| Next changeset 1:de9f53630349 (2021-12-15) |
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Commit message:
Uploaded rpbasicdesign 0.3.4 |
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added:
rpbasicdesign/rpbasicdesign.xml rpbasicdesign/test-data/BASIC_construct_A1.xml rpbasicdesign/test-data/BASIC_construct_B1.xml rpbasicdesign/test-data/BASIC_construct_C1.xml rpbasicdesign/test-data/biolegio_plate.csv rpbasicdesign/test-data/constructs.csv rpbasicdesign/test-data/lycopene_CrtEBI_from_selenzy.xml rpbasicdesign/test-data/user_parts_plate.csv |
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| diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/rpbasicdesign.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/rpbasicdesign.xml Thu Nov 18 13:17:02 2021 +0000 |
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| @@ -0,0 +1,121 @@ +<tool id="rpbasicdesign" name="BasicDesign" version="0.3.4"> + <description>Build DNA-BOT input files from rpSBML</description> + <requirements> + <requirement type="package" version="0.3.4">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} - ${rpsbml_file.name}: constructs" /> + <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} - ${rpsbml_file.name}: User parts plate"/> + <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} - ${rpsbml_file.name}: Biolegio plate"/> + <collection name="sbol_dir" type="list" label="${tool.name} - ${rpsbml_file.name}: SBOL constructs"> + <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" /> + </collection> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced --> + <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" /> + <param name="sample_size" value="3" /> + <output name="Constructs" file="constructs.csv" ftype="csv" compare="diff"/> + <output name="User parts plate" file="user_parts_plate.csv" ftype="csv" compare="diff"/> + <output name="Biolegio plate" file="biolegio_plate.csv" ftype="csv" compare="diff"/> + <output_collection name="sbol_dir" type="list"> + <discovered_dataset designation="BASIC_construct_A1" ftype="xml" file="BASIC_construct_A1.xml"/> + <discovered_dataset designation="BASIC_construct_B1" ftype="xml" file="BASIC_construct_B1.xml"/> + <discovered_dataset designation="BASIC_construct_C1" ftype="xml" file="BASIC_construct_C1.xml"/> + </output_collection> + </test> + </tests> + <help><![CDATA[ +rpbasicdesign +================ + +Convert rpSBML enzyme info in to BASIC construct. UniProt IDs corresponding +enzyme variants are extracted rpSBMl files. Promoters and RBSs are randomly +chosen from a default list. CDSs, in other words gene variants, of enzymes are +randomly chosen from amongst the UniProt IDs extracted. Constructs generated +can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as SBOL +files. + +Input +----- + +Required: + +* **rpsbml_file**\ : (string) rpSBML file from which enzymes UniProt IDs will be collected. + +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] +* **lms_id**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS. +* **lmp_id**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP. +* **backbone_id**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1. +* **sample_size**\ : (int) Number of construct to generate.Default: 3. +* **cds_permutation**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. + +Output +------ + +* **o_dnabot_dir**\ : (string) Output folder to write construct and plate files. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/dnabot_in. +* **o_sbol_dir**\ : (string) Output folder to write SBOL depictions of constructs. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/sbol_export. + +Project Links +------------------ + +* `GitHub <https://github.com/brsynth/rpbasicdesign>`_ + +License +------- + +* `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_ + + ]]></help> + <citations> + <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 |
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| diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/test-data/BASIC_construct_A1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/BASIC_construct_A1.xml Thu Nov 18 13:17:02 2021 +0000 |
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| b'@@ -0,0 +1,339 @@\n+<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#">\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1">\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n+ <sbol:displayId>LMS</sbol:displayId>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1">\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1">\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n+ <sbol:displayId>LMP</sbol:displayId>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23119_BASIC/1">\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:displayId>PJ23119_BASIC</sbol:displayId>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23119_BASIC/1"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1">\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n+ <sbol:displayId>U1_RBS1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1">\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/>\n+ <sbol:displayId>P21684</sbol:displayId>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1">\n+ <sbol:displayId>U2_RBS1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/>\n+ </sbol:ComponentDefinition>\n+ <sbol:C'..b'ion/BASIC_construct_A1/P21684_0/1"/>\n+ <sbol:displayId>constraint_4</sbol:displayId>\n+ </sbol:SequenceConstraint>\n+ </sbol:sequenceConstraint>\n+ </sbol:ComponentDefinition>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>\n+ <sbol:displayId>LMS</sbol:displayId>\n+ <sbol:elements></sbol:elements>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1">\n+ <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:elements></sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:displayId>LMP</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/>\n+ <sbol:elements></sbol:elements>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23119_BASIC/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23119_BASIC"/>\n+ <sbol:elements></sbol:elements>\n+ <sbol:displayId>PJ23119_BASIC</sbol:displayId>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1">\n+ <sbol:elements></sbol:elements>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:displayId>U1_RBS1</sbol:displayId>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:elements>atgc</sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/>\n+ <sbol:displayId>P21684</sbol:displayId>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1">\n+ <sbol:displayId>U2_RBS1</sbol:displayId>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:elements></sbol:elements>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1">\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:displayId>P21683</sbol:displayId>\n+ <sbol:elements>atgc</sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/>\n+ <sbol:displayId>U3_RBS2</sbol:displayId>\n+ <sbol:elements></sbol:elements>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1">\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/>\n+ <sbol:elements>atgc</sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ <sbol:displayId>P21685</sbol:displayId>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ </sbol:Sequence>\n+</rdf:RDF>\n' |
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| diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/test-data/BASIC_construct_B1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/BASIC_construct_B1.xml Thu Nov 18 13:17:02 2021 +0000 |
