Index

A

AbsTerm (class in bioscrape.types) add_event() (bioscrape.lineage.LineageModel method) add_lineage_rule() (bioscrape.lineage.LineageModel method) add_parameter() (in module bioscrape.sbmlutil) add_reaction() (in module bioscrape.sbmlutil)

add_rule() (in module bioscrape.sbmlutil) add_species() (in module bioscrape.sbmlutil) AdditiveAssignmentRule (class in bioscrape.types) ArrayDelayQueue (class in bioscrape.simulator) AssignmentVolumeRule (class in bioscrape.lineage)

B

beta_prior() (bioscrape.pid_interfaces.PIDInterface method) BimolecularPropensity (class in bioscrape.types) BinaryTerm (class in bioscrape.types) bioscrape.analysis module bioscrape.inference module bioscrape.inference_setup module bioscrape.lineage module

bioscrape.pid_interfaces module bioscrape.random module bioscrape.sbmlutil module bioscrape.simulator module bioscrape.types module BulkData (class in bioscrape.inference)

C

CappedStateQueue (class in bioscrape.lineage) CellState (class in bioscrape.simulator) check_parameters() (bioscrape.types.Model method) check_prior() (bioscrape.pid_interfaces.PIDInterface method) check_species() (bioscrape.types.Model method) compute_J() (bioscrape.analysis.SensitivityAnalysis method) compute_SSM() (bioscrape.analysis.SensitivityAnalysis method) compute_Zj() (bioscrape.analysis.SensitivityAnalysis method) ConstantTerm (class in bioscrape.types) ConstitutivePropensity (class in bioscrape.types) copy() (bioscrape.types.Schnitz method) cost_function() (bioscrape.inference_setup.InferenceSetup method)

create_death_event() (bioscrape.lineage.LineageModel method) create_death_rule() (bioscrape.lineage.LineageModel method) create_division_event() (bioscrape.lineage.LineageModel method) create_division_rule() (bioscrape.lineage.LineageModel method) create_parameter() (bioscrape.types.Model method) create_propensity() (bioscrape.types.Model method) create_reaction() (bioscrape.types.Model method) create_rule() (bioscrape.types.Model method) create_sbml_model() (in module bioscrape.sbmlutil) create_volume_event() (bioscrape.lineage.LineageModel method) create_volume_rule() (bioscrape.lineage.LineageModel method) CSimInterface (class in bioscrape.simulator) CustomSplitter (class in bioscrape.simulator)

D

Data (class in bioscrape.inference) DeathEvent (class in bioscrape.lineage) DeathRule (class in bioscrape.lineage) Delay (class in bioscrape.types) DelayCellState (class in bioscrape.simulator) DelayQueue (class in bioscrape.simulator) DelaySimulator (class in bioscrape.simulator) DelaySSAResult (class in bioscrape.simulator) DelaySSASimulator (class in bioscrape.simulator) DelayVolumeCellState (class in bioscrape.simulator) DelayVolumeSimulator (class in bioscrape.simulator)

DelayVolumeSplitter (class in bioscrape.simulator) DelayVolumeSSAResult (class in bioscrape.simulator) DelayVolumeSSASimulator (class in bioscrape.simulator) DeltaVDivisionRule (class in bioscrape.lineage) DeterministicDilutionSimulator (class in bioscrape.simulator) DeterministicInference (class in bioscrape.inference) (class in bioscrape.pid_interfaces) DeterministicLikelihood (class in bioscrape.inference) DeterministicSimulator (class in bioscrape.simulator) Distribution (class in bioscrape.inference) DivisionEvent (class in bioscrape.lineage) DivisionRule (class in bioscrape.lineage)

E

Event (class in bioscrape.lineage) ExperimentalLineage (class in bioscrape.types)

exponential_prior() (bioscrape.pid_interfaces.PIDInterface method) ExpTerm (class in bioscrape.types) extract_data() (bioscrape.inference_setup.InferenceSetup method)

F

FixedDelay (class in bioscrape.types)

FlowData (class in bioscrape.inference)

