Index

A

add_condition() (pybool.constraints.MetaData method) add_edge() (pybool.io.GraphBuilder method) (pybool.io.NetworkXGraphBuilder method) add_external_input() (pybool.constraints.MetaData method) add_gene() (pybool.constraints.MetaData method) add_gene_headers_to_matrix() (in module pybool.io)

aggregate_possible_inputs() (in module pybool.analysis) aggregate_possible_regulations() (in module pybool.analysis) aggregate_possible_thetas() (in module pybool.analysis) analyse_dependencies() (in module pybool.analysis)

B

BooleanNetwork (class in pybool.network) BooleanNetworkGenerator (class in pybool.network)

build_chow_liu_tree() (in module pybool.chow_liu_trees)

C

c_calculate_change_points() (in module pybool.network) c_execute_time_step() (in module pybool.network) calculate_change_points() (in module pybool.network) calculate_gene_change_points() (in module pybool.network) calculate_mutual_information() (in module pybool.chow_liu_trees) centre_string() (in module pybool.io) ChangePointChecker (class in pybool.constraints) CHECK_ALL_DIFFERENT (in module pybool.constraints) check_all_different() (pybool.constraints.ChangePointChecker method) CHECK_CONSECUTIVE_DIFFERENT (in module pybool.constraints) check_consecutive_different() (pybool.constraints.ChangePointChecker method) CHECK_DIFFERENT (in module pybool.constraints) check_different() (pybool.constraints.ChangePointChecker method) CHECK_EXPRESSES_BEFORE (in module pybool.constraints) check_expresses_before() (pybool.constraints.ChangePointChecker method) CHECK_NULL_EXPRESSION (in module pybool.constraints) check_null_expression() (pybool.constraints.ChangePointChecker method)

CHECK_OFF_TO_ON_SWITCH (in module pybool.constraints) check_off_to_on_switch() (pybool.constraints.ChangePointChecker method) CHECK_ON_TO_OFF_SWITCH (in module pybool.constraints) check_on_to_off_switch() (pybool.constraints.ChangePointChecker method) CHECK_ORDER_OF_EXPRESSION (in module pybool.constraints) check_order_of_expression() (pybool.constraints.ChangePointChecker method) color (pybool.constraints.Gene attribute) combinations() (in module pybool.constraints) (in module pybool.network) combine() (in module pybool.constraints) Condition (class in pybool.constraints) configure_matplotlib_for_tex() (in module pybool.io) consecutive() (in module pybool.constraints) constraints (pybool.constraints.Condition attribute) count_possible_inputs() (in module pybool.analysis) count_possible_regulations() (in module pybool.analysis) count_possible_thetas() (in module pybool.analysis) cp (pybool.constraints.ChangePointChecker attribute)

E

ensure_dir_exists() (in module pybool.io) evaluate_all_conditions() (in module pybool.network)

evaluate_condition() (in module pybool.network) execute_time_step() (pybool.network.BooleanNetwork method)

F

feature_string() (in module pybool.network)

filter_unique_Js() (in module pybool.network)

G

G (pybool.constraints.MetaData attribute) Gene (class in pybool.constraints) gene_off() (in module pybool.constraints) gene_on() (in module pybool.constraints)

generate_realisation() (pybool.network.BooleanNetwork method) graph_network() (in module pybool.io) graph_restrictions() (in module pybool.io) GraphBuilder (class in pybool.io)

I

input_parameters (pybool.network.BooleanNetwork attribute)

inputs (pybool.constraints.Condition attribute)

J

J (pybool.network.BooleanNetwork attribute)

M

marginal_distribution() (in module pybool.chow_liu_trees) marginal_pair_distribution() (in module pybool.chow_liu_trees) merged_inputs (pybool.constraints.Condition attribute)

meta_data (pybool.network.BooleanNetwork attribute) MetaData (class in pybool.constraints) (class in pybool.examples.neurogenesis) (class in pybool.examples.tutorial)

N

name (pybool.constraints.Condition attribute) (pybool.constraints.Gene attribute) network_to_features() (in module pybool.network)

NetworkXGraphBuilder (class in pybool.io) number_possible_combinations() (in module pybool.network)

O

output_file() (in module pybool.io)

P

plot_network_realisation() (in module pybool.io) plot_network_realisations() (in module pybool.io) position (pybool.constraints.Gene attribute) py_execute_time_step() (in module pybool.network) pybool (module) pybool.analysis (module) pybool.chow_liu_trees (module)

pybool.constraints (module) pybool.examples (module) pybool.examples.neurogenesis (module) pybool.examples.tutorial (module) pybool.io (module) pybool.network (module)

R

R (pybool.constraints.ChangePointChecker attribute) regulation_as_str() (in module pybool.io)

regulatory_matrix_as_string() (in module pybool.io) rgb_as_string() (in module pybool.io)

S

summarise_meta_data() (in module pybool.io) summarise_possible_networks() (in module pybool.io)

svp_external_input() (in module pybool.examples.neurogenesis) (in module pybool.examples.tutorial)

T

theta (pybool.network.BooleanNetwork attribute)

V

version_string() (in module pybool)

W

which_network_feature() (in module pybool.network)

write_graph() (in module pybool.io)

X

X_external_input() (in module pybool.examples.tutorial)