Index

_

__author__ (in module robustnet) __call__() (robustnet.sampling.SamplingCallback method) __repr__() (robustnet.Model method) (robustnet.model.Model method) (robustnet.utils.FluxFitResults method) __version__ (in module robustnet) _augment_stoichiometric_matrix() (robustnet.kinetics.Simulator method) _check_bounds() (robustnet.kinetics.Simulator method) _check_data_consistency() (robustnet.Model method) (robustnet.model.Model method) _check_efflux_set_inclusion() (robustnet.sensitivity.EnsembleSimulator method) _check_enzyme_set_inclusion() (robustnet.sensitivity.EnsembleSimulator method) _check_fluxomics() (robustnet.kinetics.Fitter method) _check_fold_change() (robustnet.sensitivity.EnsembleSimulator method) _check_influx_set_inclusion() (robustnet.sensitivity.EnsembleSimulator method) _check_kinetic_parameter_set_inclusion() (robustnet.sensitivity.EnsembleSimulator method) _check_metabolite_set_inclusion() (robustnet.sensitivity.EnsembleSimulator method) _check_method() (robustnet.kinetics.Fitter method) _check_nan() (robustnet.kinetics.Simulator static method) _check_optimizer() (robustnet.kinetics.Fitter method) _check_simulation_results() (robustnet.utils.EnsembleResults method) _compute_dvde() (robustnet.sensitivity.EnsembleSimulator method) _compute_dvdx() (robustnet.sensitivity.EnsembleSimulator method) _compute_v() (robustnet.sensitivity.EnsembleSimulator method) _euler() (robustnet.sensitivity.EnsembleSimulator method) _fit_flux_with_nlopt() (robustnet.kinetics.Fitter method) _fit_flux_with_scipy() (robustnet.kinetics.Fitter method) _get_bounds() (robustnet.kinetics.Simulator method) _get_initial_values() (robustnet.kinetics.Simulator method)

_get_involved_enzymes() (robustnet.kinetics.Simulator method) _get_live_metabolites() (robustnet.Model static method) (robustnet.model.Model static method) _get_perturbation_bounds() (robustnet.sensitivity.EnsembleSimulator method) _get_plural() (robustnet.sensitivity.EnsembleSimulator method) _get_robust_model_probability() (robustnet.utils.EnsembleResults method) _get_split_chunks() (robustnet.sensitivity.EnsembleSimulator method) _lambdify_e() (robustnet.kinetics.Simulator method) _lambdify_v() (robustnet.kinetics.Simulator method) _make_stoichiometric_matrix() (robustnet.Model static method) (robustnet.model.Model static method) _make_value_array() (robustnet.sampling.Sampler method) _parse_expression() (robustnet.Model method) (robustnet.model.Model method) _parse_reactants() (robustnet.Model method) (robustnet.model.Model method) _plot_helper_distribution_plot() (robustnet.utils.EnsembleResults method) _plot_helper_pert_direction() (robustnet.utils.EnsembleResults method) _plot_helper_sensitivity_sample_plot() (robustnet.utils.EnsembleResults method) _plot_helper_sensitivity_stats_plot() (robustnet.utils.EnsembleResults method) _prepare_prior() (robustnet.sampling.Sampler method) _rank_decomposition() (robustnet.kinetics.Simulator method) _refresh_pbar() (robustnet.utils.Prograss method) _select_parameter_sets() (robustnet.sensitivity.EnsembleSimulator method) _simulate_flux() (robustnet.kinetics.Simulator static method) _simulation_worker() (robustnet.sensitivity.EnsembleSimulator method) _solve_sensitivity() (robustnet.sensitivity.EnsembleSimulator method) _to_ser() (robustnet.sampling.Sampler method) _update_model() (robustnet.Model method) (robustnet.model.Model method)

A

add_reaction() (robustnet.Model method) (robustnet.model.Model method)

aug_stoy_mat (robustnet.kinetics.Simulator attribute)

B

bar_format (robustnet.utils.Prograss attribute)

bifurcation_diagram() (robustnet.utils.EnsembleResults method)

C

context() (robustnet.utils.Prograss method)

