}, - note = {ysaa010}, - eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf}, - } - </citation> + <citation type="doi">10.1093/synbio/ysaa010</citation> </citations> </tool> \ No newline at end of file
--- a/test-data/BASIC_construct_A1.xml Wed Dec 15 15:10:43 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: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/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: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/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_A1/1"> - <sbol:component> - <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: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_5/1"> - <sbol:version>1</sbol:version> - <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: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_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: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:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/> - <sbol:displayId>LMS_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/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/LMP/1"/> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <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: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/PJ23119_BASIC/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/PJ23119_BASIC"/> - <sbol:elements></sbol:elements> - <sbol:displayId>PJ23119_BASIC</sbol:displayId> - </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/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>
--- a/test-data/BASIC_construct_B1.xml Wed Dec 15 15:10:43 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: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>
--- a/test-data/BASIC_construct_C1.xml Wed Dec 15 15:10:43 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: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/test-data/biolegio_plate.csv Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -Part/linker,Well,Part concentration (ng/uL) -L1-S,A1, -L1-P,B1, -L2-S,A2, -L2-P,B2, -L3-S,A3, -L3-P,B3, -L4-S,A4, -L4-P,B4, -L5-S,A5, -L5-P,B5, -L6-S,A6, -L6-P,B6, -LMP-S,A7, -LMP-P,B7, -LMS-S,A8, -LMS-P,B8, -U1-S,C1, -U2-S,C2, -U3-S,C3, -U1-RBS1-P,C4, -U1-RBS2-P,C5, -U1-RBS3-P,C6, -U1-A01-P,D1, -U1-A02-P,D2, -U1-A03-P,D3, -U1-A04-P,D4, -U1-A05-P,D5, -U1-A06-P,D6, -U1-A07-P,D7, -U1-A08-P,D8, -U1-A09-P,D9, -U1-A10-P,D10, -U1-A11-P,D11 -U1-A12-P,D12, -U2-RBS1-P,C7, -U2-RBS2-P,C8, -U2-RBS3-P,C9, -U2-A01-P,E1, -U2-A02-P,E2, -U2-A03-P,E3, -U2-A04-P,E4, -U2-A05-P,E5, -U2-A06-P,E6, -U2-A07-P,E7, -U2-A08-P,E8, -U2-A09-P,E9, -U2-A10-P,E10, -U2-A11-P,E11 -U2-A12-P,E12, -U3-RBS1-P,C10, -U3-RBS2-P,C11, -U3-RBS3-P,C12, -U3-A01-P,F1, -U3-A02-P,F2, -U3-A03-P,F3, -U3-A04-P,F4, -U3-A05-P,F5, -U3-A06-P,F6, -U3-A07-P,F7, -U3-A08-P,F8, -U3-A09-P,F9, -U3-A10-P,F10, -U3-A11-P,F11 -U3-A12-P,F12, -U1-AM12-P,A10, -U1-AM24-P,B10, -U2-AM12-P,A11, -U2-AM24-P,B11, -U3-AM12-P,A12, -U3-AM24-P,B12, -LF1-S,A9, -LF1-P,B9, -LF2-S,G1, -LF2-P,H1, -LF3-S,G2, -LF3-P,H2, -LF4-S,G3, -LF4-P,H3, -LF5-S,G4, -LF5-P,H4, -LF6-S,G5, -LF6-P,H5, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biolegio_plate_lycopene.csv Mon Mar 28 14:16:59 2022 +0000 @@ -0,0 +1,83 @@ +Part/linker,Well,Part concentration (ng/uL) +L1-S,A1, +L1-P,B1, +L2-S,A2, +L2-P,B2, +L3-S,A3, +L3-P,B3, +L4-S,A4, +L4-P,B4, +L5-S,A5, +L5-P,B5, +L6-S,A6, +L6-P,B6, +LMP-S,A7, +LMP-P,B7, +LMS-S,A8, +LMS-P,B8, +U1-S,C1, +U2-S,C2, +U3-S,C3, +U1-RBS1-P,C4, +U1-RBS2-P,C5, +U1-RBS3-P,C6, +U1-A01-P,D1, +U1-A02-P,D2, +U1-A03-P,D3, +U1-A04-P,D4, +U1-A05-P,D5, +U1-A06-P,D6, +U1-A07-P,D7, +U1-A08-P,D8, +U1-A09-P,D9, +U1-A10-P,D10, +U1-A11-P,D11 +U1-A12-P,D12, +U2-RBS1-P,C7, +U2-RBS2-P,C8, +U2-RBS3-P,C9, +U2-A01-P,E1, +U2-A02-P,E2, +U2-A03-P,E3, +U2-A04-P,E4, +U2-A05-P,E5, +U2-A06-P,E6, +U2-A07-P,E7, +U2-A08-P,E8, +U2-A09-P,E9, +U2-A10-P,E10, +U2-A11-P,E11 +U2-A12-P,E12, +U3-RBS1-P,C10, +U3-RBS2-P,C11, +U3-RBS3-P,C12, +U3-A01-P,F1, +U3-A02-P,F2, +U3-A03-P,F3, +U3-A04-P,F4, +U3-A05-P,F5, +U3-A06-P,F6, +U3-A07-P,F7, +U3-A08-P,F8, +U3-A09-P,F9, +U3-A10-P,F10, +U3-A11-P,F11 +U3-A12-P,F12, +U1-AM12-P,A10, +U1-AM24-P,B10, +U2-AM12-P,A11, +U2-AM24-P,B11, +U3-AM12-P,A12, +U3-AM24-P,B12, +LF1-S,A9, +LF1-P,B9, +LF2-S,G1, +LF2-P,H1, +LF3-S,G2, +LF3-P,H2, +LF4-S,G3, +LF4-P,H3, +LF5-S,G4, +LF5-P,H4, +LF6-S,G5, +LF6-P,H5, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biolegio_plate_muconate.csv