G

gamma_prior() (bioscrape.pid_interfaces.PIDInterface method) GammaDelay (class in bioscrape.types) gaussian_prior() (bioscrape.pid_interfaces.PIDInterface method) GaussianDelay (class in bioscrape.types) GeneralAssignmentRule (class in bioscrape.types) GeneralDeathRule (class in bioscrape.lineage) GeneralDivisionRule (class in bioscrape.lineage) GeneralODERule (class in bioscrape.types) GeneralPropensity (class in bioscrape.types) GeneralVolumeEvent (class in bioscrape.lineage) GeneralVolumeSplitter (class in bioscrape.simulator) generate_sbml_model() (bioscrape.types.Model method) get_delays() (bioscrape.types.Model method) get_derivative_strings() (bioscrape.types.Model method) get_global_crn_results() (bioscrape.lineage.InteractingLineageSSASimulator method) get_global_species_array() (bioscrape.lineage.InteractingLineageSSASimulator method) get_likelihood_function() (bioscrape.pid_interfaces.DeterministicInference method) (bioscrape.pid_interfaces.StochasticInference method) get_lineage_list() (bioscrape.lineage.InteractingLineageSSASimulator method) get_minimizer_results() (bioscrape.pid_interfaces.LMFitInference method) get_minimum_dt() (bioscrape.inference.BulkData method) get_model() (bioscrape.inference_setup.InferenceSetup method) get_number_of_params() (bioscrape.types.Model method) get_number_of_species() (bioscrape.types.Model method) get_param_index() (bioscrape.types.Model method) get_param_list() (bioscrape.types.Model method) get_param_value() (bioscrape.types.Model method) get_parameter_dictionary() (bioscrape.types.Model method) get_parameter_values() (bioscrape.types.Model method) get_parameters() (bioscrape.inference_setup.InferenceSetup method) get_params() (bioscrape.types.Model method) get_params2index() (bioscrape.types.Model method) get_propensities() (bioscrape.types.Model method) get_reaction_strings() (bioscrape.types.Model method) get_reactions() (bioscrape.types.Model method) get_rules() (bioscrape.types.Model method) get_samples() (bioscrape.lineage.InteractingLineageSSASimulator method) get_schnitzes_by_generation() (bioscrape.types.Lineage method) get_species() (bioscrape.types.Model method) get_species2index() (bioscrape.types.Model method) get_species_and_parameters() (bioscrape.lineage.AssignmentVolumeRule method) (bioscrape.lineage.DeathEvent method) (bioscrape.lineage.DeathRule method) (bioscrape.lineage.DeltaVDivisionRule method) (bioscrape.lineage.DivisionEvent method) (bioscrape.lineage.DivisionRule method) (bioscrape.lineage.Event method) (bioscrape.lineage.GeneralDeathRule method) (bioscrape.lineage.GeneralDivisionRule method) (bioscrape.lineage.GeneralVolumeEvent method) (bioscrape.lineage.LineageRule method) (bioscrape.lineage.LinearVolumeEvent method) (bioscrape.lineage.LinearVolumeRule method) (bioscrape.lineage.MultiplicativeVolumeEvent method) (bioscrape.lineage.MultiplicativeVolumeRule method) (bioscrape.lineage.ODEVolumeRule method) (bioscrape.lineage.ParamDeathRule method) (bioscrape.lineage.SpeciesDeathRule method) (bioscrape.lineage.TimeDivisionRule method) (bioscrape.lineage.VolumeDivisionRule method) (bioscrape.lineage.VolumeEvent method) (bioscrape.types.AdditiveAssignmentRule method) (bioscrape.types.BimolecularPropensity method) (bioscrape.types.ConstitutivePropensity method) (bioscrape.types.Delay method) (bioscrape.types.FixedDelay method) (bioscrape.types.GammaDelay method) (bioscrape.types.GaussianDelay method) (bioscrape.types.GeneralAssignmentRule method) (bioscrape.types.GeneralODERule method) (bioscrape.types.GeneralPropensity method) (bioscrape.types.MassActionPropensity method) (bioscrape.types.NegativeHillPropensity method) (bioscrape.types.NegativeProportionalHillPropensity method) (bioscrape.types.PositiveHillPropensity method) (bioscrape.types.PositiveProportionalHillPropensity method) (bioscrape.types.Propensity method) (bioscrape.types.Rule method) (bioscrape.types.UnimolecularPropensity method)

