Index

A

add_amount_expressions() (in module basico.model_info) add_compartment() (in module basico.model_info) add_default_plot() (in module basico.model_info) add_equation() (in module basico.model_info) add_event() (in module basico.model_info) add_event_assignment() (in module basico.model_info) add_experiment() (in module basico.task_parameterestimation) add_experiment_from_dict() (in module basico.task_parameterestimation) add_function() (in module basico.model_info) add_parameter() (in module basico.model_info) add_parameter_set() (in module basico.model_info) add_plot() (in module basico.model_info) add_reaction() (in module basico.model_info) add_report() (in module basico.model_info) add_scan_item() (in module basico.task_scan) add_species() (in module basico.model_info)

ALL_INITIAL_VALUES (basico.task_sensitivities.SENS attribute) ALL_LOCAL_PARAMETER_VALUES (basico.task_sensitivities.SENS attribute) all_method_names() (basico.task_parameterestimation.PE class method) ALL_ODE_VARIABLES (basico.task_sensitivities.SENS attribute) ALL_PARAMETER_AND_INITIAL_VALUES (basico.task_sensitivities.SENS attribute) ALL_PARAMETER_VALUES (basico.task_sensitivities.SENS attribute) all_task_names() (basico.model_info.T class method) ALL_VARIABLES (basico.task_sensitivities.SENS attribute) animate_rectangular_time_course() (in module basico.compartment_array_tools) animate_rectangular_time_course_as_image() (in module basico.compartment_array_tools) apply_parameter_set() (in module basico.model_info) as_dict() (in module basico.model_info) ASS_COMPARTMENT_VOLUMES (basico.task_sensitivities.SENS attribute) ASS_GLOBAL_PARAMETER_VALUES (basico.task_sensitivities.SENS attribute) ASS_METAB_CONCENTRATIONS (basico.task_sensitivities.SENS attribute) ASS_METAB_NUMBERS (basico.task_sensitivities.SENS attribute) assign_report() (in module basico.model_info)

B

basico module basico.biomodels module basico.compartment_array_tools module basico.jws_online module basico.model_info module basico.model_io module

basico.task_optimization module basico.task_parameterestimation module basico.task_scan module basico.task_sensitivities module basico.task_steadystate module basico.task_timecourse module

C

COMPARTMENT_INITIAL_VOLUMES (basico.task_sensitivities.SENS attribute) COMPARTMENT_RATES (basico.task_sensitivities.SENS attribute) COMPARTMENT_VOLUMES (basico.task_sensitivities.SENS attribute) COMPARTMENTS (basico.task_sensitivities.SENS attribute) CONST_COMPARTMENT_VOLUMES (basico.task_sensitivities.SENS attribute) CONST_GLOBAL_PARAMETER_INITIAL_VALUES (basico.task_sensitivities.SENS attribute) CONST_METAB_CONCENTRATIONS (basico.task_sensitivities.SENS attribute)

CONST_METAB_NUMBERS (basico.task_sensitivities.SENS attribute) create_data_handler() (in module basico.task_timecourse) create_datamodel() (in module basico.model_io) create_linear_array() (in module basico.compartment_array_tools) create_rectangular_array() (in module basico.compartment_array_tools) CROSS_SECTION (basico.model_info.T attribute) CrossSection (basico.task_sensitivities.SENS_ST attribute) CURRENT_SOLUTION (basico.task_parameterestimation.PE attribute)

D

delete_compartments() (in module basico.compartment_array_tools) DIFFERENTIAL_EVOLUTION (basico.task_parameterestimation.PE attribute) download_from() (in module basico.biomodels) (in module basico.jws_online)

download_json() (in module basico.biomodels) (in module basico.jws_online)

E

EFM (basico.model_info.T attribute) EMPTY_LIST (basico.task_sensitivities.SENS attribute) EnumHelper (class in basico.task_sensitivities)

Evaluation (basico.task_sensitivities.SENS_ST attribute) EVOLUTIONARY_PROGRAMMING (basico.task_parameterestimation.PE attribute) EVOLUTIONARY_STRATEGY_SRES (basico.task_parameterestimation.PE attribute)

F

from_enum() (basico.model_info.T class method) (basico.task_parameterestimation.PE class method) (basico.task_sensitivities.EnumHelper class method)

