Index

A

add_constraint() (cameo.util.ProblemCache method) add_demand() (cameo.core.solver_based_model.SolverBasedModel method) add_exchange() (cameo.core.solver_based_model.SolverBasedModel method) add_metabolite() (cameo.core.solver_based_model.SolverBasedModel method) add_metabolites() (cameo.core.reaction.Reaction method) (cameo.core.solver_based_model.SolverBasedModel method) add_objective() (cameo.util.ProblemCache method) add_palettalbe_palette() (cameo.visualization.palette.PaletteMapper method) add_ratio_constraint() (cameo.core.solver_based_model.SolverBasedModel method) add_reactions() (cameo.core.solver_based_model.SolverBasedModel method) add_variable() (cameo.util.ProblemCache method)

apply() (cameo.core.strain_design.StrainDesign method) (cameo.core.target.GeneKnockoutTarget method) (cameo.core.target.ReactionCofactorSwapTarget method) (cameo.core.target.ReactionKnockinTarget method) (cameo.core.target.ReactionKnockoutTarget method) (cameo.parallel.MultiprocessingView method) (cameo.parallel.SequentialView method) apply_async() (cameo.parallel.MultiprocessingView method) (cameo.parallel.SequentialView method) as_cobrapy_solution() (cameo.core.solution.SolutionBase method) AutoVivification (class in cameo.util)

B

begin_transaction() (cameo.util.ProblemCache method)

bold() (in module cameo.ui)

C

cameo (module) cameo.api (module) cameo.api.designer (module) cameo.api.hosts (module) cameo.api.products (module) cameo.config (module) cameo.core (module) cameo.core.gene (module) cameo.core.manipulation (module) cameo.core.metabolite (module) cameo.core.pathway (module) cameo.core.reaction (module) cameo.core.result (module) cameo.core.solution (module) cameo.core.solver_based_model (module) cameo.core.solver_based_model_dual (module) cameo.core.strain_design (module) cameo.core.target (module) cameo.data (module) cameo.data.metanetx (module) cameo.exceptions (module) cameo.flux_analysis (module) cameo.flux_analysis.analysis (module) cameo.flux_analysis.simulation (module) cameo.flux_analysis.structural (module) cameo.flux_analysis.util (module) cameo.io (module) cameo.models (module) cameo.models.universal (module) cameo.models.webmodels (module)

cameo.network_analysis (module) cameo.network_analysis.networkx_based (module) cameo.network_analysis.util (module) cameo.parallel (module) cameo.strain_design (module) cameo.strain_design.deterministic (module) cameo.strain_design.deterministic.flux_variability_based (module) cameo.strain_design.deterministic.linear_programming (module) cameo.strain_design.heuristic (module) cameo.strain_design.heuristic.evolutionary_based (module) cameo.strain_design.pathway_prediction (module) cameo.strain_design.pathway_prediction.pathway_predictor (module) cameo.strain_design.pathway_prediction.util (module) cameo.ui (module) cameo.util (module) cameo.visualization (module) cameo.visualization.escher_ext (module) cameo.visualization.palette (module) cameo.visualization.plotting_old (module) cameo.visualization.sympy_ext (module) cameo.visualization.visualization (module) change_bounds() (cameo.core.reaction.Reaction method) change_objective() (cameo.core.solver_based_model.SolverBasedModel method) clone() (cameo.core.gene.Gene class method) (cameo.core.metabolite.Metabolite class method) (cameo.core.reaction.Reaction class method) constraint (cameo.core.metabolite.Metabolite attribute) convert_to_dual() (in module cameo.core.solver_based_model_dual) copy() (cameo.core.solver_based_model.SolverBasedModel method) create_adapter_reactions() (in module cameo.strain_design.pathway_prediction.util) current_solver_name() (in module cameo.util)