get_species_array() (bioscrape.types.Model method) get_species_dictionary() (bioscrape.types.Model method) get_species_index() (bioscrape.types.Model method) get_species_list() (bioscrape.types.Model method) get_species_value() (bioscrape.types.Model method) get_state_set() (bioscrape.lineage.LineageVolumeCellState method) get_sub_lineage() (bioscrape.types.Schnitz method) getAllIds() (in module bioscrape.sbmlutil) getSpeciesByName() (in module bioscrape.sbmlutil) getValidIdForName() (bioscrape.sbmlutil.SetIdFromNames method)

H

has_delays() (bioscrape.types.Model method)

has_multiple_timepoints() (bioscrape.inference.BulkData method) (bioscrape.inference.StochasticTrajectories method)

I

import_sbml() (in module bioscrape.sbmlutil) import_sbml_parameters() (in module bioscrape.sbmlutil) import_sbml_reactions() (in module bioscrape.sbmlutil) import_sbml_rules() (in module bioscrape.sbmlutil) import_sbml_species() (in module bioscrape.sbmlutil) InferenceSetup (class in bioscrape.inference_setup) initialize() (bioscrape.lineage.AssignmentVolumeRule method) (bioscrape.lineage.DeathRule method) (bioscrape.lineage.DeltaVDivisionRule method) (bioscrape.lineage.DivisionRule method) (bioscrape.lineage.GeneralDeathRule method) (bioscrape.lineage.GeneralDivisionRule method) (bioscrape.lineage.LineageRule method) (bioscrape.lineage.LinearVolumeRule method) (bioscrape.lineage.MultiplicativeVolumeRule method) (bioscrape.lineage.ODEVolumeRule method) (bioscrape.lineage.ParamDeathRule method) (bioscrape.lineage.SpeciesDeathRule method) (bioscrape.lineage.TimeDivisionRule method) (bioscrape.lineage.VolumeDivisionRule method) (bioscrape.types.AdditiveAssignmentRule method) (bioscrape.types.BimolecularPropensity method) (bioscrape.types.ConstitutivePropensity method) (bioscrape.types.Delay method) (bioscrape.types.FixedDelay method) (bioscrape.types.GammaDelay method) (bioscrape.types.GaussianDelay method) (bioscrape.types.GeneralAssignmentRule method) (bioscrape.types.GeneralODERule method) (bioscrape.types.GeneralPropensity method) (bioscrape.types.MassActionPropensity method) (bioscrape.types.NegativeHillPropensity method) (bioscrape.types.NegativeProportionalHillPropensity method) (bioscrape.types.PositiveHillPropensity method) (bioscrape.types.PositiveProportionalHillPropensity method) (bioscrape.types.Propensity method) (bioscrape.types.Rule method) (bioscrape.types.UnimolecularPropensity method)

initialize_inference() (in module bioscrape.inference_setup) InteractingLineageSSASimulator (class in bioscrape.lineage) is_still_heap() (bioscrape.lineage.CappedStateQueue method)

L

Likelihood (class in bioscrape.inference) Lineage (class in bioscrape.types) LineageCSimInterface (class in bioscrape.lineage) LineageModel (class in bioscrape.lineage) LineageRule (class in bioscrape.lineage) LineageSSASimulator (class in bioscrape.lineage) LineageVolumeCellState (class in bioscrape.lineage)

LineageVolumeSplitter (class in bioscrape.lineage) LinearVolumeEvent (class in bioscrape.lineage) LinearVolumeRule (class in bioscrape.lineage) LMFitInference (class in bioscrape.pid_interfaces) log_gaussian_prior() (bioscrape.pid_interfaces.PIDInterface method) log_uniform_prior() (bioscrape.pid_interfaces.PIDInterface method) LogTerm (class in bioscrape.types)

