Index

A

ABSPATH (in module BioSANS2020.BioSSL) acos() (in module BioSANS2020.math_functs.sbml_math) acosh() (in module BioSANS2020.math_functs.sbml_math) acot() (in module BioSANS2020.math_functs.sbml_math) acoth() (in module BioSANS2020.math_functs.sbml_math) acsc() (in module BioSANS2020.math_functs.sbml_math) acsch() (in module BioSANS2020.math_functs.sbml_math) ACTUALSP (in module BioSANS2020.propagation.recalculate_globals) add2_spaces_sep() (in module BioSANS2020.model.fileconvert.process_sbml) analysis_case() (in module BioSANS2020.BioSANS) analyt_soln() (in module BioSANS2020.propagation.symbolic.analytical_sol) And() (in module BioSANS2020.math_functs.sbml_math) apply_rules() (in module BioSANS2020.propagation.recalculate_globals) arccos() (in module BioSANS2020.math_functs.sbml_math) arccosh() (in module BioSANS2020.math_functs.sbml_math) arccot() (in module BioSANS2020.math_functs.sbml_math) arccoth() (in module BioSANS2020.math_functs.sbml_math)

arccsc() (in module BioSANS2020.math_functs.sbml_math) arccsch() (in module BioSANS2020.math_functs.sbml_math) arcsec() (in module BioSANS2020.math_functs.sbml_math) arcsech() (in module BioSANS2020.math_functs.sbml_math) arcsin() (in module BioSANS2020.math_functs.sbml_math) arcsinh() (in module BioSANS2020.math_functs.sbml_math) arctan() (in module BioSANS2020.math_functs.sbml_math) arctanh() (in module BioSANS2020.math_functs.sbml_math) asech() (in module BioSANS2020.math_functs.sbml_math) asin() (in module BioSANS2020.math_functs.sbml_math) asinh() (in module BioSANS2020.math_functs.sbml_math) atan() (in module BioSANS2020.math_functs.sbml_math) atanh() (in module BioSANS2020.math_functs.sbml_math) author (in module conf) autoapi_dirs (in module conf) ave_abs_dev() (in module BioSANS2020.model.param_est.param_estimate) ave_traj_calc() (in module BioSANS2020.analysis.numeric.transform_data)

B

BioSANS() (in module BioSANS2020.RunBioSANS) biosans() (in module BioSANS2020.RunBioSANS) BioSANS2020 module BioSANS2020.__main__ module BioSANS2020.analysis module BioSANS2020.analysis.numeric module BioSANS2020.analysis.numeric.sample_points module BioSANS2020.analysis.numeric.transform_data module BioSANS2020.analysis.plotting module BioSANS2020.analysis.plotting.plot_traj module BioSANS2020.BioSANS module BioSANS2020.BioSSL module BioSANS2020.cli_functs module BioSANS2020.cli_functs.ssl_calls module BioSANS2020.gui_functs module BioSANS2020.gui_functs.draw_figure module BioSANS2020.gui_functs.prepare_canvas module BioSANS2020.gui_functs.scrollable_text module BioSANS2020.math_functs module BioSANS2020.math_functs.sbml_math module BioSANS2020.model module BioSANS2020.model.fileconvert module BioSANS2020.model.fileconvert.convtopotosbml module BioSANS2020.model.fileconvert.process_sbml module BioSANS2020.model.new_file module BioSANS2020.model.ode_parse module BioSANS2020.model.ode_parse.ode_extract module BioSANS2020.model.param_est module BioSANS2020.model.param_est.my_mcem module BioSANS2020.model.param_est.param_estimate module BioSANS2020.model.param_est.param_slider module

