Index

A

ABSOLUTE_TOL (optimModels.utils.configurations.SolverConfigurations attribute) AdamsBashforth2 (optimModels.utils.constantes.solverMethod attribute) AdamsBashMoulton2 (optimModels.utils.constantes.solverMethod attribute)

add_child() (optimModels.utils.utils.MyTree method) analysis_growth() (in module optimModels.unittests.gecko_simulation) (in module optimModels.unittests.presentation) analysis_ko() (in module optimModels.unittests.gecko_simulation)

B

BP_MinModifications (class in optimModels.optimization.evaluation_functions) BPCY (class in optimModels.optimization.evaluation_functions)

build_evaluation_function() (in module optimModels.optimization.evaluation_functions) build_ode() (optimModels.model.kineticModel.KineticModel method)

C

cameo_optim() (in module optimModels.unittests.framed_cobrapy) cbm_simualtion() (in module optimModels.unittests.cbm_simulation) cbm_simualtion_iAF() (in module optimModels.unittests.cbm_simulation)

cbm_strain_optim() (in module optimModels.optimization.run) cobra_optim() (in module optimModels.unittests.framed_cobrapy) COMPOSITION (optimModels.utils.constantes.optimType attribute)

D

daemon (optimModels.utils.utils.NoDaemonProcess attribute) decode_candidate() (optimModels.optimization.decoders.Decoder method) (optimModels.optimization.decoders.DecoderMedium method) (optimModels.optimization.decoders.DecoderMediumLevels method) (optimModels.optimization.decoders.DecoderMediumReacKO method) (optimModels.optimization.decoders.DecoderProtKnockouts method) (optimModels.optimization.decoders.DecoderProtUnderOverExpression method) (optimModels.optimization.decoders.DecoderReacKnockouts method) (optimModels.optimization.decoders.DecoderReacUnderOverExpression method) decode_candidate_ids_to_index() (optimModels.optimization.decoders.DecoderMedium method) (optimModels.optimization.decoders.DecoderMediumLevels method) (optimModels.optimization.decoders.DecoderMediumReacKO method) (optimModels.optimization.decoders.DecoderProtKnockouts method) (optimModels.optimization.decoders.DecoderProtUnderOverExpression method) (optimModels.optimization.decoders.DecoderReacKnockouts method) (optimModels.optimization.decoders.DecoderReacUnderOverExpression method)

Decoder (class in optimModels.optimization.decoders) DecoderMedium (class in optimModels.optimization.decoders) DecoderMediumLevels (class in optimModels.optimization.decoders) DecoderMediumReacKO (class in optimModels.optimization.decoders) DecoderProtKnockouts (class in optimModels.optimization.decoders) DecoderProtUnderOverExpression (class in optimModels.optimization.decoders) DecoderReacKnockouts (class in optimModels.optimization.decoders) DecoderReacUnderOverExpression (class in optimModels.optimization.decoders) DEFAULT_LB (optimModels.utils.configurations.StoicConfigurations attribute) DEFAULT_UB (optimModels.utils.configurations.StoicConfigurations attribute) Dop853 (optimModels.utils.constantes.solverMethod attribute) Dopri5 (optimModels.utils.constantes.solverMethod attribute) DORMAN_PRINCE (optimModels.utils.constantes.solverMethod attribute)

E

EAConfigurations (class in optimModels.optimization.evolutionary_computation) ERROR (optimModels.utils.constantes.solverStatus attribute) essential_prot() (in module optimModels.unittests.presentation)

essential_prot_scale() (in module optimModels.unittests.presentation) EULER (optimModels.utils.constantes.solverMethod attribute) EvaluationFunction (class in optimModels.optimization.evaluation_functions) evaluator() (in module optimModels.optimization.evaluators)

F

find_essential_drains() (optimModels.simulation.simul_problems.StoicSimulationProblem method) find_essential_proteins() (optimModels.simulation.simul_problems.GeckoSimulationProblem method)

findBestSolutions() (in module optimModels.optimization.run) fix_exchange_reactions_model() (in module optimModels.utils.utils) framed_optim() (in module optimModels.unittests.framed_cobrapy)