M

MassActionPropensity (class in bioscrape.types) MaxTerm (class in bioscrape.types) MinTerm (class in bioscrape.types) Model (class in bioscrape.types) ModelCSimInterface (class in bioscrape.simulator) ModelLikelihood (class in bioscrape.inference) module bioscrape.analysis bioscrape.inference bioscrape.inference_setup bioscrape.lineage bioscrape.pid_interfaces bioscrape.random bioscrape.sbmlutil bioscrape.simulator bioscrape.types

MultiplicativeVolumeEvent (class in bioscrape.lineage) MultiplicativeVolumeRule (class in bioscrape.lineage)

N

nameToSbmlId() (bioscrape.sbmlutil.SetIdFromNames method) NegativeHillPropensity (class in bioscrape.types)

NegativeProportionalHillPropensity (class in bioscrape.types) NoDelay (class in bioscrape.types) normalize_SSM() (bioscrape.analysis.SensitivityAnalysis method)

O

ODEVolumeRule (class in bioscrape.lineage)

P

ParamDeathRule (class in bioscrape.lineage) ParameterTerm (class in bioscrape.types) parse_expression() (in module bioscrape.types) parse_general_expression() (bioscrape.types.Model method) parse_model() (bioscrape.types.Model method) PerfectBinomialDelayVolumeSplitter (class in bioscrape.simulator) PerfectBinomialVolumeSplitter (class in bioscrape.simulator) PIDInterface (class in bioscrape.pid_interfaces) plot_mcmc_results() (bioscrape.inference_setup.InferenceSetup method) PositiveHillPropensity (class in bioscrape.types) PositiveProportionalHillPropensity (class in bioscrape.types) PowerTerm (class in bioscrape.types) prepare_inference() (bioscrape.inference_setup.InferenceSetup method) prepare_initial_conditions() (bioscrape.inference_setup.InferenceSetup method) prepare_parameter_conditions() (bioscrape.inference_setup.InferenceSetup method) Prior (class in bioscrape.inference) ProductTerm (class in bioscrape.types) Propensity (class in bioscrape.types) py_add_reaction() (bioscrape.simulator.DelayQueue method) py_add_schnitz() (bioscrape.types.Lineage method) py_add_term() (bioscrape.types.BinaryTerm method) py_advance_time() (bioscrape.simulator.DelayQueue method) py_apply_repeated_rules() (bioscrape.simulator.CSimInterface method) py_apply_repeated_volume_rules() (bioscrape.simulator.CSimInterface method) py_approx_binom_rnd() (in module bioscrape.random) py_approx_binom_rnd_f() (in module bioscrape.random) py_array_sum() (in module bioscrape.random) py_binom_rnd() (in module bioscrape.random) py_binom_rnd_f() (in module bioscrape.random) py_binomial_partition() (bioscrape.simulator.DelayQueue method) py_calculate_deterministic_derivative() (bioscrape.simulator.CSimInterface method) py_cell_divided() (bioscrape.simulator.VolumeSSAResult method) (bioscrape.types.Volume method) py_clear_copy() (bioscrape.simulator.DelayQueue method) py_copy() (bioscrape.simulator.DelayQueue method) (bioscrape.types.Volume method) py_correlations() (bioscrape.simulator.SSAResult method) py_create_propensity_buffer() (bioscrape.lineage.LineageSSASimulator method) py_delay_simulate() (bioscrape.simulator.DelaySimulator method) py_delay_volume_simulate() (bioscrape.simulator.DelayVolumeSimulator method) py_dim() (bioscrape.inference.Distribution method) py_empirical_distribution() (bioscrape.simulator.SSAResult method) py_erlang_rv() (in