Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | V | W A accession_type (biggr_models.handlers.gene_handlers.GenesInGenomeListViewHandler attribute) accession_value (biggr_models.handlers.gene_handlers.GenesInGenomeListViewHandler attribute) agg_strings() (in module biggr_models.handlers.advanced_search_handlers) ALLOWED_SEARCH_ALPHABET (in module biggr_models.handlers.advanced_search_handlers) ANNOTATION_TYPES (in module biggr_models.queries.metabolite_queries) api (biggr_models.handlers.utils.DataHandler attribute) APIVersionHandler (class in biggr_models.handlers.utils) apply_search_query (biggr_models.handlers.utils.DataColumnSpec attribute) B BASE_URL (in module biggr_models.handlers.db_interop_handlers) BaseHandler (class in biggr_models.handlers.utils) BaseInteropQueryHandler (class in biggr_models.handlers.db_interop_handlers) bigg_id (biggr_models.handlers.compartment_handlers.ModelsWithCompartmentListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteInModelsListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteInReactionsListViewHandler attribute) biggr_json_object_hook() (in module biggr_models.handlers.utils) biggr_models module biggr_models.handlers module biggr_models.handlers.advanced_search_handlers module biggr_models.handlers.compartment_handlers module biggr_models.handlers.data_access_handlers module biggr_models.handlers.db_interop_handlers module biggr_models.handlers.download_handlers module biggr_models.handlers.escher_handlers module biggr_models.handlers.gene_handlers module biggr_models.handlers.genome_handlers module biggr_models.handlers.home_handlers module biggr_models.handlers.identifiers_handlers module biggr_models.handlers.metabolite_handlers module biggr_models.handlers.model_handlers module biggr_models.handlers.object_handlers module biggr_models.handlers.reaction_handlers module biggr_models.handlers.utils module biggr_models.queries module biggr_models.queries.compartment_queries module biggr_models.queries.download_queries module biggr_models.queries.escher_map_queries module biggr_models.queries.escher_queries module biggr_models.queries.gene_queries module biggr_models.queries.genome_queries module biggr_models.queries.memote_queries module biggr_models.queries.metabolite_queries module biggr_models.queries.model_queries module biggr_models.queries.object_queries module biggr_models.queries.reaction_queries module biggr_models.queries.summary_queries module biggr_models.queries.utils module biggr_models.routes module biggr_models.server module biggr_models.version module BiGGrJSONEncoder (class in biggr_models.handlers.utils) breadcrumbs() (biggr_models.handlers.compartment_handlers.CompartmentListViewHandler method) (biggr_models.handlers.compartment_handlers.ModelsWithCompartmentListViewHandler method) (biggr_models.handlers.gene_handlers.GeneListViewHandler method) (biggr_models.handlers.genome_handlers.GenomeListViewHandler method) (biggr_models.handlers.metabolite_handlers.MetaboliteListViewHandler method) (biggr_models.handlers.metabolite_handlers.UniversalMetaboliteListViewHandler method) (biggr_models.handlers.model_handlers.ModelCollectionHandler method) (biggr_models.handlers.model_handlers.ModelsListViewHandler method) (biggr_models.handlers.reaction_handlers.ReactionListViewHandler method) (biggr_models.handlers.reaction_handlers.UniversalReactionListViewHandler method) (biggr_models.handlers.utils.DataHandler method) build_model_chart() (in module biggr_models.handlers.home_handlers) build_reaction_string() (in module biggr_models.queries.utils) build_special_tab_page() (biggr_models.handlers.advanced_search_handlers.SearchResultsHandler method) builder_to_html_string() (in module biggr_models.handlers.escher_handlers) C children (biggr_models.queries.model_queries.TreeNode attribute) clean_search_query() (biggr_models.handlers.advanced_search_handlers.SearchResultsHandler method) col_bool_search() (in module biggr_models.handlers.utils) col_number_search() (in module biggr_models.handlers.utils) col_str_search() (in module biggr_models.handlers.utils) collection (biggr_models.queries.model_queries.CollectionTreeNode attribute) collection_bigg_id (biggr_models.handlers.model_handlers.ModelCollectionHandler attribute) CollectionTreeNode (class in biggr_models.queries.model_queries) column_specs (biggr_models.handlers.advanced_search_handlers.GeneSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.GenomeSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.MetaboliteAnnotationSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.MetaboliteInChIKeySearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.MetaboliteReferenceSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.ModelSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalMetaboliteSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionAnnotationSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionECSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionReferenceSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionSearchHandler attribute) (biggr_models.handlers.compartment_handlers.CompartmentListViewHandler attribute) (biggr_models.handlers.compartment_handlers.ModelsWithCompartmentListViewHandler attribute) (biggr_models.handlers.gene_handlers.GeneListViewHandler attribute) (biggr_models.handlers.gene_handlers.GenesInGenomeListViewHandler attribute) (biggr_models.handlers.genome_handlers.GenomeListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteInModelsListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteInReactionsListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.UniversalMetaboliteListViewHandler attribute) (biggr_models.handlers.model_handlers.ModelCollectionHandler attribute) (biggr_models.handlers.model_handlers.ModelsListViewHandler attribute) (biggr_models.handlers.reaction_handlers.ReactionListViewHandler attribute) (biggr_models.handlers.reaction_handlers.UniversalReactionListViewHandler attribute) (biggr_models.handlers.utils.DataHandler attribute) columns (biggr_models.handlers.utils.DataHandler attribute) COMP_ANNOTATIONS_SUBQ (in module biggr_models.queries.metabolite_queries) CompartmentHandler (class in biggr_models.handlers.compartment_handlers) CompartmentListViewHandler (class in biggr_models.handlers.compartment_handlers) convert_id_to_query_filter() (in module biggr_models.queries.utils) D data_query() (biggr_models.handlers.utils.DataHandler method) data_source (biggr_models.handlers.advanced_search_handlers.MetaboliteAnnotationSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.MetaboliteInChIKeySearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionAnnotationSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionECSearchHandler attribute) DATA_SOURCE_IDS (in module biggr_models.handlers.advanced_search_handlers) data_url (biggr_models.handlers.utils.DataHandler property) DataAccessPageHandler (class in biggr_models.handlers.data_access_handlers) database_version() (in module biggr_models.queries.utils) DataColumn (class in biggr_models.handlers.utils) DataColumnSpec (class in biggr_models.handlers.utils) DataHandler (class in biggr_models.handlers.utils) default() (biggr_models.handlers.utils.BiGGrJSONEncoder method) determine_query_signature() (in module biggr_models.handlers.object_handlers) directory (in module biggr_models.handlers.utils) do_safe_query() (in module biggr_models.handlers.utils) draw (biggr_models.handlers.utils.DataHandler attribute) E env (in module biggr_models.handlers.utils) ESCHER_CSS (in module biggr_models.handlers.escher_handlers) EscherHandler (class in biggr_models.handlers.escher_handlers) extract_reaction_participants() (in module biggr_models.queries.download_queries) extract_universal_reaction_participants() (in module biggr_models.queries.download_queries) F format_bigg_id() (in module biggr_models.handlers.utils) format_gene_reaction_rule() (in module biggr_models.handlers.utils) format_reference() (in module biggr_models.handlers.utils) G GENE_TESTS (in module biggr_models.queries.memote_queries) GeneHandler (class in biggr_models.handlers.gene_handlers) GeneListHandler (class in biggr_models.handlers.db_interop_handlers) GeneListViewHandler (class in biggr_models.handlers.gene_handlers) GeneSearchHandler (class in biggr_models.handlers.advanced_search_handlers) GenesInGenomeListViewHandler (class in biggr_models.handlers.gene_handlers) GeneStrainPairListHandler (class in biggr_models.handlers.db_interop_handlers) GenomeGeneHandler (class in biggr_models.handlers.gene_handlers) GenomeHandler (class in biggr_models.handlers.genome_handlers) GenomeListViewHandler (class in biggr_models.handlers.genome_handlers) GenomeSearchHandler (class in biggr_models.handlers.advanced_search_handlers) get() (biggr_models.handlers.advanced_search_handlers.SearchResultsHandler method) (biggr_models.handlers.compartment_handlers.CompartmentHandler method) (biggr_models.handlers.data_access_handlers.DataAccessPageHandler method) (biggr_models.handlers.db_interop_handlers.GeneListHandler method) (biggr_models.handlers.db_interop_handlers.GeneStrainPairListHandler method) (biggr_models.handlers.db_interop_handlers.StrainListHandler method) (biggr_models.handlers.download_handlers.MetabolitesDownloadHandler method) (biggr_models.handlers.download_handlers.ReactionsDownloadHandler method) (biggr_models.handlers.escher_handlers.EscherHandler method) (biggr_models.handlers.gene_handlers.GeneHandler method) (biggr_models.handlers.gene_handlers.GenomeGeneHandler method) (biggr_models.handlers.genome_handlers.GenomeHandler method) (biggr_models.handlers.home_handlers.HomeHandler