Examples with Activity spold2.Activity used on opensource projects

Example 21 with Activity

use of spold2.Activity in project libSBOLj by SynBioDex.

the class Provenance_SpecifyBuildOperations method specifyAmplifyOperation.

/**
 * specifies the amplify operation, which amplifies a linear DNA construct using
 * 5' and 3' primers
 *
 * @throws Exception
 */
public static void specifyAmplifyOperation() throws Exception {
    // instantiate a document
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(BUILD_PREFIX);
    // the linear DNA construct
    ComponentDefinition dnaConstruct = document.createComponentDefinition("dna_construct", LINEAR_SINGLE_STRANDED_DNA);
    dnaConstruct.setName("dna_construct");
    // the 5' primer for amplification
    ComponentDefinition fivePrimer = document.createComponentDefinition("five_primer", FORWARD_PRIMER);
    fivePrimer.setName("five_primer");
    // the 3' primer for amplification
    ComponentDefinition threePrimer = document.createComponentDefinition("three_primer", REVERSE_PRIMER);
    threePrimer.setName("three_primer");
    // Create the generic top level entity for the amplify operation
    Activity amplifyOperation = document.createActivity("amplify_" + dnaConstruct.getName() + "_with_" + fivePrimer.getName() + "_and_" + threePrimer.getName());
    amplifyOperation.setName("amplify(" + dnaConstruct.getName() + ", " + fivePrimer.getName() + ", " + threePrimer.getName() + ")");
    // create the qualifiedUsage annotation to describe the inputs of the amplification operation
    // -- the amplicon
    Usage usageDNAConstruct = amplifyOperation.createUsage("dna_construct", dnaConstruct.getIdentity());
    usageDNAConstruct.addRole(URI.create("http://sbols.org/v2#source"));
    usageDNAConstruct.addRole(PCR_PRODUCT);
    // -- the forward primer
    Usage usageFwdPrimer = amplifyOperation.createUsage("forward_primer", fivePrimer.getIdentity());
    usageFwdPrimer.addRole(FORWARD_PRIMER);
    usageFwdPrimer.addRole(FORWARD_PRIMER);
    // -- the reverse primer
    Usage usageRevPrimer = amplifyOperation.createUsage("reverse_primer", threePrimer.getIdentity());
    usageRevPrimer.addRole(REVERSE_PRIMER);
    usageRevPrimer.addRole(REVERSE_PRIMER);
    // the result of the amplification operation
    ComponentDefinition amplified_construct = document.createComponentDefinition("my_amplified_dna", AMPLIFIED_CONSTRUCT);
    amplified_construct.setName("my_amplified_dna");
    amplified_construct.addWasGeneratedBy(amplifyOperation.getIdentity());
    // serialize the document to a file
    SBOLWriter.write(document, System.out);
}

Example 22 with Activity

use of spold2.Activity in project libSBOLj by SynBioDex.

the class Provenance_CodonOptimization method main.

public static void main(String[] args) throws Exception {
    NamespaceBinding myAppNs = NamespaceBinding("http://myapp.com/", "myapp");
    SBOLDocument document = new SBOLDocument();
    document.addNamespace(URI.create(myAppNs.getNamespaceURI()), myAppNs.getPrefix());
    document.setDefaultURIprefix(myAppNs.getNamespaceURI());
    ComponentDefinition optimizedCds = getCds(document, "codon_optimized", "Codon optimised CDS");
    ComponentDefinition sourceCds = getCds(document, "non_codon_optimized", "Non Codon optimised CDS");
    optimizedCds.addWasDerivedFrom(sourceCds.getIdentity());
    // Create the agent definition for the codon optimization software
    Agent agent = document.createAgent("codon_optimization_software");
    agent.setName("Codon Optimization Software");
    // Create the generic top level entity for the codon optimization activity
    Activity activity = document.createActivity("codon_optimization_activity");
    activity.setName("Codon Optimization Activity");
    // Create the qualifiedUsage annotation to describe the use of the non codon optimized CDS component
    activity.createUsage("usage", sourceCds.getIdentity()).addRole(URI.create("http://sbols.org/v2#source"));
    // Create the qualifiedAssociation annotation to describe the use of the software agent used in the activity
    activity.createAssociation("association", agent.getIdentity()).addRole(myAppNs.namespacedUri("codonoptimiser"));
    optimizedCds.addWasGeneratedBy(activity.getIdentity());
    SBOLWriter.write(document, System.out);
}

