Index

_

__len__() (booldog.BoolDogModel method) (booldog.network.BoolDogModel method) __post_init__() (booldog.classes.BoolDogModelInfo method) (booldog.classes.BoolDogNode method) __repr__() (booldog.BoolDogModel method) (booldog.boolean.modifications.Modification method) (booldog.BooleanStateSpace method) (booldog.classes.BoolDogModelInfo method) (booldog.classes.BoolDogNode method) (booldog.network.BoolDogModel method) (booldog.simulation_result.boolean_result.BooleanStateSpace method) (booldog.simulation_result.BooleanStateSpace method) __version__ (in module booldog) _A1 (booldog.continuous.ode_factory.SquadODE attribute) _a1 (booldog.continuous.ode_factory.SquadODE attribute) _add_species() (booldog.io.sbml.SBMLQualWriter method) _add_transitions() (booldog.io.sbml.SBMLQualWriter method) _B1 (booldog.continuous.ode_factory.SquadODE attribute) _b1 (booldog.continuous.ode_factory.SquadODE attribute) _CYTOSCAPE_AVAILABLE (in module booldog.io.cytoscape) (in module booldog.simulation_result.boolean_result) _CYTOSCAPE_STYLE_XML (in module booldog.resources) _download() (in module booldog.io.biomodels) _dxdt_transform() (booldog.continuous.ode_factory.SquadODE method) _from_reader() (booldog.io.BoolDogModelIOFromMixin class method) _get_all_rules() (booldog.io.sbml.SBMLQualReader method) _get_all_species() (booldog.io.sbml.SBMLQualReader method) _get_all_transitions() (booldog.io.sbml.SBMLQualReader method)

_get_qual_plugin() (booldog.io.sbml.SBMLQualReader method) _get_rules() (booldog.io.bnet.BnetParser method) _get_system() (booldog.continuous.ode_factory.BooleCubeODE method) (booldog.continuous.ode_factory.SquadODE method) _handle_comparison() (booldog.io.sbml.MathMLParser static method) _handle_operator() (booldog.io.sbml.MathMLParser static method) _handle_xor() (booldog.io.sbml.MathMLParser static method) _IGRAPH_AVAILABLE (in module booldog.io.igraph) (in module booldog.io.interaction_networks) _MPL_STYLE_SHEET (in module booldog.resources) _normalise_and_collect_regulators() (in module booldog.io.interaction_logic) _omega() (booldog.continuous.ode_factory.SquadODE method) _PILLOW_AVALIBLE (in module booldog.simulation_result.boolean_result) _plot_one_ax() (booldog.simulation_result.continuous_result.ContinuousSimulationResult method) (booldog.simulation_result.ContinuousSimulationResult method) _primes_cached (booldog.BoolDogModel attribute) (booldog.network.BoolDogModel attribute) _rule_to_formula() (booldog.io.sbml.SBMLQualWriter method) _SBML_AVAILABLE (in module booldog.io.sbml) _set_node_ids_and_index() (booldog.BoolDogModel method) (booldog.network.BoolDogModel method) _TABULARQUAL_AVAILABLE (in module booldog.io.tabularqual) _test_node_removabilty() (booldog.boolean.BooleanNetworkModificationMixin method) (booldog.boolean.modifications.BooleanNetworkModificationMixin method) _to_writer() (booldog.io.BoolDogModelIOToMixin class method) _track_network_modifications() (booldog.boolean.BooleanNetworkModificationMixin method) (booldog.boolean.modifications.BooleanNetworkModificationMixin method) _update_model_object() (booldog.boolean.BooleanNetworkModificationMixin method) (booldog.boolean.modifications.BooleanNetworkModificationMixin method)

A

activate_state() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method) activations (booldog.continuous.ode_factory.SquadODE attribute) ADD (booldog.boolean.modifications.ModificationTypes attribute) add_and() (booldog.io.circuit.BooleanDiGraph method) add_node() (booldog.boolean.BooleanNetworkModificationMixin method) (booldog.boolean.modifications.BooleanNetworkModificationMixin method)

add_not() (booldog.io.circuit.BooleanDiGraph method) add_or() (booldog.io.circuit.BooleanDiGraph method) all_species (booldog.io.sbml.SBMLQualReader attribute) AND (booldog.io.circuit.BooleanOperators attribute) and_count (booldog.io.circuit.BooleanDiGraph attribute)

