Index

_

__call__() (skimpy.ConcentrationControlFunction method), [1] (skimpy.ElasticityFunction method) (skimpy.ExpressionModifier method), [1] (skimpy.FluxControlFunction method), [1] (skimpy.FluxFunction method), [1], [2], [3] (skimpy.FluxParameterFunction method), [1] (skimpy.inference.experiment.Observable method) (skimpy.JacobianFunction method), [1] (skimpy.ODEFunction method), [1], [2] (skimpy.SaturationParameterFunction method), [1] (skimpy.SymbolicJacobianFunction method) (skimpy.VolumeRatioFunction method) __del__() (skimpy.ConstantConcentration method), [1] __dir__() (skimpy.TabDict method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22] __getattr__() (skimpy.TabDict method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22] __getitem__() (skimpy.ParameterValuePopulation method), [1] (skimpy.ParameterValues method), [1], [2], [3] __iter__() (skimpy.ItterableSeries method), [1] (skimpy.ParameterValuePopulation method), [1] __len__() (skimpy.ParameterValuePopulation method), [1] __next__() (skimpy.ParameterValuePopulation method), [1] __reduce__() (pytfa.ItemSet method) (skimpy.ItemSet method) (skimpy.KineticMechanism method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] __repr__() (pytfa.Item method) (skimpy.ElementrayReactionStep method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] (skimpy.Item method) __setitem__() (skimpy.ParameterValues method), [1], [2], [3] __str__() (pytfa.Item method) (skimpy.ElementrayReactionStep method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] (skimpy.Item method) (skimpy.Reaction method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16]

_compile_sampling_functions() (skimpy.CMAESParameterSampler method), [1] (skimpy.GaParameterSampler method), [1] (skimpy.SimpleParameterSampler method), [1], [2] _data (skimpy.Tensor attribute), [1], [2] _dataframe() (skimpy.ParameterValuePopulation method), [1] _dict (skimpy.inference.experiment.Observable attribute) _dist (skimpy.inference.parameters.SecureMultivariateNormal attribute) _distribution_observables (skimpy.inference.experiment.SteadyStateExperiment attribute) _generate_symbol() (pytfa.Item method) (skimpy.Item method) _i (skimpy.Tensor attribute), [1], [2] _j (skimpy.Tensor attribute), [1], [2] _k (skimpy.Tensor attribute), [1], [2] _lower_bound (pytfa.Item attribute) (skimpy.Item attribute) _modified (skimpy.KineticModel attribute), [1] (skimpy.Reactor attribute) _name (skimpy.ExpressionModifier attribute), [1] _parameter_values (skimpy.ParameterValues attribute), [1], [2], [3] _parameters (skimpy.KineticMechanism attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] (skimpy.ODEFunction attribute), [1], [2] _reaction (skimpy.ExpressionModifier attribute), [1] _recompiled (skimpy.KineticModel attribute), [1] _sample_saturation_step_compiled() (skimpy.SimpleParameterSampler method), [1], [2] _simtype (skimpy.KineticModel attribute), [1] _suffix (pytfa.Item attribute) (skimpy.Item attribute) _sym_to_str (skimpy.ParameterValues attribute), [1], [2], [3] _symbol (pytfa.Item attribute) (skimpy.Item attribute) _upper_bound (pytfa.Item attribute) (skimpy.Item attribute)

A

ActivationModifier (class in skimpy), [1] add_boundary_condition() (skimpy.KineticModel method), [1] (skimpy.Reactor method) add_compartment() (skimpy.KineticModel method), [1] add_constraint() (skimpy.KineticModel method), [1] add_dummy_delta_g() (in module skimpy), [1] add_min_flux_requirements() (in module skimpy), [1] add_min_log_displacement() (in module skimpy), [1] add_ratio_constraints() (in module skimpy), [1]

add_reaction() (skimpy.KineticModel method), [1] add_to_tabdict() (skimpy.KineticModel method), [1] (skimpy.Reactor method) add_undefined_delta_g() (in module skimpy), [1] add_units() (in module skimpy) AdditiveConcentrationRate (class in skimpy), [1] ALL_GENERIC_MECHANISM_SUBCLASSES (in module skimpy) animate_fluxes() (in module skimpy.viz.escher) AVOGADROS_NUMBER (in module skimpy)

B

BIGM (in module skimpy), [1], [2], [3], [4], [5], [6] BIGM_DG (in module skimpy), [1], [2], [3], [4] BIGM_P (in module skimpy), [1], [2], [3], [4] BIGM_THERMO (in module skimpy), [1], [2], [3], [4] BinUseVariable (class in skimpy), [1] BinVariable (class in skimpy), [1] biomass_reactions (skimpy.Reactor attribute) biomass_scaling (skimpy.Reactor attribute) biomass_variables (skimpy.Reactor attribute) BiUniReversibleHill (class in skimpy), [1]

BiUniReversibleHill.ElementaryReactions (class in skimpy), [1] boundary_condition_representer() (in module skimpy) boundary_conditions (skimpy.KineticModel attribute), [1] (skimpy.Reactor attribute) BoundaryCondition (class in skimpy), [1] BoundaryFlux (class in skimpy), [1] bounds (pytfa.Item property) (skimpy.Item property) boxplot() (in module skimpy) build_index_dict() (skimpy.Tensor method), [1], [2]

