Index

A

add_cycle() (CNOGraph method) add_edge() (CNOGraph method) add_edges_from() (CNOGraph method) add_experiment() (XMIDAS method) add_gaussian_noise() (XMIDAS method) add_measurements() (Measurements method) (MIDASBuilder method) add_node() (CNOGraph method) add_nodes_from() (CNOGraph method) add_path() (CNOGraph method) add_reaction() (CNOGraph method) (Reactions method) (SIF method) (SOP2SIF method) add_reactions() (CNOGraph method) (Reactions method) (SIF method) (SOP2SIF method) add_section() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) add_star() (CNOGraph method)

add_uniform_distributed_noise() (XMIDAS method) add_weighted_edges_from() (CNOGraph method) ADJ2SIF (class in cno.io.adj2sif) adjacency_matrix() (CNOGraph method) alpha (Trend attribute) analyse() (GTTBool method) and_nodes (SIF attribute) and_symbol (SIF attribute) (SOP2SIF attribute) ands2ors() (Reaction method) append() (Measurements method) args (CNOError attribute) attributes (CNOGraph attribute) average_replicates() (XMIDAS method)

B

best_score (BooleanResults attribute) (DTResults attribute) (FuzzyResults attribute) (ODEResults attribute) BooleanModels (class in cno.core.models)

BooleanResults (class in cno.core.results) boxplot() (XMIDAS method)

C

cellLine (Measurement attribute) (XMIDAS attribute) cellLines (XMIDAS attribute) centrality_betweeness() (CNOGraph method) centrality_closeness() (CNOGraph method) centrality_degree() (CNOGraph method) centrality_eigenvector() (CNOGraph method) check_data_compatibility() (CNOGraph method) clean() (DistributeRPackage method) clean_orphan_ands() (CNOGraph method) clear() (CNOGraph method) (SIF method) close_body() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) close_html() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) CNA (class in cno.io.cna) cno.admin.distribute (module) cno.admin.install (module) cno.core.base (module) cno.core.cnor (module) cno.core.gtt (module) cno.core.models (module) cno.core.params (module) cno.core.report (module) cno.core.results (module) cno.io.adj2sif (module) cno.io.cna (module) cno.io.cnograph (module) cno.io.eda (module) cno.io.measurements (module) cno.io.midas (module) cno.io.reactions (module)

cno.io.sif (module) cno.io.sif2asp (module) cno.io.sop2sif (module) cno.io.xcnograph (module) cno.io.xmlmidas (module) cno.misc.matfun (module) cno.misc.tools (module) CNOBase (class in cno.core.base) CNOError CNOGraph (class in cno.io.cnograph) cnograph (CNOBase attribute) CNOGraphAttributes (class in cno.io.cnograph) CNORBase (class in cno.core.base) collapse_node() (CNOGraph method) CompareTwoModels (class in cno.core.models) compress() (CNOGraph method) compressable_nodes (CNOGraph attribute) compute_average() (BooleanModels method) (DTModels method) constant() (Trend method) copy() (BooleanModels method) (DTModels method) (FuzzyModels method) (XMIDAS method) corr() (XMIDAS method) count() (Measurements method) create_empty_simulation() (XMIDAS method) create_picture_cnorfuzzy_package() (in module cno.misc.matfun) create_random_simulation() (XMIDAS method) create_report() (CNOBase method) create_report_images() (CNOBase method) cues_as_dict() (Measurement method) cutnonc() (CNOGraph method)

D

data (CNOBase attribute) (Measurement attribute) debugLevel (CNOBase attribute) (Report attribute) (ReportBool attribute) (ReportDT attribute) (ReportFuzzy attribute) (ReportODE attribute) degree_histogram() (XCNOGraph method) dependency_matrix() (XCNOGraph method) difference() (CNOGraph method) discretise() (XMIDAS method) discretize() (XMIDAS method)

distribute() (DistributeRPackage method) DistributeRPackage (class in cno.admin.distribute) draw() (CNOGraph method) drop_duplicates() (BooleanModels method) (DTModels method) drop_scores_above() (BooleanModels method) (DTModels method) (FuzzyModels method) (Models method) DTModels (class in cno.core.models) DTResults (class in cno.core.results)

