sbol2.dbtl

Module Contents

Classes

Design	This class represents a biological Design.
Build	A Build is a realization of a Design. For practical purposes,
Test	All SBOL classes derived from TopLevel appear as top level nodes
Analysis	All SBOL classes derived from TopLevel appear as top level nodes
SampleRoster	A SampleRoster is a container used to group Builds that are included in an experiment together.
AliasedProperty
TranscriptionRepressionInteraction
SmallMoleculeInhibitionInteraction
GeneProductionInteraction
TranscriptionalActivationInteraction
SmallMoleculeActivationInteraction
EnzymeCatalysisInteraction

class sbol2.dbtl.Design(uri='example', version=VERSION_STRING, structure=None, function=None)

Bases: sbol2.toplevel.TopLevel

This class represents a biological Design. A Design is a conceptual representation of a biological system that a synthetic biologist intends to build. A Design is the first object created in libSBOL’s formalized Design-Build-Test-Analysis workflow.

abstract generateDesign(self, uri, agent=None, plan=None, usages=None)

class sbol2.dbtl.Build(uri=URIRef('example'), version=VERSION_STRING, structure=None, behavior=None)

Bases: sbol2.implementation.Implementation

A Build is a realization of a Design. For practical purposes, a Build can represent a biological clone, a plasmid, or other laboratory sample. For a given Design, there may be multiple Builds realized in the lab. A Build represents the second step in libSBOL’s formalized Design-Build-Test-Analyze workflow.

property sysbio_type(self)

class sbol2.dbtl.Test(uri=URIRef('example'), version=VERSION_STRING)

Bases: sbol2.experiment.ExperimentalData

All SBOL classes derived from TopLevel appear as top level nodes in the RDF/XML document tree and SBOL files.

class sbol2.dbtl.Analysis(uri=URIRef('example'), version=VERSION_STRING)

Bases: sbol2.toplevel.TopLevel

All SBOL classes derived from TopLevel appear as top level nodes in the RDF/XML document tree and SBOL files.

abstract verifyTarget(self, consensus_sequence)

abstract reportIdentity(self)

abstract reportCoverage(self)

abstract reportAmbiguity(self)

abstract generate_analysis(self, uri, agent=None, plan=None, usages=None)

class sbol2.dbtl.SampleRoster(uri=URIRef('example'), version=VERSION_STRING)

Bases: sbol2.collection.Collection

A SampleRoster is a container used to group Builds that are included in an experiment together.

A SampleRoster can be used to generate a Test in a Design-Build-Test-Learn workflow.

property sysbio_type(self)

class sbol2.dbtl.AliasedProperty

class sbol2.dbtl.TranscriptionRepressionInteraction

class sbol2.dbtl.SmallMoleculeInhibitionInteraction

class sbol2.dbtl.GeneProductionInteraction

class sbol2.dbtl.TranscriptionalActivationInteraction

class sbol2.dbtl.SmallMoleculeActivationInteraction

class sbol2.dbtl.EnzymeCatalysisInteraction