Examples with Sequence com.google.showcase.v1beta1.Sequence used on opensource projects

Example 1 with Sequence

use of com.google.showcase.v1beta1.Sequence in project libSBOLj by SynBioDex.

the class GettingStartedExample method main.

public static void main(String[] args) throws IOException, SBOLValidationException, SBOLConversionException {
    String prURI = "http://partsregistry.org/";
    String prPrefix = "pr";
    String myersLabURI = "http://www.async.ece.utah.edu/";
    String myersLabPrefix = "myersLab";
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    document.setComplete(true);
    document.setCreateDefaults(true);
    document.addNamespace(URI.create(prURI), prPrefix);
    document.addNamespace(URI.create(myersLabURI), myersLabPrefix);
    // Creating a Top-level SBOL Data Object
    HashSet<URI> types = new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA_REGION, URI.create("http://identifiers.org/chebi/CHEBI:4705")));
    ComponentDefinition TetR_promoter = document.createComponentDefinition("BBa_R0040", types);
    ComponentDefinition LacI_repressor = document.createComponentDefinition("BBa_C0012", types);
    ComponentDefinition pIKELeftCassette = document.createComponentDefinition("pIKELeftCassette", types);
    Sequence seq_187 = document.createSequence("partseq_187", "tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac", Sequence.IUPAC_DNA);
    String element2 = "atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtc" + "tcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcggga" + "aaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactgg" + "cgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcg" + "caaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgat" + "ggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcg" + "tcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcc" + "tgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattat" + "tttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagc" + "aaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctgg" + "cataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgc" + "catgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgc" + "tggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgc" + "gttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatccc" + "gccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgc" + "tgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaa" + "agaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcatt" + "aatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaact" + "acgctttagtagcttaataa";
    Sequence seq_153 = document.createSequence("partseq_153", element2, Sequence.IUPAC_DNA);
    // Setting and editing optional fields
    TetR_promoter.setName("p(tetR)");
    LacI_repressor.setName("lacI");
    TetR_promoter.setDescription("TetR repressible promoter");
    LacI_repressor.setDescription("lacI repressor from E. coli (+LVA)");
    if (TetR_promoter.isSetName()) {
        TetR_promoter.unsetName();
    }
    TetR_promoter.setName("p(tetR)");
    TetR_promoter.addRole(SequenceOntology.PROMOTER);
    LacI_repressor.addRole(SequenceOntology.CDS);
    URI TetR_promoter_role2 = URI.create("http://identifiers.org/so/SO:0000613");
    TetR_promoter.addRole(TetR_promoter_role2);
    if (TetR_promoter.containsRole(TetR_promoter_role2)) {
        TetR_promoter.removeRole(TetR_promoter_role2);
    }
    TetR_promoter.clearRoles();
    if (!TetR_promoter.getRoles().isEmpty()) {
        System.out.println("TetR_promoter set is not empty");
    }
    TetR_promoter.setRoles(new HashSet<URI>(Arrays.asList(SequenceOntology.PROMOTER)));
    // Creating and editing references
    TetR_promoter.addSequence(seq_187);
    LacI_repressor.addSequence(seq_153);
    pIKELeftCassette.addSequence(seq_187);
    pIKELeftCassette.clearSequences();
    // Adding the sequence below causes an exception because it cannot be found
    // pIKELeftCassette.addSequence(URI.create("http://partsregistry.org/seq/partseq_154"));
    // Creating Annotations
    TetR_promoter.createAnnotation(new QName(prURI, "experience", prPrefix), URI.create("http://parts.igem.org/Part:BBa_R0040"));
    // Creating Generic TopLevel Object
    GenericTopLevel datasheet = document.createGenericTopLevel("datasheet", "1.0", new QName(myersLabURI, "datasheet", myersLabPrefix));
    datasheet.setName("Datasheet for Custom Parameters");
    datasheet.createAnnotation(new QName(myersLabURI, "characterizationData", myersLabPrefix), URI.create(myersLabURI + "/measurement/Part:BBa_R0040"));
    datasheet.createAnnotation(new QName(myersLabURI, "transcriptionRate", myersLabPrefix), "0.75");
    TetR_promoter.createAnnotation(new QName(myersLabURI, "datasheet", myersLabPrefix), datasheet.getIdentity());
    // Creating and editing Child Objects
    // For pIKELeftCassette, create sequence constraint that says BBa_R0040 precedes BBa_C0012.
    // Note that with CreateDefaults that components get created automatically.
    // The position of the subject Component MUST precede that of the object Component.
    pIKELeftCassette.createSequenceConstraint("pIKELeftCassette_sc", RestrictionType.PRECEDES, TetR_promoter.getDisplayId(), LacI_repressor.getDisplayId());
    if (pIKELeftCassette.getComponent("BBa_R0040") == null) {
        System.out.println("TetR_promoter component is missing");
    }
    if (pIKELeftCassette.getComponent("BBa_C0012") == null) {
        System.out.println("LacI_repressor component is missing");
    }
    // Removing the subject component below causes an exception.
    // pIKELeftCassette.removeComponent(pIKELeftCassette.getComponent("BBa_R0040"));
    // Copying objects
    ComponentDefinition TetR_promoter_copy = (ComponentDefinition) document.createCopy(TetR_promoter, "BBa_K137046");
    Sequence seq = document.createSequence("seq_K137046", "gtgctcagtatctctatcactgatagggatgtcaatctctatcactgatagggactctagtatat" + "aaacgcagaaaggcccacccgaaggtgagccagtgtgactctagtagagagcgttcaccgaca" + "aacaacagataaaacgaaaggc", Sequence.IUPAC_DNA);
    TetR_promoter_copy.addSequence(seq);
    SBOLWriter.write(document, "GettingStartedExample.rdf");
    writeThenRead(document);
}