C

calc_max_eigenvalue() (in module skimpy), [1], [2], [3] calc_parameters() (in module skimpy), [1], [2], [3] calculate_rate_constants() (skimpy.ActivationModifier method), [1] (skimpy.BiUniReversibleHill method), [1] (skimpy.DisplacementSmallMoleculeModifier method), [1] (skimpy.FirstOrderSmallMoleculeModifier method), [1] (skimpy.HillActivationModifier method), [1] (skimpy.HillInhibitionModifier method), [1] (skimpy.InhibitionModifier method), [1] (skimpy.IrreversibleHill method), [1] (skimpy.KineticMechanism method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] (skimpy.RandBiBiReversibleMichaelisMenten method), [1] (skimpy.ReversibleMichaelisMenten method), [1] (skimpy.SimpleHillActivationModifier method), [1] (skimpy.SimpleRegulatedGeneExpression method), [1] (skimpy.UniBiReversibleHill method), [1] check() (in module skimpy) check_boundary_reaction() (in module skimpy) check_dependency() (skimpy.BoundaryFlux method), [1] check_is_symbol() (in module skimpy), [1] check_rev_michaelis_menten() (in module skimpy) CMAESParameterSampler (class in skimpy), [1] CMAESParameterSampler.Parameters (class in skimpy), [1] COLORS (in module skimpy) columns (skimpy.ElasticityFunction attribute) (skimpy.SymbolicJacobianFunction attribute) Compartment (class in skimpy) compartment (pytfa.Reactant attribute) (skimpy.Reactant attribute), [1] compartment_representer() (in module skimpy)

compartments (skimpy.KineticModel attribute), [1] compile_jacobian() (skimpy.KineticModel method), [1] compile_mca() (skimpy.KineticModel method), [1] compile_ode() (skimpy.KineticModel method), [1] (skimpy.Reactor method) COMPILER (in module skimpy) complementary_indexes (skimpy.Tensor attribute), [1], [2] concat_populations() (in module skimpy), [1] concentration_control_fun (skimpy.FluxControlFunction attribute), [1] CONCENTRATION_SCALING (skimpy.ScalingParameters attribute) ConcentrationControlFunction (class in skimpy), [1] concentrations (skimpy.ODESolution attribute) conservation_relation (skimpy.ConcentrationControlFunction attribute), [1] (skimpy.FluxControlFunction attribute), [1] (skimpy.JacobianFunction attribute), [1] const_index (skimpy.inference.parameters.SecureMultivariateNormal attribute) constant_parameters (skimpy.inference.parameters.SecureMultivariateNormal attribute) ConstantConcentration (class in skimpy), [1] constraints (skimpy.KineticModel attribute), [1] convex_mating() (in module skimpy), [1] copy() (skimpy.ODESolution method) cov() (skimpy.ParameterValuePopulation method), [1] create_linear_model() (in module skimpy) (in module skimpy.analysis.ode.sample_concentrations) create_reaction_from_data() (in module skimpy) create_reaction_from_stoich() (in module skimpy) crossover_scaling (skimpy.GaFluxConcentrationSampler.Parameters attribute), [1] cum_weights (skimpy.inference.parameters.PosteriorLogNormalParameterPopulation attribute) (skimpy.inference.parameters.PosteriorNormalParameterPopulation attribute) custom_ode_update (skimpy.ODEFunction attribute), [1], [2] custom_variables (skimpy.Reactor attribute)

D

data (skimpy.ItterableSeries attribute), [1] (skimpy.ODESolutionPopulation attribute) DEFAULT_CHROME (in module skimpy.viz.escher) default_fitness() (in module skimpy), [1] deltag0_to_keq() (in module skimpy), [1], [2] DENSITY (skimpy.ScalingParameters attribute) dependent_elasticity_function (skimpy.ConcentrationControlFunction attribute), [1] (skimpy.FluxControlFunction attribute), [1] (skimpy.JacobianFunction attribute), [1]

dependent_variable_ix (skimpy.ConcentrationControlFunction attribute), [1] (skimpy.FluxControlFunction attribute), [1] (skimpy.JacobianFunction attribute), [1] displacement_function (skimpy.ConcentrationControlFunction attribute), [1] DisplacementSmallMoleculeModifier (class in skimpy), [1] dummy_dgo (skimpy.ModelGenerator attribute)

E

educts (skimpy.ElementrayReactionStep attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] ElasticityFunction (class in skimpy) ELEMENTARY (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] ElementrayReactionStep (class in skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] EMBEDD_CSS (in module skimpy.viz.utils) enzyme (skimpy.KineticMechanism attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] (skimpy.Reaction attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] EPSILON (in module skimpy), [1], [2], [3], [4], [5], [6], [7] (in module skimpy.analysis.ode.sample_concentrations) (in module skimpy.inference.parameters)

export_sbml() (in module skimpy) export_to_yaml() (in module skimpy) expr (skimpy.FluxFunction attribute), [1], [2], [3] ExpressionModifier (class in skimpy), [1] expressions (skimpy.ElasticityFunction attribute) (skimpy.FluxParameterFunction attribute), [1] (skimpy.ODEFunction attribute), [1], [2] (skimpy.SymbolicJacobianFunction attribute) extracellular_compartment (skimpy.Reactor attribute)

F

FIELDS_TO_SERIALIZE (in module skimpy) FirstOrderSmallMoleculeModifier (class in skimpy), [1] fitness() (skimpy.CMAESParameterSampler method), [1] (skimpy.GaFluxConcentrationSampler method), [1] fix_directionality() (in module skimpy), [1] flux_value (skimpy.AdditiveConcentrationRate attribute), [1] FluxConcentrationSampler (class in skimpy), [1] FluxControlFunction (class in skimpy), [1] FluxFunction (class in skimpy), [1], [2], [3] FluxParameterFunction (class in skimpy), [1]

FluxRatioCons (class in skimpy), [1] FromCobra (class in skimpy) FromPyTFA (class in skimpy), [1] function (skimpy.ElasticityFunction attribute) (skimpy.FluxFunction attribute), [1], [2], [3] (skimpy.FluxParameterFunction attribute), [1] (skimpy.ODEFunction attribute), [1], [2] (skimpy.SymbolicJacobianFunction attribute) FUNCTION_DEFINITION_FOOTER (in module skimpy) FUNCTION_DEFINITION_HEADER (in module skimpy)