E

earlier() (Trend method) EDA (class in cno.io.eda) edge2reaction() (CNOGraph method) edges (SIF attribute) errorbar() (BooleanModels method) (DTModels method) excludeInLogical (CNA attribute)

expand_and_gates() (CNOGraph method) expand_or_gates() (CNOGraph method) experiments (XMIDAS attribute) export2sif() (EDA method) (SOP2SIF method) extend() (Measurements method)

F

findnonc() (CNOGraph method) focus_exp() (XMIDAS method)

FuzzyModels (class in cno.core.models) FuzzyResults (class in cno.core.results)

G

G (ADJ2SIF attribute) get_average_model() (BooleanModels method) (DTModels method) (FuzzyModels method) (Models method) get_bestfit() (Trend method) get_bestfit_color() (Trend method) get_both() (CompareTwoModels method) get_both_off() (CompareTwoModels method) get_cell() (Measurements method) get_colnames() (MIDASBuilder method) get_consensus_model() (BooleanModels method) (DTModels method) get_cues() (Measurement method) get_cv_model() (BooleanModels method) (DTModels method) get_data() (Measurements method) get_default_edge_attributes() (CNOGraph method) get_df_data() (MIDASBuilder method) get_df_exps() (MIDASBuilder method) get_diff() (XMIDAS method) get_footer() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) get_header() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) get_html_reproduce() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method)

get_intersection() (CompareTwoModels method) get_jaccard() (BooleanModels method) (DTModels method) get_m1_only() (CompareTwoModels method) get_m2_only() (CompareTwoModels method) get_main_reactions() (BooleanModels method) (DTModels method) get_max_errors() (XMIDAS method) get_max_rank() (CNOGraph method) get_node_attributes() (CNOGraph method) get_protein() (Measurements method) get_residual_errors() (XMIDAS method) get_same_rank() (CNOGraph method) get_signed_lhs_species() (Reaction method) get_stats() (CNOGraph method) get_table_dependencies() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) get_time() (Measurements method) get_time_now() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) get_toc() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) get_union() (CompareTwoModels method) GTTBool (class in cno.core.gtt)

H

hcluster() (XCNOGraph method) (XMIDAS method) heatmap() (BooleanModels method) (DTModels method) (XMIDAS method) help() (DistributeRPackage static method)

hist2d_scores_vs_model_size() (BooleanResults method) (DTResults method) hist_scores() (BooleanResults method) (DTResults method)

I

imshow() (XMIDAS method) incTruthTable (CNA attribute) index() (Measurements method) inhibitors (CNOGraph attribute) (MIDASBuilder attribute) (Measurement attribute) (Measurements attribute) (XMIDAS attribute) insert() (Measurements method) install_all_cellnopt_dependencies() (in module cno.admin.install) install_dependencies_cellnoptr() (in module cno.core.cnor)

install_dependencies_ode() (in module cno.core.cnor) intersect() (CNOGraph method) inverse_sustained() (Trend method) is_and() (SIF method) is_compressable() (CNOGraph method) is_reaction_in() (CNOGraph method) isand() (CNOGraph method)

K

keys() (CNOGraphAttributes method)

L

later() (Trend method) level (CNOBase attribute) (Report attribute) (ReportBool attribute) (ReportDT attribute) (ReportFuzzy attribute) (ReportODE attribute) lhs (Reaction attribute) lhs_species (Reaction attribute)

load_adjacency() (ADJ2SIF method) load_names() (ADJ2SIF method) lookfor() (CNOGraph method)

M

mapping (SOP2SIF attribute) Measurement (class in cno.io.measurements) Measurements (class in cno.io.measurements) merge_nodes() (CNOGraph method) merge_times() (XMIDAS method) message (CNOError attribute) midas (CNOBase attribute) (CNOGraph attribute)

