Expand description

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

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

(internal) Utility methods for BinaryOp.

(internal) Utility methods for BooleanNetwork.

(internal) BooleanNetwork to .aeon string.

(internal) Implements experimental .bnet parser for BooleanNetwork.

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

(internal) Utility methods for FnUpdate.

(internal) Utility methods for Parameter.

(internal) Utility methods for ParameterId.

(internal) Utility methods for Regulation.

(internal) Utility methods for RegulatoryGraph.

(internal) RegulatoryGraph to .aeon string.

(internal) Equivalence relation for RegulatoryGraph.

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

(internal) Utility methods for Variable.

(internal) Utility methods for VariableId.

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

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

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

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

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

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

A Boolean network, possibly parametrised with uninterpreted Boolean functions.

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

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

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

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

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

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

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

Enums

Possible binary Boolean operators that can appear in FnUpdate.

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

Possible monotonous effects of a Regulation in a RegulatoryGraph.

Constants

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

Type Definitions

An iterator over all ParameterIds of a BooleanNetwork.

An iterator over all Regulations of a RegulatoryGraph.

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