D

DEFAULT_FOLD_CHANGE (in module robustnet.sensitivity)

dof (robustnet.utils.FluxFitResults attribute) done (robustnet.utils.Prograss attribute)

E

e_exp_mu (robustnet.utils.NonTCSampleResults attribute) e_exp_sigma (robustnet.utils.NonTCSampleResults attribute) e_fun (robustnet.kinetics.Simulator attribute) effective_models (robustnet.utils.EnsembleResults property) eigreal_distribution() (robustnet.utils.EnsembleResults method) eigreal_sensitivity() (robustnet.utils.EnsembleResults method) EnsembleResults (class in robustnet.utils) EnsembleSimulator (class in robustnet.sensitivity) enz (robustnet.model.Ratelaw attribute) enz_vars (robustnet.kinetics.Simulator attribute) enzs (robustnet.utils.NonTCSampleResults attribute) enzyme (robustnet.model.Reaction attribute)

enzyme_list (robustnet.Model attribute) (robustnet.model.Model attribute) enzyme_list_temp (robustnet.Model attribute) (robustnet.model.Model attribute) estimate_reference_fluxes() (robustnet.Model method) (robustnet.model.Model method) estimated_flux_errors (robustnet.utils.FluxFitResults property) estimated_fluxes (robustnet.utils.FluxFitResults property) evaluate_robustness() (robustnet.Model method) (robustnet.model.Model method) exclude_metabs (robustnet.kinetics.Simulator attribute) expr (robustnet.model.Ratelaw attribute)

F

fin_pros (robustnet.kinetics.Simulator attribute) final_products() (robustnet.Model method) (robustnet.model.Model method) fit_reference_fluxes() (robustnet.kinetics.Fitter method)

Fitter (class in robustnet.kinetics) flux_distribution() (robustnet.utils.EnsembleResults method) FLUX_SEN_PLOT_YLIM (in module robustnet.utils) flux_sensitivity() (robustnet.utils.EnsembleResults method) FluxFitResults (class in robustnet.utils)

G

generate_distribution() (in module robustnet.utils)

generate_parameter_sets() (robustnet.Model method) (robustnet.model.Model method)

I

idata (robustnet.utils.NonTCSampleResults attribute) ini_subs (robustnet.kinetics.Simulator attribute)

initial_substrates() (robustnet.Model method) (robustnet.model.Model method)

K

k_exp_mu (robustnet.utils.NonTCSampleResults attribute) k_exp_sigma (robustnet.utils.NonTCSampleResults attribute)

kparams (robustnet.kinetics.Simulator attribute) (robustnet.model.Ratelaw attribute) (robustnet.utils.NonTCSampleResults attribute)

L

load_parameter_sets() (robustnet.Model method) (robustnet.model.Model method) load_priors() (robustnet.Model method) (robustnet.model.Model method)

log_transform() (robustnet.sampling.Sampler static method) logger (in module robustnet.sampling)

M

METAB_SEN_PLOT_YLIM (in module robustnet.utils) metab_vars (robustnet.kinetics.Simulator attribute) metabolite_distribution() (robustnet.utils.EnsembleResults method) metabolite_list (robustnet.Model attribute) (robustnet.model.Model attribute) metabolite_list_temp (robustnet.Model attribute) (robustnet.model.Model attribute) metabolite_sensitivity() (robustnet.utils.EnsembleResults method) metabs (robustnet.model.Ratelaw attribute) (robustnet.utils.EnsembleResults attribute) (robustnet.utils.NonTCSampleResults attribute) metabs_only_in_rate (robustnet.kinetics.Simulator attribute)

mininterval (robustnet.utils.Prograss attribute) miniters (robustnet.utils.Prograss attribute) Model (class in robustnet) (class in robustnet.model) model (robustnet.kinetics.Simulator attribute) module robustnet robustnet.kinetics robustnet.model robustnet.sampling robustnet.sensitivity robustnet.utils

N

n_eff_models (robustnet.utils.EnsembleResults attribute) n_steps (robustnet.utils.EnsembleResults attribute)

name (robustnet.Model attribute) (robustnet.model.Model attribute) NonTCSampleResults (class in robustnet.utils)

O

opt_obj (robustnet.utils.FluxFitResults attribute)

