basico

• basico package
  • Submodules
  • basico.array_tools module
    • compartment_names()
    • plot_arrays_1d()
    • remove_arrays()
    • remove_template()
  • basico.biomodels module
    • download_from()
    • download_json()
    • get_content_for_model()
    • get_files_for_model()
    • get_model_info()
    • search_for_model()
  • basico.compartment_array_tools module
    • animate_rectangular_time_course()
    • animate_rectangular_time_course_as_image()
    • create_linear_array()
    • create_rectangular_array()
    • delete_compartments()
    • plot_linear_time_course()
    • plot_rectangular_time_course()
  • basico.jws_online module
    • download_from()
    • download_json()
    • get_all_models()
    • get_manuscript()
    • get_mathematica_model()
    • get_model_info()
    • get_models_for_reaction()
    • get_models_for_species()
    • get_sbml_model()
  • basico.model_info module
    • T
      • T.CROSS_SECTION
      • T.EFM
      • T.LNA
      • T.LYAPUNOV_EXPONENTS
      • T.MCA
      • T.MOIETIES
      • T.OPTIMIZATION
      • T.PARAMETER_ESTIMATION
      • T.SCAN
      • T.SENSITIVITIES
      • T.STEADY_STATE
      • T.TIME_COURSE
      • T.TIME_COURSE_SENSITIVITIES
      • T.TIME_SCALE_SEPARATION
      • T.all_task_names()
      • T.from_enum()
      • T.to_enum()
    • add_amount_expressions()
    • add_compartment()
    • add_default_plot()
    • add_equation()
    • add_event()
    • add_event_assignment()
    • add_function()
    • add_parameter()
    • add_plot()
    • add_reaction()
    • add_report()
    • add_species()
    • as_dict()
    • assign_report()
    • get_cn()
    • get_compartments()
    • get_default_plot_names()
    • get_events()
    • get_functions()
    • get_jacobian_matrix()
    • get_miriam_annotation()
    • get_miriam_resources()
    • get_model_units()
    • get_notes()
    • get_parameters()
    • get_plot_dict()
    • get_plots()
    • get_reaction_mapping()
    • get_reaction_parameters()
    • get_reactions()
    • get_reduced_jacobian_matrix()
    • get_reduced_stoichiometry_matrix()
    • get_report_dict()
    • get_reports()
    • get_scheduled_tasks()
    • get_species()
    • get_stoichiometry_matrix()
    • get_task_settings()
    • get_time_unit()
    • get_value()
    • have_miriam_resources()
    • remove_amount_expressions()
    • remove_compartment()
    • remove_event()
    • remove_function()
    • remove_parameter()
    • remove_plot()
    • remove_reaction()
    • remove_report()
    • remove_report_from_task()
    • remove_species()
    • remove_user_defined_functions()
    • set_compartment()
    • set_element_name()
    • set_event()
    • set_miriam_annotation()
    • set_model_name()
    • set_model_unit()
    • set_notes()
    • set_parameters()
    • set_plot_curves()
    • set_plot_dict()
    • set_reaction()
    • set_reaction_mapping()
    • set_reaction_parameters()
    • set_report_dict()
    • set_scheduled_tasks()
    • set_species()
    • set_task_settings()
    • set_time_unit()
    • set_value()
    • update_miriam_resources()
  • basico.model_io module
    • create_datamodel()
    • get_current_model()
    • get_examples()
    • get_model_from_dict_or_default()
    • get_num_loaded_models()
    • load_biomodel()
    • load_example()
    • load_model()
    • load_model_from_string()
    • load_model_from_url()
    • new_model()
    • open_copasi()
    • overview()
    • print_model()
    • remove_datamodel()
    • save_model()
    • save_model_and_data()
    • save_model_to_string()
    • set_current_model()
  • basico.task_parameterestimation module
    • PE
      • PE.CURRENT_SOLUTION
      • PE.DIFFERENTIAL_EVOLUTION
      • PE.EVOLUTIONARY_PROGRAMMING
      • PE.EVOLUTIONARY_STRATEGY_SRES
      • PE.GENETIC_ALGORITHM
      • PE.GENETIC_ALGORITHM_SR
      • PE.HOOKE_JEEVES
      • PE.LEVENBERG_MARQUARDT
      • PE.NELDER_MEAD
      • PE.NL2SOL
      • PE.PARTICLE_SWARM
      • PE.PRAXIS
      • PE.RANDOM_SEARCH
      • PE.SCATTER_SEARCH
      • PE.SIMULATED_ANNEALING
      • PE.STEEPEST_DESCENT
      • PE.TRUNCATED_NEWTON
      • PE.all_method_names()
      • PE.from_enum()
      • PE.to_enum()
    • add_experiment()
    • add_experiment_from_dict()
    • get_data_from_experiment()
    • get_experiment()
    • get_experiment_data_from_model()
    • get_experiment_dict()
    • get_experiment_filenames()
    • get_experiment_mapping()
    • get_experiment_names()
    • get_fit_item_template()
    • get_fit_parameters()
    • get_fit_statistic()
    • get_parameters_solution()
    • get_simulation_results()
    • load_experiments_from_dict()
    • load_experiments_from_yaml()
    • num_experiment_files()
    • num_validations_files()
    • plot_per_dependent_variable()
    • plot_per_experiment()
    • prune_simulation_results()
    • remove_experiments()
    • remove_fit_parameters()
    • run_parameter_estimation()
    • save_experiments_to_dict()
    • save_experiments_to_yaml()
    • set_fit_parameters()
  • basico.task_steadystate module
    • run_steadystate()
  • basico.task_timecourse module
    • create_data_handler()
    • get_data_from_data_handler()
    • run_time_course()
    • run_time_course_with_output()
  • basico.task_scan module
    • add_scan_item()
    • get_scan_items()
    • get_scan_items_frame()
    • get_scan_settings()
    • run_scan()
    • set_scan_items()
    • set_scan_settings()
  • basico.task_optimization module
    • get_opt_item_template()
    • get_opt_parameters()
    • get_opt_settings()
    • get_opt_solution()
    • get_opt_statistic()
    • run_optimization()
    • set_objective_function()
    • set_opt_parameters()
    • set_opt_settings()