BioSANS2020.model.topology_view module BioSANS2020.myglobal module BioSANS2020.myglobal.mglobals module BioSANS2020.myglobal.proc_global module BioSANS2020.prepcodes module BioSANS2020.prepcodes.process module BioSANS2020.prepcodes.processes_hub module BioSANS2020.propagation module BioSANS2020.propagation.create_wxmaxima_command module BioSANS2020.propagation.deterministic module BioSANS2020.propagation.deterministic.euler_mod module BioSANS2020.propagation.deterministic.lna_approx module BioSANS2020.propagation.deterministic.lna_function_of_time module BioSANS2020.propagation.deterministic.ode_int module BioSANS2020.propagation.deterministic.runge_kutta4 module BioSANS2020.propagation.law_of_localization module BioSANS2020.propagation.propensity module BioSANS2020.propagation.recalculate_globals module BioSANS2020.propagation.stochastic module BioSANS2020.propagation.stochastic.gillespie_ssa module BioSANS2020.propagation.stochastic.mystiffcle module BioSANS2020.propagation.stochastic.mytauleap module BioSANS2020.propagation.stochastic.tau_leaping module BioSANS2020.propagation.stochastic.tau_leaping2 module BioSANS2020.propagation.symbolic module BioSANS2020.propagation.symbolic.analytical_sol module BioSANS2020.propagation.symbolic.lna_approx2 module BioSANS2020.RunBioSANS module BioSSL() (in module BioSANS2020.RunBioSANS) biossl() (in module BioSANS2020.RunBioSANS)

C

calc_average_conc_at_tend() (in module BioSANS2020.cli_functs.ssl_calls) calc_covariance() (in module BioSANS2020.analysis.numeric.transform_data) (in module BioSANS2020.cli_functs.ssl_calls) calc_covariance2() (in module BioSANS2020.analysis.numeric.transform_data) calc_covariance_bootsrap() (in module BioSANS2020.cli_functs.ssl_calls) calc_covariance_per_traj() (in module BioSANS2020.cli_functs.ssl_calls) calc_cross_corr() (in module BioSANS2020.analysis.numeric.transform_data) canvas_update_widgets() (in module BioSANS2020.BioSANS) (in module BioSANS2020.gui_functs.draw_figure) (in module BioSANS2020.gui_functs.scrollable_text) ceil() (in module BioSANS2020.math_functs.sbml_math) ceiling() (in module BioSANS2020.math_functs.sbml_math) cle2_calculate() (in module BioSANS2020.propagation.stochastic.mystiffcle) cle_calculate() (in module BioSANS2020.propagation.stochastic.mystiffcle) cle_model() (in module BioSANS2020.propagation.stochastic.mystiffcle) CON_BOUNDARY (in module BioSANS2020.myglobal.mglobals) CONCP (in module BioSANS2020.propagation.recalculate_globals)

CONCP2 (in module BioSANS2020.propagation.recalculate_globals) conf module CONTAINER (in module BioSANS2020.myglobal.mglobals) convert() (in module BioSANS2020.BioSANS) copyright (in module conf) cos() (in module BioSANS2020.math_functs.sbml_math) cosh() (in module BioSANS2020.math_functs.sbml_math) cost_value() (in module BioSANS2020.model.param_est.my_mcem) cot() (in module BioSANS2020.math_functs.sbml_math) coth() (in module BioSANS2020.math_functs.sbml_math) create_file() (in module BioSANS2020.BioSANS) cs_to_csr() (in module BioSANS2020.propagation.symbolic.analytical_sol) csc() (in module BioSANS2020.math_functs.sbml_math) csch() (in module BioSANS2020.math_functs.sbml_math) CURRENT_DATA (in module BioSANS2020.BioSANS) custom_likelihood() (in module BioSANS2020.model.param_est.param_estimate) CWD (in module BioSANS2020.BioSSL)

D

delay() (in module BioSANS2020.propagation.recalculate_globals) DELAY_LIST (in module BioSANS2020.myglobal.mglobals) delay_part1() (in module BioSANS2020.propagation.recalculate_globals) delay_part2() (in module BioSANS2020.propagation.recalculate_globals) delete_this() (in module BioSANS2020.BioSANS) (in module BioSANS2020.gui_functs.draw_figure) (in module BioSANS2020.gui_functs.scrollable_text)

dict_trans() (in module BioSANS2020.BioSANS) divide() (in module BioSANS2020.math_functs.sbml_math) DONE_PARSING (in module BioSANS2020.model.ode_parse.ode_extract) draw_figure() (in module BioSANS2020.gui_functs.draw_figure)