module bioscrape.random) py_evaluate() (bioscrape.types.Term method) py_execute_rule() (bioscrape.types.Rule method) py_execute_volume_rule() (bioscrape.types.Rule method) py_exponential_rv() (in module bioscrape.random) py_first_moment() (bioscrape.simulator.SSAResult method) py_gamma_rv() (in module bioscrape.random) py_get_data() (bioscrape.inference.DeterministicLikelihood method) (bioscrape.inference.StochasticTrajectoriesLikelihood method) (bioscrape.types.Schnitz method) py_get_dataframe() (bioscrape.simulator.CellState method) (bioscrape.simulator.SSAResult method) (bioscrape.simulator.VolumeCellState method) (bioscrape.simulator.VolumeSSAResult method) (bioscrape.types.Schnitz method) py_get_daughters() (bioscrape.types.Schnitz method) py_get_dead() (bioscrape.lineage.SingleCellSSAResult method) py_get_delay() (bioscrape.types.Delay method) py_get_delay_queue() (bioscrape.simulator.DelayCellState method) (bioscrape.simulator.DelaySSAResult method) (bioscrape.simulator.DelayVolumeCellState method) (bioscrape.simulator.DelayVolumeSSAResult method) py_get_delay_update_array() (bioscrape.simulator.CSimInterface method) (bioscrape.types.Model method) py_get_divided() (bioscrape.lineage.SingleCellSSAResult method) py_get_dt() (bioscrape.simulator.CSimInterface method) py_get_event_counts() (bioscrape.lineage.LineageModel method) py_get_final_cell_state() (bioscrape.simulator.VolumeSSAResult method) py_get_initial_state() (bioscrape.simulator.CSimInterface method) py_get_initial_time() (bioscrape.lineage.LineageVolumeCellState method) (bioscrape.simulator.CSimInterface method) py_get_initial_volume() (bioscrape.lineage.LineageVolumeCellState method) py_get_jacobian() (in module bioscrape.analysis) py_get_lineage_propensities() (bioscrape.lineage.LineageModel method) py_get_measured_species() (bioscrape.inference.Data method) py_get_measurements() (bioscrape.inference.Data method) py_get_N_simulations() (bioscrape.inference.StochasticTrajectoriesLikelihood method) py_get_next_queue_time() (bioscrape.simulator.DelayQueue method) py_get_next_reactions() (bioscrape.simulator.DelayQueue method) py_get_norm_order() (bioscrape.inference.DeterministicLikelihood method) (bioscrape.inference.StochasticTrajectoriesLikelihood method) py_get_num_death_events() (bioscrape.lineage.LineageModel method) py_get_num_death_rules() (bioscrape.lineage.LineageModel method) py_get_num_division_events() (bioscrape.lineage.LineageModel method) py_get_num_division_rules() (bioscrape.lineage.LineageModel method) py_get_num_lineage_propensities() (bioscrape.lineage.LineageModel method) py_get_num_parameters() (bioscrape.simulator.CSimInterface method) py_get_num_reactions() (bioscrape.simulator.CSimInterface method) py_get_num_species() (bioscrape.simulator.CSimInterface method) py_get_num_volume_events() (bioscrape.lineage.LineageModel method) py_get_num_volume_rules() (bioscrape.lineage.LineageModel method) py_get_number_of_rules() (bioscrape.simulator.CSimInterface method) py_get_param_values() (bioscrape.simulator.CSimInterface method) (bioscrape.simulator.ModelCSimInterface method) py_get_parent() (bioscrape.types.Schnitz method) py_get_propensity() (bioscrape.types.Propensity method)