Example 2 with Sequence

use of com.google.showcase.v1beta1.Sequence in project libSBOLj by SynBioDex.

the class ModuleDefinitionOutput method addSequence.

private static Sequence addSequence(SBOLDocument document, ComponentDefinition componentDef, String displayId, URI sequenceType, String elements) throws SBOLValidationException {
    Sequence sequence = document.createSequence(displayId, elements, sequenceType);
    componentDef.addSequence(sequence.getIdentity());
    return sequence;
}

Example 3 with Sequence

use of com.google.showcase.v1beta1.Sequence in project libSBOLj by SynBioDex.

the class RepressionModel method main.

public static void main(String[] args) throws SBOLValidationException, SBOLConversionException, IOException {
    SBOLDocument doc = new SBOLDocument();
    doc.setDefaultURIprefix("http://sbols.org/CRISPR_Example/");
    doc.setComplete(true);
    doc.setCreateDefaults(true);
    String version = "1.0.0";
    // Create ComponentDefinition for cas9_generic protein
    doc.createComponentDefinition("cas9_generic", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefinition for gRNA_generic RNA
    doc.createComponentDefinition("gRNA_generic", version, ComponentDefinition.RNA_REGION).addRole(SequenceOntology.SGRNA);
    // Create ComponentDefinition for cas9_gRNA_complex
    doc.createComponentDefinition("cas9_gRNA_complex", version, ComponentDefinition.COMPLEX);
    // Create ComponentDefinition for target gene
    doc.createComponentDefinition("target_gene", version, ComponentDefinition.DNA_REGION).addRole(SequenceOntology.PROMOTER);
    // Create ComponentDefinition for target protein
    doc.createComponentDefinition("target", version, ComponentDefinition.PROTEIN);
    // Create ModuleDefinition for CRISPR_Repression_Template
    ModuleDefinition CRISPR_Template = doc.createModuleDefinition("CRISPR_Template", version);
    // Complex Formation Interaction for Cas9m_BFP and gRNA
    Interaction Cas9Complex_Formation = CRISPR_Template.createInteraction("cas9_complex_formation", SystemsBiologyOntology.NON_COVALENT_BINDING);
    Cas9Complex_Formation.createParticipation("cas9_generic", "cas9_generic", SystemsBiologyOntology.REACTANT);
    Cas9Complex_Formation.createParticipation("gRNA_generic", "gRNA_generic", SystemsBiologyOntology.REACTANT);
    Cas9Complex_Formation.createParticipation("cas9_gRNA_complex", "cas9_gRNA_complex", SystemsBiologyOntology.PRODUCT);
    // Production of target from target gene
    Interaction EYFP_production = CRISPR_Template.createInteraction("target_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    EYFP_production.createParticipation("target_gene", "target_gene", SystemsBiologyOntology.PROMOTER);
    EYFP_production.createParticipation("target", "target", SystemsBiologyOntology.PRODUCT);
    // Inhibition of target by cas9m_BFP_gRNA
    Interaction target_generic_gene_inhibition = CRISPR_Template.createInteraction("target_gene_inhibition", SystemsBiologyOntology.INHIBITION);
    target_generic_gene_inhibition.createParticipation("cas9_gRNA_complex", "cas9_gRNA_complex", SystemsBiologyOntology.INHIBITOR);
    target_generic_gene_inhibition.createParticipation("target_gene", "target_gene", SystemsBiologyOntology.PROMOTER);
    // Create Sequence for CRa_U6 promoter
    String CRa_U6_seq_elements = "GGTTTACCGAGCTCTTATTGGTTTTCAAACTTCATTGACTGTGCC" + "AAGGTCGGGCAGGAAGAGGGCCTATTTCCCATGATTCCTTCATAT" + "TTGCATATACGATACAAGGCTGTTAGAGAGATAATTAGAATTAAT" + "TTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGA" + "AAGTAATAATTTCTTGGGTAGTTTGCAGTTTTAAAATTATGTTTT" + "AAAATGGACTATCATATGCTTACCGTAACTTGAAATATAGAACCG" + "ATCCTCCCATTGGTATATATTATAGAACCGATCCTCCCATTGGCT" + "TGTGGAAAGGACGAAACACCGTACCTCATCAGGAACATGTGTTTA" + "AGAGCTATGCTGGAAACAGCAGAAATAGCAAGTTTAAATAAGGCT" + "AGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTT" + "TTGGTGCGTTTTTATGCTTGTAGTATTGTATAATGTTTTT";
    doc.createSequence("CRa_U6_seq", version, CRa_U6_seq_elements, Sequence.IUPAC_DNA);
    // Create Sequence for gRNA_b coding sequence