E

eq() (in module BioSANS2020.math_functs.sbml_math) euler2_int() (in module BioSANS2020.propagation.deterministic.euler_mod) euler2_model() (in module BioSANS2020.propagation.deterministic.euler_mod) euler_help() (in module BioSANS2020.propagation.deterministic.euler_mod) euler_int() (in module BioSANS2020.propagation.deterministic.euler_mod) euler_model() (in module BioSANS2020.propagation.deterministic.euler_mod) euler_wer_est() (in module BioSANS2020.propagation.deterministic.euler_mod) eval2() (in module BioSANS2020.BioSANS) (in module BioSANS2020.BioSSL) (in module BioSANS2020.propagation.recalculate_globals) eval_dict() (in module BioSANS2020.prepcodes.process)

eval_exp() (in module BioSANS2020.model.fileconvert.process_sbml) exclude_patterns (in module conf) EXEC_FUNCTIONS (in module BioSANS2020.myglobal.mglobals) exp() (in module BioSANS2020.math_functs.sbml_math) exptn_maxtn() (in module BioSANS2020.model.param_est.my_mcem) extensions (in module conf), [1] extract_function() (in module BioSANS2020.model.fileconvert.process_sbml) extract_ode() (in module BioSANS2020.BioSANS) extract_par_num() (in module BioSANS2020.model.fileconvert.process_sbml) extract_species() (in module BioSANS2020.model.fileconvert.process_sbml) extract_var_func() (in module BioSANS2020.model.fileconvert.process_sbml)

F

factorial() (in module BioSANS2020.math_functs.sbml_math) fano_factor() (in module BioSANS2020.analysis.numeric.transform_data) FILE_NAME (in module BioSANS2020.BioSANS) floor() (in module BioSANS2020.math_functs.sbml_math)

FOOTER (in module BioSANS2020.BioSANS) for_wxmaxima() (in module BioSANS2020.propagation.create_wxmaxima_command) FRAME (in module BioSANS2020.BioSANS) funct_redefine_var() (in module BioSANS2020.model.fileconvert.process_sbml)

G

geq() (in module BioSANS2020.math_functs.sbml_math) get_checked() (in module BioSANS2020.BioSANS) get_compartments_details() (in module BioSANS2020.model.fileconvert.process_sbml) get_exponent_sp() (in module BioSANS2020.model.fileconvert.process_sbml) get_globals() (in module BioSANS2020.propagation.recalculate_globals) get_initial_conc() (in module BioSANS2020.model.fileconvert.process_sbml) get_input() (in module BioSANS2020.BioSSL) get_param_details() (in module BioSANS2020.model.fileconvert.process_sbml)

get_prop_stoich() (in module BioSANS2020.model.ode_parse.ode_extract) get_rule_details() (in module BioSANS2020.model.fileconvert.process_sbml) get_sbml_units() (in module BioSANS2020.model.fileconvert.process_sbml) get_sets() (in module BioSANS2020.propagation.symbolic.analytical_sol) get_species_details() (in module BioSANS2020.model.fileconvert.process_sbml) gillespie_ssa() (in module BioSANS2020.propagation.stochastic.gillespie_ssa) grab_rxn_ksn() (in module BioSANS2020.model.ode_parse.ode_extract) grab_steady_state() (in module BioSANS2020.propagation.symbolic.analytical_sol) gt() (in module BioSANS2020.math_functs.sbml_math)

H

HEADER (in module BioSANS2020.BioSANS)

htmlstatic_path (in module conf) html_theme (in module conf)

I

init() (in module BioSANS2020.myglobal.mglobals) (in module BioSANS2020.myglobal.proc_global)

INT_VARS (in module BioSANS2020.myglobal.mglobals) is_number() (in module BioSANS2020.prepcodes.process)

