Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | O | P | Q | R | S | T | U | V | W | Y _ __add__() (micom.workflows.GrowthResults method) (micom.workflows.results.GrowthResults method) __add_exchanges() (micom.Community method) (micom.community.Community method) __db_metrics (micom.Community attribute) (micom.community.Community attribute) __repr__() (micom.solution.CommunitySolution method) __taxonomy (micom.Community attribute) (micom.community.Community attribute) __update_community_objective() (micom.Community method) (micom.community.Community method) __update_exchanges() (micom.Community method) (micom.community.Community method) _annotate() (in module micom.workflows.db_media) _apply_min_growth() (in module micom.util) _derivatives() (in module micom.elasticity) _fix_medium() (in module micom.workflows.media) _format_min_growth() (in module micom.util) _get_fluxes() (in module micom.elasticity) _group_taxa() (in module micom.solution) _grow() (in module micom.workflows.db_media) _growth() (in module micom.workflows.grow) _has_manifest (in module micom.qiime_formats) _interact() (in module micom.interaction.focal) _medium() (in module micom.workflows.media) _mes() (in module micom.interaction.scores) _metabolite_interaction() (in module micom.interaction.focal) _methods (in module micom.optcom) _modification (micom.Community attribute) (micom.community.Community attribute) _read_funcs (in module micom.util) _read_model() (in module micom.util) _reduce_group() (in module micom.workflows.build) _repr_html_() (micom.solution.CommunitySolution method) _rtol (micom.Community attribute) (micom.community.Community attribute) _run_corr() (in module micom.stats) _run_test() (in module micom.stats) _summarize() (in module micom.interaction.summary) _summarize_models() (in module micom.workflows.build) _tradeoff() (in module micom.workflows.tradeoff) _try_complete() (in module micom.workflows.db_media) A abundances (micom.Community property) (micom.community.Community property) add_dualized_optcom() (in module micom.optcom) add_linear_obj() (in module micom.media) add_mip_obj() (in module micom.media) add_moma_optcom() (in module micom.optcom) add_pfba_objective() (in module micom.solution) add_var_from_expression() (in module micom.util) adjust_solver_config() (in module micom.util) agora (in module micom.data) annotate() (in module micom.annotation) annotate_metabolites_from_exchanges() (in module micom.annotation) annotations (micom.workflows.GrowthResults attribute) (micom.workflows.results.GrowthResults attribute) ARGS (in module micom.workflows.grow) B build() (in module micom.workflows) (in module micom.workflows.build) build_and_save() (in module micom.workflows.build) build_database() (in module micom.workflows) (in module micom.workflows.build) build_from_qiime() (in module micom.taxonomy) build_metrics (micom.Community property) (micom.community.Community property) C check_db_medium() (in module micom.workflows) (in module micom.workflows.db_media) check_modification() (in module micom.util) chr_or_input() (in module micom.util) clean_ids() (in module micom.util) combine_results() (in module micom.workflows.results) Community (class in micom) (class in micom.community) CommunitySolution (class in micom.solution) compare_groups() (in module micom.stats) compartment_id() (in module micom.util) COMPARTMENT_RE (in module micom.util) complete_community_medium() (in module micom.workflows) (in module micom.workflows.media) complete_db_medium() (in module micom.workflows) (in module micom.workflows.db_media) complete_medium() (in module micom.media) consumption_rates() (in module micom.measures) cooperative_tradeoff() (in module micom.problems) (micom.Community method) (micom.community.Community method) correlate_fluxes() (in module micom.stats) crossover() (in module micom.solution) D data (micom.viz.core.Visualization attribute), [1] (micom.viz.Visualization attribute), [1] db_annotations() (in module micom.workflows.db_media) DIRECTION (in module micom.solution) (in module micom.workflows.grow) (in module micom.workflows.media) (in module micom.workflows.results) download_model() (in module micom.util) E elasticities() (in module micom.elasticity) elasticities_by_abundance() (in module micom.elasticity) elasticities_by_medium() (in module micom.elasticity) env (in module micom.viz.core) euclidean() (in module micom.algorithms) ex_metabolite() (in module micom.util) exchanges (micom.Community property) (micom.community.Community property) (micom.workflows.GrowthResults attribute) (micom.workflows.results.GrowthResults attribute) F fast_dual() (in module micom.duality) fdr_adjust() (in module micom.stats) filename (micom.viz.core.Visualization attribute), [1] (micom.viz.Visualization attribute), [1] fix_demands() (in module micom.util) flatten() (in module micom.annotation) fluxes (micom.solution.CommunitySolution attribute) fluxes_from_primals() (in module micom.util) formatter (in module micom.logger) from_solution() (micom.workflows.GrowthResults static method) (micom.workflows.results.GrowthResults static method) G good (in module micom.solution) grow() (in module micom.workflows) (in module micom.workflows.grow) growth_rate (micom.solution.CommunitySolution attribute), [1] growth_rates (micom.workflows.GrowthResults attribute) (micom.workflows.results.GrowthResults attribute) GrowthResults (class in micom.workflows) (class in micom.workflows.results) H handler (in module micom.logger) I interactions() (in module micom.interaction) (in module micom.interaction.focal) internal_exchanges (micom.Community property) (micom.community.Community property) is_active_demand() (in module micom.util) J jaccard() (in module micom.algorithms) join_models() (in module micom.util) K knockout_taxa() (in module micom.problems) (micom.Community method) (micom.community.Community method) L load() (micom.workflows.GrowthResults static method) (micom.workflows.results.GrowthResults static method) load_manifest() (in module micom.db) load_model() (in module micom.util) load_pickle() (in module micom) (in module micom.util) load_qiime_feature_table() (in module micom.qiime_formats) load_qiime_manifest() (in