py_get_result() (bioscrape.simulator.SSAResult method) py_get_rule_counts() (bioscrape.lineage.LineageModel method) py_get_schnitz() (bioscrape.simulator.VolumeSSAResult method) (bioscrape.types.Lineage method) py_get_sensitivity_to_parameter() (in module bioscrape.analysis) py_get_species_index() (bioscrape.types.ExperimentalLineage method) py_get_state() (bioscrape.simulator.CellState method) py_get_term() (bioscrape.types.GeneralPropensity method) py_get_time() (bioscrape.simulator.CellState method) (bioscrape.types.Schnitz method) py_get_timepoints() (bioscrape.inference.Data method) (bioscrape.simulator.SSAResult method) py_get_underlying_array() (bioscrape.lineage.CappedStateQueue method) py_get_update_array() (bioscrape.simulator.CSimInterface method) (bioscrape.types.Model method) py_get_volume() (bioscrape.simulator.VolumeCellState method) (bioscrape.simulator.VolumeSSAResult method) (bioscrape.types.Schnitz method) (bioscrape.types.Volume method) py_get_volume_object() (bioscrape.simulator.VolumeCellState method) py_get_volume_propensity() (bioscrape.types.Propensity method) py_get_volume_splitters() (bioscrape.lineage.LineageModel method) py_get_volume_step() (bioscrape.types.Volume method) py_global_derivative_buffer() (in module bioscrape.simulator) py_inference() (in module bioscrape.inference) py_initialize() (bioscrape.lineage.LineageModel method) (bioscrape.types.Model method) (bioscrape.types.Volume method) py_initialize_single_cell_interface() (bioscrape.lineage.LineageSSASimulator method) py_initialize_single_cell_results_arrays() (bioscrape.lineage.LineageSSASimulator method) py_log_likelihood() (bioscrape.inference.Likelihood method) py_normal_rv() (in module bioscrape.random) py_partition() (bioscrape.simulator.DelayVolumeSplitter method) (bioscrape.simulator.VolumeSplitter method) py_pop_event() (bioscrape.lineage.CappedStateQueue method) py_prep_deterministic_simulation() (bioscrape.simulator.CSimInterface method) py_prob() (bioscrape.inference.Distribution method) py_PropagateCells() (bioscrape.lineage.LineageSSASimulator method) (in module bioscrape.lineage) py_PropagateInteractingCells() (bioscrape.lineage.InteractingLineageSSASimulator method) (in module bioscrape.lineage) py_push_event() (bioscrape.lineage.CappedStateQueue method) py_rand_int() (in module bioscrape.random) py_sample_discrete() (in module bioscrape.random) py_second_moment() (bioscrape.simulator.SSAResult method) py_seed_random() (in module bioscrape.random) py_sensitivity_analysis() (in module bioscrape.analysis) py_set_c_timepoints() (bioscrape.lineage.LineageSSASimulator method) py_set_c_truncated_timepoints() (bioscrape.lineage.LineageSSASimulator method) py_set_current_time() (bioscrape.simulator.DelayQueue method) py_set_data() (bioscrape.types.Schnitz method) py_set_daughters() (bioscrape.types.Schnitz method) py_set_dead() (bioscrape.lineage.SingleCellSSAResult method) py_set_delay_queue() (bioscrape.simulator.DelayCellState method) (bioscrape.simulator.DelayVolumeCellState method) py_set_divided() (bioscrape.lineage.SingleCellSSAResult method) py_set_dt() (bioscrape.simulator.CSimInterface method) py_set_globals() (in module bioscrape.simulator) py_set_hmax() (bioscrape.inference.DeterministicLikelihood method) (bioscrape.simulator.DeterministicSimulator method) py_set_initial_state() (bioscrape.simulator.CSimInterface method) py_set_initial_time() (bioscrape.lineage.SingleCellSSAResult method) (bioscrape.simulator.CSimInterface method) py_set_initial_volume() (bioscrape.lineage.SingleCellSSAResult method) py_set_mxstep() (bioscrape.simulator.DeterministicSimulator method) py_set_param_values() (bioscrape.simulator.ModelCSimInterface method) py_set_parent() (bioscrape.types.Schnitz method) py_set_partition_noise() (bioscrape.simulator.GeneralVolumeSplitter method) py_set_partitioning() (bioscrape.simulator.GeneralVolumeSplitter method) py_set_species() (bioscrape.simulator.CellState method) py_set_species_indices() (bioscrape.types.ExperimentalLineage method) py_set_state() (bioscrape.lineage.LineageVolumeCellState method) (bioscrape.simulator.CellState method) py_set_time() (bioscrape.simulator.CellState method) py_set_tolerance() (bioscrape.simulator.DeterministicSimulator method) py_set_underlying_array() (bioscrape.lineage.CappedStateQueue method) py_set_up_InteractingLineage() (in module bioscrape.lineage) py_set_volume() (bioscrape.simulator.VolumeCellState method) (bioscrape.types.Volume method) py_set_volume_object() (bioscrape.simulator.VolumeCellState method) py_simulate() (bioscrape.simulator.DeterministicSimulator method) (bioscrape.simulator.RegularSimulator method) py_simulate_model() (in module bioscrape.simulator) py_SimulateCellLineage() (bioscrape.lineage.LineageSSASimulator method) (in module bioscrape.lineage) py_SimulateInteractingCellLineage() (bioscrape.lineage.InteractingLineageSSASimulator method) (in module bioscrape.lineage) py_SimulateSingleCell() (bioscrape.lineage.LineageSSASimulator method) (in module bioscrape.lineage) py_SimulateTurbidostat() (bioscrape.lineage.LineageSSASimulator method) (in module bioscrape.lineage) py_SingleCellLineage() (bioscrape.lineage.LineageSSASimulator method) (in module bioscrape.lineage) py_size() (bioscrape.types.Lineage method) py_standard_deviation() (bioscrape.simulator.SSAResult method) py_uniform_rv() (in module bioscrape.random) py_unprob() (bioscrape.inference.Distribution method) py_volume_evaluate() (bioscrape.types.Term method) py_volume_simulate() (bioscrape.simulator.VolumeSimulator method)