G

GaFluxConcentrationSampler (class in skimpy), [1] GaFluxConcentrationSampler.Parameters (class in skimpy), [1] GammaFunction (class in skimpy), [1] GaParameterSampler (class in skimpy), [1] GaParameterSampler.Parameters (class in skimpy), [1] GDW_GWW_RATIO (skimpy.ScalingParameters attribute) GENERAL_GAS_CONSTANT (in module skimpy) generate_a_code_line() (in module skimpy) generate_a_code_line_simplfied() (in module skimpy) generate_vectorized_code() (in module skimpy) get_all_reactants() (in module skimpy) get_all_subclasses() (in module skimpy) get_bistream_logger() (in module skimpy) get_boundary_subclasses() (in module skimpy), [1] get_dep_indep_vars_from_basis() (in module skimpy) get_dependent_weights() (skimpy.ElasticityFunction method) get_dlogx_dlogy() (in module skimpy) get_equlibrium_constant() (skimpy.FromPyTFA method), [1] get_expressions_from_model() (in module skimpy), [1] get_full_rate_expression() (skimpy.ActivationModifier method), [1] (skimpy.BiUniReversibleHill method), [1] (skimpy.DisplacementSmallMoleculeModifier method), [1] (skimpy.FirstOrderSmallMoleculeModifier method), [1] (skimpy.HillActivationModifier method), [1] (skimpy.HillInhibitionModifier method), [1] (skimpy.InhibitionModifier method), [1] (skimpy.IrreversibleHill method), [1] (skimpy.KineticMechanism method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] (skimpy.RandBiBiReversibleMichaelisMenten method), [1] (skimpy.ReversibleMichaelisMenten method), [1] (skimpy.SimpleHillActivationModifier method), [1] (skimpy.SimpleRegulatedGeneExpression method), [1] (skimpy.UniBiReversibleHill method), [1]

get_generic_constructor() (in module skimpy) get_mechanism() (in module skimpy) get_mechanism_subclasses() (in module skimpy) get_medium() (in module skimpy) get_modifier_subclasses() (in module skimpy) get_parameters_from_expression() (skimpy.KineticMechanism method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] get_params() (skimpy.ODEFunction method), [1], [2] get_qssa_rate_expression() (skimpy.ActivationModifier method), [1] (skimpy.BiUniReversibleHill method), [1] (skimpy.DisplacementSmallMoleculeModifier method), [1] (skimpy.FirstOrderSmallMoleculeModifier method), [1] (skimpy.HillActivationModifier method), [1] (skimpy.HillInhibitionModifier method), [1] (skimpy.InhibitionModifier method), [1] (skimpy.IrreversibleHill method), [1] (skimpy.KineticMechanism method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] (skimpy.RandBiBiReversibleMichaelisMenten method), [1] (skimpy.ReversibleMichaelisMenten method), [1] (skimpy.SimpleHillActivationModifier method), [1] (skimpy.SimpleRegulatedGeneExpression method), [1] (skimpy.UniBiReversibleHill method), [1] get_reduced_stoichiometry() (in module skimpy) get_reversible_fluxes() (in module skimpy), [1] get_reversiblity() (in module skimpy) get_slice_index() (skimpy.Tensor method), [1], [2] get_stoich() (in module skimpy) get_stoichiometry() (in module skimpy) get_timestr() (in module skimpy) get_unit() (in module skimpy) guess_mechanism() (in module skimpy)

H

HillActivationModifier (class in skimpy), [1] HillInhibitionModifier (class in skimpy), [1]

hook (pytfa.Item attribute) (skimpy.Item attribute)

I

iloc() (skimpy.TabDict method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22] import_model() (skimpy.FromCobra method) (skimpy.FromPyTFA method), [1] (skimpy.ModelGenerator method) import_reaction() (skimpy.FromCobra method) (skimpy.ModelGenerator method) import_sbml() (in module skimpy) impose_turnover_concentation_ratios() (in module skimpy), [1] INCLUDE (in module skimpy) independent_elasticity_function (skimpy.ConcentrationControlFunction attribute), [1] (skimpy.FluxControlFunction attribute), [1] (skimpy.JacobianFunction attribute), [1] independent_variable_ix (skimpy.ConcentrationControlFunction attribute), [1] (skimpy.FluxControlFunction attribute), [1] (skimpy.JacobianFunction attribute), [1]

InhibitionModifier (class in skimpy), [1] inhibitors (skimpy.KineticMechanism attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] init_parameters() (in module skimpy), [1], [2], [3] initial_conditions (skimpy.KineticModel attribute), [1] (skimpy.Reactor attribute) initialize() (skimpy.Reactor method) integer_left_basis_semipos() (in module pytfa) IrreversibleHill (class in skimpy), [1] IrreversibleHill.ElementaryReactions (class in skimpy), [1] Item (class in pytfa) (class in skimpy) items() (skimpy.ParameterValues method), [1], [2], [3] ItemSet (class in pytfa) (class in skimpy) iterable_to_tabdict() (in module skimpy), [1], [2] ItterableSeries (class in skimpy), [1]

J

JacobianFunction (class in skimpy), [1] join_dicts() (in module skimpy), [1]

JOULE (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23]

K

KCAL (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] KCAL_IN_JOULE (in module skimpy) keys() (skimpy.ParameterValues method), [1], [2], [3] KineticMechanism (class in skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18]

KineticModel (class in skimpy), [1] KJ (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] KJ_IN_JOULE (in module skimpy) kmodel (skimpy.ParameterValuePopulation attribute), [1]