G

gecko_strain_optim() (in module optimModels.optimization.run) GeckoConfigurations (class in optimModels.utils.configurations) GeckoSimulationProblem (class in optimModels.simulation.simul_problems) GeckoSimulationResult (class in optimModels.simulation.simul_results) GENE_KO (optimModels.utils.constantes.optimType attribute) GENE_UO (optimModels.utils.constantes.optimType attribute) generator_single_int_set() (in module optimModels.optimization.generators) generator_single_int_tuple() (in module optimModels.optimization.generators) generator_tuple_int_set() (in module optimModels.optimization.generators) get_bounds() (optimModels.simulation.simul_problems.GeckoSimulationProblem method) (optimModels.simulation.simul_problems.StoicSimulationProblem method) get_constraints_reacs() (optimModels.simulation.simul_problems.GeckoSimulationProblem method) (optimModels.simulation.simul_problems.StoicSimulationProblem method) get_decoder() (optimModels.optimization.evolutionary_computation.OptimProblemConfiguration method) get_default_config() (optimModels.optimization.evolutionary_computation.EAConfigurations method) get_drains() (optimModels.simulation.simul_problems.GeckoSimulationProblem method) (optimModels.simulation.simul_problems.StoicSimulationProblem method) get_ea_configurations() (optimModels.optimization.evolutionary_computation.OptimProblemConfiguration method) get_evaluation_function() (optimModels.optimization.evolutionary_computation.OptimProblemConfiguration method) get_fitness() (optimModels.optimization.evaluation_functions.BP_MinModifications method) (optimModels.optimization.evaluation_functions.BPCY method) (optimModels.optimization.evaluation_functions.EvaluationFunction method) (optimModels.optimization.evaluation_functions.MinCandSize method) (optimModels.optimization.evaluation_functions.MinCandSizeAndMaxTarget method) (optimModels.optimization.evaluation_functions.MinCandSizeWithLevelsAndMaxTarget method) (optimModels.optimization.evaluation_functions.TargetFlux method) get_fluxes_distribution() (optimModels.simulation.simul_results.SimulationResult method) get_id() (optimModels.optimization.evaluation_functions.BP_MinModifications static method) (optimModels.optimization.evaluation_functions.BPCY static method) (optimModels.optimization.evaluation_functions.MinCandSize static method) (optimModels.optimization.evaluation_functions.MinCandSizeAndMaxTarget static method) (optimModels.optimization.evaluation_functions.MinCandSizeWithLevelsAndMaxTarget static method) (optimModels.optimization.evaluation_functions.TargetFlux static method) get_initial_concentrations() (optimModels.simulation.simul_problems.KineticSimulationProblem method) get_internal_reactions() (optimModels.simulation.simul_problems.GeckoSimulationProblem method) (optimModels.simulation.simul_problems.StoicSimulationProblem method) get_method() (optimModels.simulation.simul_problems.SimulationProblem method) get_model() (optimModels.simulation.simul_problems.SimulationProblem method) get_modifications() (optimModels.simulation.override_simul_problem.OverrideKineticSimulProblem method) (optimModels.simulation.override_simul_problem.OverrideSimulationProblem method) (optimModels.simulation.override_simul_problem.OverrideStoicSimulProblem method)