B

B1 (booldog.continuous.ode_factory.BooleCubeODE attribute) BIOMODELS_BASE_URL (in module booldog.io.biomodels) bnet (booldog.io.bnet.BnetParser attribute) BNET_HEADER (in module booldog.io.bnet) BNET_LINE_REGEX (in module booldog.io.bnet) BNET_REGULATORS_REGEX (in module booldog.io.bnet) BnetParser (class in booldog.io.bnet) booldog module booldog.boolean module booldog.boolean.boolean module booldog.boolean.modifications module booldog.classes module booldog.continuous module booldog.continuous.ode_factory module booldog.continuous.semi_quantitative module booldog.io module booldog.io.biomodels module booldog.io.bnet module booldog.io.circuit module booldog.io.cytoscape module booldog.io.igraph module booldog.io.interaction_logic module booldog.io.interaction_networks module booldog.io.networkx module booldog.io.primes module booldog.io.sbml module booldog.io.tabularqual module booldog.network module booldog.resources module

booldog.simulation_result module booldog.simulation_result.boolean_result module booldog.simulation_result.continuous_result module booldog.utils module booldog.utils.boolean_normal_forms module booldog.utils.cytoscape_utils module booldog.utils.decorators module booldog.utils.logger module booldog.utils.misc module booldog2circuit() (in module booldog.io.circuit) booldog2cytoscape() (in module booldog.io) (in module booldog.io.cytoscape) booldog2igraph() (in module booldog.io) (in module booldog.io.igraph) booldog2networkx() (in module booldog.io) (in module booldog.io.networkx) BoolDogModel (class in booldog) (class in booldog.network) BoolDogModelInfo (class in booldog.classes) BoolDogModelIOFromMixin (class in booldog.io) BoolDogModelIOToMixin (class in booldog.io) BoolDogNode (class in booldog.classes) BoolDogSBMLException boolean_network (booldog.continuous.ode_factory.ODE attribute) boolean_simulation() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method) BooleanDiGraph (class in booldog.io.circuit) BooleanNetworkMixin (class in booldog.boolean) (class in booldog.boolean.boolean) BooleanNetworkModificationMixin (class in booldog.boolean) (class in booldog.boolean.modifications) BooleanOperators (class in booldog.io.circuit) BooleanSimulationResult (class in booldog.simulation_result) (class in booldog.simulation_result.boolean_result) BooleanStateSpace (class in booldog) (class in booldog.simulation_result) (class in booldog.simulation_result.boolean_result) BooleCubeODE (class in booldog.continuous.ode_factory) build() (booldog.io.interaction_logic.LogicBuilder method) (booldog.io.interaction_logic.SquadLogic method)

C

clean_line() (in module booldog.io.circuit) continuous_simulation() (booldog.continuous.ContinuousMixin method) (booldog.continuous.semi_quantitative.ContinuousMixin method) ContinuousMixin (class in booldog.continuous) (class in booldog.continuous.semi_quantitative)

ContinuousSimulationResult (class in booldog.simulation_result) (class in booldog.simulation_result.continuous_result) cytoscape_style_xml (in module booldog.resources)

D

debug() (in module booldog.utils.decorators) DEFAULT_COLOURS (in module booldog.simulation_result.boolean_result) doc (booldog.io.sbml.SBMLQualWriter attribute)

document (booldog.io.sbml.SBMLQualReader attribute) dxdt (booldog.continuous.ode_factory.BooleCubeODE attribute), [1] (booldog.continuous.ode_factory.SquadODE attribute), [1]

E

edge_events (booldog.simulation_result.continuous_result.ContinuousSimulationResult attribute) (booldog.simulation_result.ContinuousSimulationResult attribute) ensure_ndarray() (in module booldog.utils) (in module booldog.utils.misc) event_function() (booldog.continuous.ode_factory.ODE method) EXAMPLE_MODEL_ID (in module booldog.io.biomodels)

export() (booldog.simulation_result.boolean_result.BooleanSimulationResult method) (booldog.simulation_result.BooleanSimulationResult method) (booldog.simulation_result.continuous_result.ContinuousSimulationResult method) (booldog.simulation_result.ContinuousSimulationResult method) export_network() (in module booldog.utils.cytoscape_utils) ExtendedEnum (class in booldog.utils) (class in booldog.utils.misc)