G

GENETIC_ALGORITHM (basico.task_parameterestimation.PE attribute) GENETIC_ALGORITHM_SR (basico.task_parameterestimation.PE attribute) get_all_models() (in module basico.jws_online) get_all_names() (basico.task_sensitivities.EnumHelper class method) get_cn() (in module basico.model_info) get_compartments() (in module basico.model_info) get_content_for_model() (in module basico.biomodels) get_copasi_messages() (in module basico.model_info) get_current_model() (in module basico.model_io) get_data_from_data_handler() (in module basico.task_timecourse) get_data_from_experiment() (in module basico.task_parameterestimation) get_default_plot_names() (in module basico.model_info) get_events() (in module basico.model_info) get_examples() (in module basico.model_io) get_experiment() (in module basico.task_parameterestimation) get_experiment_data_from_model() (in module basico.task_parameterestimation) get_experiment_dict() (in module basico.task_parameterestimation) get_experiment_filenames() (in module basico.task_parameterestimation) get_experiment_mapping() (in module basico.task_parameterestimation) get_experiment_names() (in module basico.task_parameterestimation) get_files_for_model() (in module basico.biomodels) get_fit_constraints() (in module basico.task_parameterestimation) get_fit_item_template() (in module basico.task_parameterestimation) get_fit_parameters() (in module basico.task_parameterestimation) get_fit_statistic() (in module basico.task_parameterestimation) get_functions() (in module basico.model_info) get_jacobian_matrix() (in module basico.model_info) get_manuscript() (in module basico.jws_online) get_mathematica_model() (in module basico.jws_online) get_miriam_annotation() (in module basico.model_info) get_miriam_resources() (in module basico.model_info) get_model_from_dict_or_default() (in module basico.model_io) get_model_info() (in module basico.biomodels) (in module basico.jws_online) get_model_name() (in module basico.model_info) get_model_units() (in module basico.model_info) get_models_for_reaction() (in module basico.jws_online) get_models_for_species() (in module basico.jws_online)

get_notes() (in module basico.model_info) get_num_loaded_models() (in module basico.model_io) get_opt_constraints() (in module basico.task_optimization) get_opt_item_template() (in module basico.task_optimization) get_opt_parameters() (in module basico.task_optimization) get_opt_settings() (in module basico.task_optimization) get_opt_solution() (in module basico.task_optimization) get_opt_statistic() (in module basico.task_optimization) get_parameter_sets() (in module basico.model_info) get_parameters() (in module basico.model_info) get_parameters_solution() (in module basico.task_parameterestimation) get_plot_dict() (in module basico.model_info) get_plots() (in module basico.model_info) get_reaction_mapping() (in module basico.model_info) get_reaction_parameters() (in module basico.model_info) get_reactions() (in module basico.model_info) get_reduced_jacobian_matrix() (in module basico.model_info) get_reduced_stoichiometry_matrix() (in module basico.model_info) get_report_dict() (in module basico.model_info) get_reports() (in module basico.model_info) get_sbml_model() (in module basico.jws_online) get_scaled_sensitivities() (in module basico.task_sensitivities) get_scan_items() (in module basico.task_scan) get_scan_items_frame() (in module basico.task_scan) get_scan_settings() (in module basico.task_scan) get_scheduled_tasks() (in module basico.model_info) get_sensitivity_settings() (in module basico.task_sensitivities) get_simulation_results() (in module basico.task_parameterestimation) get_species() (in module basico.model_info) get_stoichiometry_matrix() (in module basico.model_info) get_summarized_sensitivities() (in module basico.task_sensitivities) get_task_settings() (in module basico.model_info) get_time_unit() (in module basico.model_info) get_unscaled_sensitivities() (in module basico.task_sensitivities) get_value() (in module basico.model_info) GLOBAL_PARAMETER_INITIAL_VALUES (basico.task_sensitivities.SENS attribute) GLOBAL_PARAMETER_RATES (basico.task_sensitivities.SENS attribute) GLOBAL_PARAMETER_VALUES (basico.task_sensitivities.SENS attribute) GLOBAL_PARAMETERS (basico.task_sensitivities.SENS attribute)

H

have_miriam_resources() (in module basico.model_info)

