Index A | B | C | D | E | F | I | M | N | O | P | R | S | T | V A all_control_strategies() (biobalm.control.Intervention method) attractor_candidates (biobalm.types.NodeData attribute) attractor_candidates_limit (biobalm.types.SuccessionDiagramConfiguration attribute) attractor_seeds (biobalm.types.NodeData attribute) attractor_sets (biobalm.types.NodeData attribute) B biobalm module biobalm.control module biobalm.drivers module biobalm.interaction_graph_utils module biobalm.petri_net_translation module biobalm.space_utils module biobalm.succession_diagram module biobalm.symbolic_utils module biobalm.trappist_core module biobalm.types module BooleanSpace (in module biobalm.types) build() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) C cleanup_network() (in module biobalm.interaction_graph_utils) component_subdiagram() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) compute_fixed_point_reduced_STG() (in module biobalm.trappist_core) compute_fixed_point_reduced_STG_async() (in module biobalm.trappist_core) config (biobalm.succession_diagram.SuccessionDiagram attribute) (biobalm.SuccessionDiagram attribute) (biobalm.types.SuccessionDiagramState attribute) control (biobalm.control.Intervention property) ControlOverrides (in module biobalm.types) controls_are_equal() (in module biobalm.control) D dag (biobalm.succession_diagram.SuccessionDiagram attribute) (biobalm.SuccessionDiagram attribute) (biobalm.types.SuccessionDiagramState attribute) debug (biobalm.types.SuccessionDiagramConfiguration attribute) DEBUG (in module biobalm.petri_net_translation) default_config() (biobalm.succession_diagram.SuccessionDiagram static method) (biobalm.SuccessionDiagram static method) depth (biobalm.types.NodeData attribute) depth() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) dnf_function_is_true() (in module biobalm.space_utils) drivers_of_succession() (in module biobalm.control) E edge_all_stable_motifs() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) edge_stable_motif() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expand_attractor_seeds() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expand_bfs() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expand_block() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expand_dfs() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expand_minimal_spaces() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expand_scc() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expand_to_target() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expanded (biobalm.types.NodeData attribute) expanded_attractor_candidates() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expanded_attractor_seeds() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expanded_attractor_sets() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expanded_ids() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) expression_to_space_list() (in module biobalm.space_utils) extract_source_variables() (in module biobalm.petri_net_translation) extract_variable_names() (in module biobalm.petri_net_translation) F feedback_vertex_set() (in module biobalm.interaction_graph_utils) find_drivers() (in module biobalm.control) find_node() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) find_single_drivers() (in module biobalm.drivers) find_single_node_LDOIs() (in module biobalm.drivers) from_file() (biobalm.succession_diagram.SuccessionDiagram static method) (biobalm.SuccessionDiagram static method) from_rules() (biobalm.succession_diagram.SuccessionDiagram static method) (biobalm.SuccessionDiagram static method) function_eval() (in module biobalm.symbolic_utils) function_is_true() (in module biobalm.symbolic_utils) I intersect() (in module biobalm.space_utils) Intervention (class in biobalm.control) is_isomorphic() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) is_subgraph() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) is_subspace() (in module biobalm.space_utils) M max_motifs_per_node (biobalm.types.SuccessionDiagramConfiguration attribute) minimal_trap_spaces() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) minimum_simulation_budget (biobalm.types.SuccessionDiagramConfiguration attribute) module biobalm biobalm.control biobalm.drivers biobalm.interaction_graph_utils biobalm.petri_net_translation biobalm.space_utils biobalm.succession_diagram biobalm.symbolic_utils biobalm.trappist_core biobalm.types N network (biobalm.succession_diagram.SuccessionDiagram attribute) (biobalm.SuccessionDiagram attribute) network_rules (biobalm.types.SuccessionDiagramState attribute) network_to_petrinet() (in module biobalm.petri_net_translation) nfvs (biobalm.succession_diagram.SuccessionDiagram attribute) (biobalm.SuccessionDiagram attribute) (biobalm.types.SuccessionDiagramState attribute) nfvs_size_threshold (biobalm.types.SuccessionDiagramConfiguration attribute) node_attractor_candidates() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) node_attractor_seeds() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) node_attractor_sets() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) node_data() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) node_ids() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) node_indices (biobalm.succession_diagram.SuccessionDiagram attribute) (biobalm.SuccessionDiagram attribute) (biobalm.types.SuccessionDiagramState attribute) node_is_minimal() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) node_percolated_network() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) node_percolated_nfvs() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) node_percolated_petri_net() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) node_successors() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) NodeData (class in biobalm.types) O optimized_recursive_dnf_generator() (in module biobalm.petri_net_translation) P parent_node (biobalm.types.NodeData attribute) percolate_network() (in module biobalm.space_utils) percolate_space() (in module biobalm.space_utils) percolate_space_strict() (in module biobalm.space_utils) percolated_network (biobalm.types.NodeData attribute) percolated_nfvs (biobalm.types.NodeData attribute) percolated_petri_net (biobalm.types.NodeData attribute) percolation_conflicts() (in module biobalm.space_utils) petri_net (biobalm.succession_diagram.SuccessionDiagram attribute) (biobalm.SuccessionDiagram attribute) (biobalm.types.SuccessionDiagramState attribute) pint_goal_size_limit (biobalm.types.SuccessionDiagramConfiguration attribute) place_to_variable() (in module biobalm.petri_net_translation) R reclaim_node_data() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) remove_state_from_dnf() (in module biobalm.space_utils) restrict_expression() (in module biobalm.space_utils) restrict_petrinet_to_subspace() (in module biobalm.petri_net_translation) retained_set_optimization_threshold (biobalm.types.SuccessionDiagramConfiguration attribute) root() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) S sanitize_network_names() (in module biobalm.petri_net_translation) skip_remaining() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) skip_to_minimal() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) skipped (biobalm.types.NodeData attribute) source_nodes() (in module biobalm.interaction_graph_utils) source_scc_subdiagrams() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) source_SCCs() (in module biobalm.interaction_graph_utils) space (biobalm.types.NodeData attribute) space_unique_key() (in module biobalm.space_utils) state_list_to_bdd() (in module biobalm.symbolic_utils) state_to_bdd() (in module biobalm.symbolic_utils) strategy (biobalm.control.Intervention property) stub_ids() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) SubspaceSuccession (in module biobalm.types) successful (biobalm.control.Intervention property) succession (biobalm.control.Intervention property) succession_control() (in module biobalm.control) SuccessionDiagram (class in biobalm) (class in biobalm.succession_diagram) SuccessionDiagramConfiguration (class in biobalm.types) SuccessionDiagramState (class in biobalm.types) successions_to_target() (in module biobalm.control) summary() (biobalm.succession_diagram.SuccessionDiagram method) (biobalm.SuccessionDiagram method) symbolic (biobalm.succession_diagram.SuccessionDiagram attribute) (biobalm.SuccessionDiagram attribute) T trappist() (in module biobalm.trappist_core) trappist_async() (in module biobalm.trappist_core) V valuation_to_state() (in module biobalm.symbolic_utils) variable_to_place() (in module biobalm.petri_net_translation)