    String gRNA_b_elements = "AAGGTCGGGCAGGAAGAGGGCCTATTTCCCATGATTCCTTCATAT" + "TTGCATATACGATACAAGGCTGTTAGAGAGATAATTAGAATTAAT" + "TTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGA" + "AAGTAATAATTTCTTGGGTAGTTTGCAGTTTTAAAATTATGTTTT" + "AAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCGAT" + "TTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTACCT" + "CATCAGGAACATGTGTTTAAGAGCTATGCTGGAAACAGCAGAAAT" + "AGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGG" + "CACCGAGTCGGTGCTTTTTTT";
    doc.createSequence("gRNA_b_seq", version, gRNA_b_elements, Sequence.IUPAC_DNA);
    // Create Sequence for mKate
    String mKate_seq_elements = "TCTAAGGGCGAAGAGCTGATTAAGGAGAACATGCACATGAAGCTG" + "TACATGGAGGGCACCGTGAACAACCACCACTTCAAGTGCACATCC" + "GAGGGCGAAGGCAAGCCCTACGAGGGCACCCAGACCATGAGAATC" + "AAGGTGGTCGAGGGCGGCCCTCTCCCCTTCGCCTTCGACATCCTG" + "GCTACCAGCTTCATGTACGGCAGCAAAACCTTCATCAACCACACC" + "CAGGGCATCCCCGACTTCTTTAAGCAGTCCTTCCCTGAGGTAAGT" + "GGTCCTACCTCATCAGGAACATGTGTTTTAGAGCTAGAAATAGCA" + "AGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACC" + "GAGTCGGTGCTACTAACTCTCGAGTCTTCTTTTTTTTTTTCACAG" + "GGCTTCACATGGGAGAGAGTCACCACATACGAAGACGGGGGCGTG" + "CTGACCGCTACCCAGGACACCAGCCTCCAGGACGGCTGCCTCATC" + "TACAACGTCAAGATCAGAGGGGTGAACTTCCCATCCAACGGCCCT" + "GTGATGCAGAAGAAAACACTCGGCTGGGAGGCCTCCACCGAGATG" + "CTGTACCCCGCTGACGGCGGCCTGGAAGGCAGAAGCGACATGGCC" + "CTGAAGCTCGTGGGCGGGGGCCACCTGATCTGCAACTTGAAGACC" + "ACATACAGATCCAAGAAACCCGCTAAGAACCTCAAGATGCCCGGC" + "GTCTACTATGTGGACAGAAGACTGGAAAGAATCAAGGAGGCCGAC" + "AAAGAGACCTACGTCGAGCAGCACGAGGTGGCTGTGGCCAGATAC" + "TGCG";
    doc.createSequence("mKate_seq", version, mKate_seq_elements, Sequence.IUPAC_DNA);
    // Create Sequence for CRP_b promoter
    String CRP_b_seq_elements = "GCTCCGAATTTCTCGACAGATCTCATGTGATTACGCCAAGCTACG" + "GGCGGAGTACTGTCCTCCGAGCGGAGTACTGTCCTCCGAGCGGAG" + "TACTGTCCTCCGAGCGGAGTACTGTCCTCCGAGCGGAGTTCTGTC" + "CTCCGAGCGGAGACTCTAGATACCTCATCAGGAACATGTTGGAAT" + "TCTAGGCGTGTACGGTGGGAGGCCTATATAAGCAGAGCTCGTTTA" + "GTGAACCGTCAGATCGCCTCGAGTACCTCATCAGGAACATGTTGG" + "ATCCAATTCGACC";
    doc.createSequence("CRP_b_seq", version, CRP_b_seq_elements, Sequence.IUPAC_DNA);
    // Create ComponentDefinition for a Constitutive Promoter
    doc.createComponentDefinition("pConst", version, ComponentDefinition.DNA_REGION).addRole(SequenceOntology.PROMOTER);
    // Create ComponentDefinition for cas9m_BFP coding sequence
    doc.createComponentDefinition("cas9m_BFP_cds", version, ComponentDefinition.DNA_REGION).addRole(SequenceOntology.CDS);
    // Create ComponentDefinition for cas9m_BFP gene
    ComponentDefinition cas9m_BFP_gene = doc.createComponentDefinition("cas9m_BFP_gene", version, ComponentDefinition.DNA_REGION);
    cas9m_BFP_gene.addRole(SequenceOntology.PROMOTER);
    cas9m_BFP_gene.createSequenceConstraint("cas9m_BFP_gene_constraint", RestrictionType.PRECEDES, "pConst", "cas9m_BFP_cds");
    // Create ComponentDefintion for cas9m_BFP protein
    doc.createComponentDefinition("cas9m_BFP", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefintion for CRa_U6 promoter
    ComponentDefinition CRa_U6 = doc.createComponentDefinition("CRa_U6", version, ComponentDefinition.DNA_REGION);
    CRa_U6.addRole(SequenceOntology.PROMOTER);
    CRa_U6.addSequence("CRa_U6_seq");
    // Create ComponentDefintion for gRNA_b coding sequence
    ComponentDefinition gRNA_b_nc = doc.createComponentDefinition("gRNA_b_nc", version, ComponentDefinition.DNA_REGION);
    gRNA_b_nc.addRole(SequenceOntology.CDS);
    gRNA_b_nc.addSequence("gRNA_b_seq");
    // Create ComponentDefinition for gRNA_b terminator
    doc.createComponentDefinition("gRNA_b_terminator", version, ComponentDefinition.DNA_REGION).addRole(SequenceOntology.TERMINATOR);
    // Create ComponentDefinition for gRNA_b gene
    ComponentDefinition gRNA_b_gene = doc.createComponentDefinition("gRNA_b_gene", version, ComponentDefinition.DNA_REGION);
    gRNA_b_gene.addRole(SequenceOntology.PROMOTER);
