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.

Core Classes

Prefix: biocrnpyler.core

Chemical reaction networks and BioCRNpyler base classes.

The core classes in BioCRNpyler define the low-level objects that are used to specify chemical reaction networks as well as defining the base classes for components, mechanisms as mixtures.

Chemical Reaction Networks (CRNs)

Low-level chemical reaction networks can be implemented by defining species and reactions directly. The following classes are used to implement this functionality.

ChemicalReactionNetwork	Container for chemical species and their reactions.
Compartment	Spatial compartment for organizing species in a CRN model.
ModelParameter	Parameter with search and found keys for defaulting behavior.
Reaction	Chemical reaction in a CRN with species and rate law.
Species	A formal species object for a chemical reaction network (CRN).

Species types

A number of different species are used internally to keep track of different types of molecular constructs. These are normally not accessed at the user level, but are useful when defining components and mechanisms.

Complex	Metaclass for creating chemical complexes.
ComplexSpecies	Species formed from multiple bound species.
MonomerCollection	Collection of ordered monomers without any particular structure.
NamedPolymer	An OrderedPolymer with an associated name and circularity flag.
OrderedComplexSpecies	Complex species where species order is significant.
OrderedMonomer	A unit that belongs to an OrderedPolymer.
OrderedPolymer	A polymer made up of OrderedMonomers with a specific order.
OrderedPolymerSpecies	Ordered polymer that can participate in chemical reactions.
PolymerConformation	Set of polymers and their connections via ComplexSpecies.
WeightedSpecies	Container for a species with stoichiometric coefficient.

Propensities

Propensities define the rate laws for chemical reactions in a CRN. Different propensity types implement different kinetic models such as mass action, Hill functions, and custom formulas. Propensities can be deterministic (ODE) or stochastic (Gillespie).

Propensity	Base class for reaction propensity functions in BioCRNpyler.
GeneralPropensity	Propensity with user-defined formula string.
Hill	Base class for Hill-type propensities.
HillNegative	Negative Hill function propensity (repression).
HillPositive	Positive Hill function propensity (activation).
MassAction	Mass action kinetics propensity.
ProportionalHillPositive	Proportional positive Hill function propensity.
ProportionalHillNegative	Proportional negative Hill function propensity.

Parameter databases

Parameters are organized into databases that allow hierarchical searching.

ParameterDatabase	Database for storing and retrieving parameters with defaulting.
ParameterEntry	Parameter with database lookup key and metadata.

Base classes

The base classes define the primary objects used to represent a model and compile it into a chemical reaction network. These classes are not called directly, but are utilized for the components, mechanisms, and mixtures that make up the BioCRNpyler library.

Component	Base class for biomolecular components in BioCRNpyler.
Mechanism	Base class for mechanisms that generate species and reactions.
Mixture	Container for components, mechanisms, and parameters in a CRN model.
Parameter	Base class for representing parameters in BioCRNpyler.

Components

Prefix: biocrnpyler.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.

Basic

DNA	DNA sequence component with specified length.
RNA	RNA sequence component with specified length.
Protein	Protein component with specified length.
Metabolite	Metabolic compound that can be produced, utilized, or degraded.
ChemicalComplex	Complex formed by binding of two or more molecular species.
Enzyme	Enzyme that catalyzes conversion of substrates to products.

Combinatorial Complex

CombinatorialComplex

Complex formed through combinatorial binding of multiple species.

Combinatorial Conformation

CombinatorialConformation	Polymer conformation with combinatorial internal binding complexes.
CombinatorialConformationPromoter	Combinatorial conformation with transcriptionally active states.

Component Enumerator

ComponentEnumerator	Base class for enumerating new components from existing components.
LocalComponentEnumerator	Component enumerator that operates on individual components.
GlobalComponentEnumerator	Component enumerator that operates on all mixture components.

Construct Explorer

ConstructExplorer
TxExplorer
TlExplorer

Integrase Enumerator

Polymer_transformation	Template for transforming polymer sequences through recombination.
IntegraseRule	Rules defining integrase recombination reactions and products.
Integrase_Enumerator	Global enumerator for integrase-mediated DNA recombination products.

Membrane

DiffusibleMolecule	Molecule that diffuses passively through a membrane.
IntegralMembraneProtein	Transmembrane protein that integrates into the membrane.
MembraneChannel	Membrane channel for facilitated transport across membranes.
MembranePump	ATP-dependent membrane pump for active transport.
MembraneSensor	Two-component system (TCS) membrane sensor protein.

