The BioCRNpyler Library
This chapter contains documentation on the classes and functions that make up the BioCRNplyer package. All objects and functions available in the package can be access through the subpackages in which they are contained. For convenience, a list of low-level (core) classes, components, mechanisms, and mixtures is also included here, in individual sections of this chapter.
Subpackages
The BioCRNpyler package is organized as a set of subpackages that define the differrent functions and objects used to model a system. Information on the individual subpackages can be accessed via the table below. Information on all components, mechanisms, and mixtures contained in the package are described further down on the page.
Chemical reaction networks and BioCRNpyler base classes. |
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BioCRNpyler component library (including DNA components). |
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BioCRNpyler mechanism library. |
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BioCRNpyler mixture library. |
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Utility functions, including SBML support and plotting. |
Low-Level Classes
Low-level chemical reaction networks can be implemented by defining species and reactions directly. The following classes are used to implement this functionality.
Container for chemical species and their reactions. |
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Metaclass for creating chemical complexes. |
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Base class for representing parameters in BioCRNpyler. |
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Chemical reaction in a CRN with species and rate law. |
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A formal species object for a chemical reaction network (CRN). |
More detailed information about specialized subclasses for
representing species can be found in the
biocrnpyler.core.species module.
Components
BioCRNpyler component library (including DNA components).
Components are the primary building blocks of models in BioCRNpyler.
They represent biomolecular parts or motifs such as promoters,
enzymes, transcriptional units, or complexes, and serve as an
abstraction layer above the core chemical species and reactions
defined in the biocrnpyler.core module.
The following subsections provide a list of all components currently available in the BioCRNpyler package.
Components
biocrnpyler.components.combinatorial_complex.CombinatorialComplexbiocrnpyler.components.combinatorial_conformation.CombinatorialConformationbiocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoterbiocrnpyler.components.component_enumerator.ComponentEnumeratorbiocrnpyler.components.component_enumerator.LocalComponentEnumeratorbiocrnpyler.components.component_enumerator.GlobalComponentEnumeratorbiocrnpyler.components.integrase_enumerator.Polymer_transformationbiocrnpyler.components.integrase_enumerator.Integrase_Enumerator
DNA: Assembly
DNA: Cds
DNA: Construct
DNA: Misc
DNA: Promoter
DNA: Rbs
DNA: Terminator
Mechanisms
BioCRNpyler mechanism library.
Mechanisms in BioCRNpyler define “reaction schemas” that describe the biochemical processes generating species and reactions during model compilation. They sit between the abstract design of components and the concrete chemical reactions and species described in the Chemical Reaction Networks section.
The following subsections provide a list of all mechanisms currently available in the BioCRNpyler package.
Binding
Conformation
Enzyme
Global Mechanisms
biocrnpyler.mechanisms.global_mechanisms.AnitDilutionConstiutiveCreationbiocrnpyler.mechanisms.global_mechanisms.Degradation_mRNA_MMbiocrnpyler.mechanisms.global_mechanisms.Deg_Tagged_Degradation
Integrase
Metabolite
Signaling
Transport
Txtl
Mixtures
BioCRNpyler mixture library.
A mixture in BioCRNpyler defines the context in which components are compiled into a chemical reaction network (CRN). A mixture ties together components, mechanisms, and parameters by specifying which Mechanisms are available, which components are present, and what parameters to use.
The following subsections provide a list of all mixtures currently available in the BioCRNpyler package.