L

label_param() (in module BioSANS2020.model.param_est.param_estimate) law_loc_symbolic() (in module BioSANS2020.propagation.law_of_localization) leq() (in module BioSANS2020.math_functs.sbml_math) ln() (in module BioSANS2020.math_functs.sbml_math) lna_cov_model() (in module BioSANS2020.propagation.deterministic.lna_function_of_time) lna_model_ss() (in module BioSANS2020.propagation.deterministic.lna_approx) lna_non_steady_state() (in module BioSANS2020.propagation.deterministic.lna_function_of_time) lna_non_steady_state2() (in module BioSANS2020.propagation.deterministic.lna_function_of_time) lna_ode_model() (in module BioSANS2020.propagation.deterministic.lna_function_of_time) lna_ss_jacobian() (in module BioSANS2020.propagation.deterministic.lna_approx) lna_steady_state() (in module BioSANS2020.propagation.deterministic.lna_approx)

lna_symbolic2() (in module BioSANS2020.propagation.symbolic.lna_approx2) load_data() (in module BioSANS2020.BioSANS) (in module BioSANS2020.model.param_est.param_estimate) (in module BioSANS2020.model.param_est.param_slider) load_data2() (in module BioSANS2020.BioSANS) load_data_traj() (in module BioSANS2020.cli_functs.ssl_calls) load_image() (in module BioSANS2020.BioSANS) log() (in module BioSANS2020.math_functs.sbml_math) log10() (in module BioSANS2020.math_functs.sbml_math) log_likelihood() (in module BioSANS2020.model.param_est.my_mcem) LST (in module BioSANS2020.myglobal.proc_global) lt() (in module BioSANS2020.math_functs.sbml_math)

M

MANAGER (in module BioSANS2020.myglobal.proc_global) MENUBUT1 (in module BioSANS2020.BioSANS) minus() (in module BioSANS2020.math_functs.sbml_math) MODIFIED (in module BioSANS2020.myglobal.mglobals) module BioSANS2020 BioSANS2020.__main__ BioSANS2020.analysis BioSANS2020.analysis.numeric BioSANS2020.analysis.numeric.sample_points BioSANS2020.analysis.numeric.transform_data BioSANS2020.analysis.plotting BioSANS2020.analysis.plotting.plot_traj BioSANS2020.BioSANS BioSANS2020.BioSSL BioSANS2020.cli_functs BioSANS2020.cli_functs.ssl_calls BioSANS2020.gui_functs BioSANS2020.gui_functs.draw_figure BioSANS2020.gui_functs.prepare_canvas BioSANS2020.gui_functs.scrollable_text BioSANS2020.math_functs BioSANS2020.math_functs.sbml_math BioSANS2020.model BioSANS2020.model.fileconvert BioSANS2020.model.fileconvert.convtopotosbml BioSANS2020.model.fileconvert.process_sbml BioSANS2020.model.new_file BioSANS2020.model.ode_parse BioSANS2020.model.ode_parse.ode_extract BioSANS2020.model.param_est BioSANS2020.model.param_est.my_mcem BioSANS2020.model.param_est.param_estimate BioSANS2020.model.param_est.param_slider BioSANS2020.model.topology_view BioSANS2020.myglobal BioSANS2020.myglobal.mglobals BioSANS2020.myglobal.proc_global BioSANS2020.prepcodes BioSANS2020.prepcodes.process BioSANS2020.prepcodes.processes_hub BioSANS2020.propagation BioSANS2020.propagation.create_wxmaxima_command BioSANS2020.propagation.deterministic BioSANS2020.propagation.deterministic.euler_mod BioSANS2020.propagation.deterministic.lna_approx BioSANS2020.propagation.deterministic.lna_function_of_time BioSANS2020.propagation.deterministic.ode_int BioSANS2020.propagation.deterministic.runge_kutta4 BioSANS2020.propagation.law_of_localization BioSANS2020.propagation.propensity BioSANS2020.propagation.recalculate_globals BioSANS2020.propagation.stochastic BioSANS2020.propagation.stochastic.gillespie_ssa BioSANS2020.propagation.stochastic.mystiffcle BioSANS2020.propagation.stochastic.mytauleap BioSANS2020.propagation.stochastic.tau_leaping BioSANS2020.propagation.stochastic.tau_leaping2 BioSANS2020.propagation.symbolic BioSANS2020.propagation.symbolic.analytical_sol BioSANS2020.propagation.symbolic.lna_approx2 BioSANS2020.RunBioSANS conf

mrun_propagation() (in module BioSANS2020.BioSANS) multiply() (in module BioSANS2020.math_functs.sbml_math)

