Reference

Shorthand for QualitativeNetwork.

struct QualitativeNetwork{N, S} <: GraphDynamicalSystem{N, S}

A qualitative network model as described in "Qualitative networks: a symbolic approach to analyze biological signaling networks".

This implementation encompasses both the synchronous and asynchonous cases. In the paper, it is assumed that the synchronous case is used. As such, the default constructor uses a synchronous schedule.

• graph: Graph containing the topology and target functions of the network

• state: State of the network

Systems that include the model semantics wrap around this struct with an ArbitrarySteppable from DynamicalSystems. See create_qn_system for an example.

get_state(gds::GraphDynamicalSystem) -> Any

Get the state of the GDS.

get_state(qn::QualitativeNetwork, component) -> Any

set_state!(
    qn::QualitativeNetwork,
    entity::Symbol,
    value::Integer
) -> Integer

async_qn_step!(qn::QualitativeNetwork) -> Integer

build_qn_grammar(
    entity_names;
    ...
) -> HerbGrammar.ContextSensitiveGrammar
build_qn_grammar(
    entity_names,
    constants;
    unique_constr
) -> HerbGrammar.ContextSensitiveGrammar

Builds a grammar based on the base QN grammar adding entity_names and constants to the grammar.

The following constraints are currently included

1. removing symmetry due to commutativity of +/*/min/max
2. forbidding same arguments of two argument functions
3. forbidding constant arguments to 2-argument functions
4. forbidding constant arguments to 1-argument functions
5. using each of the entities only once per function
6. forbidding adding or subtracting zero
7. forbidding multiplication and division by 1 or 0
8. forcing the first operator inside ceil and floor to be ÷
9. forbidding max(□, X) and min(□, X) where X is either the max or min

constant in the grammar.

create_qn_system(
    qn::QualitativeNetwork
) -> Union{DynamicalSystemsBase.ArbitrarySteppable{U, M, typeof(GraphDynamicalSystems.async_qn_step!), typeof(GraphDynamicalSystems.reset_model!), typeof(GraphDynamicalSystems.extract_state), typeof(GraphDynamicalSystems.extract_parameters), P, DynamicalSystemsBase.var"#22#24"{typeof(GraphDynamicalSystems.reset_model!)}} where {U<:(StaticArraysCore.MVector{N, Int64} where N), M<:QualitativeNetwork, P<:MetaGraphsNext.MetaGraph}, DynamicalSystemsBase.ArbitrarySteppable{U, M, typeof(GraphDynamicalSystems.sync_qn_step!), typeof(GraphDynamicalSystems.reset_model!), typeof(GraphDynamicalSystems.extract_state), typeof(GraphDynamicalSystems.extract_parameters), P, DynamicalSystemsBase.var"#22#24"{typeof(GraphDynamicalSystems.reset_model!)}} where {U<:(StaticArraysCore.MVector{N, Int64} where N), M<:QualitativeNetwork, P<:MetaGraphsNext.MetaGraph}}

Construct an asynchronous QualitativeNetwork system using the async_qn_step! as a step function.

entities(gds::GraphDynamicalSystem) -> Any

List all entities in gds.

get_domain(
    qn::QualitativeNetwork,
    entity_label::Symbol
) -> Any

Get the domain of the entity entity_label in qn.

get_domain(qn::QualitativeNetwork) -> Any

Get all of the domains of the entities in qn.

get_graph(gds::GraphDynamicalSystem) -> Any

Get the underlying graph of the GDS.

get_n_entities(_::GraphDynamicalSystem{N, S}) -> Any

Get the number of entities N in the GDS.

get_schedule(_::GraphDynamicalSystem{N, S}) -> Any

Get the schedule for the GDS.

interpret(
    e::Union{Int64, Expr, Symbol},
    qn::QualitativeNetwork
) -> Any

Interpret target functions from a QualitativeNetwork.

limit_change(
    prev_value::Integer,
    next_value::Integer,
    min_level::Integer,
    max_level::Integer
) -> Any

Returns the limited value of next_value which is at most 1 different than prev_value.

It is also never negative, or larger than N.

sample_qualitative_network(
    entities::AbstractVector{Symbol},
    domains::AbstractVector{UnitRange{Int64}},
    max_eq_depth::Int64;
    schedule
) -> QualitativeNetwork

sync_qn_step!(qn::QualitativeNetwork)

target_functions(qn::QualitativeNetwork) -> Dict

update_functions_to_interaction_graph(
    entities::AbstractVector{Symbol},
    update_functions::AbstractVector{Union{Expr, Integer, Symbol}},
    domains::AbstractVector{UnitRange{Int64}};
    schedule
) -> MetaGraphsNext.MetaGraph{Int64, Graphs.SimpleGraphs.SimpleDiGraph{Int64}, Symbol, GraphDynamicalSystems.Entity{Int64}, Nothing, DataType, MetaGraphsNext.var"#11#13", Float64}