MIDASBuilder (class in cno.io.measurements) MIDASReader (class in cno.io.midas) models (BooleanResults attribute) Models (class in cno.core.models) models (DTResults attribute) (FuzzyResults attribute) (ODEResults attribute) monotony (CNA attribute) MultiModels (class in cno.core.models)

N

name (Reaction attribute) names (ADJ2SIF attribute) names_cues (XMIDAS attribute) names_inhibitors (XMIDAS attribute) names_signals (XMIDAS attribute) names_species (XMIDAS attribute) names_stimuli (XMIDAS attribute) nExps (XMIDAS attribute) nodes1 (SIF attribute)

nodes2 (SIF attribute) nonc (CNOGraph attribute) normalise() (XMIDAS method) normed_times (Trend attribute) normed_values (Trend attribute) normhill_tf() (in module cno.misc.matfun) notedge() (SIF method) nSignals (XMIDAS attribute)

O

ODEResults (class in cno.core.results)

onweb() (CNOBase method)

P

pca() (XMIDAS method) pknmodel (CNOBase attribute) plot() (BooleanModels method) (CNOGraph method) (DTModels method) (EDA method) (SIF method) (Trend method) (XMIDAS method) plot2() (XMIDAS method) plot_adjacency_matrix() (XCNOGraph method) plot_data() (XMIDAS method) plot_degree_rank() (XCNOGraph method) plot_feedback_loops_histogram() (XCNOGraph method) plot_feedback_loops_species() (XCNOGraph method) plot_fit() (BooleanResults method) (DTResults method) (ODEResults method) plot_fitness() (CNOBase method) (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) plot_in_out_degrees() (XCNOGraph method) plot_layout() (XMIDAS method) plot_mapback_model() (CNOBase method)

plot_midas() (CNOBase method) plot_model() (CNOBase method) plot_mse() (XMIDAS method) plot_mse_grouped_by_size() (BooleanResults method) (DTResults method) plot_multigraph() (CompareTwoModels method) plot_ode_transfer_function() (in module cno.misc.matfun) plot_optimised_model() (CNOBase method) plot_pknmodel() (CNOBase method) plot_sim_data() (XMIDAS method) png (CNOGraph attribute) pop() (Measurements method) predecessors_as_reactions() (CNOGraph method) preprocessing() (CNOBase method) (CNOGraph method) protein_name (Measurement attribute)

R

radviz() (XMIDAS method) random_cnograph() (XCNOGraph method) random_poisson_graph() (XCNOGraph method) reac2edges() (CNOGraph method) reacBoxes (CNA attribute) reacText (CNA attribute) Reaction (class in cno.io.reactions) Reactions (class in cno.io.reactions) reactions (CNOGraph attribute) (Reactions attribute) (SIF attribute) (SOP2SIF attribute) read() (MIDASReader method) (XMIDAS method) read_json() (CNOGraph method) read_sbmlqual() (CNOGraph method) (SIF method) read_sif() (CNOGraph method) (SIF method) readXML() (XMLMIDAS method) relabel_nodes() (CNOGraph method) remove() (Measurements method) remove_and_gates() (CNOGraph method) (SIF method) remove_cellLine() (XMIDAS method) remove_edge() (CNOGraph method) remove_edges_from() (CNOGraph method) remove_experiments() (XMIDAS method) remove_inhibitors() (XMIDAS method) remove_node() (CNOGraph method) remove_nodes_from() (CNOGraph method) remove_reaction() (Reactions method) (SIF method) (SOP2SIF method)

remove_self_loops() (CNOGraph method) remove_species() (Reactions method) (SIF method) (SOP2SIF method) (XMIDAS method) remove_stimuli() (XMIDAS method) remove_times() (XMIDAS method) rename_cellLine() (XMIDAS method) rename_experiments() (XMIDAS method) rename_inhibitors() (XMIDAS method) rename_species() (Reaction method) (Reactions method) (SIF method) (SOP2SIF method) (XMIDAS method) rename_stimuli() (XMIDAS method) rename_time() (XMIDAS method) Report (class in cno.core.report) report() (CNOBase method) (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) report_directory (CNOBase attribute) ReportBool (class in cno.core.report) ReportDT (class in cno.core.report) ReportFuzzy (class in cno.core.report) ReportODE (class in cno.core.report) reset() (XMIDAS method) reset_edge_attributes() (CNOGraph method) reset_experiments() (XMIDAS method) reset_index() (XMIDAS method) results (BooleanResults attribute) (DTResults attribute) (FuzzyResults attribute) (ODEResults attribute) reverse() (Measurements method) rhs (Reaction attribute) round() (XMIDAS method)