    gRNA_b_gene.createSequenceConstraint("gRNA_b_gene_constraint1", RestrictionType.PRECEDES, "CRa_U6", "gRNA_b_nc");
    gRNA_b_gene.createSequenceConstraint("gRNA_b_gene_constraint2", RestrictionType.PRECEDES, "gRNA_b_nc", "gRNA_b_terminator");
    // Create ComponentDefinition for gRNA_b RNA
    doc.createComponentDefinition("gRNA_b", version, ComponentDefinition.RNA_REGION).addRole(SequenceOntology.SGRNA);
    SequenceOntology so = new SequenceOntology();
    URI sgrna = so.getURIbyName("sgRNA");
    // Create ComponentDefinition for cas9m_BFP gRNA_b complex
    doc.createComponentDefinition("cas9m_BFP_gRNA_b", version, ComponentDefinition.COMPLEX);
    // Create ComponentDefinition for mKate coding sequence
    ComponentDefinition mKate_cds = doc.createComponentDefinition("mKate_cds", version, ComponentDefinition.DNA_REGION);
    mKate_cds.addRole(SequenceOntology.CDS);
    mKate_cds.addSequence("mKate_seq");
    // Create ComponentDefinition for mKate gene
    ComponentDefinition mKate_gene = doc.createComponentDefinition("mKate_gene", version, ComponentDefinition.DNA_REGION);
    mKate_gene.addRole(SequenceOntology.PROMOTER);
    mKate_gene.createSequenceConstraint("mKate_gene_constraint", RestrictionType.PRECEDES, "pConst", "mKate_cds");
    // Create ComponentDefinition for mKate protein
    doc.createComponentDefinition("mKate", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefinition for Gal4VP16 coding sequence
    ComponentDefinition Gal4VP16_cds = doc.createComponentDefinition("Gal4VP16_cds", version, ComponentDefinition.DNA_REGION);
    Gal4VP16_cds.addRole(SequenceOntology.CDS);
    // Create ComponentDefintion for Gal4VP16 gene
    ComponentDefinition Gal4VP16_gene = doc.createComponentDefinition("Gal4VP16_gene", version, ComponentDefinition.DNA_REGION);
    Gal4VP16_gene.addRole(SequenceOntology.PROMOTER);
    Gal4VP16_gene.createSequenceConstraint("GAL4VP16_gene_constraint", RestrictionType.PRECEDES, "pConst", "Gal4VP16_cds");
    // Create ComponentDefintion for Gal4VP16 protein
    doc.createComponentDefinition("Gal4VP16", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefinition for CRP_b promoter
    ComponentDefinition CRP_b = doc.createComponentDefinition("CRP_b", version, ComponentDefinition.DNA_REGION);
    CRP_b.addRole(SequenceOntology.PROMOTER);
    CRP_b.addSequence("CRP_b_seq");
    // Create ComponentDefintiion for EYFP coding sequence
    ComponentDefinition EYFP_cds = doc.createComponentDefinition("EYFP_cds", version, ComponentDefinition.DNA_REGION);
    EYFP_cds.addRole(SequenceOntology.CDS);
    // Create ComponentDefinition for EYFP gene
    ComponentDefinition EYFP_gene = doc.createComponentDefinition("EYFP_gene", version, ComponentDefinition.DNA_REGION);
    EYFP_gene.addRole(SequenceOntology.PROMOTER);
    EYFP_gene.createSequenceConstraint("EYFP_gene_constraint", RestrictionType.PRECEDES, "CRP_b", "EYFP_cds");
    // Create ComponentDefintiion for EYFP protein
    doc.createComponentDefinition("EYFP", version, ComponentDefinition.PROTEIN);
    // Create ModuleDefintion for CRISPR Repression
    ModuleDefinition CRPb_circuit = doc.createModuleDefinition("CRPb_characterization_circuit", version);
    // Create the FunctionalComponents for the ModuleDefinition CRISPR_Repression
    CRPb_circuit.createFunctionalComponent("cas9m_BFP", AccessType.PRIVATE, "cas9m_BFP", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("cas9m_BFP_gene", AccessType.PRIVATE, "cas9m_BFP_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("gRNA_b", AccessType.PRIVATE, "gRNA_b", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("gRNA_b_gene", AccessType.PRIVATE, "gRNA_b_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("mKate", AccessType.PRIVATE, "mKate", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("mKate_gene", AccessType.PRIVATE, "mKate_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("Gal4VP16", AccessType.PRIVATE, "Gal4VP16", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("Gal4VP16_gene", AccessType.PRIVATE, "Gal4VP16_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("EYFP", AccessType.PRIVATE, "EYFP", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("EYFP_gene", AccessType.PRIVATE, "EYFP_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("cas9m_BFP_gRNA_b", AccessType.PRIVATE, "cas9m_BFP_gRNA_b", version, DirectionType.NONE);