L

LIN (in module skimpy), [1] link() (skimpy.ExpressionModifier method), [1] link_parameters_and_reactants() (skimpy.KineticMechanism method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] load_concentrations() (in module skimpy), [1], [2] load_enzyme_regulation() (in module skimpy) load_equilibrium_constants() (in module skimpy), [1], [2] load_fluxes() (in module skimpy), [1], [2] load_parameter_population() (in module skimpy), [1]

load_yaml_model() (in module skimpy) local_gcd() (in module pytfa) LOG (in module skimpy), [1] log_cov() (skimpy.ParameterValuePopulation method), [1] log_mean() (skimpy.ParameterValuePopulation method), [1] log_var() (skimpy.ParameterValuePopulation method), [1] LOGFOLDERNAME (in module skimpy) logger (skimpy.KineticModel attribute), [1] LogNormalPriorParameterDistribution (class in skimpy.inference.parameters)

M

make_batch_reactor() (in module skimpy) make_convenience() (in module skimpy), [1] make_convenience_with_inhibition() (in module skimpy), [1] make_cython_function() (in module skimpy), [1], [2] make_df() (skimpy.Tensor method), [1], [2] make_elasticity_fun() (in module skimpy) make_elasticity_fun_multicore() (in module skimpy) make_elasticity_fun_single_cpu() (in module skimpy) make_elasticity_single_row() (in module skimpy) make_expressions() (in module skimpy), [1] make_expresson_single_var() (in module skimpy), [1] make_flux_fun() (in module skimpy), [1] make_gamma_fun() (in module skimpy), [1] make_generalized_elementary_kinetics() (in module skimpy), [1] make_generalized_reversible_hill_n_n() (in module skimpy), [1] make_generalized_reversible_hill_n_n_h1() (in module skimpy), [1] make_generalized_reversible_hill_n_n_h1_with_inhibition() (in module skimpy), [1] make_irrev_m_n_hill() (in module skimpy), [1] make_irrev_m_n_michaelis_menten() (in module skimpy), [1] make_irrev_massaction() (in module skimpy), [1] make_mca_functions() (in module skimpy) make_mechanism_from_expression() (in module skimpy) make_ode_fun() (in module skimpy), [1] make_parameter_set() (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] make_reactant_set() (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] make_reactor_ode_fun() (in module skimpy) make_rev_massaction() (in module skimpy), [1] make_subclasses_dict() (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] make_symbolic_jacobian() (in module skimpy) make_symbolic_jacobian_row() (in module skimpy) MAX_C (in module skimpy), [1] max_eigenvalue (skimpy.GaFluxConcentrationSampler.Parameters attribute), [1] max_generation (skimpy.GaFluxConcentrationSampler.Parameters attribute), [1] max_revesible_deltag_0 (skimpy.FromPyTFA attribute), [1] MAX_STOICH (in module skimpy), [1] MCA (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] mca_type (skimpy.ConcentrationControlFunction attribute), [1] (skimpy.FluxControlFunction attribute), [1] mean() (skimpy.ParameterValuePopulation method), [1] (skimpy.Tensor method), [1], [2] mechanism (pytfa.ItemSet attribute) (skimpy.ItemSet attribute) mechanism_representer() (in module skimpy) medium (skimpy.Reactor attribute) metabolite (skimpy.MetWithStoich attribute) MetWithStoich (class in skimpy) MIN_C (in module skimpy), [1] min_eigenvalue (skimpy.GaFluxConcentrationSampler.Parameters attribute), [1] MinFLux (class in skimpy), [1] MinFLuxVariable (class in skimpy), [1] modal_matrix() (in module skimpy), [1] model (pytfa.Item attribute) (skimpy.ConcentrationControlFunction attribute), [1] (skimpy.FluxControlFunction attribute), [1] (skimpy.Item attribute) (skimpy.ODEFunction attribute), [1], [2] model_gen (in module skimpy), [1] ModelGenerator (class in skimpy) models (skimpy.Reactor attribute) modifier (skimpy.ExpressionModifier property), [1] modifier() (skimpy.ActivationModifier method), [1] (skimpy.AdditiveConcentrationRate method), [1] (skimpy.ConstantConcentration method), [1] (skimpy.DisplacementSmallMoleculeModifier method), [1] (skimpy.FirstOrderSmallMoleculeModifier method), [1] (skimpy.HillActivationModifier method), [1] (skimpy.HillInhibitionModifier method), [1] (skimpy.InhibitionModifier method), [1] (skimpy.SimpleHillActivationModifier method), [1] modifiers (skimpy.Reaction attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] module pytfa, [1], [2] skimpy, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66], [67], [68], [69], [70], [71], [72], [73], [74], [75], [76], [77], [78], [79], [80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91] skimpy.analysis skimpy.analysis.gsa skimpy.analysis.mca skimpy.analysis.mca.concentration_control_fun skimpy.analysis.mca.elasticity_fun skimpy.analysis.mca.flux_control_fun skimpy.analysis.mca.jacobian_fun skimpy.analysis.mca.make skimpy.analysis.mca.prepare skimpy.analysis.mca.utils skimpy.analysis.mca.volume_ratio_function skimpy.analysis.modal skimpy.analysis.modal.modal_matrix skimpy.analysis.ode skimpy.analysis.ode.flux_fun skimpy.analysis.ode.gamma_fun skimpy.analysis.ode.ode_fun skimpy.analysis.ode.sample_concentrations skimpy.analysis.ode.symbolic_jacobian_fun skimpy.analysis.ode.utils skimpy.analysis.oracle skimpy.analysis.oracle.add_min_displacement skimpy.analysis.oracle.dummy_free_energies skimpy.analysis.oracle.fix_directionality skimpy.analysis.oracle.flux_concentration_ratios skimpy.analysis.oracle.load_pytfa_solution skimpy.analysis.oracle.minimum_fluxes skimpy.core skimpy.core.compartments skimpy.core.itemsets skimpy.core.kinmodel skimpy.core.modifiers skimpy.core.parameters skimpy.core.reactions skimpy.core.reactor skimpy.core.solution skimpy.inference skimpy.inference.experiment skimpy.inference.parameters skimpy.io skimpy.io.generate_from_cobra skimpy.io.generate_from_pytfa skimpy.io.model_generator skimpy.io.regulation skimpy.io.sbml skimpy.io.utils skimpy.io.yaml skimpy.mechanisms skimpy.mechanisms.bi_uni_reversible_hill skimpy.mechanisms.convenience skimpy.mechanisms.convenience_with_inihibition skimpy.mechanisms.direct_expression skimpy.mechanisms.gene_expression skimpy.mechanisms.generalized_elementary_kinetics skimpy.mechanisms.generalized_reversible_hill_n_n skimpy.mechanisms.generalized_reversible_hill_n_n_h1 skimpy.mechanisms.generalized_reversible_hill_n_n_h1_with_inhibition skimpy.mechanisms.irrev_hill skimpy.mechanisms.irrev_m_n_hill skimpy.mechanisms.irrev_m_n_michaelis_menten skimpy.mechanisms.irrev_massaction skimpy.mechanisms.mechanism skimpy.mechanisms.michaelis_menten skimpy.mechanisms.rand_bi_bi_michaelis_menten skimpy.mechanisms.rev_massaction skimpy.mechanisms.uni_bi_reversible_hill skimpy.mechanisms.utils skimpy.sampling skimpy.sampling.cma_es_parameter_sampler skimpy.sampling.flux_concentration_sampler skimpy.sampling.flux_parameter_function skimpy.sampling.ga_flux_concentration_sampler skimpy.sampling.ga_parameter_sampler skimpy.sampling.parameter_sampler skimpy.sampling.saturation_parameter_function skimpy.sampling.simple_parameter_sampler skimpy.sampling.simple_resampler skimpy.sampling.utils skimpy.simulations skimpy.simulations.reactor skimpy.utils skimpy.utils.compile_sympy skimpy.utils.constants skimpy.utils.constructors skimpy.utils.conversions skimpy.utils.general skimpy.utils.logger skimpy.utils.medium skimpy.utils.moieties skimpy.utils.namespace skimpy.utils.scaling skimpy.utils.tabdict skimpy.utils.tensor skimpy.viz skimpy.viz.controll_coefficients skimpy.viz.escher skimpy.viz.flux_profile skimpy.viz.modal skimpy.viz.plotting skimpy.viz.sensitivty skimpy.viz.utils