S

save() (SIF method) save_config_file() (CNOBase method) savefig() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) scale_max() (XMIDAS method) scale_max_across_experiments() (XMIDAS method) scale_min_max() (XMIDAS method) scale_min_max_across_experiments() (XMIDAS method) scatter_scores_vs_model_size() (BooleanResults method) (DTResults method) scores (BooleanResults attribute) (DTResults attribute) (FuzzyResults attribute) (ODEResults attribute) search() (Reactions method) (SIF method) (SOP2SIF method) set() (Trend method) set_default_node_attributes() (CNOGraph method) set_edge_attribute() (CNOGraph method) set_edge_visibility_from_reactions() (CNOGraph method) set_index() (XMIDAS method) set_node_attributes() (CNOGraph method) show() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method) shuffle() (XMIDAS method) SIF (class in cno.io.sif) SIF2ASP (class in cno.io.sif2asp)

sign (Reaction attribute) sign_operator_to_number() (SIF method) signals (CNOGraph attribute) (XMIDAS attribute) signed_predecessors() (CNOGraph method) signs (SIF2ASP attribute) simplify() (Reaction method) sizes (BooleanModels attribute) (BooleanResults attribute) (DTModels attribute) (DTResults attribute) SOP2SIF (class in cno.io.sop2sif) sop2sif() (SOP2SIF method) sort() (Measurements method) (Reaction method) sort_experiments_by_inhibitors() (XMIDAS method) sort_experiments_by_stimuli() (XMIDAS method) species (CNOGraph attribute) (Measurements attribute) (Reaction attribute) (Reactions attribute) (SIF attribute) (SOP2SIF attribute) (XMIDAS attribute) split_node() (CNOGraph method) stimuli (CNOGraph attribute) (MIDASBuilder attribute) (Measurement attribute) (Measurements attribute) (XMIDAS attribute) summary() (CNOGraph method) sustained() (Trend method) svg (CNOGraph attribute) swap_edges() (CNOGraph method)

T

test_example() (MIDASBuilder method) time (Measurement attribute) times (Trend attribute) (XMIDAS attribute) timeScale (CNA attribute) to_cnograph() (SIF method) to_csv() (BooleanModels method) (DTModels method) (FuzzyModels method) (Models method) (XMIDAS method) to_directed() (CNOGraph method) to_gexf() (CNOGraph method) to_json() (CNOGraph method) (SIF method)

to_list() (Reactions method) (SIF method) (SOP2SIF method) to_measurements() (XMIDAS method) to_midas() (XMIDAS method) to_net() (SIF2ASP method) to_reactions() (SIF method) to_sbmlqual() (CNOGraph method) (SIF method) to_sif() (ADJ2SIF method) (BooleanModels method) (CNA method) (CNOGraph method) (DTModels method) (FuzzyModels method) (Models method) transient() (Trend method) Trend (class in cno.io.midas)

U

union() (CNOGraph method)

units (Measurement attribute)

V

valid_symbols (SIF attribute) (SOP2SIF attribute) values (Trend attribute)

verbose (CNOGraph attribute) verboseR (CNORBase attribute)

W

write() (Report method) (ReportBool method) (ReportDT method) (ReportFuzzy method) (ReportODE method)

X

XCNOGraph (class in cno.io.xcnograph) XMIDAS (class in cno.io.midas) xmidas (MIDASBuilder attribute) (XMLMIDAS attribute)

XMLMIDAS (class in cno.io.xmlmidas) xplot() (XMIDAS method)