get_name() (optimModels.optimization.evaluation_functions.BP_MinModifications static method) (optimModels.optimization.evaluation_functions.BPCY static method) (optimModels.optimization.evaluation_functions.MinCandSize static method) (optimModels.optimization.evaluation_functions.MinCandSizeAndMaxTarget static method) (optimModels.optimization.evaluation_functions.MinCandSizeWithLevelsAndMaxTarget static method) (optimModels.optimization.evaluation_functions.TargetFlux static method) get_number_reactions() (optimModels.optimization.evolutionary_computation.OptimProblemConfiguration method) get_ode() (optimModels.model.kineticModel.KineticModel method) get_optim_type_name() (optimModels.utils.constantes.optimType method) get_order_nodes() (in module optimModels.utils.utils) get_override_simul_problem() (optimModels.optimization.decoders.Decoder method) (optimModels.optimization.decoders.DecoderMedium method) (optimModels.optimization.decoders.DecoderMediumLevels method) (optimModels.optimization.decoders.DecoderMediumReacKO method) (optimModels.optimization.decoders.DecoderProtKnockouts method) (optimModels.optimization.decoders.DecoderProtUnderOverExpression method) (optimModels.optimization.decoders.DecoderReacKnockouts method) (optimModels.optimization.decoders.DecoderReacUnderOverExpression method) (optimModels.simulation.simul_results.SimulationResult method) get_parameters_ids() (optimModels.optimization.evaluation_functions.BP_MinModifications static method) (optimModels.optimization.evaluation_functions.BPCY static method) (optimModels.optimization.evaluation_functions.MinCandSize static method) (optimModels.optimization.evaluation_functions.MinCandSizeAndMaxTarget static method) (optimModels.optimization.evaluation_functions.MinCandSizeWithLevelsAndMaxTarget static method) (optimModels.optimization.evaluation_functions.TargetFlux static method) get_params_set() (optimModels.unittests.kinetic_simulation.Params method) get_protein_concentrations() (optimModels.simulation.simul_results.GeckoSimulationResult method) get_reactions_ids() (optimModels.simulation.simul_problems.GeckoSimulationProblem method) (optimModels.simulation.simul_problems.StoicSimulationProblem method) get_simulation_problem() (optimModels.optimization.evolutionary_computation.OptimProblemConfiguration method) get_solver() (optimModels.simulation.solvers.odespySolver method) get_solver_id() (optimModels.simulation.simul_problems.SimulationProblem method) get_solver_method_name() (optimModels.utils.constantes.solverMethod method) get_solver_status() (optimModels.simulation.simul_results.SimulationResult method) get_status_str() (optimModels.utils.constantes.solverStatus static method) get_steady_state_concentrations() (optimModels.simulation.simul_results.kineticSimulationResult method) get_time_steps() (optimModels.simulation.simul_problems.KineticSimulationProblem method) get_uptake_reactions() (optimModels.simulation.simul_problems.GeckoSimulationProblem method) (optimModels.simulation.simul_problems.StoicSimulationProblem method) grow_mutation_intSetRep() (in module optimModels.optimization.variators) grow_mutation_intTupleRep() (in module optimModels.optimization.variators) grow_mutation_tuple_intSetRep() (in module optimModels.optimization.variators)

H

HEUN (optimModels.utils.constantes.solverMethod attribute)

I

INF_OR_UNB (optimModels.utils.constantes.solverStatus attribute)

INFEASIBLE (optimModels.utils.constantes.solverStatus attribute)

J

jahan_ko() (in module optimModels.unittests.simplify_solutions)

jahan_model() (in module optimModels.unittests.simplify_solutions) jahan_uo() (in module optimModels.unittests.simplify_solutions)

K

kinetic_sim() (in module optimModels.unittests.kinetic_simulation) kinetic_simulation() (in module optimModels.simulation.run) kinetic_strain_optim() (in module optimModels.optimization.run) KineticConfigurations (class in optimModels.utils.configurations) KineticModel (class in optimModels.model.kineticModel)

KineticSimulationProblem (class in optimModels.simulation.simul_problems) kineticSimulationResult (class in optimModels.simulation.simul_results) ko_chassagnole() (in module optimModels.unittests.kinetic_optim) ko_jahan() (in module optimModels.unittests.kinetic_optim) ko_millard() (in module optimModels.unittests.kinetic_optim)

L

LEVELS (in module optimModels.unittests.cbm_optim) load_kinetic_model() (in module optimModels.model.kineticModel) load_population() (in module optimModels.optimization.observers)

LSODA (optimModels.utils.constantes.solverMethod attribute) LSODAR (optimModels.utils.constantes.solverMethod attribute) LSODE (optimModels.utils.constantes.solverMethod attribute)

M

MEDIUM (optimModels.utils.constantes.optimType attribute) medium_Lactate_optim() (in module optimModels.unittests.cbm_optim) MEDIUM_LEVELS (optimModels.utils.constantes.optimType attribute) medium_optim() (in module optimModels.unittests.cbm_optim) medium_reac_ko_optim() (in module optimModels.unittests.cbm_optim) MEDIUM_REACTION_KO (optimModels.utils.constantes.optimType attribute) MEDIUM_REACTION_UO (optimModels.utils.constantes.optimType attribute) medium_SC_Etanol_Levels_optim() (in module optimModels.unittests.cbm_optim) medium_SC_Etanol_optim() (in module optimModels.unittests.cbm_optim) medium_SC_optim() (in module optimModels.unittests.cbm_optim) medium_test() (in module optimModels.unittests.cbm_simulation) merge_two_dicts() (in module optimModels.utils.utils) method_str() (optimModels.optimization.evaluation_functions.BP_MinModifications method) (optimModels.optimization.evaluation_functions.BPCY method) (optimModels.optimization.evaluation_functions.EvaluationFunction method) (optimModels.optimization.evaluation_functions.MinCandSize method) (optimModels.optimization.evaluation_functions.MinCandSizeAndMaxTarget method) (optimModels.optimization.evaluation_functions.MinCandSizeWithLevelsAndMaxTarget method) (optimModels.optimization.evaluation_functions.TargetFlux method)