moieties (skimpy.KineticModel property), [1] mu (skimpy.inference.experiment.SteadyStateExperiment attribute) (skimpy.inference.parameters.PosteriorLogNormalParameterPopulation attribute) (skimpy.inference.parameters.PosteriorNormalParameterPopulation attribute) (skimpy.inference.parameters.SecureMultivariateNormal attribute) mutate_ind() (skimpy.GaFluxConcentrationSampler method), [1] mutation_probability (skimpy.GaFluxConcentrationSampler.Parameters attribute), [1]

N

n_parameter_samples (skimpy.GaFluxConcentrationSampler.Parameters attribute), [1] n_samples (skimpy.CMAESParameterSampler.Parameters attribute), [1] (skimpy.GaFluxConcentrationSampler.Parameters attribute), [1] (skimpy.GaParameterSampler.Parameters attribute), [1] (skimpy.SimpleParameterSampler.Parameters attribute), [1], [2] name (pytfa.Item attribute) (skimpy.Compartment attribute) (skimpy.ExpressionModifier property), [1] (skimpy.inference.experiment.Observable attribute) (skimpy.Item attribute) (skimpy.KineticMechanism attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] (skimpy.KineticModel attribute), [1] (skimpy.Reaction attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16]

names (skimpy.ODESolution attribute) NET (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25] NUMERICAL (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] numpy_gcd() (in module pytfa)

O

Observable (class in skimpy.inference.experiment) observables (skimpy.inference.experiment.SteadyStateExperiment attribute) ODE (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23]

ode_expressions (skimpy.SymbolicJacobianFunction attribute) ode_solution (skimpy.ODESolution attribute) ODEFunction (class in skimpy), [1], [2] ODESolution (class in skimpy) ODESolutionPopulation (class in skimpy)

P

p() (skimpy.inference.experiment.SteadyStateExperiment method) Parameter (class in pytfa) (class in skimpy) PARAMETER (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] parameter_elasticity_function (skimpy.ConcentrationControlFunction attribute), [1] (skimpy.FluxControlFunction attribute), [1] parameter_reactant_links (skimpy.ActivationModifier attribute), [1] (skimpy.BiUniReversibleHill attribute), [1] (skimpy.DisplacementSmallMoleculeModifier attribute), [1] (skimpy.FirstOrderSmallMoleculeModifier attribute), [1] (skimpy.HillActivationModifier attribute), [1] (skimpy.HillInhibitionModifier attribute), [1] (skimpy.InhibitionModifier attribute), [1] (skimpy.IrreversibleHill attribute), [1] (skimpy.KineticMechanism attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] (skimpy.RandBiBiReversibleMichaelisMenten attribute), [1] (skimpy.ReversibleMichaelisMenten attribute), [1] (skimpy.SimpleHillActivationModifier attribute), [1] (skimpy.SimpleRegulatedGeneExpression attribute), [1] (skimpy.UniBiReversibleHill attribute), [1] parameter_representer() (in module skimpy) Parameters (skimpy.ActivationModifier attribute), [1] (skimpy.BiUniReversibleHill attribute), [1] parameters (skimpy.Compartment attribute) Parameters (skimpy.DisplacementSmallMoleculeModifier attribute), [1] parameters (skimpy.ElasticityFunction attribute) Parameters (skimpy.FirstOrderSmallMoleculeModifier attribute), [1] parameters (skimpy.FluxConcentrationSampler attribute), [1] Parameters (skimpy.FluxConcentrationSampler property), [1] parameters (skimpy.FluxFunction attribute), [1], [2], [3] Parameters (skimpy.HillActivationModifier attribute), [1] (skimpy.HillInhibitionModifier attribute), [1] (skimpy.InhibitionModifier attribute), [1] (skimpy.IrreversibleHill attribute), [1] (skimpy.KineticMechanism property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] parameters (skimpy.KineticMechanism property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] (skimpy.KineticModel property), [1] (skimpy.ODEFunction property), [1], [2] (skimpy.ParameterSampler attribute), [1] Parameters (skimpy.ParameterSampler property), [1] (skimpy.RandBiBiReversibleMichaelisMenten attribute), [1] parameters (skimpy.Reaction property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] (skimpy.Reactor property) Parameters (skimpy.ReversibleMichaelisMenten attribute), [1] (skimpy.SimpleHillActivationModifier attribute), [1] (skimpy.SimpleRegulatedGeneExpression attribute), [1]