    /* Production of mKate from the mKate gene */
    Interaction mKate_production = CRPb_circuit.createInteraction("mKate_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    mKate_production.createParticipation("mKate", "mKate", SystemsBiologyOntology.PRODUCT);
    mKate_production.createParticipation("mKate_gene", "mKate_gene", SystemsBiologyOntology.PROMOTER);
    // Production of GAL4VP16 from the GAL4VP16 gene
    Interaction GAL4VP16_production = CRPb_circuit.createInteraction("Gal4VP16_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    GAL4VP16_production.createParticipation("Gal4VP16_gene", "Gal4VP16_gene", SystemsBiologyOntology.PROMOTER);
    GAL4VP16_production.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.PRODUCT);
    // Production of cas9m_BFP from the cas9m_BFP gene
    Interaction cas9m_BFP_production = CRPb_circuit.createInteraction("cas9m_BFP_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    cas9m_BFP_production.createParticipation("cas9m_BFP_gene", "cas9m_BFP_gene", SystemsBiologyOntology.PROMOTER);
    cas9m_BFP_production.createParticipation("cas9m_BFP", "cas9m_BFP", SystemsBiologyOntology.PRODUCT);
    // Production of gRNA_b from the gRNA_b gene
    Interaction gRNA_b_production = CRPb_circuit.createInteraction("gRNA_b_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    gRNA_b_production.createParticipation("gRNA_b_gene", "gRNA_b_gene", SystemsBiologyOntology.PROMOTER);
    gRNA_b_production.createParticipation("gRNA_b", "gRNA_b", SystemsBiologyOntology.PRODUCT);
    // Activation of EYFP production by GAL4VP16
    Interaction EYFP_Activation = CRPb_circuit.createInteraction("EYFP_Activation", SystemsBiologyOntology.STIMULATION);
    EYFP_Activation.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.STIMULATOR);
    EYFP_Activation.createParticipation("EYFP_gene", "EYFP_gene", SystemsBiologyOntology.PROMOTER);
    // Degradation of mKate
    Interaction mKate_deg = CRPb_circuit.createInteraction("mKate_deg", SystemsBiologyOntology.DEGRADATION);
    mKate_deg.createParticipation("mKate", "mKate", SystemsBiologyOntology.REACTANT);
    // Degradation of GAL4VP16
    Interaction GAL4VP16_deg = CRPb_circuit.createInteraction("Gal4VP16_deg", SystemsBiologyOntology.DEGRADATION);
    GAL4VP16_deg.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.REACTANT);
    // Degradation of cas9m_BFP
    Interaction cas9m_BFP_deg = CRPb_circuit.createInteraction("cas9m_BFP_deg", SystemsBiologyOntology.DEGRADATION);
    cas9m_BFP_deg.createParticipation("cas9m_BFP", "cas9m_BFP", SystemsBiologyOntology.REACTANT);
    // Degradation of gRNA_b
    Interaction gRNA_b_deg = CRPb_circuit.createInteraction("gRNA_b_deg", SystemsBiologyOntology.DEGRADATION);
    gRNA_b_deg.createParticipation("gRNA_b", "gRNA_b", SystemsBiologyOntology.REACTANT);
    // Degradation of EYFP
    Interaction EYFP_deg = CRPb_circuit.createInteraction("EYFP_deg", SystemsBiologyOntology.DEGRADATION);
    EYFP_deg.createParticipation("EYFP", "EYFP", SystemsBiologyOntology.REACTANT);
    // Degradation of cas9m_BFP_gRNA_b
    Interaction cas9m_BFP_gRNA_b_deg = CRPb_circuit.createInteraction("cas9m_BFP_gRNA_b_deg", SystemsBiologyOntology.DEGRADATION);
    cas9m_BFP_gRNA_b_deg.createParticipation("cas9m_BFP_gRNA_b", "cas9m_BFP_gRNA_b", SystemsBiologyOntology.REACTANT);
    // Create Template Module
    Module Template_Module = CRPb_circuit.createModule("CRISPR_Template", "CRISPR_Template", version);
    // Add MapsTos to Template Module
    Template_Module.createMapsTo("cas9m_BFP_map", RefinementType.USELOCAL, "cas9m_BFP", "cas9_generic");
    Template_Module.createMapsTo("gRNA_b_map", RefinementType.USELOCAL, "gRNA_b", "gRNA_generic");