D

data_frame (cameo.core.pathway.Pathway attribute) (cameo.core.result.Result attribute) (cameo.core.solution.SolutionBase attribute) (cameo.core.strain_design.StrainDesignMethodResult attribute) decompose_reaction_groups() (in module cameo.util) decrease_flux() (in module cameo.core.manipulation) delete() (cameo.core.reaction.Reaction method)

delta() (in module cameo.ui) DifferentialFVA (class in cameo.strain_design.deterministic.flux_variability_based) display_on_map() (cameo.core.strain_design.StrainDesignMethodResult method) display_pathway() (in module cameo.strain_design.pathway_prediction.util) distance_based_on_molecular_formula() (in module cameo.network_analysis.util) downreg() (in module cameo.ui) draw_knockout_result() (in module cameo.visualization.visualization) dual_objective (cameo.core.solver_based_model_dual.SolverBasedModelDual attribute)

E

effective_lower_bound (cameo.core.reaction.Reaction attribute) effective_upper_bound (cameo.core.reaction.Reaction attribute) essential_genes() (cameo.core.solver_based_model.SolverBasedModel method)

essential_metabolites() (cameo.core.solver_based_model.SolverBasedModel method) essential_reactions() (cameo.core.solver_based_model.SolverBasedModel method) exchanges (cameo.core.solver_based_model.SolverBasedModel attribute)

F

f (cameo.core.solution.LazySolution attribute) fba() (in module cameo.flux_analysis.simulation) FeasibleButNotOptimal find_blocked_reactions() (in module cameo.flux_analysis.analysis) find_coupled_reactions() (in module cameo.flux_analysis.structural) find_dead_end_reactions() (in module cameo.flux_analysis.structural) fix_objective_as_constraint() (cameo.core.solver_based_model.SolverBasedModel method) fix_pfba_as_constraint() (in module cameo.flux_analysis.util) flatten() (in module cameo.util) float_ceil() (in module cameo.util) float_floor() (in module cameo.util)

flux (cameo.core.reaction.Reaction attribute) flux_balance_impact_degree() (in module cameo.flux_analysis.analysis) flux_expression (cameo.core.reaction.Reaction attribute) flux_variability_analysis() (in module cameo.flux_analysis.analysis) fluxes (cameo.core.solution.LazySolution attribute), [1] (cameo.core.solution.Solution attribute) forward_variable (cameo.core.reaction.Reaction attribute) from_file() (cameo.core.pathway.Pathway class method) frozendict (class in cameo.util) FSEOF (class in cameo.strain_design.deterministic.flux_variability_based) functional (cameo.core.reaction.Reaction attribute)

G

Gene (class in cameo.core.gene) gene_reaction_rule (cameo.core.reaction.Reaction attribute) GeneKnockoutTarget (class in cameo.core.target) GeneModulationTarget (class in cameo.core.target) generate_colors() (in module cameo.util)

get_model_target() (cameo.core.target.GeneModulationTarget method) (cameo.core.target.ReactionModulationTarget method) get_primal_by_id() (cameo.core.solution.LazySolution method) (cameo.core.solution.SolutionBase method) get_system_info() (in module cameo.util) graph_to_svg() (in module cameo.visualization.visualization)

H

human_readable_timestamp (cameo.core.result.MetaInformation attribute)

I

id (cameo.core.gene.Gene attribute) (cameo.core.metabolite.Metabolite attribute) (cameo.core.reaction.Reaction attribute) imap() (cameo.parallel.MultiprocessingView method) (cameo.parallel.SequentialView method) in_ipnb() (in module cameo.util) inchi_to_svg() (in module cameo.visualization.visualization) IncompatibleTargets

increase_flux() (in module cameo.core.manipulation) index_models_bigg() (in module cameo.models.webmodels) index_models_minho() (in module cameo.models.webmodels) indicator_variables (cameo.flux_analysis.structural.ShortestElementaryFluxModes attribute) Infeasible inheritdocstring() (in module cameo.util) IntelliContainer (class in cameo.util) is_exchange (cameo.core.reaction.Reaction attribute)

K

knock_out() (cameo.core.gene.Gene method) (cameo.core.metabolite.Metabolite method) (cameo.core.reaction.Reaction method)

knockin() (in module cameo.ui)

