Crate biodivine_lib_param_bn

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§

biodivine_std: Legacy utility structs and traits, such as State or Set.
fixed_points: This module contains algorithms and data structures for efficiently computing fixed-points of large Boolean networks.
sbml: Adds support for SBML-qual import and export to BooleanNetwork.
solver_context: Solver context provides a way of interfacing between lib-param-bn and the Z3 SMT prover.
symbolic_async_graph: A fully symbolic coloured graph representation of the Asynchronous Boolean Network.
trap_spaces
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.

BooleanNetwork: A Boolean network, possibly parametrised with uninterpreted Boolean functions.
ModelAnnotation: Annotations are “meta” objects that can be declared as part of AEON models to add additional properties that are not directly recognized by the main AEON toolbox.
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.
SdGraph: A more efficient representation of a signed directed graph that can be used for studying the properties of a RegulatoryGraph.
Space: Space represents a hypercube (multidimensional rectangle) in the Boolean state space.
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).

BinaryOp: Possible binary Boolean operators that can appear in FnUpdate.
ExtendedBoolean: An enum representing the possible state of each variable when describing a hypercube.
FnUpdate: A Boolean update function formula which references Variables and Parameters of a BooleanNetwork.
Monotonicity: Possible monotonous effects of a Regulation in a RegulatoryGraph.
Sign: A sign enum that describes the monotonicity of edges.

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).