R

read_model_from_sbml() (in module bioscrape.sbmlutil) RegularSimulator (class in bioscrape.simulator) renameSIds() (in module bioscrape.sbmlutil) restore_binary_term() (in module bioscrape.types) rhs_global() (in module bioscrape.simulator)

rhs_ivp() (in module bioscrape.simulator) Rule (class in bioscrape.types) run_emcee() (bioscrape.inference_setup.InferenceSetup method) run_lmfit() (bioscrape.inference_setup.InferenceSetup method) run_mcmc() (bioscrape.inference_setup.InferenceSetup method)

S

SafeLineageCSimInterface (class in bioscrape.lineage) SafeModelCSimInterface (class in bioscrape.simulator) SafeModeSSASimulator (class in bioscrape.simulator) Schnitz (class in bioscrape.types) seed_parameter_values() (bioscrape.inference_setup.InferenceSetup method) SensitivityAnalysis (class in bioscrape.analysis) set_data() (bioscrape.inference.BulkData method) (bioscrape.inference.Data method) (bioscrape.inference.DeterministicLikelihood method) (bioscrape.inference.FlowData method) (bioscrape.inference.ModelLikelihood method) (bioscrape.inference.StochasticStatesLikelihood method) (bioscrape.inference.StochasticTrajectories method) (bioscrape.inference.StochasticTrajectoriesLikelihood method) set_default_params() (bioscrape.inference.ModelLikelihood method) set_default_species() (bioscrape.inference.ModelLikelihood method) set_dimension() (bioscrape.inference_setup.InferenceSetup method) set_exp_data() (bioscrape.inference_setup.InferenceSetup method) set_frequency_flag() (bioscrape.types.Rule method) set_init_params() (bioscrape.inference.ModelLikelihood method) set_init_seed() (bioscrape.inference_setup.InferenceSetup method) set_init_species() (bioscrape.inference.ModelLikelihood method) set_initial_conditions() (bioscrape.inference_setup.InferenceSetup method) set_likelihood_options() (bioscrape.inference.DeterministicLikelihood method) (bioscrape.inference.ModelLikelihood method) (bioscrape.inference.StochasticTrajectoriesLikelihood method) (bioscrape.inference.StochasticTrajectoryMomentLikelihood method) set_measurements() (bioscrape.inference_setup.InferenceSetup method) set_method() (bioscrape.inference_setup.InferenceSetup method) set_model() (bioscrape.inference.DeterministicLikelihood method) (bioscrape.inference.ModelLikelihood method) (bioscrape.inference.StochasticStatesLikelihood method) (bioscrape.inference.StochasticTrajectoriesLikelihood method) (bioscrape.inference_setup.InferenceSetup method) set_N_simulations() (bioscrape.inference_setup.InferenceSetup method) set_norm_order() (bioscrape.inference_setup.InferenceSetup method) set_nsteps() (bioscrape.inference_setup.InferenceSetup method)