HOOKE_JEEVES (basico.task_parameterestimation.PE attribute)

L

LEVENBERG_MARQUARDT (basico.task_parameterestimation.PE attribute) LNA (basico.model_info.T attribute) load_biomodel() (in module basico.model_io) load_example() (in module basico.model_io) load_experiments_from_dict() (in module basico.task_parameterestimation)

load_experiments_from_yaml() (in module basico.task_parameterestimation) load_model() (in module basico.model_io) load_model_from_string() (in module basico.model_io) load_model_from_url() (in module basico.model_io) LYAPUNOV_EXPONENTS (basico.model_info.T attribute)

M

MCA (basico.model_info.T attribute) METAB_CONC_RATES (basico.task_sensitivities.SENS attribute) METAB_CONCENTRATIONS (basico.task_sensitivities.SENS attribute) METAB_INITIAL_CONCENTRATIONS (basico.task_sensitivities.SENS attribute) METAB_INITIAL_NUMBERS (basico.task_sensitivities.SENS attribute) METAB_NUMBERS (basico.task_sensitivities.SENS attribute) METAB_PART_RATES (basico.task_sensitivities.SENS attribute) METAB_TRANSITION_TIME (basico.task_sensitivities.SENS attribute) METABS (basico.task_sensitivities.SENS attribute) module basico basico.biomodels basico.compartment_array_tools basico.jws_online basico.model_info basico.model_io basico.task_optimization basico.task_parameterestimation basico.task_scan basico.task_sensitivities basico.task_steadystate basico.task_timecourse

MOIETIES (basico.model_info.T attribute)

N

NELDER_MEAD (basico.task_parameterestimation.PE attribute) new_model() (in module basico.model_io) NL2SOL (basico.task_parameterestimation.PE attribute) NON_CONST_COMPARTMENT_VOLUMES (basico.task_sensitivities.SENS attribute)

NON_CONST_GLOBAL_PARAMETER_VALUES (basico.task_sensitivities.SENS attribute) NON_CONST_METAB_CONCENTRATIONS (basico.task_sensitivities.SENS attribute) NON_CONST_METAB_NUMBERS (basico.task_sensitivities.SENS attribute) num_experiment_files() (in module basico.task_parameterestimation) num_validations_files() (in module basico.task_parameterestimation)

O

ODE_COMPARTMENT_VOLUMES (basico.task_sensitivities.SENS attribute) ODE_GLOBAL_PARAMETER_VALUES (basico.task_sensitivities.SENS attribute) ODE_METAB_CONCENTRATIONS (basico.task_sensitivities.SENS attribute) ODE_METAB_NUMBERS (basico.task_sensitivities.SENS attribute)

open_copasi() (in module basico.model_io) OPTIMIZATION (basico.model_info.T attribute) Optimization (basico.task_sensitivities.SENS_ST attribute) overview() (in module basico.model_io)

P

PARAMETER_ESTIMATION (basico.model_info.T attribute) ParameterEstimation (basico.task_sensitivities.SENS_ST attribute) PARTICLE_SWARM (basico.task_parameterestimation.PE attribute) PE (class in basico.task_parameterestimation) plot_linear_time_course() (in module basico.compartment_array_tools)

plot_per_dependent_variable() (in module basico.task_parameterestimation) plot_per_experiment() (in module basico.task_parameterestimation) plot_rectangular_time_course() (in module basico.compartment_array_tools) PRAXIS (basico.task_parameterestimation.PE attribute) print_model() (in module basico.model_io) prune_simulation_results() (in module basico.task_parameterestimation)

R

RANDOM_SEARCH (basico.task_parameterestimation.PE attribute) REACTION_CONC_FLUXES (basico.task_sensitivities.SENS attribute) REACTION_METAB_CONCENTRATIONS (basico.task_sensitivities.SENS attribute) REACTION_METAB_NUMBERS (basico.task_sensitivities.SENS attribute) REACTION_PART_FLUXES (basico.task_sensitivities.SENS attribute) REACTIONS (basico.task_sensitivities.SENS attribute) REDUCED_JACOBIAN_EV_IM (basico.task_sensitivities.SENS attribute) REDUCED_JACOBIAN_EV_RE (basico.task_sensitivities.SENS attribute) remove_amount_expressions() (in module basico.model_info) remove_compartment() (in module basico.model_info) remove_datamodel() (in module basico.model_io) remove_event() (in module basico.model_info) remove_experiments() (in module basico.task_parameterestimation) remove_fit_parameters() (in module basico.task_parameterestimation) remove_function() (in module basico.model_info) remove_loaded_models() (in module basico.model_io)