L

LazySolution (class in cameo.core.solution) lmoma() (in module cameo.flux_analysis.simulation) load_medium() (cameo.core.solver_based_model.SolverBasedModel method)

load_model() (in module cameo.io) loading() (in module cameo.ui) lower_bound (cameo.core.reaction.Reaction attribute)

M

manipulation_type (cameo.strain_design.heuristic.evolutionary_based.OptGene attribute) map() (cameo.parallel.MultiprocessingView method) (cameo.parallel.SequentialView method) map_palette() (cameo.visualization.palette.PaletteMapper method) medium (cameo.core.solver_based_model.SolverBasedModel attribute) memoize() (in module cameo.util) meta_information (cameo.core.result.Result attribute) Metabolite (class in cameo.core.metabolite)

MetaInformation (class in cameo.core.result) model (cameo.core.reaction.Reaction attribute) (cameo.core.solution.LazySolution attribute) (cameo.flux_analysis.structural.ShortestElementaryFluxModes attribute) (cameo.strain_design.pathway_prediction.pathway_predictor.PathwayPredictor attribute) (cameo.util.ProblemCache attribute) model_to_network() (in module cameo.network_analysis.networkx_based) moma() (in module cameo.flux_analysis.simulation) MultiprocessingView (class in cameo.parallel)

N

n_carbon (cameo.core.metabolite.Metabolite attribute) (cameo.core.reaction.Reaction attribute)

non_functional_genes (cameo.core.solver_based_model.SolverBasedModel attribute) NotebookBuilder (class in cameo.visualization.escher_ext) notice() (in module cameo.ui)

O

objective (cameo.core.solver_based_model.SolverBasedModel attribute) (cameo.core.solver_based_model_dual.SolverBasedModelDual attribute) objective_coefficient (cameo.core.reaction.Reaction attribute)

objective_value (cameo.core.solution.SolutionBase attribute) OptGene (class in cameo.strain_design.heuristic.evolutionary_based) optimize() (cameo.core.solver_based_model.SolverBasedModel method) OptKnock (class in cameo.strain_design.deterministic.linear_programming)

P

PaletteMapper (class in cameo.visualization.palette) partition() (in module cameo.util) partition_() (in module cameo.util) Pathway (class in cameo.core.pathway) PathwayPredictor (class in cameo.strain_design.pathway_prediction.pathway_predictor) pfba() (in module cameo.flux_analysis.simulation) phenotypic_phase_plane() (in module cameo.flux_analysis.analysis) pick_one() (in module cameo.util) plot (cameo.strain_design.heuristic.evolutionary_based.OptGene attribute) plot() (cameo.core.result.Result method) (cameo.core.strain_design.StrainDesignMethodResult method)

plot_2_production_envelopes() (in module cameo.visualization.plotting_old) plot_flux_variability_analysis() (in module cameo.visualization.plotting_old) plot_production_envelope() (in module cameo.visualization.plotting_old) plug_model() (cameo.core.pathway.Pathway method) pool (cameo.parallel.MultiprocessingView attribute) pop() (cameo.core.reaction.Reaction method) (cameo.util.frozendict method) popitem() (cameo.util.frozendict method) primal_objective() (cameo.core.solver_based_model_dual.SolverBasedModelDual method) ProblemCache (class in cameo.util)

R

randint() (cameo.util.RandomGenerator method) random() (cameo.util.RandomGenerator method) RandomGenerator (class in cameo.util) Reaction (class in cameo.core.reaction) ReactionCofactorSwapTarget (class in cameo.core.target) ReactionKnockinTarget (class in cameo.core.target) ReactionKnockoutTarget (class in cameo.core.target) ReactionModulationTarget (class in cameo.core.target) reactions (cameo.core.pathway.Pathway attribute) reactions_to_network() (in module cameo.network_analysis.networkx_based) redo() (cameo.util.TimeMachine method) reduce_reaction_set() (in module cameo.util) reduced_cost (cameo.core.reaction.Reaction attribute) reduced_costs (cameo.core.solution.LazySolution attribute), [1] (cameo.core.solution.Solution attribute) remove_from_model() (cameo.core.metabolite.Metabolite method) (cameo.core.reaction.Reaction method)