methods (optimModels.utils.constantes.solverMethod attribute) millard_ko() (in module optimModels.unittests.simplify_solutions) millard_model() (in module optimModels.unittests.simplify_solutions) millard_uo() (in module optimModels.unittests.simplify_solutions) MinCandSize (class in optimModels.optimization.evaluation_functions) MinCandSizeAndMaxTarget (class in optimModels.optimization.evaluation_functions) MinCandSizeWithLevelsAndMaxTarget (class in optimModels.optimization.evaluation_functions) model (optimModels.simulation.simul_problems.KineticSimulationProblem attribute) MyPool (class in optimModels.utils.utils) MyTree (class in optimModels.utils.utils)

N

N_STEPS (optimModels.utils.configurations.SolverConfigurations attribute) new_candidates_no_duplicates_replacement() (in module optimModels.optimization.replacers)

new_candidates_replacement() (in module optimModels.optimization.replacers) NoDaemonProcess (class in optimModels.utils.utils)

O

odespySolver (class in optimModels.simulation.solvers) OPTIMAL (optimModels.utils.constantes.solverStatus attribute) optimModels (module) optimModels.model (module) optimModels.model.kineticModel (module) optimModels.optimization (module) optimModels.optimization.decoders (module) optimModels.optimization.evaluation_functions (module) optimModels.optimization.evaluators (module) optimModels.optimization.evolutionary_computation (module) optimModels.optimization.generators (module) optimModels.optimization.observers (module) optimModels.optimization.replacers (module) optimModels.optimization.run (module) optimModels.optimization.variators (module) optimModels.simulation (module) optimModels.simulation.override_simul_problem (module) optimModels.simulation.run (module) optimModels.simulation.simul_problems (module) optimModels.simulation.simul_results (module)

optimModels.simulation.solvers (module) optimModels.unittests (module) optimModels.unittests.cbm_optim (module) optimModels.unittests.cbm_simulation (module) optimModels.unittests.framed_cobrapy (module) optimModels.unittests.gecko_optim (module) optimModels.unittests.gecko_simulation (module) optimModels.unittests.kinetic_optim (module) optimModels.unittests.kinetic_simulation (module) optimModels.unittests.presentation (module) optimModels.unittests.simplify_solutions (module) optimModels.utils (module) optimModels.utils.configurations (module) optimModels.utils.constantes (module) optimModels.utils.utils (module) OptimProblemConfiguration (class in optimModels.optimization.evolutionary_computation) optimType (class in optimModels.utils.constantes) OverrideKineticSimulProblem (class in optimModels.simulation.override_simul_problem) OverrideSimulationProblem (class in optimModels.simulation.override_simul_problem) OverrideStoicSimulProblem (class in optimModels.simulation.override_simul_problem)

P

parallel_evaluation_mp() (in module optimModels.optimization.evaluators) parameters (optimModels.simulation.simul_problems.KineticSimulationProblem attribute) Params (class in optimModels.unittests.kinetic_simulation) print() (optimModels.simulation.simul_results.GeckoSimulationResult method) (optimModels.simulation.simul_results.StoicSimulationResult method) (optimModels.simulation.simul_results.kineticSimulationResult method) print_drains_cobrapy() (in module optimModels.unittests.framed_cobrapy)

print_results() (in module optimModels.optimization.run) (in module optimModels.unittests.framed_cobrapy) Process (optimModels.utils.utils.MyPool attribute) prot_ko_optim() (in module optimModels.unittests.gecko_optim) (in module optimModels.unittests.presentation) PROTEIN_KO (optimModels.utils.constantes.optimType attribute) PROTEIN_UO (optimModels.utils.constantes.optimType attribute)

R

Radau5 (optimModels.utils.constantes.solverMethod attribute) reac_ko_medium_optim_CM() (in module optimModels.unittests.cbm_optim) reac_ko_optim() (in module optimModels.unittests.cbm_optim) reac_ko_optim_CM() (in module optimModels.unittests.cbm_optim) REACTION_KO (optimModels.utils.constantes.optimType attribute)