Example 23 with Activity

use of spold2.Activity in project libSBOLj by SynBioDex.

the class Provenance_StrainDerivation method main.

public static void main(String[] args) throws Exception {
    NamespaceBinding myAppNs = NamespaceBinding("http://myapp.com/", "myapp");
    SBOLDocument document = new SBOLDocument();
    document.addNamespace(URI.create(myAppNs.getNamespaceURI()), myAppNs.getPrefix());
    document.setDefaultURIprefix(myAppNs.getNamespaceURI());
    ComponentDefinition b168 = getCds(document, "bsubtilis168", "Bacillus subtilis 168");
    ComponentDefinition b3610 = getCds(document, "bsubtilisncimb3610", "Bacillus subtilis NCIMB 3610");
    b168.addWasDerivedFrom(b3610.getIdentity());
    // Create the agent definition to represent X-ray
    Agent agent = document.createAgent("x_ray");
    agent.setName("X-ray");
    // Create the generic top level entity for the X-ray mutagenesis activity
    Activity activity = document.createActivity("xraymutagenesis");
    activity.setName("X-ray mutagenesis");
    // Create the qualifiedUsage annotation to describe the use of the parent strain
    activity.createUsage("usage", b3610.getIdentity()).addRole(URI.create("http://sbols.org/v2#source"));
    // Create the qualifiedAssociation annotation to describe the use of the agent used in the activity
    activity.createAssociation("association", agent.getIdentity()).addRole(myAppNs.namespacedUri("mutagen"));
    b168.addWasGeneratedBy(activity.getIdentity());
    SBOLWriter.write(document, System.out);
}

Example 24 with Activity

use of spold2.Activity in project libSBOLj by SynBioDex.

the class SBOLWorkshop2018 method main.