N

neq() (in module BioSANS2020.math_functs.sbml_math) new_file() (in module BioSANS2020.model.new_file) none_to_list() (in module BioSANS2020.propagation.recalculate_globals)

normalize() (in module BioSANS2020.analysis.numeric.transform_data) Not() (in module BioSANS2020.math_functs.sbml_math) NUMBER_TYPE (in module BioSANS2020.math_functs.sbml_math)

O

ode_int() (in module BioSANS2020.propagation.deterministic.ode_int) ode_model() (in module BioSANS2020.propagation.deterministic.ode_int) odedxdt_to_topo() (in module BioSANS2020.model.ode_parse.ode_extract)

OPERS_LIST (in module BioSANS2020.model.fileconvert.process_sbml) OPERS_LIST2 (in module BioSANS2020.model.fileconvert.process_sbml) Or() (in module BioSANS2020.math_functs.sbml_math) ORASP (in module BioSANS2020.propagation.recalculate_globals)

P

par_substitution() (in module BioSANS2020.model.fileconvert.process_sbml) param_estimate() (in module BioSANS2020.model.param_est.param_estimate) param_ode_int() (in module BioSANS2020.model.param_est.param_slider) param_ode_model() (in module BioSANS2020.model.param_est.param_slider) param_set() (in module BioSANS2020.BioSANS) piecewise() (in module BioSANS2020.math_functs.sbml_math) PLOT_I (in module BioSANS2020.myglobal.mglobals) plot_traj() (in module BioSANS2020.analysis.plotting.plot_traj) plot_traj2() (in module BioSANS2020.analysis.plotting.plot_traj) plot_traj_d() (in module BioSANS2020.BioSANS) plot_traj_d2() (in module BioSANS2020.BioSANS) PLOTTED (in module BioSANS2020.myglobal.mglobals) plus() (in module BioSANS2020.math_functs.sbml_math) pow() (in module BioSANS2020.math_functs.sbml_math) power() (in module BioSANS2020.math_functs.sbml_math) prepare_dict1() (in module BioSANS2020.propagation.create_wxmaxima_command) prepare_dict_list1() (in module BioSANS2020.propagation.law_of_localization) prepare_ffrrint() (in module BioSANS2020.propagation.create_wxmaxima_command) (in module BioSANS2020.propagation.law_of_localization) prepare_frame_for_plot() (in module BioSANS2020.gui_functs.prepare_canvas)

prepare_list1() (in module BioSANS2020.propagation.create_wxmaxima_command) prepare_list2() (in module BioSANS2020.propagation.create_wxmaxima_command) (in module BioSANS2020.propagation.law_of_localization) prepare_scroll_text() (in module BioSANS2020.gui_functs.scrollable_text) print_stoich_prop() (in module BioSANS2020.model.ode_parse.ode_extract) prob_density_calc() (in module BioSANS2020.analysis.numeric.transform_data) (in module BioSANS2020.cli_functs.ssl_calls) prob_density_calc2() (in module BioSANS2020.analysis.numeric.transform_data) prob_density_calc3() (in module BioSANS2020.analysis.numeric.transform_data) prob_density_calc_tslice() (in module BioSANS2020.cli_functs.ssl_calls) prob_density_calc_wtime() (in module BioSANS2020.cli_functs.ssl_calls) process() (in module BioSANS2020.model.ode_parse.ode_extract) (in module BioSANS2020.prepcodes.process) process_command() (in module BioSANS2020.BioSSL) process_hub() (in module BioSANS2020.prepcodes.processes_hub) process_sbml() (in module BioSANS2020.model.fileconvert.process_sbml) project (in module conf) prop_extr() (in module BioSANS2020.model.ode_parse.ode_extract) PROP_MODIFIED (in module BioSANS2020.myglobal.mglobals) propensity_vec() (in module BioSANS2020.propagation.propensity) propensity_vec_molar() (in module BioSANS2020.propagation.propensity)

