Crate biodivine_lib_param_bn

A library for analysis of Boolean networks. As of now, the library supports:

• Regulatory graphs with monotonicity and observability constraints.
• Boolean networks, possibly with partially unknown and parametrised update functions.
• Full SBML-qual support for import/export as well as custom string format .aeon.
• Fully symbolic asynchronous state-space generator using BDDs (great overall performance).
• Semi-symbolic state-space generator, using BDDs used only for the network parameters (allows state-level parallelism for smaller networks).

For a quick introduction to Boolean networks and their symbolic manipulation, you can check out our tutorial module.

Modules

_aeon_parser

(internal) Implements .aeon parser for BooleanNetwork and RegulatoryGraph objects.

_impl_binary_op

(internal) Utility methods for BinaryOp.

_impl_boolean_network

(internal) Utility methods for BooleanNetwork.

_impl_boolean_network_display

(internal) BooleanNetwork to .aeon string.

_impl_boolean_network_from_bnet

(internal) Implements experimental .bnet parser for BooleanNetwork.

_impl_boolean_network_to_bnet

(internal) Implements an experimental .bnet writer for BooleanNetwork.

_impl_fn_update

(internal) Utility methods for FnUpdate.

_impl_parameter

(internal) Utility methods for Parameter.

_impl_parameter_id

(internal) Utility methods for ParameterId.

_impl_regulation

(internal) Utility methods for Regulation.

_impl_regulatory_graph

(internal) Utility methods for RegulatoryGraph.

_impl_regulatory_graph_display

(internal) RegulatoryGraph to .aeon string.

_impl_regulatory_graph_eq

(internal) Equivalence relation for RegulatoryGraph.

_impl_regulatory_graph_to_dot

(internal) Export of RegulatoryGraph into a .dot format.

_impl_variable

(internal) Utility methods for Variable.

_impl_variable_id

(internal) Utility methods for VariableId.

async_graph

Legacy semi-symbolic representation of the coloured asynchronous state-transition graph.

bdd_params

Legacy symbolic representation of parameter space of a BooleanNetwork using Bdds.

biodivine_std

Legacy utility structs and traits, such as State or Set.

sbml

Adds support for SBML-qual import and export to BooleanNetwork.

symbolic_async_graph

A fully symbolic coloured graph representation of the Asynchronous Boolean Network.

tutorial

This is a documentation-only module which describes how to use this crate to work with parametrised Boolean networks and construct symbolic algorithms with them.

Structs

BooleanNetwork

A Boolean network, possibly parametrised with uninterpreted Boolean functions.

ID_REGEX

A regular expression that matches the identifiers allowed as names of Boolean parameters or variables.

Parameter

An explicit parameter of a BooleanNetwork; an uninterpreted Boolean function with a given name and arity.

ParameterId

A type-safe index of a Parameter inside a BooleanNetwork.

Regulation

Describes an interaction between two Variables in a RegulatoryGraph (or a BooleanNetwork).

RegulatoryGraph

A directed graph representing relationships between a collection of Boolean variables using Regulations.

Variable

A Boolean variable of a RegulatoryGraph (or a BooleanNetwork) with a given name.

VariableId

A type-safe index of a Variable inside a RegulatoryGraph (or a BooleanNetwork).

Enums

BinaryOp

Possible binary Boolean operators that can appear in FnUpdate.

FnUpdate

A Boolean update function formula which references Variables and Parameters of a BooleanNetwork.

Monotonicity

Possible monotonous effects of a Regulation in a RegulatoryGraph.

Constants

ID_REGEX_STR

(internal) A regex string of an identifier which we currently allow to appear as a variable or parameter name.

Type Definitions

ParameterIdIterator

An iterator over all ParameterIds of a BooleanNetwork.

RegulationIterator

An iterator over all Regulations of a RegulatoryGraph.

VariableIdIterator

An iterator over all VariableIds of a RegulatoryGraph (or a BooleanNetwork).