F

fetch_model() (in module booldog.io.biomodels) fetch_model_info() (in module booldog.io.biomodels) file (booldog.io.sbml.SBMLQualReader attribute) file_writable() (in module booldog.io) (in module booldog.utils) (in module booldog.utils.misc) from_bnet() (booldog.io.BoolDogModelIOFromMixin class method) from_graphml() (booldog.io.BoolDogModelIOFromMixin class method)

from_igraph() (booldog.io.BoolDogModelIOFromMixin class method) from_interactions() (booldog.io.BoolDogModelIOFromMixin class method) from_networkx() (booldog.io.BoolDogModelIOFromMixin class method) from_primes() (booldog.io.BoolDogModelIOFromMixin class method) from_sbmlqual() (booldog.io.BoolDogModelIOFromMixin class method) from_sif() (booldog.io.BoolDogModelIOFromMixin class method) from_tabularqual() (booldog.io.BoolDogModelIOFromMixin class method) functions2mindnf() (in module booldog.utils.boolean_normal_forms) functions2primes() (in module booldog.utils.boolean_normal_forms)

G

generate_states() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method) get_interactions() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method) get_parents() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method) get_pkg_version() (in module booldog) (in module booldog.utils) (in module booldog.utils.misc)

get_primes() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method) get_resource_file_path() (in module booldog.resources) get_rule() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method)

H

hill() (booldog.continuous.ode_factory.BooleCubeODE method)

homologue_b1() (booldog.continuous.ode_factory.BooleCubeODE method)

I

identifier (booldog.classes.BoolDogModelInfo attribute) (booldog.classes.BoolDogNode attribute), [1] identity() (booldog.continuous.ode_factory.BooleCubeODE method) igraph2interactions() (in module booldog.io.interaction_networks) inactivate_state() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method) index (booldog.BoolDogModel attribute) (booldog.network.BoolDogModel attribute)

inhibitions (booldog.continuous.ode_factory.SquadODE attribute) initial_states (booldog.simulation_result.boolean_result.BooleanSimulationResult attribute) (booldog.simulation_result.BooleanSimulationResult attribute) interactions2rules() (in module booldog.io.interaction_logic) is_constant() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method)

L

list_network_inputs() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method) log (in module booldog.utils.boolean_normal_forms) logger (in module booldog) (in module booldog.boolean.boolean) (in module booldog.boolean.modifications) (in module booldog.continuous.ode_factory) (in module booldog.continuous.semi_quantitative) (in module booldog.io) (in module booldog.io.biomodels) (in module booldog.io.bnet) (in module booldog.io.circuit) (in module booldog.io.igraph) (in module booldog.io.interaction_logic) (in module booldog.io.interaction_networks) (in module booldog.io.networkx) (in module booldog.io.sbml) (in module booldog.io.tabularqual) (in module booldog.network) (in module booldog.simulation_result.boolean_result) (in module booldog.simulation_result.continuous_result) (in module booldog.utils) (in module booldog.utils.misc)

LogicBuilder (class in booldog.io.interaction_logic)

M

make_animation() (booldog.simulation_result.boolean_result.BooleanSimulationResult method) (booldog.simulation_result.BooleanSimulationResult method) MAMO_ACCESSIONS (in module booldog.io.biomodels) MathMLParser (class in booldog.io.sbml) model (booldog.io.sbml.SBMLQualReader attribute) model_id (booldog.io.sbml.SBMLQualReader attribute) model_path (booldog.io.tabularqual.TabularQualReader attribute) Modification (class in booldog.boolean.modifications) modifications (booldog.BoolDogModel attribute) (booldog.network.BoolDogModel attribute) ModificationTypes (class in booldog.boolean.modifications) modify_network() (booldog.boolean.BooleanNetworkModificationMixin method) (booldog.boolean.modifications.BooleanNetworkModificationMixin method) module booldog booldog.boolean booldog.boolean.boolean booldog.boolean.modifications booldog.classes booldog.continuous booldog.continuous.ode_factory booldog.continuous.semi_quantitative booldog.io booldog.io.biomodels booldog.io.bnet booldog.io.circuit booldog.io.cytoscape booldog.io.igraph booldog.io.interaction_logic booldog.io.interaction_networks booldog.io.networkx booldog.io.primes booldog.io.sbml booldog.io.tabularqual booldog.network booldog.resources booldog.simulation_result booldog.simulation_result.boolean_result booldog.simulation_result.continuous_result booldog.utils booldog.utils.boolean_normal_forms booldog.utils.cytoscape_utils booldog.utils.decorators booldog.utils.logger booldog.utils.misc

mpl_style_sheet (in module booldog.resources) mplugin (booldog.io.sbml.SBMLQualWriter attribute)

