Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Y _ __add__() (micom.batch.GrowthResults method) (micom.batch.results.GrowthResults method) __add_exchanges() (micom.Community method) (micom.community.Community method) __add_model() (micom.Community method) (micom.community.Community method) __db_metrics (micom.Community attribute) (micom.community.Community attribute) __repr__() (micom.Batch method) (micom.batch.Batch method) (micom.batch.batch.Batch method) (micom.solution.CommunitySolution method) __str__() (micom.Batch method) (micom.batch.Batch method) (micom.batch.batch.Batch method) (micom.batch.Configuration method) (micom.batch.configuration.Configuration method) (micom.Configuration 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.batch.db_media) _apply_min_growth() (in module micom.util) _derivatives() (in module micom.elasticity) _fix_medium() (in module micom.batch.media) _format_min_growth() (in module micom.util) _get_fluxes() (in module micom.elasticity) _group_taxa() (in module micom.solution) _grow() (in module micom.batch.db_media) _growth() (in module micom.batch.grow) _has_manifest (in module micom.qiime_formats) _interact() (in module micom.interaction.focal) _medium (micom.Batch attribute) (micom.batch.Batch attribute) (micom.batch.batch.Batch attribute) _medium() (in module micom.batch.media) _mes() (in module micom.interaction.scores) _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.batch.build) _repr_html_() (micom.Batch method) (micom.batch.Batch method) (micom.batch.batch.Batch method) (micom.batch.Configuration method) (micom.batch.configuration.Configuration method) (micom.Configuration method) (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.batch.build) _taxonomy (micom.Batch attribute) (micom.batch.Batch attribute) (micom.batch.batch.Batch attribute) _tradeoff() (in module micom.batch.tradeoff) _try_complete() (in module micom.batch.db_media) A add_coupling() (in module micom.coupling) add_coupling_constraints() (micom.Community method) (micom.community.Community method) add_dualized_optcom() (in module micom.optcom) add_host() (micom.Community method) (micom.community.Community method) 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_resource_constraint() (in module micom.coupling) add_var_from_expression() (in module micom.util) adjust_solver_config() (in module micom.util) annotate() (in module micom.annotation) annotate_metabolites_from_exchanges() (in module micom.annotation) annotations (micom.batch.GrowthResults attribute) (micom.batch.results.GrowthResults attribute) ARGS (in module micom.batch.grow) (in module micom.constants) B basic() (in module micom.interaction) (in module micom.interaction.scores) Batch (class in micom) (class in micom.batch) (class in micom.batch.batch) build (micom.batch.Configuration attribute) (micom.batch.configuration.Configuration attribute) (micom.Configuration attribute) build() (micom.Batch method) (micom.batch.Batch method) (micom.batch.batch.Batch method) build_and_save() (in module micom.batch.build) build_database() (in module micom.batch) (in module micom.batch.build) build_from_qiime() (in module micom.taxonomy) build_manifest (micom.Batch attribute) (micom.batch.Batch attribute) (micom.batch.batch.Batch attribute) build_metrics (micom.Community property) (micom.community.Community property) BuildConfig (class in micom.batch.configuration) C check_db_medium() (in module micom.batch) (in module micom.batch.db_media) check_medium() (in module micom.types) check_modification() (in module micom.util) check_taxonomy() (in module micom.types) chr_or_input() (in module micom.util) clean_ids() (in module micom.util) combine_results() (in module micom.batch.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_db_medium() (in module micom.batch) (in module micom.batch.db_media) complete_medium() (in module micom.media) (micom.Batch method) (micom.batch.Batch method) (micom.batch.batch.Batch method) Configuration (class in micom) (class in micom.batch) (class in micom.batch.configuration) constraint (micom.batch.configuration.CouplingConfig attribute) 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) coupling (micom.batch.Configuration attribute) (micom.batch.configuration.Configuration attribute) (micom.Configuration attribute) CouplingConfig (class in micom.batch.configuration) crossover() (in module micom.solution) cutoff (micom.batch.configuration.BuildConfig attribute) D data (micom.viz.core.Visualization attribute), [1] (micom.viz.Visualization attribute), [1] db_annotations() (in module micom.batch.db_media) DB_URL (in module micom.constants) DBConfig (class in micom.batch.configuration) dbs (micom.batch.Configuration attribute) (micom.batch.configuration.Configuration attribute) (micom.Configuration attribute) DIRECTION (in module micom.batch.grow) (in module micom.batch.media) (in module micom.batch.results) (in module micom.constants) (in module micom.solution) download_location (micom.batch.configuration.DBConfig attribute) 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) enabled (micom.batch.configuration.CouplingConfig attribute) env (in module micom.viz.core) euclidean() (in module micom.algorithms) ex_metabolite() (in module micom.util) exchanges (micom.batch.GrowthResults attribute) (micom.batch.results.GrowthResults attribute) (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), [1] (micom.viz.Visualization attribute), [1] files (in module micom.names.generate) fill_missing_fluxes() (in module micom.stats) fix_demands() (in module micom.util) flatten() (in module micom.annotation) flux_method (micom.batch.configuration.SimulationConfig attribute) fluxes (micom.solution.CommunitySolution attribute) fluxes_from_primals() (in module micom.util) force_rebuild (micom.batch.configuration.BuildConfig attribute) formatter (in module micom.logger) from_json() (micom.batch.Configuration class method) (micom.batch.configuration.Configuration class method) (micom.Configuration class method) from_solution() (micom.batch.GrowthResults static method) (micom.batch.results.GrowthResults static method) from_yaml() (micom.batch.Configuration class method) (micom.batch.configuration.Configuration class method) (micom.Configuration class method) G generate_random_name() (in module micom.names) (in module micom.names.generate) get_database() (in module micom.db) good (in module micom.solution) grow() (micom.Batch method) (micom.batch.Batch method) (micom.batch.batch.Batch method) growth_rate (micom.solution.CommunitySolution attribute), [1] growth_rates (micom.batch.GrowthResults attribute) (micom.batch.results.GrowthResults attribute) GrowthResults (class in micom.batch) (class in micom.batch.results) H handler (in module micom.logger) has_results (micom.Batch property) (micom.batch.Batch property) (micom.batch.batch.Batch property) has_tradeoffs (micom.Batch property) (micom.batch.Batch property) (micom.batch.batch.Batch property) host (micom.batch.configuration.DBConfig attribute) (micom.Community attribute) (micom.community.Community attribute) host_abundances (micom.Community property) (micom.community.Community property) host_exchanges (micom.Community property) (micom.community.Community property) host_growth (micom.batch.configuration.SimulationConfig attribute) host_medium (micom.Community property) (micom.community.Community property) host_method (micom.batch.configuration.SimulationConfig attribute) host_rates (micom.solution.CommunitySolution attribute) host_relative (micom.batch.configuration.SimulationConfig attribute) I include_exchanges (micom.batch.configuration.CouplingConfig attribute) interactions() (in module micom.interaction) (in module micom.interaction.focal) internal_exchanges (micom.Community property) (micom.community.Community property) internal_reactions (micom.Community property) (micom.community.Community property) is_active_demand() (in module micom.util) is_built (micom.Batch property) (micom.batch.Batch property) (micom.batch.batch.Batch property) 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.batch.GrowthResults static method) (micom.batch.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.batch) (in module micom.batch.results) load_zip_model_db() (in module micom.db) logger (in module micom.algorithms) (in module micom.batch.batch) (in module micom.batch.build) (in module micom.batch.core) (in module micom.batch.db_media) (in module micom.batch.grow) (in module micom.batch.media) (in module micom.batch.tradeoff) (in module micom.community) (in module micom.duality) (in module micom.media) (in module micom.optcom) (in module micom.problems) (in module micom.solution) (in module micom.types) (in module micom.util) (in module micom.viz.association) (in module micom.viz.core) (in module micom.viz.exchanges) (in module micom.viz.interactions) lower (micom.batch.configuration.CouplingConfig attribute) M mass (micom.Community attribute) (micom.community.Community attribute) max_exchange (micom.Community attribute) (micom.community.Community attribute) max_import (micom.batch.configuration.MediaConfig attribute) media (micom.batch.Configuration attribute) (micom.batch.configuration.Configuration attribute) (micom.Configuration attribute) MEDIA_URL (in module micom.constants) MediaConfig (class in micom.batch.configuration) medium (micom.Batch property) (micom.batch.Batch property) (micom.batch.batch.Batch property) (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.batch module micom.batch.batch module micom.batch.build module micom.batch.configuration module micom.batch.core module micom.batch.db_media module micom.batch.grow module micom.batch.media module micom.batch.results module micom.batch.tradeoff module micom.community module micom.constants module micom.coupling 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.names module micom.names.generate module micom.optcom module micom.problems module micom.qiime_formats module