public static void main(String[] args) throws SBOLValidationException, IOException, SBOLConversionException, SynBioHubException {
    /* Getting a Device from an SBOL Compliant XML */
    // Start a new SBOL Document to hold the device
    SBOLDocument doc = new SBOLDocument();
    doc.setCreateDefaults(true);
    // Set your Homespace. All new SBOL objects will be created in this namespace
    String my_namespace = "http://my_namespace.org/";
    doc.setDefaultURIprefix(my_namespace);
    // Create a new device
    ComponentDefinition my_device = doc.createComponentDefinition("my_device", version, ComponentDefinition.DNA_REGION);
    System.out.println(my_device.getIdentity());
    System.out.println("");
    // Load some genetic parts taken from the Cello paper
    // TODO: need to fill in path
    SBOLDocument cello_parts = SBOLReader.read("/Users/myers/Downloads/parts.xml");
    System.out.println(len(cello_parts));
    printCounts(cello_parts);
    System.out.println("");
    // componentDefinitions and sequences
    for (TopLevel topLevel : cello_parts.getTopLevels()) {
        System.out.println(topLevel.getIdentity());
    }
    System.out.println("");
    // Import these objects into your Document
    doc.createCopy(cello_parts);
    for (TopLevel topLevel : doc.getTopLevels()) {
        System.out.println(topLevel.getIdentity());
    }
    System.out.println("");
    // Retrieve an object from the Document using its uniform resource identifier (URI)
    Collection promoter_collection = doc.getCollection(URI.create("http://examples.org/Collection/promoters/1"));
    // A Collection contains a list of URI references to objects, not the object themselves
    for (TopLevel topLevel : promoter_collection.getMembers()) {
        System.out.println(topLevel.getIdentity());
    }
    System.out.println("");
    // Retrieve a component, using its full URI
    ComponentDefinition promoter = doc.getComponentDefinition(URI.create("http://examples.org/ComponentDefinition/pPhlF/1"));
    // Review the BioPAX and Sequence Ontology terms that describe this component
    System.out.println(promoter.getTypes());
    System.out.println(promoter.getRoles());
    System.out.println("");
    /* Getting a Device from Synbiohub */
    // Start an interface to the part shop
    SynBioHubFrontend part_shop = new SynBioHubFrontend("https://synbiohub.org");
    // Search for records from the interlab study
    ArrayList<IdentifiedMetadata> records = part_shop.getMatchingComponentDefinitionMetadata("interlab", null, null, null, 0, 50);
    for (IdentifiedMetadata record : records) {
        System.out.println(record.getDisplayId() + ": " + record.getUri());
    }
    System.out.println("");
    // Import the medium device into the user's Document
    doc.createCopy(part_shop.getSBOL(URI.create("https://synbiohub.org/public/iGEM_2016_interlab/Medium_2016Interlab/1")));
    // Explore the new parts
    for (TopLevel topLevel : doc.getTopLevels()) {
        System.out.println(topLevel.getClass().getSimpleName() + ": " + topLevel.getIdentity());
    }
    System.out.println("");
    /* Extracting a ComponentDefinition from a Pre-existing Device */
    // Extract the medium strength promoter
    ComponentDefinition medium_strength_promoter = doc.getComponentDefinition(URI.create("https://synbiohub.org/public/igem/BBa_J23106/1"));
    // Get parts for a new circuit
    ComponentDefinition rbs = doc.getComponentDefinition(URI.create("http://examples.org/ComponentDefinition/Q2/1"));
    ComponentDefinition cds = doc.getComponentDefinition(URI.create("http://examples.org/ComponentDefinition/LuxR/1"));
    ComponentDefinition terminator = doc.getComponentDefinition(URI.create("http://examples.org/ComponentDefinition/ECK120010818/1"));
    // Assemble a new gene
    my_device.createSequenceConstraint("constraint1", RestrictionType.PRECEDES, medium_strength_promoter.getIdentity(), rbs.getIdentity());
    my_device.createSequenceConstraint("constraint2", RestrictionType.PRECEDES, rbs.getIdentity(), cds.getIdentity());
    my_device.createSequenceConstraint("constraint3", RestrictionType.PRECEDES, cds.getIdentity(), terminator.getIdentity());
    // Annotate the target construct with a Sequence Ontology term
    my_device.addRole(SequenceOntology.ENGINEERED_REGION);
    // Explore the newly assembled gene
    for (Component component : my_device.getComponents()) {
        System.out.println(component.getDisplayId());
    }
    System.out.println("");
    compile(doc, my_device);
    Sequence seq = my_device.getSequenceByEncoding(Sequence.IUPAC_DNA);
    System.out.println(seq.getElements());
    System.out.println("");
    /* Managing a Design-Build-Test-Learn workflow */
    Activity workflow_step_1 = doc.createActivity("build_1", version);
    Activity workflow_step_2 = doc.createActivity("build_2", version);
    Activity workflow_step_3 = doc.createActivity("test_1", version);
    Activity workflow_step_4 = doc.createActivity("analysis_1", version);
    Plan workflow_step_1_plan = doc.createPlan("gibson_assembly", version);
    Plan workflow_step_2_plan = doc.createPlan("transformation", version);
    Plan workflow_step_3_plan = doc.createPlan("promoter_characterization", version);
    Plan workflow_step_4_plan = doc.createPlan("parameter_optimization", version);
    workflow_step_1.createAssociation("association", URI.create("mailto:jdoe@my_namespace.org")).setPlan(workflow_step_1_plan.getIdentity());
    workflow_step_2.createAssociation("association", URI.create("mailto:jdoe@my_namespace.org")).setPlan(workflow_step_2_plan.getIdentity());
    workflow_step_3.createAssociation("association", URI.create("http://sys-bio.org/plate_reader_1")).setPlan(workflow_step_3_plan.getIdentity());
    workflow_step_4.createAssociation("association", URI.create("http://tellurium.analogmachine.org")).setPlan(workflow_step_4_plan.getIdentity());
    Implementation gibson_mix = doc.createImplementation("gibson_mix", version);
    gibson_mix.setBuilt(my_device);
    gibson_mix.addWasGeneratedBy(workflow_step_1.getIdentity());
    workflow_step_1.createUsage("usage", my_device.getIdentity());
    Collection clones = doc.createCollection("clones", version);
    Implementation clone1 = doc.createImplementation("clone1", version);
    clone1.setBuilt(my_device);
    clones.addMember(clone1.getIdentity());
    Implementation clone2 = doc.createImplementation("clone2", version);
    clone2.setBuilt(my_device);
    clones.addMember(clone2.getIdentity());
    Implementation clone3 = doc.createImplementation("clone3", version);
    clone3.setBuilt(my_device);
    clones.addMember(clone3.getIdentity());
    clones.addWasGeneratedBy(workflow_step_2.getIdentity());
    workflow_step_2.createUsage("usage", gibson_mix.getIdentity());
    Collection experiment1 = doc.createCollection("experiment1", version);
    experiment1.addWasGeneratedBy(workflow_step_3.getIdentity());
    workflow_step_3.createUsage("usage", clones.getIdentity());
    Collection analysis1 = doc.createCollection("analysis1", version);
    analysis1.addWasGeneratedBy(workflow_step_4.getIdentity());
    workflow_step_4.createUsage("usage", experiment1.getIdentity());
    // Validate the Document
    SBOLValidate.validateSBOL(doc, false, false, false);
    for (String error : SBOLValidate.getErrors()) {
        System.out.println(error);
    }
    System.out.println(analysis1.getIdentity());
    System.out.println("");
    /* Uploading the Device back to SynBioHub */
    // TODO: Need to provide your credentials
    String user_name = "myers";
    String password = "MaWen69!";
    part_shop.login(user_name, password);
    // Upon submission, the Document will be converted to a Collection with the following properties
    // The new Collection will have a URI that conforms to the following pattern:
    // https://synbiohub.org/user/<USERNAME>/<DOC.DISPLAYID>/<DOC.DISPLAYID>_collection
    String displayId = "my_device";
    String name = "my device";
    String description = "a description of the cassette";
    part_shop.createCollection(displayId, version, name, description, "", true, doc);
    // TODO: need to fill in your path
    String attachment_path = "/Users/myers/Downloads/results.txt";
    // Attach raw experimental data to the Test object here. Note the pattern
    URI test_uri = URI.create("https://synbiohub.org/user/" + user_name + "/" + displayId + "/experiment1/1");
    part_shop.attachFile(test_uri, attachment_path);
    // Attach processed experimental data here
    // TODO: need to fill in your path
    String other_attachement_path = "/Users/myers/Downloads/results.txt";
    URI analysis_uri = URI.create("https://synbiohub.org/user/" + user_name + "/" + displayId + "/analysis1/1");
    part_shop.attachFile(analysis_uri, other_attachement_path);
    System.out.println("Successfully uploaded");
}