N

n (booldog.BoolDogModel attribute) (booldog.BoolDogModel property) (booldog.continuous.ode_factory.ODE attribute) (booldog.network.BoolDogModel attribute) (booldog.network.BoolDogModel property) name (booldog.classes.BoolDogNode attribute), [1] network (booldog.BooleanStateSpace attribute) (booldog.io.sbml.SBMLQualWriter attribute) (booldog.simulation_result.boolean_result.BooleanSimulationResult attribute) (booldog.simulation_result.boolean_result.BooleanStateSpace attribute) (booldog.simulation_result.BooleanSimulationResult attribute) (booldog.simulation_result.BooleanStateSpace attribute) (booldog.simulation_result.continuous_result.ContinuousSimulationResult attribute) (booldog.simulation_result.ContinuousSimulationResult attribute)

networkx2interactions() (in module booldog.io.interaction_networks) node_dict (booldog.io.sbml.SBMLQualWriter attribute) node_events (booldog.simulation_result.continuous_result.ContinuousSimulationResult attribute) (booldog.simulation_result.ContinuousSimulationResult attribute) node_id (booldog.boolean.modifications.Modification attribute) nodes (booldog.BoolDogModel attribute), [1] (booldog.network.BoolDogModel attribute), [1] normalised_hill() (booldog.continuous.ode_factory.BooleCubeODE method) NOT (booldog.io.circuit.BooleanOperators attribute) not_count (booldog.io.circuit.BooleanDiGraph attribute) notes (booldog.classes.BoolDogModelInfo attribute)

O

ODE (class in booldog.continuous.ode_factory) ode_classes (in module booldog.continuous.ode_factory) ode_factory() (in module booldog.continuous.ode_factory)

ode_system (booldog.simulation_result.continuous_result.ContinuousSimulationResult attribute) (booldog.simulation_result.ContinuousSimulationResult attribute) OR (booldog.io.circuit.BooleanOperators attribute) or_count (booldog.io.circuit.BooleanDiGraph attribute)

P

param_dict (booldog.continuous.ode_factory.BooleCubeODE attribute), [1] param_gamma (booldog.continuous.ode_factory.SquadODE attribute), [1] param_h (booldog.continuous.ode_factory.SquadODE attribute), [1] param_k (booldog.continuous.ode_factory.BooleCubeODE attribute), [1] param_n (booldog.continuous.ode_factory.BooleCubeODE attribute), [1] param_tau (booldog.continuous.ode_factory.BooleCubeODE attribute), [1] parameter_to_array() (in module booldog.utils) (in module booldog.utils.misc) PAREN_RE (in module booldog.io.circuit) parse() (booldog.io.sbml.MathMLParser static method) parse_function() (booldog.io.sbml.TransitionParser static method) parse_io() (booldog.io.sbml.TransitionParser static method) plot() (booldog.simulation_result.continuous_result.ContinuousSimulationResult method) (booldog.simulation_result.ContinuousSimulationResult method)

plot_state_space() (booldog.BooleanStateSpace method) (booldog.simulation_result.boolean_result.BooleanSimulationResult method) (booldog.simulation_result.boolean_result.BooleanStateSpace method) (booldog.simulation_result.BooleanSimulationResult method) (booldog.simulation_result.BooleanStateSpace method) plot_stg() (booldog.simulation_result.boolean_result.BooleanSimulationResult method) (booldog.simulation_result.BooleanSimulationResult method) plugin (booldog.io.sbml.SBMLQualReader attribute) primes (booldog.BoolDogModel attribute) (booldog.BoolDogModel property) (booldog.network.BoolDogModel attribute) (booldog.network.BoolDogModel property) primes_to_matrices() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method)

R

read() (booldog.io.tabularqual.TabularQualReader method) read_bnet() (in module booldog.io) (in module booldog.io.bnet) read_graphml() (in module booldog.io) (in module booldog.io.interaction_networks) read_igraph() (in module booldog.io) (in module booldog.io.interaction_networks) read_interactions() (in module booldog.io) (in module booldog.io.interaction_networks) read_networkx() (in module booldog.io) (in module booldog.io.interaction_networks) read_primes() (in module booldog.io) (in module booldog.io.primes) read_sbmlqual() (in module booldog.io) (in module booldog.io.sbml)