DNA Assemblies

DNAassembly	High-level representation of a gene expression construct.
CDS	Coding sequence component representing a protein-coding region.
Construct	Base class for ordered genetic constructs with multiple parts.
DNA_construct	DNA construct representing a functional genetic circuit.
RNA_construct	RNA construct representing a functional transcript.
DNA_part	Base class for individual DNA parts in constructs.
DNABindingSite	DNA binding site component for protein-DNA interactions.
IntegraseSite	Integrase attachment site for site-specific recombination.
UserDefined	User-defined DNA part with no intrinsic functionality.
Origin	Origin of replication component for visualization.
Operator	Operator sequence component for visualization.
Promoter	Basic promoter component for constitutive transcription.
RegulatedPromoter	Promoter with simple independent regulatory binding.
ActivatablePromoter	Promoter with Hill function-based activation.
RepressiblePromoter	Promoter with Hill function-based repression.
CombinatorialPromoter	Promoter with combinatorial regulatory logic.
RBS	Ribosome binding site component for translation control.
Terminator	Transcriptional terminator component for ending transcription.

Mechanisms

Prefix: biocrnpyler.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

One_Step_Cooperative_Binding	Cooperative binding mechanism for single-step multi-ligand binding.
Two_Step_Cooperative_Binding	Sequential cooperative binding mechanism with oligomerization.
Combinatorial_Cooperative_Binding	Combinatorial binding mechanism for multiple distinct ligands.
One_Step_Binding	Simple binding mechanism for multiple species without cooperativity.

Conformation

One_Step_Reversible_Conformation_Change

Reversible conformational change mechanism.

Enzyme

BasicCatalysis	Basic catalytic mechanism for irreversible substrate conversion.
BasicProduction	Basic catalytic production mechanism with optional substrate.
MichaelisMenten	Standard Michaelis-Menten enzyme kinetics mechanism.
MichaelisMentenReversible	Reversible Michaelis-Menten kinetics with product binding.
MichaelisMentenCopy	Michaelis-Menten kinetics with substrate preservation.

Global Mechanisms

GlobalMechanism	Base class for global mechanisms that act on all species in a mixture.
Dilution	Global mechanism for species dilution or degradation.
AntiDilutionConstitutiveCreation	Global mechanism for constitutive creation to counter dilution.
Degradation_mRNA_MM	Michaelis-Menten mRNA degradation by endonucleases.
Deg_Tagged_Degradation	Michaelis-Menten degradation of deg-tagged proteins by degradase.

Integrase

BasicIntegration	Basic DNA integration mechanism without enzyme involvement.
EnzymeIntegration	Enzyme-catalyzed DNA integration mechanism with integrase.

Metabolite

OneStepPathway

Simple one-step metabolic pathway mechanism.

Signaling

Membrane_Signaling_Pathway_MM

Two-component system membrane sensor with Michaelis-Menten kinetics.

Transport

Simple_Diffusion	Passive diffusion mechanism for substrate transport across membranes.
Membrane_Protein_Integration	Membrane protein integration mechanism for protein insertion.
Simple_Transport	Passive transport mechanism through membrane channel proteins.
Facilitated_Transport_MM	Facilitated diffusion mechanism with Michaelis-Menten kinetics.
Primary_Active_Transport_MM	Primary active transport mechanism with ATP-dependent pumping.

Txtl

OneStepGeneExpression	Single-step gene expression mechanism without explicit TX-TL steps.
SimpleTranscription	Simple catalytic transcription mechanism.
SimpleTranslation	Simple catalytic translation mechanism.
PositiveHillTranscription	Transcription regulated by positive Hill function (activation).
NegativeHillTranscription	Transcription regulated by negative Hill function (repression).
Transcription_MM	Michaelis-Menten transcription with explicit RNA polymerase.
Translation_MM	Michaelis-Menten translation with explicit ribosome.
Energy_Transcription_MM	Michaelis-Menten transcription with explicit energy consumption.
Energy_Translation_MM	Michaelis-Menten translation with explicit energy consumption.
multi_tx	Multi-polymerase transcription with isomerization and occupancy.
multi_tl	Multi-ribosome translation with isomerization and occupancy.

Mixtures

Prefix: biocrnpyler.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.

Cell

ExpressionDilutionMixture	In vivo gene expression with dilution but without cellular machinery.
SimpleTxTlDilutionMixture	In vivo TX-TL with simple mechanisms and continuous dilution.
TxTlDilutionMixture	In vivo TX-TL with explicit machinery, dilution, and background load.

Extract

ExpressionExtract	Gene expression extract without explicit TX-TL machinery.
SimpleTxTlExtract	TX-TL extract with simple transcription and translation mechanisms.
TxTlExtract	TX-TL extract with explicit transcription and translation machinery.
EnergyTxTlExtract	TX-TL cell extract with explicit machinery and energy consumption.

Pure

BasicPURE

PURE cell-free protein synthesis system with energy consumption.