    Template_Module.createMapsTo("cas9m_BFP_gRNA_map", RefinementType.USELOCAL, "cas9m_BFP_gRNA_b", "cas9_gRNA_complex");
    Template_Module.createMapsTo("EYFP_map", RefinementType.USELOCAL, "EYFP", "target");
    Template_Module.createMapsTo("EYFP_gene_map", RefinementType.USELOCAL, "EYFP_gene", "target_gene");
    // try {
    // SBOLWriter.write(doc, "/Users/myers/RepressionModel.rdf");
    // }
    // catch (XMLStreamException | FactoryConfigurationError | CoreIoException e) {
    // e.printStackTrace();
    // }
    // catch (IOException e) {
    // e.printStackTrace();
    // }
    // END of Repression Model construction. Code below uses trivial manipulations to show other major methods in the library.
    ComponentDefinition cas9_generic1 = doc.getComponentDefinition("cas9_generic", version);
    ComponentDefinition cas9_generic2 = doc.getComponentDefinition("cas9_generic", null);
    if (cas9_generic1.equals(cas9_generic2)) {
        System.out.println("Two Cas9 generic protein objects are equal.");
    }
    gRNA_b_gene.getSequenceConstraint("gRNA_b_gene_constraint1");
    CRISPR_Template.setName("C~R*I!S@P#R-based Repression Template");
    if (CRISPR_Template.isSetName()) {
        CRISPR_Template.unsetName();
        CRISPR_Template.setName("CRISPR-based Repression Template");
    }
    CRISPR_Template.setDescription("Authors: S. Kiani, J. Beal, M. Ebrahimkhani, J. Huh, R. Hall, Z. Xie, Y. Li, and R. Weiss" + "Titel: Crispr transcriptional repression devices and layered circuits in mammalian cells" + "Journal: Nature Methods, vol. 11, no. 7, pp. 723–726, 2014.");
    URI gRNA_b_gene_role2 = URI.create("http://identifiers.org/so/SO:0000613");
    gRNA_b_gene.addRole(gRNA_b_gene_role2);
    if (gRNA_b_gene.containsRole(gRNA_b_gene_role2)) {
        gRNA_b_gene.removeRole(gRNA_b_gene_role2);
    }
    gRNA_b_gene.clearRoles();
    if (!gRNA_b_gene.getRoles().isEmpty()) {
        System.out.println("gRNA_b_gene set is not empty.");
    }
    gRNA_b_gene.setRoles(new HashSet<URI>(Arrays.asList(SequenceOntology.PROMOTER)));
    CRP_b.clearSequences();
    CRP_b.addSequence("CRP_b_seq");
    // CRP_b.addSequence(
    // URI.create("http://partsregistry.org/seq/partseq_154")
    // );
    String prURI = "http://partsregistry.org/";
    String prPrefix = "pr";
    doc.addNamespace(URI.create(prURI), prPrefix);
    ComponentDefinition pConst = doc.getComponentDefinition("pConst", version);
    pConst.createAnnotation(new QName(prURI, "experience", prPrefix), URI.create("http://parts.igem.org/Part:BBa_J23119:Experience"));
    String myersLabURI = "http://www.async.ece.utah.edu/";
    String myersLabPrefix = "myersLab";
    doc.addNamespace(URI.create(myersLabURI), myersLabPrefix);
    GenericTopLevel datasheet = doc.createGenericTopLevel("datasheet", "1.1", new QName(myersLabURI, "datasheet", myersLabPrefix));
    datasheet.setName("Datasheet for Custom Parameters");
    datasheet.createAnnotation(new QName(myersLabURI, "characterizationData", myersLabPrefix), URI.create(myersLabURI + "/measurement/BBa_J23119"));
    datasheet.createAnnotation(new QName(myersLabURI, "transcriptionRate", myersLabPrefix), 0.75);
    pConst.createAnnotation(new QName(myersLabURI, "datasheet", myersLabPrefix), datasheet.getIdentity());
    ComponentDefinition pConst_alt = (ComponentDefinition) doc.createCopy(pConst, "pConst_alt");
    // pConst_alt.createAnnotation(
    // new QName(prURI, "", prPrefix),
    // URI.create("http://parts.igem.org/Part:BBa_J23100"));
    Sequence pConst_alt_seq = doc.createSequence("pConst_alt_seq", version, "ttgacggctagctcagtcctaggtacagtgctagc", Sequence.IUPAC_DNA);
    pConst_alt.addSequence(pConst_alt_seq);
    SBOLValidate.validateSBOL(doc, true, true, true);
    if (SBOLValidate.getNumErrors() > 0) {
        for (String error : SBOLValidate.getErrors()) {
            System.out.println(error);
        }
        return;
    }
    SBOLWriter.write(doc, (System.out));
    SBOLWriter.write(doc, "RepressionModel.rdf");
}

