Welcome to BNMPy’s documentation!

Contents:

• BMatrix
  • Required Packages
  • Installation
  • Function Descriptions
    • load_network_from_file(filename, initial_state=None)
    • get_equations(file)
    • get_gene_dict(equations)
    • get_upstream_genes(equations)
    • get_connectivity_matrix(equations,gene_dict,upstream_genes)
    • get_truth_table(equations,upstream_genes, show_functions = None)
    • get_mutation_dict(file)
    • get_knocking_genes(profile, mutation_dict, connectivity_matrix, gene_dict,perturbed_genes=None, perturbed_dict=None)
  • The calculating equations (which all start with cal_) are used post-simulation and calculate the phenotype scores and the final network score_
    • get_cal_upstream_genes(equations):
    • get_cal_functions(equations):
  • get_calculating_scores is to be used post-simulation, which requires the BooleanNetwork code
    • get_calculating_scores(network_traj, cal_functions, cal_upstream_genes, gene_dict, cal_range=None, scores_dict=None)
• API
  • BNMPy.BMatrix
    • get_upstream_genes()
    • load_network_from_file()
    • load_network_from_string()
    • load_pbn_from_file()
    • load_pbn_from_string()
    • rename_nodes()
  • BNMPy.booleanNetwork
    • BooleanNetwork
    • getDataFromFile()
    • getParametersFromFile()
    • getRandomInitialNodeValues()
    • getRandomParameters()
  • BNMPy.build_bn_from_kg
    • all_boolean_combos()
    • load_signor_network()
    • merge_PBN_string()
  • BNMPy.PBN
    • ProbabilisticBN
  • BNMPy.vis
    • build_igraph()
    • build_igraph_pbn()
    • create_matplotlib_extension_visualization()
    • create_matplotlib_visualization()
    • extract_logic_rules_from_network()
    • read_logic_rules()
    • vis_compression()
    • vis_extension()
    • vis_network()
  • BNMPy.steady_state
    • SteadyStateCalculator

Indices and tables

• Index

• Module Index

• Search Page