set_nwalkers() (bioscrape.inference_setup.InferenceSetup method) set_parallel() (bioscrape.inference_setup.InferenceSetup method) set_parameter() (bioscrape.types.Model method) set_parameter_conditions() (bioscrape.inference_setup.InferenceSetup method) set_parameters() (bioscrape.types.NegativeProportionalHillPropensity method) set_params() (bioscrape.types.Model method) set_params_to_estimate() (bioscrape.inference_setup.InferenceSetup method) set_prior() (bioscrape.inference_setup.InferenceSetup method) set_sim_type() (bioscrape.inference_setup.InferenceSetup method) set_species() (bioscrape.types.Model method) (bioscrape.types.NegativeProportionalHillPropensity method) set_time_column() (bioscrape.inference_setup.InferenceSetup method) set_timepoints() (bioscrape.inference_setup.InferenceSetup method) SetIdFromNames (class in bioscrape.sbmlutil) setup() (bioscrape.types.StateDependentVolume method) setup_cost_function() (bioscrape.inference_setup.InferenceSetup method) setup_global_volume_simulation() (bioscrape.lineage.InteractingLineageSSASimulator method) setup_likelihood_function() (bioscrape.pid_interfaces.DeterministicInference method) (bioscrape.pid_interfaces.StochasticInference method) setup_queue() (bioscrape.simulator.ArrayDelayQueue static method) SingleCellSSAResult (class in bioscrape.lineage) species_sbml_id() (in module bioscrape.sbmlutil) SpeciesDeathRule (class in bioscrape.lineage) SpeciesTerm (class in bioscrape.types) SSAResult (class in bioscrape.simulator) SSASimulator (class in bioscrape.simulator) StateDependentVolume (class in bioscrape.types) StepTerm (class in bioscrape.types) StochasticInference (class in bioscrape.pid_interfaces) StochasticStatesLikelihood (class in bioscrape.inference) StochasticTimeThresholdVolume (class in bioscrape.types) StochasticTrajectories (class in bioscrape.inference) StochasticTrajectoriesLikelihood (class in bioscrape.inference) StochasticTrajectoryMomentLikelihood (class in bioscrape.inference) SumTerm (class in bioscrape.types) sympy_recursion() (in module bioscrape.types) sympy_species_and_parameters() (in module bioscrape.types)

T

Term (class in bioscrape.types) TimeDependentSSASimulator (class in bioscrape.simulator) TimeDivisionRule (class in bioscrape.lineage)

TimeTerm (class in bioscrape.types) transform() (bioscrape.sbmlutil.SetIdFromNames method) truncate_lineage() (bioscrape.types.ExperimentalLineage method) (bioscrape.types.Lineage method)

U

uniform_prior() (bioscrape.pid_interfaces.PIDInterface method)

UniformDistribution (class in bioscrape.inference) UnimolecularPropensity (class in bioscrape.types)

V

Volume (class in bioscrape.types) VolumeCellState (class in bioscrape.simulator) VolumeDivisionRule (class in bioscrape.lineage) VolumeEvent (class in bioscrape.lineage) VolumeRule (class in bioscrape.lineage)

VolumeSimulator (class in bioscrape.simulator) VolumeSplitter (class in bioscrape.simulator) VolumeSSAResult (class in bioscrape.simulator) VolumeSSASimulator (class in bioscrape.simulator) VolumeTerm (class in bioscrape.types)

W

write_lmfit_results() (bioscrape.inference_setup.InferenceSetup method)

write_sbml_model() (bioscrape.types.Model method)