parameters (skimpy.SymbolicJacobianFunction attribute) Parameters (skimpy.UniBiReversibleHill attribute), [1] ParameterSampler (class in skimpy), [1] ParameterSet (class in pytfa) (class in skimpy) ParameterValuePopulation (class in skimpy), [1] ParameterValues (class in skimpy), [1], [2], [3] parametrize() (skimpy.KineticModel method), [1] (skimpy.Reaction method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] (skimpy.Reactor method) parametrize_by_reaction() (skimpy.KineticModel method), [1] pareto_dominance() (in module skimpy), [1], [2], [3] parse_expression() (in module skimpy) pdf (skimpy.inference.parameters.PosteriorLogNormalParameterPopulation attribute) (skimpy.inference.parameters.PosteriorNormalParameterPopulation attribute) plot() (skimpy.ODESolution method) (skimpy.ODESolutionPopulation method) plot_control_coefficients() (in module skimpy) plot_flux_profiles() (in module skimpy) plot_fluxes() (in module skimpy.viz.escher) plot_modal_matrix() (in module skimpy) plot_population_per_variable() (in module skimpy) plot_sobol_coefficients() (in module skimpy) PosteriorLogNormalParameterPopulation (class in skimpy.inference.parameters) PosteriorNormalParameterPopulation (class in skimpy.inference.parameters) prefix (skimpy.ActivationModifier attribute), [1] (skimpy.AdditiveConcentrationRate attribute), [1] (skimpy.BinUseVariable attribute), [1] (skimpy.BinVariable attribute), [1] (skimpy.BoundaryCondition attribute), [1] (skimpy.BoundaryFlux attribute), [1] (skimpy.ConstantConcentration attribute), [1] (skimpy.DisplacementSmallMoleculeModifier attribute), [1] (skimpy.ExpressionModifier attribute), [1] (skimpy.FirstOrderSmallMoleculeModifier attribute), [1] (skimpy.FluxRatioCons attribute), [1] (skimpy.HillActivationModifier attribute), [1] (skimpy.HillInhibitionModifier attribute), [1] (skimpy.InhibitionModifier attribute), [1] (skimpy.MinFLux attribute), [1] (skimpy.MinFLuxVariable attribute), [1] (skimpy.SimpleHillActivationModifier attribute), [1] prepare() (skimpy.KineticModel method), [1] prepare_mca() (in module skimpy) products (skimpy.ElementrayReactionStep attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] pytfa module, [1], [2]

Q

QSSA (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23]

quantile() (skimpy.Tensor method), [1], [2]

R

r1b (skimpy.ReversibleMichaelisMenten.ElementaryReactions attribute), [1] r1f (skimpy.ReversibleMichaelisMenten.ElementaryReactions attribute), [1] r2b (skimpy.ReversibleMichaelisMenten.ElementaryReactions attribute), [1] r2f (skimpy.ReversibleMichaelisMenten.ElementaryReactions attribute), [1] RandBiBiReversibleMichaelisMenten (class in skimpy), [1] RandBiBiReversibleMichaelisMenten.ElementaryReactions (class in skimpy), [1] rate_constant_name (skimpy.ElementrayReactionStep attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] rates (skimpy.Reaction property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] rational_left_basis() (in module pytfa) Reactant (class in pytfa) (class in skimpy), [1] reactant (skimpy.AdditiveConcentrationRate attribute), [1] (skimpy.ConstantConcentration attribute), [1] reactant_list (skimpy.BiUniReversibleHill attribute), [1] (skimpy.IrreversibleHill attribute), [1] (skimpy.SimpleRegulatedGeneExpression attribute), [1] (skimpy.UniBiReversibleHill attribute), [1] reactant_relations (skimpy.ModelGenerator attribute) reactant_representer() (in module skimpy) reactant_stoichiometry (skimpy.ActivationModifier attribute), [1] (skimpy.BiUniReversibleHill attribute), [1] (skimpy.HillActivationModifier attribute), [1] (skimpy.HillInhibitionModifier attribute), [1] (skimpy.InhibitionModifier attribute), [1] (skimpy.IrreversibleHill attribute), [1] (skimpy.RandBiBiReversibleMichaelisMenten attribute), [1] (skimpy.Reaction property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] (skimpy.ReversibleMichaelisMenten attribute), [1] (skimpy.SimpleHillActivationModifier attribute), [1] (skimpy.SimpleRegulatedGeneExpression attribute), [1] (skimpy.UniBiReversibleHill attribute), [1] Reactants (skimpy.ActivationModifier attribute), [1] (skimpy.BiUniReversibleHill attribute), [1] (skimpy.DisplacementSmallMoleculeModifier attribute), [1] (skimpy.FirstOrderSmallMoleculeModifier attribute), [1] (skimpy.HillActivationModifier attribute), [1] (skimpy.HillInhibitionModifier attribute), [1] (skimpy.InhibitionModifier attribute), [1] (skimpy.IrreversibleHill attribute), [1]