REACTION_UO (optimModels.utils.constantes.optimType attribute) RELATIVE_TOL (optimModels.utils.configurations.SolverConfigurations attribute) RK4 (optimModels.utils.constantes.solverMethod attribute) RKFehlberg (optimModels.utils.constantes.solverMethod attribute) run_optimization() (in module optimModels.optimization.evolutionary_computation)

S

save_all_results() (in module optimModels.optimization.observers) SCALE_CONSTANT (optimModels.utils.configurations.GeckoConfigurations attribute) set_factors() (optimModels.simulation.override_simul_problem.OverrideKineticSimulProblem method) set_objective_function() (optimModels.simulation.simul_problems.GeckoSimulationProblem method) (optimModels.simulation.simul_problems.StoicSimulationProblem method) set_reactions_parameters_factors() (optimModels.model.kineticModel.KineticModel method) shrink_mutation() (in module optimModels.optimization.variators) shrink_mutation_tuple() (in module optimModels.optimization.variators) simplify_modifications() (optimModels.simulation.override_simul_problem.OverrideSimulationProblem method) (optimModels.simulation.override_simul_problem.OverrideStoicSimulProblem method) simplify_solution() (in module optimModels.unittests.simplify_solutions) simplifySolutions() (in module optimModels.optimization.run) simulate() (optimModels.simulation.simul_problems.GeckoSimulationProblem method) (optimModels.simulation.simul_problems.KineticSimulationProblem method) (optimModels.simulation.simul_problems.SimulationProblem method) (optimModels.simulation.simul_problems.StoicSimulationProblem method) simulate_prot() (in module optimModels.unittests.gecko_simulation) simulate_solutions() (in module optimModels.unittests.simplify_solutions) simulate_wt() (in module optimModels.unittests.gecko_simulation)

simulate_wt_multi() (in module optimModels.unittests.gecko_simulation) SimulationProblem (class in optimModels.simulation.simul_problems) SimulationResult (class in optimModels.simulation.simul_results) single_mutation_intSetRep() (in module optimModels.optimization.variators) single_mutation_intTupleRep() (in module optimModels.optimization.variators) single_mutation_tuple_intSetRep() (in module optimModels.optimization.variators) SOLVER (optimModels.utils.configurations.KineticConfigurations attribute) (optimModels.utils.configurations.StoicConfigurations attribute) SOLVER_METHOD (optimModels.utils.configurations.KineticConfigurations attribute) (optimModels.utils.configurations.StoicConfigurations attribute) SOLVER_TIMEOUT (optimModels.utils.configurations.KineticConfigurations attribute) SolverConfigurations (class in optimModels.utils.configurations) solverMethod (class in optimModels.utils.constantes) solverStatus (class in optimModels.utils.constantes) STEADY_STATE_TIME (optimModels.utils.configurations.KineticConfigurations attribute) StoicConfigurations (class in optimModels.utils.configurations) StoicSimulationProblem (class in optimModels.simulation.simul_problems) StoicSimulationResult (class in optimModels.simulation.simul_results) SUBOPTIMAL (optimModels.utils.constantes.solverStatus attribute)

T

t_steps (optimModels.simulation.simul_problems.KineticSimulationProblem attribute) TargetFlux (class in optimModels.optimization.evaluation_functions) timeout (optimModels.simulation.simul_problems.KineticSimulationProblem attribute)

toy_model() (in module optimModels.unittests.kinetic_simulation) toy_model2() (in module optimModels.unittests.kinetic_simulation) types (optimModels.utils.constantes.optimType attribute)

U

UNBOUNDED (optimModels.utils.constantes.solverStatus attribute) under_over_chassagnole() (in module optimModels.unittests.kinetic_optim) under_over_millard() (in module optimModels.unittests.kinetic_optim)

uniform_crossover() (in module optimModels.optimization.variators) uniform_crossover_intTupleRep() (in module optimModels.optimization.variators) uniform_crossover_tuple() (in module optimModels.optimization.variators) UNKNOWN (optimModels.utils.constantes.solverStatus attribute)

V

Vode (optimModels.utils.constantes.solverMethod attribute)

Y

yield_solutions() (in module optimModels.unittests.simplify_solutions)