basico
- basico package
- Submodules
- basico.biomodels module
- basico.compartment_array_tools module
- basico.jws_online module
- basico.model_info module
Tadd_amount_expressions()add_compartment()add_default_plot()add_equation()add_event()add_event_assignment()add_function()add_parameter()add_parameter_set()add_plot()add_reaction()add_report()add_species()apply_parameter_set()as_dict()assign_report()collect_data()ensure_unique_names()get_cn()get_compartments()get_copasi_messages()get_default_plot_names()get_events()get_functions()get_jacobian_matrix()get_miriam_annotation()get_miriam_resources()get_model_name()get_model_units()get_notes()get_parameter_sets()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_valid_methods()get_value()have_miriam_resources()remove_all_events()remove_amount_expressions()remove_compartment()remove_event()remove_function()remove_parameter()remove_parameter_sets()remove_plot()remove_reaction()remove_report()remove_report_from_task()remove_species()remove_user_defined_functions()run_scheduled_tasks()run_task()set_compartment()set_element_name()set_event()set_miriam_annotation()set_model_name()set_model_unit()set_notes()set_parameter_set()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()simplify_names()update_miriam_resources()update_parameter_set()wrap_copasi_string()
- basico.model_io module
create_datamodel()get_current_model()get_examples()get_model_from_dict_or_default()get_num_loaded_models()import_sbml()load_biomodel()load_example()load_model()load_model_from_string()load_model_from_url()new_model()open_copasi()overview()print_model()remove_annotations()remove_datamodel()remove_loaded_models()save_model()save_model_and_data()save_model_to_string()set_current_model()to_python_ode_string()
- basico.task_parameterestimation module
PEPE.CURRENT_SOLUTIONPE.DIFFERENTIAL_EVOLUTIONPE.EVOLUTIONARY_PROGRAMMINGPE.EVOLUTIONARY_STRATEGY_SRESPE.GENETIC_ALGORITHMPE.GENETIC_ALGORITHM_SRPE.HOOKE_JEEVESPE.LEVENBERG_MARQUARDTPE.NELDER_MEADPE.NL2SOLPE.PARTICLE_SWARMPE.PRAXISPE.RANDOM_SEARCHPE.SCATTER_SEARCHPE.SIMULATED_ANNEALINGPE.STEEPEST_DESCENTPE.TRUNCATED_NEWTONPE.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_constraints()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_constraints()set_fit_parameters()
- basico.task_steadystate module
- basico.task_timecourse module
- basico.task_scan module
- basico.task_optimization module
- basico.task_sensitivities module
EnumHelperSENSSENS.ALL_INITIAL_VALUESSENS.ALL_LOCAL_PARAMETER_VALUESSENS.ALL_ODE_VARIABLESSENS.ALL_PARAMETER_AND_INITIAL_VALUESSENS.ALL_PARAMETER_VALUESSENS.ALL_VARIABLESSENS.ASS_COMPARTMENT_VOLUMESSENS.ASS_GLOBAL_PARAMETER_VALUESSENS.ASS_METAB_CONCENTRATIONSSENS.ASS_METAB_NUMBERSSENS.COMPARTMENTSSENS.COMPARTMENT_INITIAL_VOLUMESSENS.COMPARTMENT_RATESSENS.COMPARTMENT_VOLUMESSENS.CONST_COMPARTMENT_VOLUMESSENS.CONST_GLOBAL_PARAMETER_INITIAL_VALUESSENS.CONST_METAB_CONCENTRATIONSSENS.CONST_METAB_NUMBERSSENS.EMPTY_LISTSENS.GLOBAL_PARAMETERSSENS.GLOBAL_PARAMETER_INITIAL_VALUESSENS.GLOBAL_PARAMETER_RATESSENS.GLOBAL_PARAMETER_VALUESSENS.METABSSENS.METAB_CONCENTRATIONSSENS.METAB_CONC_RATESSENS.METAB_INITIAL_CONCENTRATIONSSENS.METAB_INITIAL_NUMBERSSENS.METAB_NUMBERSSENS.METAB_PART_RATESSENS.METAB_TRANSITION_TIMESENS.NON_CONST_COMPARTMENT_VOLUMESSENS.NON_CONST_GLOBAL_PARAMETER_VALUESSENS.NON_CONST_METAB_CONCENTRATIONSSENS.NON_CONST_METAB_NUMBERSSENS.ODE_COMPARTMENT_VOLUMESSENS.ODE_GLOBAL_PARAMETER_VALUESSENS.ODE_METAB_CONCENTRATIONSSENS.ODE_METAB_NUMBERSSENS.REACTIONSSENS.REACTION_CONC_FLUXESSENS.REACTION_METAB_CONCENTRATIONSSENS.REACTION_METAB_NUMBERSSENS.REACTION_PART_FLUXESSENS.REDUCED_JACOBIAN_EV_IMSENS.REDUCED_JACOBIAN_EV_RESENS.SINGLE_OBJECT
SENS_STget_scaled_sensitivities()get_sensitivity_settings()get_summarized_sensitivities()get_unscaled_sensitivities()run_sensitivities()set_sensitivity_settings()