method) (biggr_models.handlers.home_handlers.StatisticsHandler method) (biggr_models.handlers.metabolite_handlers.MetaboliteHandler method) (biggr_models.handlers.metabolite_handlers.UniversalMetaboliteHandler method) (biggr_models.handlers.model_handlers.ModelCollectionsTreeViewHandler method) (biggr_models.handlers.model_handlers.ModelDownloadHandler method) (biggr_models.handlers.model_handlers.ModelHandler method) (biggr_models.handlers.reaction_handlers.ReactionHandler method) (biggr_models.handlers.reaction_handlers.ReactionWithStoichHandler method) (biggr_models.handlers.reaction_handlers.UniversalReactionHandler method) (biggr_models.handlers.utils.APIVersionHandler method) (biggr_models.handlers.utils.BaseHandler method) (biggr_models.handlers.utils.DataHandler method) (biggr_models.handlers.utils.HealthHandler method) get_absolute_path() (biggr_models.handlers.utils.StaticFileHandlerWithEncoding method) get_all_gene_strain_pairs() (in module biggr_models.queries.gene_queries) get_all_genes() (in module biggr_models.queries.gene_queries) get_all_genes_with_urls() (in module biggr_models.queries.gene_queries) get_all_genomes() (in module biggr_models.queries.genome_queries) get_any_components_by_identifiers() (in module biggr_models.queries.metabolite_queries) get_application() (in module biggr_models.server) get_compartment() (in module biggr_models.queries.compartment_queries) get_compartmentalized_component_object() (in module biggr_models.queries.metabolite_queries) get_component_object() (in module biggr_models.queries.metabolite_queries) get_content_type() (biggr_models.handlers.utils.StaticFileDownloadHandler method) (biggr_models.handlers.utils.StaticFileHandlerWithEncoding method) get_data_source_id() (in module biggr_models.handlers.advanced_search_handlers) get_database_links_for_gene() (in module biggr_models.queries.gene_queries) get_escher_maps_for_metabolite() (in module biggr_models.queries.escher_map_queries) get_escher_maps_for_model() (in module biggr_models.queries.escher_map_queries) get_escher_maps_for_reaction() (in module biggr_models.queries.escher_map_queries) get_gene() (in module biggr_models.queries.gene_queries) get_gene_ids_for_gene_name() (in module biggr_models.queries.gene_queries) get_gene_list_for_model() (in module biggr_models.queries.utils) get_general_results_for_model() (in module biggr_models.queries.memote_queries) get_genes() (in module biggr_models.queries.gene_queries) get_genes_with_genome_region() (in module biggr_models.queries.gene_queries) get_genome_and_models() (in module biggr_models.queries.genome_queries) get_genome_region_for_gene_id() (in module biggr_models.queries.gene_queries) get_genomes() (in module biggr_models.queries.genome_queries) get_genomes_count() (in module biggr_models.queries.genome_queries) get_genomes_with_chromosomes() (in module biggr_models.queries.genome_queries) get_list() (in module biggr_models.queries.utils) get_memote_results_for_gene() (in module biggr_models.queries.memote_queries) get_memote_results_for_metabolite() (in module biggr_models.queries.memote_queries) get_memote_results_for_reaction() (in module biggr_models.queries.memote_queries) get_metabolite() (in module biggr_models.queries.metabolite_queries) get_metabolites() (in module biggr_models.queries.download_queries) get_metabolites_for_genome() (in module biggr_models.queries.genome_queries) get_model_and_counts() (in module biggr_models.queries.model_queries) get_model_collections_and_taxons() (in module biggr_models.queries.model_queries) get_model_comp_metabolite() (in module biggr_models.queries.metabolite_queries) get_model_compartmentalized_component_object() (in module biggr_models.queries.metabolite_queries) get_model_gene() (in module biggr_models.queries.gene_queries) get_model_genes() (in module biggr_models.queries.gene_queries) get_model_genes_count() (in module biggr_models.queries.gene_queries) get_model_genes_for_gene_ids() (in module biggr_models.queries.gene_queries) get_model_json_string() (in module biggr_models.queries.model_queries) get_model_list() (in module biggr_models.queries.model_queries) get_model_list_for_metabolite() (in module biggr_models.queries.metabolite_queries) get_model_list_for_reaction() (in module biggr_models.queries.reaction_queries) get_model_metabolites() (in module biggr_models.queries.metabolite_queries) get_model_metabolites_count() (in module biggr_models.queries.metabolite_queries) get_model_object() (in module biggr_models.queries.model_queries) get_model_reaction() (in module biggr_models.queries.reaction_queries) get_model_reactions() (in module biggr_models.queries.reaction_queries) get_model_reactions_count() (in module biggr_models.queries.reaction_queries) get_model_reactions_for_escher_map() (in module