Index

A

add_to_database() (in module BMSS.models.model_handler) (in module BMSS.models.settings_handler)

analyze() (in module BMSS.sensitivityanalysis) analyze_sg_args() (in module BMSS.strike_goldd_simplified)

B

BMSS module BMSS.curvefitting module BMSS.icanalysis module BMSS.models.ia_results module BMSS.models.model_handler module BMSS.models.settings_handler module BMSS.models.setup_cf module BMSS.models.setup_sen module

BMSS.models.setup_sg module BMSS.models.setup_sim module BMSS.sbml.OnlinetoConfig module BMSS.sensitivityanalysis module BMSS.simulation module BMSS.strike_goldd_simplified module BMSS.traceanalysis module build_section() (in module BMSS.sbml.OnlinetoConfig) build_section_top() (in module BMSS.sbml.OnlinetoConfig) build_settings() (in module BMSS.sbml.OnlinetoConfig)

C

calculate_ic() (in module BMSS.icanalysis) calculate_rhat() (in module BMSS.traceanalysis) check_kurtosis() (in module BMSS.traceanalysis) check_skewness() (in module BMSS.traceanalysis) clean_compartment() (in module BMSS.sbml.OnlinetoConfig) clean_eqns() (in module BMSS.sbml.OnlinetoConfig) clean_id() (in module BMSS.sbml.OnlinetoConfig) clean_reactions() (in module BMSS.sbml.OnlinetoConfig)

clean_units() (in module BMSS.sbml.OnlinetoConfig) clean_value() (in module BMSS.sbml.OnlinetoConfig) config_to_database() (in module BMSS.models.model_handler) (in module BMSS.models.settings_handler) Convert() (in module BMSS.sbml.OnlinetoConfig) Convertplus() (in module BMSS.sbml.OnlinetoConfig) create_connection() (in module BMSS.models.model_handler) create_table() (in module BMSS.models.model_handler)

D

delete() (in module BMSS.models.model_handler) (in module BMSS.models.settings_handler)

dump_sg_results() (in module BMSS.models.ia_results)

E

eqnreplace() (in module BMSS.sbml.OnlinetoConfig)

export_sg_results() (in module BMSS.models.ia_results) export_simulation_results() (in module BMSS.simulation)

F

from_config() (in module BMSS.models.model_handler) (in module BMSS.models.settings_handler) (in module BMSS.models.setup_cf) (in module BMSS.models.setup_sen) (in module BMSS.models.setup_sg) (in module BMSS.models.setup_sim)

G

gen_cleanvalue() (in module BMSS.sbml.OnlinetoConfig) gen_config() (in module BMSS.sbml.OnlinetoConfig) gen_description() (in module BMSS.sbml.OnlinetoConfig) gen_dictionary() (in module BMSS.sbml.OnlinetoConfig) gen_eqns() (in module BMSS.sbml.OnlinetoConfig) gen_prior_bounds() (in module BMSS.sbml.OnlinetoConfig) gen_reactions() (in module BMSS.sbml.OnlinetoConfig) gen_reference() (in module BMSS.sbml.OnlinetoConfig) gen_settingstemplate() (in module BMSS.sbml.OnlinetoConfig) gen_species_parameter_descriptions() (in module BMSS.sbml.OnlinetoConfig) get_models_and_params() (in module BMSS.models.setup_sim)

get_negreaction() (in module BMSS.sbml.OnlinetoConfig) get_params_for_model() (in module BMSS.curvefitting) get_posreaction() (in module BMSS.sbml.OnlinetoConfig) get_sampler_args() (in module BMSS.models.setup_cf) get_sampler_args_bh() (in module BMSS.models.setup_cf) get_sampler_args_da() (in module BMSS.models.setup_cf) get_sampler_args_de() (in module BMSS.models.setup_cf) get_sampler_args_op() (in module BMSS.models.setup_cf) get_sampler_args_sa() (in module BMSS.models.setup_cf) get_sensitivity_args() (in module BMSS.models.setup_sen) get_SSE_data() (in module BMSS.curvefitting) get_strike_goldd_args() (in module BMSS.models.setup_sg)

I

import_trace() (in module BMSS.traceanalysis)

integrate_models() (in module BMSS.simulation) integrate_samples() (in module BMSS.sensitivityanalysis)

L

list_models() (in module BMSS.models.model_handler)

list_settings() (in module BMSS.models.settings_handler)

M

make_AX() (in module BMSS.curvefitting) (in module BMSS.simulation) make_columns() (in module BMSS.models.ia_results) make_core_model() (in module BMSS.models.model_handler) make_new_nested_dict() (in module BMSS.models.ia_results) make_new_row() (in module BMSS.models.ia_results) make_new_row_template() (in module BMSS.models.ia_results) make_samples() (in module BMSS.sensitivityanalysis) make_settings() (in module BMSS.models.settings_handler) make_settings_template() (in module BMSS.models.settings_handler) (in module BMSS.models.setup_cf) (in module BMSS.models.setup_sen) (in module BMSS.models.setup_sg) (in module BMSS.models.setup_sim) module BMSS BMSS.curvefitting BMSS.icanalysis BMSS.models.ia_results BMSS.models.model_handler BMSS.models.settings_handler BMSS.models.setup_cf BMSS.models.setup_sen BMSS.models.setup_sg BMSS.models.setup_sim BMSS.sbml.OnlinetoConfig BMSS.sensitivityanalysis BMSS.simulation BMSS.strike_goldd_simplified BMSS.traceanalysis

N

normalize_ic() (in module BMSS.icanalysis)

P

pairplot_kde() (in module BMSS.traceanalysis) pairplot_steps() (in module BMSS.traceanalysis) piecewise_integrate() (in module BMSS.simulation) plot() (in module BMSS.curvefitting) plot_data() (in module BMSS.curvefitting) plot_first_order() (in module BMSS.sensitivityanalysis)

plot_hist() (in module BMSS.traceanalysis) plot_kde() (in module BMSS.traceanalysis) plot_model() (in module BMSS.curvefitting) (in module BMSS.simulation) plot_second_order() (in module BMSS.sensitivityanalysis) plot_steps() (in module BMSS.traceanalysis)

Q

quick_search() (in module BMSS.models.model_handler) (in module BMSS.models.settings_handler)

R

rank_ic() (in module BMSS.icanalysis) read_ia() (in module BMSS.models.model_handler)

restore() (in module BMSS.models.model_handler) (in module BMSS.models.settings_handler)

S

sbmltoconfig() (in module BMSS.sbml.OnlinetoConfig) scipy_basinhopping() (in module BMSS.curvefitting) scipy_differential_evolution() (in module BMSS.curvefitting) scipy_dual_annealing() (in module BMSS.curvefitting) scipy_optimize() (in module BMSS.curvefitting)

search_database() (in module BMSS.models.model_handler) (in module BMSS.models.settings_handler) setup_helper() (in module BMSS.models.setup_sim) simulated_annealing() (in module BMSS.curvefitting) split_at_top_level() (in module BMSS.models.model_handler)

T

to_config() (in module BMSS.models.model_handler)

to_df() (in module BMSS.models.model_handler) (in module BMSS.models.settings_handler)

U

update_core_model() (in module BMSS.models.ia_results)

update_ia() (in module BMSS.models.model_handler) update_row_with_sg_result() (in module BMSS.models.ia_results)

W

write_new_row_to_file() (in module BMSS.models.ia_results)

X

xmlclean() (in module BMSS.sbml.OnlinetoConfig)