Mon Mar 28 14:16:59 2022 +0000 @@ -0,0 +1,83 @@ +Part/linker,Well,Part concentration (ng/uL) +L1-S,A1, +L1-P,B1, +L2-S,A2, +L2-P,B2, +L3-S,A3, +L3-P,B3, +L4-S,A4, +L4-P,B4, +L5-S,A5, +L5-P,B5, +L6-S,A6, +L6-P,B6, +LMP-S,A7, +LMP-P,B7, +LMS-S,A8, +LMS-P,B8, +U1-S,C1, +U2-S,C2, +U3-S,C3, +U1-RBS1-P,C4, +U1-RBS2-P,C5, +U1-RBS3-P,C6, +U1-A01-P,D1, +U1-A02-P,D2, +U1-A03-P,D3, +U1-A04-P,D4, +U1-A05-P,D5, +U1-A06-P,D6, +U1-A07-P,D7, +U1-A08-P,D8, +U1-A09-P,D9, +U1-A10-P,D10, +U1-A11-P,D11 +U1-A12-P,D12, +U2-RBS1-P,C7, +U2-RBS2-P,C8, +U2-RBS3-P,C9, +U2-A01-P,E1, +U2-A02-P,E2, +U2-A03-P,E3, +U2-A04-P,E4, +U2-A05-P,E5, +U2-A06-P,E6, +U2-A07-P,E7, +U2-A08-P,E8, +U2-A09-P,E9, +U2-A10-P,E10, +U2-A11-P,E11 +U2-A12-P,E12, +U3-RBS1-P,C10, +U3-RBS2-P,C11, +U3-RBS3-P,C12, +U3-A01-P,F1, +U3-A02-P,F2, +U3-A03-P,F3, +U3-A04-P,F4, +U3-A05-P,F5, +U3-A06-P,F6, +U3-A07-P,F7, +U3-A08-P,F8, +U3-A09-P,F9, +U3-A10-P,F10, +U3-A11-P,F11 +U3-A12-P,F12, +U1-AM12-P,A10, +U1-AM24-P,B10, +U2-AM12-P,A11, +U2-AM24-P,B11, +U3-AM12-P,A12, +U3-AM24-P,B12, +LF1-S,A9, +LF1-P,B9, +LF2-S,G1, +LF2-P,H1, +LF3-S,G2, +LF3-P,H2, +LF4-S,G3, +LF4-P,H3, +LF5-S,G4, +LF5-P,H4, +LF6-S,G5, +LF6-P,H5, \ No newline at end of file
--- a/test-data/constructs.csv Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 -A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, -B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, -C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,P21684,U3-RBS2,P21685,U2-RBS2,P21683,,,,,,,,,,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/constructs_lycopene.csv Mon Mar 28 14:16:59 2022 +0000 @@ -0,0 +1,4 @@ +Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 +A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,P21684,U3-RBS2,P21685,U2-RBS2,P21683,,,,,,,,,,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/constructs_muconate.csv Mon Mar 28 14:16:59 2022 +0000 @@ -0,0 +1,89 @@ +Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 +A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS2,O33948,U1-RBS2,O85675,,,,,,,,,,,, +B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,O85675,U2-RBS2,O33948,,,,,,,,,,,, +C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,, +D1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,, +E1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS1,O33948,U1-RBS3,O85675,,,,,,,,,,,, +F1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS2,O85675,U2-RBS3,O33948,,,,,,,,,,,, +G1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,, 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<brsynth:global_score value="-1"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="rxn_1"/> + <groups:member groups:idRef="rxn_2"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="CMPD_0000000003"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="CMPD_0000000003"/> + <groups:member groups:idRef="MNXM4"/> + <groups:member groups:idRef="MNXM188"/> + <groups:member groups:idRef="TARGET_0000000001"/> + <groups:member groups:idRef="MNXM6"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM15"/> + <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM5"/> + <groups:member groups:idRef="MNXM13"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM5"/> + <groups:member groups:idRef="MNXM4"/> + <groups:member groups:idRef="MNXM188"/> + <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM6"/> + <groups:member groups:idRef="MNXM13"/> + <groups:member groups:idRef="MNXM15"/> + </groups:listOfMembers> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>
--- a/test-data/user_parts_plate.csv Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -Part/linker,Well,Part concentration (ng/uL) -BASIC_SEVA_37_CmR-p15A.1,A1, -P21683,B1, -P21684,C1, -P21685,D1, -PJ23101_BASIC,E1, -PJ23119_BASIC,F1,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/user_parts_plate_lycopene.csv Mon Mar 28 14:16:59 2022 +0000 @@ -0,0 +1,7 @@ +Part/linker,Well,Part concentration (ng/uL) +BASIC_SEVA_37_CmR-p15A.1,A1, +P21683,B1, +P21684,C1, +P21685,D1, +PJ23101_BASIC,E1, +PJ23119_BASIC,F1,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/user_parts_plate_muconate.csv Mon Mar 28 14:16:59 2022 +0000 @@ -0,0 +1,9 @@ +Part/linker,Well,Part concentration (ng/uL) +BASIC_SEVA_37_CmR-p15A.1,A1, +O33948,B1, +O85675,C1, +PJ23101_BASIC,D1, +PJ23104_BASIC,E1, +PJ23108_BASIC,F1, +PJ23111_BASIC,G1, +PJ23119_BASIC,H1,