Mercurial > repos > tduigou > rpbasicdesign
changeset 0:37185c8a8f46 draft
upload rpbasicdesign v0.3.1
| author | tduigou |
|---|---|
| date | Tue, 12 Oct 2021 15:24:00 +0000 |
| parents | |
| children | a9e9eb8a392c |
| 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/biolegio_plate.csv rpbasicdesign/test-data/constructs.csv rpbasicdesign/test-data/muconate_example.xml rpbasicdesign/test-data/user_parts_plate.csv |
| diffstat | 8 files changed, 2003 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/rpbasicdesign.xml Tue Oct 12 15:24:00 2021 +0000 @@ -0,0 +1,124 @@ +<tool id="rpbasicdesign" name="BasicDesign" version="0.3.1"> + <description>Build DNA-BOT input files from rpSBML</description> + <requirements> + <requirement type="package" version="0.3.1">rpbasicdesign</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python -m rpbasicdesign.cli + --rpsbml_file '$rpsbml_file' + #if $adv.parts_files + #set files = '" "'.join([str($file) for $file in $adv.parts_files]) + --parts_files "${files}" + #end if + --lms_id '$adv.lms_id' + --lmp_id '$adv.lmp_id' + --backbone_id '$backbone_id' + --sample_size '$sample_size' + #if str($adv.cds_permutation) == "true" + --cds_permutation true + #else + --cds_permutation false + #end if + --o_dnabot_dir 'out/dnabot_in' + --o_sbol_dir 'out/sbol_export' + ]]></command> + <inputs> + <param name="rpsbml_file" type="data" format="xml" label="rpSBML file"/> + <param name="backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" /> + <param name="sample_size" type="integer" value="3" label="Number of construct to generate" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" /> + <param name="lms_id" type="text" value="LMS" label="LMS part ID" /> + <param name="lmp_id" type="text" value="LMP" label="LMP part ID" /> + <param name="cds_permutation" type="boolean" label="Perform CDS permutation?" checked="true" /> + </section> + </inputs> + <outputs> + <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${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"> + <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="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"/> + </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] + +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. + +optional arguments: + -h, --help show this help message and exit + --rpsbml_file RPSBML_FILE + rpSBML file from which enzymes UniProt IDs will be + collected + + --parts_files PARTS_FILES [PARTS_FILES ...] + List of files providing available linkers and user + parts (backbone, promoters, ...) for constructs. + + --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 + + ]]></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> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/BASIC_construct_A1.xml Tue Oct 12 15:24:00 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: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/PJ23119_BASIC/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC"/> + <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: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: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: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:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + </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: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/Q8FB35"/> + </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: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: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: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: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: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:SequenceConstraint> + </sbol:sequenceConstraint> + <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: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: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: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: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:Component> + </sbol:component> + </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/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:elements></sbol:elements> + </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: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:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/Q84BZ3/1"> + <sbol:elements>atgc</sbol:elements> + <sbol:displayId>Q84BZ3</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/Q84BZ3"/> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS2/1"> + <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/U1_RBS2"/> + <sbol:displayId>U1_RBS2</sbol:displayId> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/Q8FB35/1"> + <sbol:version>1</sbol:version> + <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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/BASIC_construct_A2.xml Tue Oct 12 15:24:00 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: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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/BASIC_construct_A3.xml Tue Oct 12 15:24:00 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: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/biolegio_plate.csv Tue Oct 12 15:24:00 2021 +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/rpbasicdesign/test-data/constructs.csv Tue Oct 12 15:24:00 2021 +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,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,,,,,,,,,,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/muconate_example.xml Tue Oct 12 15:24:00 2021 +0000 @@ -0,0 +1,762 @@ +<?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> + 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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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/user_parts_plate.csv Tue Oct 12 15:24:00 2021 +0000 @@ -0,0 +1,13 @@ +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,