micom.solution module micom.stats module micom.taxonomy module micom.types 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_console (in module micom.logger) microbial (micom.batch.configuration.DBConfig attribute) microbial_abundances (micom.Community property) (micom.community.Community property) minimal_medium() (in module micom.media) (micom.Batch method) (micom.batch.Batch method) (micom.batch.batch.Batch method) model (in module micom.duality) modification (micom.Community property) (micom.community.Community property) module micom micom.algorithms micom.annotation micom.batch micom.batch.batch micom.batch.build micom.batch.configuration micom.batch.core micom.batch.db_media micom.batch.grow micom.batch.media micom.batch.results micom.batch.tradeoff micom.community micom.constants micom.coupling 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.names micom.names.generate micom.optcom micom.problems micom.qiime_formats micom.solution micom.stats micom.taxonomy micom.types micom.util micom.viz micom.viz.association micom.viz.core micom.viz.exchanges micom.viz.growth micom.viz.interactions micom.viz.tradeoff N name (micom.Batch attribute) (micom.batch.Batch attribute) (micom.batch.batch.Batch attribute) 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_host() (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) out_folder (micom.Batch attribute) (micom.batch.Batch attribute) (micom.batch.batch.Batch attribute) P pathify() (in module micom.types) plot_association() (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) (in module micom.viz.tradeoff) prefix (in module micom.duality) process_medium() (in module micom.batch.media) production_rates() (in module micom.measures) progress (micom.batch.Configuration attribute) (micom.batch.configuration.Configuration attribute) (micom.Configuration attribute) 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.batch.build) reset_min_community_growth() (in module micom.util) reset_solver() (in module micom.solution) results (micom.Batch attribute) (micom.batch.Batch attribute) (micom.batch.batch.Batch attribute) S safe_weight() (in module micom.media) sample_interactions() (in module micom.interaction.focal) save() (micom.batch.GrowthResults method) (micom.batch.results.GrowthResults method) (micom.viz.core.Visualization method) (micom.viz.Visualization method) save_results() (in module micom.batch) (in module micom.batch.results) scale (micom.Community property) (micom.community.Community property) serialize_models() (in module micom.util) set_host_abundance() (micom.Community method) (micom.community.Community method) set_microbial_abundance() (micom.Community method) (micom.community.Community method) shadow_prices (micom.solution.CommunitySolution attribute) show_versions() (in module micom) (in module micom.deps) simulation (micom.batch.Configuration attribute) (micom.batch.configuration.Configuration attribute) (micom.Configuration attribute) SimulationConfig (class in micom.batch.configuration) solve() (in module micom.solution) solver (micom.batch.Configuration attribute) (micom.batch.configuration.Configuration attribute) (micom.Community attribute) (micom.community.Community attribute) (micom.Configuration attribute) status (micom.solution.CommunitySolution attribute) STEP (in module micom.elasticity) strategy (micom.batch.configuration.CouplingConfig attribute) (micom.batch.configuration.SimulationConfig attribute) (micom.solution.CommunitySolution attribute), [1] summarize_interactions() (in module micom.interaction) (in module micom.interaction.summary) symbols (in module micom.batch.configuration) T taxa (micom.Community attribute) (micom.community.Community attribute) taxon_id() (in module micom.taxonomy) taxonomy (micom.Batch property) (micom.batch.Batch property) (micom.batch.batch.Batch property) (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] this_dir (in module micom.names.generate) threads (micom.batch.Configuration attribute) (micom.batch.configuration.Configuration attribute) (micom.Configuration attribute) to_json() (micom.batch.Configuration method) (micom.batch.configuration.Configuration method) (micom.Configuration method) to_pickle() (micom.Community method) (micom.community.Community method) to_yaml() (micom.batch.Configuration method) (micom.batch.configuration.Configuration method) (micom.Configuration method) tolerance (micom.batch.Configuration attribute) (micom.batch.configuration.Configuration attribute) (micom.Configuration attribute) tradeoff (micom.batch.configuration.SimulationConfig attribute) tradeoff() (micom.Batch method) (micom.batch.Batch method) (micom.batch.batch.Batch method) tradeoffs (micom.Batch attribute) (micom.batch.Batch attribute) (micom.batch.batch.Batch attribute) 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) weights (micom.batch.configuration.MediaConfig attribute) workflow() (in module micom.batch) (in module micom.batch.core) Y yaml (in module micom.qiime_formats)