Crate biodivine_lib_param_bn

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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.

Structs§

  • 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 (multi-dimensional 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).

Enums§

  • 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.

Type Aliases§