P

parsed_kinetic_parameters() (robustnet.Model method) (robustnet.model.Model method) pbar (robustnet.sampling.SamplingCallback attribute) pert_enzs (robustnet.utils.EnsembleResults attribute) plot_sampled_vs_prior_distribution() (in module robustnet.utils) plot_sampled_vs_prior_enzymes() (robustnet.utils.NonTCSampleResults method)

plot_sampled_vs_prior_fluxes() (robustnet.utils.NonTCSampleResults method) plot_sampled_vs_prior_kinetic_parameters() (robustnet.utils.NonTCSampleResults method) plot_sampled_vs_prior_metabolites() (robustnet.utils.NonTCSampleResults method) plot_simulated_vs_measured_fluxes() (robustnet.utils.FluxFitResults method) posterior (robustnet.utils.NonTCSampleResults attribute) products (robustnet.model.Reaction attribute) Prograss (class in robustnet.utils)

R

rate_exprs (robustnet.kinetics.Simulator attribute) Ratelaw (class in robustnet.model) ratelaw (robustnet.model.Reaction attribute) Reaction (class in robustnet.model) reaction_info (robustnet.Model attribute) (robustnet.model.Model attribute) reaction_info_temp (robustnet.Model attribute) (robustnet.model.Model attribute) reaction_list (robustnet.Model attribute) (robustnet.model.Model attribute) reaction_list_temp (robustnet.Model attribute) (robustnet.model.Model attribute) read_data_file() (in module robustnet.utils) read_from_file() (robustnet.Model method) (robustnet.model.Model method) read_reaction_file() (in module robustnet.utils) remove_reaction() (robustnet.Model method) (robustnet.model.Model method)

robust_index (robustnet.utils.EnsembleResults property) robust_model_probability() (robustnet.utils.EnsembleResults method) robustnet module robustnet.kinetics module robustnet.model module robustnet.sampling module robustnet.sensitivity module robustnet.utils module rxn_vars (robustnet.kinetics.Simulator attribute) rxns (robustnet.utils.EnsembleResults attribute) (robustnet.utils.NonTCSampleResults attribute)

S

sample_with_omics() (robustnet.sampling.Sampler method) sampled_enzyme_concentrations (robustnet.utils.NonTCSampleResults property) sampled_es (robustnet.utils.NonTCSampleResults attribute) sampled_kinetic_parameters (robustnet.utils.NonTCSampleResults property) sampled_kparams (robustnet.utils.NonTCSampleResults attribute) sampled_metabolite_concentrations (robustnet.utils.NonTCSampleResults property) sampled_reference_fluxes (robustnet.utils.NonTCSampleResults property) sampled_vs (robustnet.utils.NonTCSampleResults attribute) sampled_xs (robustnet.utils.NonTCSampleResults attribute)

Sampler (class in robustnet.sampling) SamplingCallback (class in robustnet.sampling) SEN_PLOT_N_BINS (in module robustnet.utils) sim_res (robustnet.utils.EnsembleResults attribute) simulate() (robustnet.sensitivity.EnsembleSimulator method) Simulator (class in robustnet.kinetics) stoichiometric_matrix() (robustnet.Model method) (robustnet.model.Model method) stoy_mat (robustnet.kinetics.Simulator attribute) substrates (robustnet.model.Reaction attribute)

T

trace (robustnet.utils.NonTCSampleResults property)

traces (robustnet.sampling.SamplingCallback attribute)

V

v_exp (robustnet.utils.FluxFitResults attribute) v_exp_mu (robustnet.utils.NonTCSampleResults attribute) v_exp_sigma (robustnet.utils.NonTCSampleResults attribute) v_fun (robustnet.kinetics.Simulator attribute)

v_fun_simple (robustnet.kinetics.Simulator attribute) v_sen (robustnet.utils.EnsembleResults attribute) var_names (robustnet.kinetics.Simulator attribute) vs (robustnet.utils.FluxFitResults attribute) vs_std (robustnet.utils.FluxFitResults attribute)

X

x_exp_mu (robustnet.utils.NonTCSampleResults attribute)

x_exp_sigma (robustnet.utils.NonTCSampleResults attribute)