remove_highly_connected_nodes() (in module cameo.network_analysis.networkx_based) remove_infeasible_cycles() (in module cameo.flux_analysis.util) remove_reactions() (cameo.core.solver_based_model.SolverBasedModel method) reset() (cameo.util.ProblemCache method) (cameo.util.TimeMachine method) responsible (cameo.core.result.MetaInformation attribute) Result (class in cameo.core.result) reverse_flux() (in module cameo.core.manipulation) reverse_variable (cameo.core.reaction.Reaction attribute) reversibility (cameo.core.reaction.Reaction attribute) rollback() (cameo.util.ProblemCache method) room() (in module cameo.flux_analysis.simulation) run() (cameo.core.strain_design.StrainDesignMethod method) (cameo.strain_design.deterministic.flux_variability_based.DifferentialFVA method) (cameo.strain_design.deterministic.flux_variability_based.FSEOF method) (cameo.strain_design.deterministic.linear_programming.OptKnock method) (cameo.strain_design.heuristic.evolutionary_based.OptGene method) (cameo.strain_design.pathway_prediction.pathway_predictor.PathwayPredictor method)

S

S (cameo.core.solver_based_model.SolverBasedModel attribute) sample() (cameo.util.RandomGenerator method) sanitize_ids() (in module cameo.io) searching() (in module cameo.ui) seed() (cameo.util.RandomGenerator method) SequentialView (class in cameo.parallel) setdefault() (cameo.util.frozendict method) shadow_prices (cameo.core.solution.LazySolution attribute) ShortestElementaryFluxModes (class in cameo.flux_analysis.structural) shutdown() (cameo.parallel.MultiprocessingView method) (cameo.parallel.SequentialView method) Singleton (class in cameo.util) Solution (class in cameo.core.solution) SolutionBase (class in cameo.core.solution)

solve() (cameo.core.solver_based_model.SolverBasedModel method) SolveError solver (cameo.core.solver_based_model.SolverBasedModel attribute) SolverBasedModel (class in cameo.core.solver_based_model) SolverBasedModelDual (class in cameo.core.solver_based_model_dual) status (cameo.core.solution.LazySolution attribute) stop_loader() (in module cameo.ui) str_to_valid_variable_name() (in module cameo.util) StrainDesign (class in cameo.core.strain_design) StrainDesignMethod (class in cameo.core.strain_design) StrainDesignMethodResult (class in cameo.core.strain_design) swap_cofactors() (in module cameo.core.manipulation) swap_str (cameo.core.target.ReactionCofactorSwapTarget attribute) system_info (cameo.core.result.MetaInformation attribute)

T

TimeMachine (class in cameo.util) Timer (class in cameo.util) timestamp (cameo.core.result.MetaInformation attribute) to_dual_model() (in module cameo.core.solver_based_model_dual) to_file() (cameo.core.pathway.Pathway method)

to_gnomic() (cameo.core.strain_design.StrainDesign method) (cameo.core.target.GeneKnockoutTarget method) (cameo.core.target.ReactionCofactorSwapTarget method) (cameo.core.target.ReactionKnockinTarget method) to_solver_based_model() (in module cameo.core.solver_based_model)

U

Unbounded UndefinedSolution undo() (cameo.util.TimeMachine method) uniform() (cameo.util.RandomGenerator method)

update() (cameo.util.frozendict method) (cameo.visualization.escher_ext.NotebookBuilder method) upper_bound (cameo.core.reaction.Reaction attribute) upreg() (in module cameo.ui)

X

x (cameo.core.solution.SolutionBase attribute)

x_dict (cameo.core.solution.SolutionBase attribute)

Y

y (cameo.core.solution.SolutionBase attribute)

y_dict (cameo.core.solution.SolutionBase attribute)

Z

zip_repeat() (in module cameo.util)