read_sif() (in module booldog.io) (in module booldog.io.interaction_networks) read_tabularqual() (in module booldog.io) (in module booldog.io.tabularqual) REMOVE (booldog.boolean.modifications.ModificationTypes attribute) remove_node() (booldog.boolean.BooleanNetworkModificationMixin method) (booldog.boolean.modifications.BooleanNetworkModificationMixin method) remove_nodes() (booldog.boolean.BooleanNetworkModificationMixin method) (booldog.boolean.modifications.BooleanNetworkModificationMixin method) resolve_factor() (in module booldog.io.circuit) resolve_rule() (in module booldog.io.circuit) rule (booldog.boolean.modifications.Modification attribute) (booldog.classes.BoolDogNode attribute), [1] rules (booldog.io.bnet.BnetParser attribute) (booldog.io.sbml.SBMLQualReader attribute)

S

SBML_INT_MAX (in module booldog.io.sbml) SBMLQualReader (class in booldog.io.sbml) SBMLQualWriter (class in booldog.io.sbml) set_node_state() (booldog.BooleanStateSpace method) (booldog.simulation_result.boolean_result.BooleanStateSpace method) (booldog.simulation_result.BooleanStateSpace method) setup_logger() (in module booldog) (in module booldog.utils.logger) silence_p4c_loggers() (in module booldog.io.cytoscape) silence_stdout() (in module booldog.utils.decorators) source (booldog.classes.BoolDogModelInfo attribute), [1] source_format (booldog.classes.BoolDogModelInfo attribute)

species_names (booldog.io.sbml.SBMLQualReader attribute) SquadLogic (class in booldog.io.interaction_logic) SquadODE (class in booldog.continuous.ode_factory) standard_states_format() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method) state_space (booldog.BooleanStateSpace attribute) (booldog.simulation_result.boolean_result.BooleanStateSpace attribute) (booldog.simulation_result.BooleanStateSpace attribute) steady_states() (booldog.boolean.boolean.BooleanNetworkMixin method) (booldog.boolean.BooleanNetworkMixin method) stg (booldog.simulation_result.boolean_result.BooleanSimulationResult attribute) (booldog.simulation_result.BooleanSimulationResult attribute)

T

t (booldog.simulation_result.continuous_result.ContinuousSimulationResult attribute) (booldog.simulation_result.ContinuousSimulationResult attribute) TabularQualReader (class in booldog.io.tabularqual) terminal (booldog.continuous.ode_factory.ODE attribute) test_cytoscape_connection() (in module booldog.io.cytoscape) timer() (in module booldog.utils.decorators) to_bnet() (booldog.io.BoolDogModelIOToMixin method) (booldog.io.sbml.SBMLQualReader method) to_cytoscape() (booldog.io.BoolDogModelIOToMixin method) to_igraph() (booldog.io.BoolDogModelIOToMixin method)

to_networkx() (booldog.io.BoolDogModelIOToMixin method) to_primes() (booldog.io.BoolDogModelIOToMixin method) to_sbmlqual() (booldog.io.BoolDogModelIOToMixin method) TOKEN_REGEX (in module booldog.io.sbml) transform (booldog.continuous.ode_factory.ODE attribute) transform_bool_to_continuous() (booldog.continuous.ContinuousMixin method) (booldog.continuous.semi_quantitative.ContinuousMixin method) transforms (in module booldog.continuous.ode_factory) TransitionParser (class in booldog.io.sbml) transitions (booldog.io.sbml.SBMLQualReader attribute) type (booldog.boolean.modifications.Modification attribute)

U

UPDATE (booldog.boolean.modifications.ModificationTypes attribute) update() (booldog.continuous.ode_factory.ODE method)

update_node() (booldog.boolean.BooleanNetworkModificationMixin method) (booldog.boolean.modifications.BooleanNetworkModificationMixin method)

V

validate_node_argument() (in module booldog.utils.decorators)

values() (booldog.utils.ExtendedEnum class method) (booldog.utils.misc.ExtendedEnum class method)

W

write() (booldog.io.sbml.SBMLQualWriter method) write_bnet() (in module booldog.io) (in module booldog.io.bnet) write_c_code() (booldog.continuous.ode_factory.BooleCubeODE method)

write_primes() (in module booldog.io) (in module booldog.io.primes) write_sbmlqual() (in module booldog.io) (in module booldog.io.sbml)

Y

y (booldog.simulation_result.continuous_result.ContinuousSimulationResult attribute) (booldog.simulation_result.ContinuousSimulationResult attribute)