R

range_prep() (in module BioSANS2020.BioSANS) range_trans() (in module BioSANS2020.BioSANS) rate_of() (in module BioSANS2020.propagation.recalculate_globals) RATESP (in module BioSANS2020.propagation.recalculate_globals) release (in module conf) rem_rowcol_zero() (in module BioSANS2020.propagation.deterministic.lna_approx) replace_crucial_funct() (in module BioSANS2020.model.fileconvert.process_sbml) reserve_events_words (in module BioSANS2020.propagation.recalculate_globals) rk4_model() (in module BioSANS2020.propagation.deterministic.runge_kutta4)

rkck() (in module BioSANS2020.propagation.deterministic.runge_kutta4) rkqs() (in module BioSANS2020.propagation.deterministic.runge_kutta4) root() (in module BioSANS2020.math_functs.sbml_math) run_mcem() (in module BioSANS2020.model.param_est.my_mcem) run_ssl() (in module BioSANS2020.BioSANS) runge_kutta_forth() (in module BioSANS2020.propagation.deterministic.runge_kutta4) rungek4_int() (in module BioSANS2020.propagation.deterministic.runge_kutta4) rungek4a_int() (in module BioSANS2020.propagation.deterministic.runge_kutta4) runpy_file() (in module BioSANS2020.BioSANS)

S

sample_points() (in module BioSANS2020.analysis.numeric.sample_points) save_file() (in module BioSANS2020.BioSANS) (in module BioSANS2020.gui_functs.scrollable_text) SBML_FUNCT_DICT (in module BioSANS2020.math_functs.sbml_math) sbml_to_topo2() (in module BioSANS2020.BioSANS) sec() (in module BioSANS2020.math_functs.sbml_math) sech() (in module BioSANS2020.math_functs.sbml_math) SETTINGS (in module BioSANS2020.myglobal.mglobals) show_file_dir() (in module BioSANS2020.BioSANS) (in module BioSANS2020.BioSSL) sim_tauLeap() (in module BioSANS2020.propagation.stochastic.mytauleap) sin() (in module BioSANS2020.math_functs.sbml_math)

sinh() (in module BioSANS2020.math_functs.sbml_math) SIP (in module BioSANS2020.propagation.recalculate_globals) solve_with_timeout() (in module BioSANS2020.propagation.symbolic.analytical_sol) sp_substitution() (in module BioSANS2020.model.fileconvert.process_sbml) sqr() (in module BioSANS2020.math_functs.sbml_math) sqrt() (in module BioSANS2020.math_functs.sbml_math) ssa_support() (in module BioSANS2020.propagation.stochastic.tau_leaping2) step_3to5() (in module BioSANS2020.propagation.stochastic.tau_leaping2) submit() (in module BioSANS2020.model.param_est.param_slider) subs2() (in module BioSANS2020.propagation.law_of_localization) (in module BioSANS2020.propagation.symbolic.lna_approx2) SUPER_THREAD_RUN (in module BioSANS2020.BioSANS)

T

tab() (in module BioSANS2020.gui_functs.scrollable_text) tan() (in module BioSANS2020.math_functs.sbml_math) tanh() (in module BioSANS2020.math_functs.sbml_math) tau_leaping() (in module BioSANS2020.propagation.stochastic.tau_leaping) tau_leaping2() (in module BioSANS2020.propagation.stochastic.tau_leaping2) TCHECK (in module BioSANS2020.myglobal.mglobals) templates_path (in module conf) TEMPORARY_FOLDER (in module BioSANS2020.BioSANS) term_ext() (in module BioSANS2020.model.ode_parse.ode_extract)

times() (in module BioSANS2020.math_functs.sbml_math) tload_data2() (in module BioSANS2020.BioSANS) TO_CONVERT (in module BioSANS2020.myglobal.mglobals) tofloat() (in module BioSANS2020.prepcodes.process) TOP (in module BioSANS2020.BioSANS) topo_to_sbml() (in module BioSANS2020.model.fileconvert.convtopotosbml) tprocess() (in module BioSANS2020.BioSANS) TRAJ (in module BioSANS2020.BioSSL) transform_to_rxn() (in module BioSANS2020.model.ode_parse.ode_extract)

U

update() (in module BioSANS2020.model.param_est.param_slider)

update_range() (in module BioSANS2020.model.param_est.param_slider)

V

var_substitution() (in module BioSANS2020.model.fileconvert.process_sbml)

view_topo() (in module BioSANS2020.model.topology_view)

X

xor() (in module BioSANS2020.math_functs.sbml_math)