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| b'@@ -0,0 +1,339 @@\n+<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#">\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1">\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n+ <sbol:displayId>LMS</sbol:displayId>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1">\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1">\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n+ <sbol:displayId>LMP</sbol:displayId>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1">\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:displayId>PJ23101_BASIC</sbol:displayId>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS3/1">\n+ <sbol:displayId>U1_RBS3</sbol:displayId>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS3/1"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS3"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1">\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/>\n+ <sbol:displayId>P21684</sbol:displayId>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1">\n+ <sbol:displayId>U2_RBS1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/>\n+ </sbol:ComponentDefinition>\n+ <sbol:C'..b'tity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_2"/>\n+ </sbol:SequenceConstraint>\n+ </sbol:sequenceConstraint>\n+ </sbol:ComponentDefinition>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>\n+ <sbol:displayId>LMS</sbol:displayId>\n+ <sbol:elements></sbol:elements>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1">\n+ <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:elements></sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:displayId>LMP</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/>\n+ <sbol:elements></sbol:elements>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1">\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/>\n+ <sbol:displayId>PJ23101_BASIC</sbol:displayId>\n+ <sbol:elements></sbol:elements>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS3/1">\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS3"/>\n+ <sbol:elements></sbol:elements>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:displayId>U1_RBS3</sbol:displayId>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:elements>atgc</sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/>\n+ <sbol:displayId>P21684</sbol:displayId>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1">\n+ <sbol:displayId>U2_RBS1</sbol:displayId>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:elements></sbol:elements>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1">\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:displayId>P21683</sbol:displayId>\n+ <sbol:elements>atgc</sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/>\n+ <sbol:displayId>U3_RBS2</sbol:displayId>\n+ <sbol:elements></sbol:elements>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1">\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/>\n+ <sbol:elements>atgc</sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ <sbol:displayId>P21685</sbol:displayId>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ </sbol:Sequence>\n+</rdf:RDF>\n' |
| b |
| diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/test-data/BASIC_construct_C1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/BASIC_construct_C1.xml Thu Nov 18 13:17:02 2021 +0000 |
| b |
| b'@@ -0,0 +1,339 @@\n+<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#">\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1">\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n+ <sbol:displayId>LMS</sbol:displayId>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1">\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1">\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n+ <sbol:displayId>LMP</sbol:displayId>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1">\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:displayId>PJ23101_BASIC</sbol:displayId>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1">\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n+ <sbol:displayId>U1_RBS1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1">\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/>\n+ <sbol:displayId>P21684</sbol:displayId>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1">\n+ <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/>\n+ <sbol:displayId>U3_RBS2</sbol:displayId>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ </sbol:ComponentDefinition>\n+ <sbol:C'..b'_BASIC_0"/>\n+ <sbol:displayId>PJ23101_BASIC_0</sbol:displayId>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Component>\n+ </sbol:component>\n+ </sbol:ComponentDefinition>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>\n+ <sbol:displayId>LMS</sbol:displayId>\n+ <sbol:elements></sbol:elements>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1">\n+ <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:elements></sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:displayId>LMP</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/>\n+ <sbol:elements></sbol:elements>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1">\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/>\n+ <sbol:displayId>PJ23101_BASIC</sbol:displayId>\n+ <sbol:elements></sbol:elements>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1">\n+ <sbol:elements></sbol:elements>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:displayId>U1_RBS1</sbol:displayId>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:elements>atgc</sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/>\n+ <sbol:displayId>P21684</sbol:displayId>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1">\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/>\n+ <sbol:displayId>U3_RBS2</sbol:displayId>\n+ <sbol:elements></sbol:elements>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1">\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/>\n+ <sbol:elements>atgc</sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ <sbol:displayId>P21685</sbol:displayId>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS2/1">\n+ <sbol:displayId>U2_RBS2</sbol:displayId>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:elements></sbol:elements>\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS2"/>\n+ </sbol:Sequence>\n+ <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1">\n+ <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/>\n+ <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n+ <sbol:displayId>P21683</sbol:displayId>\n+ <sbol:elements>atgc</sbol:elements>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Sequence>\n+</rdf:RDF>\n' |
| b |
| diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/test-data/biolegio_plate.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/biolegio_plate.csv Thu Nov 18 13:17:02 2021 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/test-data/constructs.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/constructs.csv Thu Nov 18 13:17:02 2021 +0000 |
| b |
| @@ -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,,,,,,,,,, |
| b |
| diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/test-data/lycopene_CrtEBI_from_selenzy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/lycopene_CrtEBI_from_selenzy.xml Thu Nov 18 13:17:02 2021 +0000 |
| [ |
| b'@@ -0,0 +1,393 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<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">\n+ <model metaid="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">\n+ <listOfCompartments>\n+ <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">\n+ <bqbiol:is>\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>\n+ <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>\n+ <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed/c"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>\n+ <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </annotation>\n+ </compartment>\n+ </listOfCompartments>\n+ <listOfSpecies>\n+ <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>\n+ <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc" id="MNXM132" name="MNXM132" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ '..b':rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:global_score value="-1"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="rxn_1"/>\n+ <groups:member groups:idRef="rxn_2"/>\n+ <groups:member groups:idRef="rxn_3"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n+ <groups:member groups:idRef="MNXM132"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="MNXM83"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM8975"/>\n+ <groups:member groups:idRef="MNXM24"/>\n+ <groups:member groups:idRef="MNXM11"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="MNXM132"/>\n+ <groups:member groups:idRef="MNXM11"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ </groups:listOfGroups>\n+ </model>\n+</sbml>\n' |
| b |
| diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/test-data/user_parts_plate.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/user_parts_plate.csv Thu Nov 18 13:17:02 2021 +0000 |
| b |
| @@ -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, |