remove_parameter() (in module basico.model_info) remove_parameter_sets() (in module basico.model_info) remove_plot() (in module basico.model_info) remove_reaction() (in module basico.model_info) remove_report() (in module basico.model_info) remove_report_from_task() (in module basico.model_info) remove_species() (in module basico.model_info) remove_user_defined_functions() (in module basico.model_info) run_optimization() (in module basico.task_optimization) run_parameter_estimation() (in module basico.task_parameterestimation) run_scan() (in module basico.task_scan) run_scheduled_tasks() (in module basico.model_info) run_sensitivities() (in module basico.task_sensitivities) run_steadystate() (in module basico.task_steadystate) run_task() (in module basico.model_info) run_time_course() (in module basico.task_timecourse) run_time_course_with_output() (in module basico.task_timecourse)

S

save_experiments_to_dict() (in module basico.task_parameterestimation) save_experiments_to_yaml() (in module basico.task_parameterestimation) save_model() (in module basico.model_io) save_model_and_data() (in module basico.model_io) save_model_to_string() (in module basico.model_io) SCAN (basico.model_info.T attribute) SCATTER_SEARCH (basico.task_parameterestimation.PE attribute) search_for_model() (in module basico.biomodels) SENS (class in basico.task_sensitivities) SENS_ST (class in basico.task_sensitivities) SENSITIVITIES (basico.model_info.T attribute) set_compartment() (in module basico.model_info) set_current_model() (in module basico.model_io) set_element_name() (in module basico.model_info) set_event() (in module basico.model_info) set_fit_constraints() (in module basico.task_parameterestimation) set_fit_parameters() (in module basico.task_parameterestimation) set_miriam_annotation() (in module basico.model_info) set_model_name() (in module basico.model_info) set_model_unit() (in module basico.model_info) set_notes() (in module basico.model_info) set_objective_function() (in module basico.task_optimization) set_opt_constraints() (in module basico.task_optimization)

set_opt_parameters() (in module basico.task_optimization) set_opt_settings() (in module basico.task_optimization) set_parameter_set() (in module basico.model_info) set_parameters() (in module basico.model_info) set_plot_curves() (in module basico.model_info) set_plot_dict() (in module basico.model_info) set_reaction() (in module basico.model_info) set_reaction_mapping() (in module basico.model_info) set_reaction_parameters() (in module basico.model_info) set_report_dict() (in module basico.model_info) set_scan_items() (in module basico.task_scan) set_scan_settings() (in module basico.task_scan) set_scheduled_tasks() (in module basico.model_info) set_sensitivity_settings() (in module basico.task_sensitivities) set_species() (in module basico.model_info) set_task_settings() (in module basico.model_info) set_time_unit() (in module basico.model_info) set_value() (in module basico.model_info) simplify_names() (in module basico.model_info) SIMULATED_ANNEALING (basico.task_parameterestimation.PE attribute) SINGLE_OBJECT (basico.task_sensitivities.SENS attribute) STEADY_STATE (basico.model_info.T attribute) SteadyState (basico.task_sensitivities.SENS_ST attribute) STEEPEST_DESCENT (basico.task_parameterestimation.PE attribute)

T

T (class in basico.model_info) TIME_COURSE (basico.model_info.T attribute) TIME_COURSE_SENSITIVITIES (basico.model_info.T attribute) TIME_SCALE_SEPARATION (basico.model_info.T attribute)

TimeSeries (basico.task_sensitivities.SENS_ST attribute) to_enum() (basico.model_info.T class method) (basico.task_parameterestimation.PE class method) (basico.task_sensitivities.EnumHelper class method) TRUNCATED_NEWTON (basico.task_parameterestimation.PE attribute)

U

update_miriam_resources() (in module basico.model_info)

update_parameter_set() (in module basico.model_info)

W

wrap_copasi_string() (in module basico.model_info)