Index _ | A | B | C | D | E | F | G | I | J | K | L | M | O | P | Q | R | S | T | V | W | Y _ __add_exchanges() (micom.Community method) (micom.community.Community method) __repr__() (micom.solution.CommunitySolution method) __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) _medium() (in module micom.workflows.media) _methods (in module micom.optcom) _ranks (in module micom.community) _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) _run_corr() (in module micom.stats) _run_test() (in module micom.stats) _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) 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) 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_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) (micom.viz.Visualization attribute) db_annotations() (in module micom.workflows.db_media) DIRECTION (in module micom.workflows.grow) 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) exchanges (micom.Community property) (micom.community.Community property) F fast_dual() (in module micom.duality) fdr_adjust() (in module micom.stats) filename (micom.viz.core.Visualization attribute) (micom.viz.Visualization attribute) fix_demands() (in module micom.util) fix_medium() (in module micom.workflows) (in module micom.workflows.media) flatten() (in module micom.annotation) fluxes (micom.solution.CommunitySolution attribute) fluxes_from_primals() (in module micom.util) FORMAT (in module micom.logger) G good (in module micom.solution) grow() (in module micom.workflows) (in module micom.workflows.grow) growth_rate (micom.solution.CommunitySolution attribute) GrowthResults (in module micom.workflows) (in module micom.workflows.core) I 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_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.core) load_zip_model_db() (in module micom.db) logger (in module micom.logger) M medium (micom.Community property) (micom.community.Community property) members (micom.solution.CommunitySolution attribute) metabolic_dist() (in module micom.algorithms) metadata() (in module micom.qiime_formats) micom module micom.algorithms module micom.annotation module micom.community module micom.data module, [1] micom.db module micom.deps module micom.duality module micom.elasticity 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.core module micom.viz.exchanges module micom.viz.growth module micom.viz.prediction 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.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.data, [1] micom.db micom.deps micom.duality micom.elasticity 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.core micom.viz.exchanges micom.viz.growth micom.viz.prediction micom.viz.tradeoff micom.workflows micom.workflows.build micom.workflows.core micom.workflows.db_media micom.workflows.grow micom.workflows.media micom.workflows.tradeoff O 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_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_fit() (in module micom.viz) (in module micom.viz.prediction) plot_growth() (in module micom.viz) (in module micom.viz.growth) 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 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) save() (micom.viz.core.Visualization method) (micom.viz.Visualization method) save_results() (in module micom.workflows) (in module micom.workflows.core) 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) status (micom.solution.CommunitySolution attribute) STEP (in module micom.elasticity) strategy (micom.solution.CommunitySolution attribute) T taxonomy (micom.Community property) (micom.community.Community property) template (micom.viz.core.Visualization attribute) (micom.viz.Visualization attribute) 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) 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)