module micom.qiime_formats) load_qiime_medium() (in module micom.qiime_formats) load_qiime_model() (in module micom.qiime_formats) load_qiime_model_db() (in module micom.qiime_formats) load_qiime_taxonomy() (in module micom.qiime_formats) load_results() (in module micom.workflows) (in module micom.workflows.results) load_zip_model_db() (in module micom.db) logger (in module micom) (in module micom.community) (in module micom.logger) (in module micom.workflows.build) (in module micom.workflows.core) M mass (micom.Community attribute) (micom.community.Community attribute) medium (micom.Community property) (micom.community.Community property) members (micom.solution.CommunitySolution attribute), [1] MES() (in module micom.interaction) (in module micom.interaction.scores) metabolic_dist() (in module micom.algorithms) metadata() (in module micom.qiime_formats) micom module micom.algorithms module micom.annotation module micom.community module micom.constants module micom.data module, [1] micom.db module micom.deps module micom.duality module micom.elasticity module micom.interaction module micom.interaction.focal module micom.interaction.scores module micom.interaction.summary module micom.logger module micom.measures module micom.media module micom.optcom module micom.problems module micom.qiime_formats module micom.solution module micom.stats module micom.taxonomy module micom.util module micom.viz module micom.viz.association module micom.viz.core module micom.viz.exchanges module micom.viz.growth module micom.viz.interactions module micom.viz.tradeoff module micom.workflows module micom.workflows.build module micom.workflows.core module micom.workflows.db_media module micom.workflows.grow module micom.workflows.media module micom.workflows.results module micom.workflows.tradeoff module minimal_media() (in module micom.workflows) (in module micom.workflows.media) minimal_medium() (in module micom.media) model (in module micom.duality) modification (micom.Community property) (micom.community.Community property) module micom micom.algorithms micom.annotation micom.community micom.constants micom.data, [1] micom.db micom.deps micom.duality micom.elasticity micom.interaction micom.interaction.focal micom.interaction.scores micom.interaction.summary micom.logger micom.measures micom.media micom.optcom micom.problems micom.qiime_formats micom.solution micom.stats micom.taxonomy micom.util micom.viz micom.viz.association micom.viz.core micom.viz.exchanges micom.viz.growth micom.viz.interactions micom.viz.tradeoff micom.workflows micom.workflows.build micom.workflows.core micom.workflows.db_media micom.workflows.grow micom.workflows.media micom.workflows.results micom.workflows.tradeoff O objective (micom.Community attribute) (micom.community.Community attribute) objective_value (micom.solution.CommunitySolution attribute) optcom() (in module micom.optcom) (micom.Community method) (micom.community.Community method) optimize() (micom.Community method) (micom.community.Community method) optimize_all() (micom.Community method) (micom.community.Community method) optimize_single() (micom.Community method) (micom.community.Community method) optimize_with_fraction() (in module micom.solution) optimize_with_retry() (in module micom.solution) P plot_association() (in module micom.viz) (in module micom.viz.association) plot_exchanges_per_sample() (in module micom.viz) (in module micom.viz.exchanges) plot_exchanges_per_taxon() (in module micom.viz) (in module micom.viz.exchanges) plot_focal_interactions() (in module micom.viz) (in module micom.viz.interactions) plot_growth() (in module micom.viz) (in module micom.viz.growth) plot_mes() (in module micom.viz) (in module micom.viz.interactions) plot_tradeoff() (in module micom.viz.tradeoff) prefix (in module micom.duality) process_medium() (in module micom.workflows.media) production_rates() (in module micom.measures) Q qiime_to_micom() (in module micom.taxonomy) R rank_prefixes() (in module micom.taxonomy) RANKS (in module micom.constants) reaction_matrix() (in module micom.algorithms) reduced_costs (micom.solution.CommunitySolution attribute) regularize_l2_norm() (in module micom.problems) REQ_FIELDS (in module micom.workflows.build) reset_min_community_growth() (in module micom.util) reset_solver() (in module micom.solution) S safe_weight() (in module micom.media) sample_interactions() (in module micom.interaction.focal) save() (micom.viz.core.Visualization method) (micom.viz.Visualization method) (micom.workflows.GrowthResults method) (micom.workflows.results.GrowthResults method) save_results() (in module micom.workflows) (in module micom.workflows.results) scale (micom.Community property) (micom.community.Community property) serialize_models() (in module micom.util) set_abundance() (micom.Community method) (micom.community.Community method) shadow_prices (micom.solution.CommunitySolution attribute) show_versions() (in module micom) (in module micom.deps) solve() (in module micom.solution) solver (micom.Community attribute) (micom.community.Community attribute) status (micom.solution.CommunitySolution attribute) STEP (in module micom.elasticity) strategy (micom.solution.CommunitySolution attribute), [1] summarize_interactions() (in module micom.interaction) (in module micom.interaction.summary) T taxa (micom.Community attribute) (micom.community.Community attribute) taxon_id() (in module micom.taxonomy) taxonomy (micom.Community property) (micom.community.Community property) template (micom.viz.core.Visualization attribute), [1] (micom.viz.Visualization attribute), [1] test_taxonomy() (in module micom.data), [1] to_pickle() (micom.Community method) (micom.community.Community method) tradeoff() (in module micom.workflows) (in module micom.workflows.tradeoff) U unify_rank_prefixes() (in module micom.taxonomy) UNITS (in module micom.viz.interactions) V view() (micom.viz.core.Visualization method) (micom.viz.Visualization method) Visualization (class in micom.viz) (class in micom.viz.core) W weight() (in module micom.media) workflow() (in module micom.workflows) (in module micom.workflows.core) Y yaml (in module micom.qiime_formats)