Example 4 with Sequence

use of com.google.showcase.v1beta1.Sequence in project libSBOLj by SynBioDex.

the class SimpleComponentDefinitionExample method main.

public static void main(String[] args) throws Exception {
    String prURI = "http://partsregistry.org/";
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    ComponentDefinition promoter = document.createComponentDefinition("BBa_J23119", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA_REGION, URI.create("http://identifiers.org/chebi/CHEBI:4705"))));
    promoter.addRole(SequenceOntology.PROMOTER);
    promoter.addRole(URI.create("http://identifiers.org/so/SO:0000613"));
    promoter.setName("J23119 promoter");
    promoter.setDescription("Constitutive promoter");
    promoter.addWasDerivedFrom(URI.create("http://partsregistry.org/Part:BBa_J23119"));
    document.setDefaultURIprefix(prURI);
    Sequence seq = document.createSequence("BBa_J23119", "", "ttgacagctagctcagtcctaggtataatgctagc", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    seq.addWasDerivedFrom(URI.create("http://parts.igem.org/Part:BBa_J23119:Design"));
    promoter.addSequence(seq.getIdentity());
    SBOLWriter.write(document, (System.out));
}

Example 5 with Sequence

use of com.google.showcase.v1beta1.Sequence in project libSBOLj by SynBioDex.

the class ComponentDefinitionOutput method createComponentDefinitionOutput.