Example 25 with Activity

use of spold2.Activity in project olca-modules by GreenDelta.

the class ProcessImport method getProcessName.

/**
 * The name of the process has the following pattern:
 * <p>
 * <process name> | <product name> | <system model>, <process type>
 * <p>
 * Where <system model> is a mnemonic like "APOS" or "Cutoff" and the process
 * type is "U" when it is a unit process or "S" when it is a LCI result
 */
private String getProcessName(DataSet ds) {
    // the process and ref. product name
    Activity a = Spold2.getActivity(ds);
    String name = a != null ? a.name : "?";
    IntermediateExchange qRef = Spold2.getReferenceProduct(ds);
    if (qRef != null && qRef.name != null) {
        name += " | " + qRef.name;
    }
    // we try to infer a short name for the system model here
    // because the short name is part of the master data which
    // is not always available (or can be found) when importing
    // a data set
    String model = null;
    Representativeness repri = Spold2.getRepresentativeness(ds);
    if (repri.systemModelName != null) {
        String sys = repri.systemModelName.toLowerCase();
        if (sys.contains("consequential")) {
            model = "Consequential";
        } else if (sys.contains("apos") || sys.contains("allocation at the point of substitution")) {
            model = "APOS";
        } else if (sys.contains("cut-off") || sys.contains("cutoff")) {
            model = "Cutoff";
        } else if (sys.contains("legacy")) {
            model = "Legacy";
        } else {
            model = repri.systemModelName;
        }
    }
    if (model != null) {
        name += " | " + model;
    }
    // the process type
    String type = a != null && a.type == 2 ? "S" : "U";
    name += ", " + type;
    return name;
}