reactants (skimpy.KineticMechanism attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] Reactants (skimpy.KineticMechanism property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] reactants (skimpy.KineticModel property), [1] Reactants (skimpy.RandBiBiReversibleMichaelisMenten attribute), [1] reactants (skimpy.Reaction property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] Reactants (skimpy.ReversibleMichaelisMenten attribute), [1] (skimpy.SimpleHillActivationModifier attribute), [1] (skimpy.SimpleRegulatedGeneExpression attribute), [1] (skimpy.UniBiReversibleHill attribute), [1] reactants (skimpy.VolumeRatioFunction attribute) ReactantSet (class in pytfa) (class in skimpy) Reaction (class in skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] reaction_groups (skimpy.ModelGenerator attribute) reaction_representer() (in module skimpy) reactions (skimpy.KineticModel attribute), [1] Reactor (class in skimpy) rebuild_dependent_mets() (in module skimpy) reduced_stoichometry (skimpy.ConcentrationControlFunction attribute), [1] (skimpy.FluxControlFunction attribute), [1] (skimpy.JacobianFunction attribute), [1] refresh_representers() (in module skimpy) regulator_list (skimpy.SimpleRegulatedGeneExpression attribute), [1] Regulators (skimpy.SimpleRegulatedGeneExpression attribute), [1] relax_min_flux() (in module skimpy), [1] repair() (skimpy.KineticModel method), [1] required_for (pytfa.ParameterSet property) (skimpy.ParameterSet property) resample() (skimpy.inference.parameters.PosteriorLogNormalParameterPopulation method) (skimpy.inference.parameters.PosteriorNormalParameterPopulation method) respective_variables (skimpy.ElasticityFunction attribute) reversible_michaelis_menten_from_thermo_data() (in module skimpy) ReversibleMichaelisMenten (class in skimpy), [1] ReversibleMichaelisMenten.ElementaryReactions (class in skimpy), [1] robust_index() (in module skimpy), [1] rows (skimpy.ElasticityFunction attribute) (skimpy.SymbolicJacobianFunction attribute) run_ea() (in module skimpy), [1], [2], [3] (skimpy.GaFluxConcentrationSampler method), [1] rvs() (skimpy.inference.parameters.SecureMultivariateNormal method)

S

sample() (skimpy.CMAESParameterSampler method), [1] (skimpy.FluxConcentrationSampler method), [1] (skimpy.GaFluxConcentrationSampler method), [1] (skimpy.GaParameterSampler method), [1] (skimpy.ParameterSampler method), [1] (skimpy.SimpleParameterSampler method), [1], [2] (skimpy.SimpleResampler method) sample_initial_concentrations() (in module skimpy) (in module skimpy.analysis.ode.sample_concentrations) sample_ix (in module skimpy) sample_parameters() (in module skimpy), [1] sample_tfa_model() (skimpy.GaFluxConcentrationSampler method), [1] sanitize_cobra_vars() (in module skimpy), [1], [2] saturation_parameters (skimpy.SaturationParameterFunction attribute), [1] SaturationParameterFunction (class in skimpy), [1] save() (skimpy.ParameterValuePopulation method), [1] scaling_parameters (skimpy.GaFluxConcentrationSampler.Parameters attribute), [1] ScalingParameters (class in skimpy) SecureMultivariateNormal (class in skimpy.inference.parameters) seed (skimpy.GaFluxConcentrationSampler.Parameters attribute), [1] shape (skimpy.ElasticityFunction attribute) (skimpy.SymbolicJacobianFunction attribute) sigma (skimpy.inference.parameters.PosteriorLogNormalParameterPopulation attribute) (skimpy.inference.parameters.PosteriorNormalParameterPopulation attribute) sim_type (skimpy.KineticModel property), [1] SimpleHillActivationModifier (class in skimpy), [1] SimpleParameterSampler (class in skimpy), [1], [2] SimpleParameterSampler.Parameters (class in skimpy), [1], [2] SimpleRegulatedGeneExpression (class in skimpy), [1] SimpleRegulatedGeneExpression.ElementaryReactions (class in skimpy), [1] SimpleResampler (class in skimpy) SingleRegulator (skimpy.SimpleRegulatedGeneExpression attribute), [1] skimpy module, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66], [67], [68], [69], [70], [71], [72], [73], [74], [75], [76], [77], [78], [79], [80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91] skimpy.analysis module skimpy.analysis.gsa module skimpy.analysis.mca module skimpy.analysis.mca.concentration_control_fun module skimpy.analysis.mca.elasticity_fun module skimpy.analysis.mca.flux_control_fun module skimpy.analysis.mca.jacobian_fun module skimpy.analysis.mca.make module skimpy.analysis.mca.prepare module skimpy.analysis.mca.utils module skimpy.analysis.mca.volume_ratio_function module skimpy.analysis.modal module skimpy.analysis.modal.modal_matrix module skimpy.analysis.ode module skimpy.analysis.ode.flux_fun module skimpy.analysis.ode.gamma_fun module skimpy.analysis.ode.ode_fun module skimpy.analysis.ode.sample_concentrations module skimpy.analysis.ode.symbolic_jacobian_fun module skimpy.analysis.ode.utils module skimpy.analysis.oracle module skimpy.analysis.oracle.add_min_displacement module skimpy.analysis.oracle.dummy_free_energies module skimpy.analysis.oracle.fix_directionality module skimpy.analysis.oracle.flux_concentration_ratios module skimpy.analysis.oracle.load_pytfa_solution module skimpy.analysis.oracle.minimum_fluxes module skimpy.core module skimpy.core.compartments module skimpy.core.itemsets module skimpy.core.kinmodel module skimpy.core.modifiers module skimpy.core.parameters module skimpy.core.reactions module skimpy.core.reactor module skimpy.core.solution module skimpy.inference module skimpy.inference.experiment module skimpy.inference.parameters module skimpy.io module skimpy.io.generate_from_cobra module skimpy.io.generate_from_pytfa module skimpy.io.model_generator module skimpy.io.regulation module skimpy.io.sbml module skimpy.io.utils module skimpy.io.yaml module skimpy.mechanisms module