public static SBOLDocument createComponentDefinitionOutput() throws SBOLValidationException {
    String prURI = "http://partsregistry.org/";
    String prPrefix = "pr";
    SBOLDocument document = new SBOLDocument();
    document.setTypesInURIs(true);
    document.addNamespace(URI.create(prURI), prPrefix);
    document.setDefaultURIprefix(prURI);
    Sequence seqpTetR = document.createSequence("BBa_R0040", "", "tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqRbs = document.createSequence("BBa_B0034", "", "aaagaggagaaa", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqCds = document.createSequence("BBa_C0062", "", "atgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattaataacactgatagtgctagtgtagatcac", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqTer = document.createSequence("BBa_B0015", "", "ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqPluxR = document.createSequence("BBa_R0062", "", "acctgtaggatcgtacaggtttacgcaagaaaatggtttgttatagtcgaataaa", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    ComponentDefinition pTetR = document.createComponentDefinition("BBa_R0040", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA_REGION)));
    pTetR.addRole(SequenceOntology.PROMOTER);
    pTetR.setName("pTetR");
    pTetR.setDescription("TetR repressible promoter");
    pTetR.addSequence(seqpTetR.getIdentity());
    ComponentDefinition rbs = document.createComponentDefinition("BBa_B0034", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA_REGION)));
    rbs.addRole(SequenceOntology.RIBOSOME_ENTRY_SITE);
    rbs.setName("BBa_B0034");
    rbs.setDescription("RBS based on Elowitz repressilator");
    rbs.addSequence(seqRbs.getIdentity());
    ComponentDefinition cds = document.createComponentDefinition("BBa_C0062", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA_REGION)));
    cds.addRole(SequenceOntology.CDS);
    cds.setName("luxR");
    cds.setDescription("luxR coding sequence");
    cds.addSequence(seqCds.getIdentity());
    ComponentDefinition ter = document.createComponentDefinition("BBa_B0015", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA_REGION)));
    ter.addRole(URI.create("http://identifiers.org/so/SO:0000141"));
    ter.setName("BBa_B0015");
    ter.setDescription("Double terminator");
    ter.addSequence(seqTer.getIdentity());
    ComponentDefinition pluxR = document.createComponentDefinition("BBa_R0062", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA_REGION)));
    // 
    pluxR.addRole(SequenceOntology.PROMOTER);
    pluxR.setName("pLuxR");
    pluxR.setDescription("LuxR inducible promoter");
    pluxR.addSequence(seqPluxR.getIdentity());
    ComponentDefinition device = document.createComponentDefinition("BBa_F2620", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA_REGION)));
    // biological region
    device.addRole(URI.create("http://identifiers.org/so/SO:00001411"));
    device.setName("BBa_F2620");
    device.setDescription("3OC6HSL -> PoPS Receiver");
    Component comPtetR = device.createComponent("pTetR", AccessType.PUBLIC, pTetR.getIdentity());
    Component comRbs = device.createComponent("rbs", AccessType.PUBLIC, rbs.getIdentity());
    Component comCds = device.createComponent("luxR", AccessType.PUBLIC, cds.getIdentity());
    Component comTer = device.createComponent("ter", AccessType.PUBLIC, ter.getIdentity());
    Component comPluxR = device.createComponent("pLuxR", AccessType.PUBLIC, pluxR.getIdentity());
    int start = 1;
    int end = seqPluxR.getElements().length();
    SequenceAnnotation anno = device.createSequenceAnnotation("anno1", "location1", start, end, OrientationType.INLINE);
    anno.setComponent(comPtetR.getIdentity());
    start = end + 1;
    end = seqRbs.getElements().length() + end + 1;
    SequenceAnnotation anno2 = device.createSequenceAnnotation("anno2", "location2", start, end, OrientationType.INLINE);
    anno2.setComponent(comRbs.getIdentity());
    start = end + 1;
    end = seqCds.getElements().length() + end + 1;
    SequenceAnnotation anno3 = device.createSequenceAnnotation("anno3", "location3", start, end, OrientationType.INLINE);
    anno3.setComponent(comCds.getIdentity());
    start = end + 1;
    end = seqTer.getElements().length() + end + 1;
    SequenceAnnotation anno4 = device.createSequenceAnnotation("anno4", "location4", start, end, OrientationType.INLINE);
    anno4.setComponent(comTer.getIdentity());
    start = end + 1;
    end = seqPluxR.getElements().length() + end + 1;
    SequenceAnnotation anno5 = device.createSequenceAnnotation("anno5", "location5", start, end, OrientationType.INLINE);
    anno5.setComponent(comPluxR.getIdentity());
    return document;
}