basiCO
stable
Getting started
Getting Started
Examples
Accessing Models from the database
Creating and simulating a simple model
Getting and setting reaction parameters and reactions
Editing reaction kinetics
Parameter Estimation
Parameter estimation setup
Parameter Estimation (import / export)
Optimization
Simple simulations and plotting
Simulating a model with basico
Simulating with custom results
Parameter Scans
Sensitivity Analysis
Working with arrays of Compartments
Using callbacks
Working with Plots
Working with Reports
Working with SBML Ids
Working with Annotations
Working with
ipyparallel
Working with PEtab
Model Selection
Working with Parameter Sets
Profile likelihood
Metabolic Control Analysis
Working with Widgets
API
basico
basiCO
Index
Edit on GitHub
Index
A
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B
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C
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D
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E
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F
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G
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H
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L
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M
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N
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O
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P
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R
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S
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T
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U
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W
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)
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