skimpy.mechanisms.bi_uni_reversible_hill module skimpy.mechanisms.convenience module skimpy.mechanisms.convenience_with_inihibition module skimpy.mechanisms.direct_expression module skimpy.mechanisms.gene_expression module skimpy.mechanisms.generalized_elementary_kinetics module skimpy.mechanisms.generalized_reversible_hill_n_n module skimpy.mechanisms.generalized_reversible_hill_n_n_h1 module skimpy.mechanisms.generalized_reversible_hill_n_n_h1_with_inhibition module skimpy.mechanisms.irrev_hill module skimpy.mechanisms.irrev_m_n_hill module skimpy.mechanisms.irrev_m_n_michaelis_menten module skimpy.mechanisms.irrev_massaction module skimpy.mechanisms.mechanism module skimpy.mechanisms.michaelis_menten module skimpy.mechanisms.rand_bi_bi_michaelis_menten module skimpy.mechanisms.rev_massaction module skimpy.mechanisms.uni_bi_reversible_hill module skimpy.mechanisms.utils module skimpy.sampling module skimpy.sampling.cma_es_parameter_sampler module skimpy.sampling.flux_concentration_sampler module skimpy.sampling.flux_parameter_function module skimpy.sampling.ga_flux_concentration_sampler module skimpy.sampling.ga_parameter_sampler module skimpy.sampling.parameter_sampler module skimpy.sampling.saturation_parameter_function module skimpy.sampling.simple_parameter_sampler module skimpy.sampling.simple_resampler module skimpy.sampling.utils module skimpy.simulations module skimpy.simulations.reactor module skimpy.utils module skimpy.utils.compile_sympy module skimpy.utils.constants module skimpy.utils.constructors module skimpy.utils.conversions module skimpy.utils.general module skimpy.utils.logger module skimpy.utils.medium module skimpy.utils.moieties module skimpy.utils.namespace module skimpy.utils.scaling module skimpy.utils.tabdict module skimpy.utils.tensor module skimpy.viz module skimpy.viz.controll_coefficients module skimpy.viz.escher module skimpy.viz.flux_profile module skimpy.viz.modal module skimpy.viz.plotting module skimpy.viz.sensitivty module skimpy.viz.utils module slice_by() (skimpy.Tensor method), [1], [2] solve_ode() (skimpy.KineticModel method), [1] (skimpy.Reactor method) sparse_matrix (in module skimpy) species (skimpy.ODESolution attribute) SPLIT (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25] std() (skimpy.Tensor method), [1], [2] SteadyStateExperiment (class in skimpy.inference.experiment) stoichiometry (skimpy.MetWithStoich attribute) stringify_stoichiometry() (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] SUBSTANCE (in module skimpy) suffix (pytfa.Item property) (skimpy.Item property) sym_concentrations (skimpy.FluxParameterFunction attribute), [1] (skimpy.SaturationParameterFunction attribute), [1] sym_parameters (skimpy.FluxParameterFunction attribute), [1] symbol (pytfa.Item property) (skimpy.Item property) SYMBOLIC (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] SymbolicJacobianFunction (class in skimpy)

T

TabDict (class in skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22] Tensor (class in skimpy), [1], [2] TIME (in module skimpy) time (skimpy.ODESolution attribute) TIME_SCALING (skimpy.ScalingParameters attribute) timetrace_plot() (in module skimpy) TQSSA (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23]

TRANSFORMATIONS (in module skimpy) type (pytfa.Item attribute) (pytfa.Parameter attribute) (pytfa.Reactant attribute) (skimpy.Item attribute) (skimpy.Parameter attribute) (skimpy.Reactant attribute), [1]

U

UniBiReversibleHill (class in skimpy), [1] UniBiReversibleHill.ElementaryReactions (class in skimpy), [1] update_parameters() (skimpy.CMAESParameterSampler method), [1] update_qssa_rate_expression() (skimpy.ActivationModifier method), [1] (skimpy.BiUniReversibleHill method), [1] (skimpy.DisplacementSmallMoleculeModifier method), [1] (skimpy.FirstOrderSmallMoleculeModifier method), [1] (skimpy.HillActivationModifier method), [1] (skimpy.HillInhibitionModifier method), [1] (skimpy.InhibitionModifier method), [1] (skimpy.IrreversibleHill method), [1] (skimpy.KineticMechanism method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] (skimpy.RandBiBiReversibleMichaelisMenten method), [1] (skimpy.ReversibleMichaelisMenten method), [1] (skimpy.SimpleHillActivationModifier method), [1] (skimpy.SimpleRegulatedGeneExpression method), [1] (skimpy.UniBiReversibleHill method), [1]

V

value (pytfa.Item attribute) (skimpy.Item attribute) values() (skimpy.ParameterValues method), [1], [2], [3] var (skimpy.inference.experiment.SteadyStateExperiment attribute) var() (skimpy.ParameterValuePopulation method), [1] VARIABLE (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] variable_index (skimpy.inference.parameters.SecureMultivariateNormal attribute) variable_parameters (skimpy.inference.parameters.SecureMultivariateNormal attribute)

variables (skimpy.ElasticityFunction attribute) (skimpy.FluxFunction attribute), [1], [2], [3] (skimpy.ODEFunction attribute), [1], [2] (skimpy.Reactor property) (skimpy.SymbolicJacobianFunction attribute) VOLUME (in module skimpy) volume_ratio_function (skimpy.ConcentrationControlFunction attribute), [1] (skimpy.JacobianFunction attribute), [1] VolumeRatioFunction (class in skimpy)

W

WATER_FORMULA (in module pytfa) (in module skimpy), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23]

with_time (skimpy.ODEFunction attribute), [1], [2] write_code_to_tempfile() (in module skimpy)