biggr_models.queries.escher_queries) get_models() (in module biggr_models.queries.model_queries) get_models_count() (in module biggr_models.queries.model_queries) get_object() (in module biggr_models.queries.object_queries) get_object_property() (in module biggr_models.queries.object_queries) get_reaction() (in module biggr_models.queries.reaction_queries) get_reaction_object() (in module biggr_models.queries.reaction_queries) get_reactions() (in module biggr_models.queries.download_queries) get_reactions_for_genome() (in module biggr_models.queries.genome_queries) get_reactions_for_model() (in module biggr_models.queries.reaction_queries) get_reference_for_reaction() (in module biggr_models.queries.reaction_queries) get_reverse_url() (in module biggr_models.handlers.utils) get_routes() (in module biggr_models.routes) get_search_list() (in module biggr_models.queries.utils) get_summary_counts() (in module biggr_models.queries.summary_queries) get_summary_history() (in module biggr_models.queries.summary_queries) get_taxons_recursively() (in module biggr_models.queries.model_queries) get_universal_component_object() (in module biggr_models.queries.metabolite_queries) get_universal_metabolites() (in module biggr_models.queries.metabolite_queries) get_universal_metabolites_count() (in module biggr_models.queries.metabolite_queries) get_universal_reaction_and_models() (in module biggr_models.queries.reaction_queries) get_universal_reactions() (in module biggr_models.queries.reaction_queries) get_universal_reactions_count() (in module biggr_models.queries.reaction_queries) get_urls_for_gene_ids() (in module biggr_models.queries.gene_queries) global_search (biggr_models.handlers.utils.DataColumnSpec attribute) H head() (biggr_models.handlers.utils.BaseHandler method) (biggr_models.handlers.utils.HealthHandler method) HealthHandler (class in biggr_models.handlers.utils) hidden_taxons (biggr_models.queries.model_queries.TaxonTreeNode attribute) HomeHandler (class in biggr_models.handlers.home_handlers) hyperlink (biggr_models.handlers.utils.DataColumnSpec attribute) I identifier (biggr_models.handlers.utils.DataColumnSpec attribute) IdentifiersHandler (class in biggr_models.handlers.identifiers_handlers) IDType (in module biggr_models.queries.utils) initialize() (biggr_models.handlers.escher_handlers.EscherHandler method) (biggr_models.handlers.utils.DataHandler method) (biggr_models.handlers.utils.TemplateHandler method) J json_for_map() (in module biggr_models.queries.escher_map_queries) L length (biggr_models.handlers.utils.DataHandler attribute) LINKOUT_PROPERTY_KEYS (in module biggr_models.queries.metabolite_queries) M METABOLITE_TESTS (in module biggr_models.queries.memote_queries) MetaboliteAnnotationSearchHandler (class in biggr_models.handlers.advanced_search_handlers) MetaboliteHandler (class in biggr_models.handlers.metabolite_handlers) MetaboliteInChIKeySearchHandler (class in biggr_models.handlers.advanced_search_handlers) MetaboliteInModelsListViewHandler (class in biggr_models.handlers.metabolite_handlers) MetaboliteInReactionsListViewHandler (class in biggr_models.handlers.metabolite_handlers) MetaboliteListViewHandler (class in biggr_models.handlers.metabolite_handlers) MetaboliteReferenceSearchHandler (class in biggr_models.handlers.advanced_search_handlers) MetabolitesDownloadHandler (class in biggr_models.handlers.download_handlers) model (biggr_models.queries.model_queries.ModelTreeNode attribute) model_bigg_id (biggr_models.handlers.gene_handlers.GeneListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteInReactionsListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteListViewHandler attribute) (biggr_models.handlers.reaction_handlers.ReactionListViewHandler attribute) ModelCollectionHandler (class in biggr_models.handlers.model_handlers) ModelCollectionsTreeViewHandler (class in biggr_models.handlers.model_handlers) ModelDownloadHandler (class in biggr_models.handlers.model_handlers) ModelHandler (class in biggr_models.handlers.model_handlers) MODELS_ALLOWED_PROPERTIES (in module biggr_models.handlers.object_handlers) MODELS_CLASS_MAP (in module biggr_models.handlers.identifiers_handlers) (in module biggr_models.handlers.object_handlers) (in module biggr_models.handlers.utils) MODELS_MAP (in module biggr_models.handlers.identifiers_handlers) (in module biggr_models.handlers.object_handlers) MODELS_PROPERTY_MAP (in module biggr_models.handlers.object_handlers) MODELS_SIGNATURE (in module biggr_models.handlers.identifiers_handlers) (in module biggr_models.handlers.object_handlers) ModelSearchHandler (class in biggr_models.handlers.advanced_search_handlers) ModelsListViewHandler (class in biggr_models.handlers.model_handlers) ModelsWithCompartmentListViewHandler (class in biggr_models.handlers.compartment_handlers) ModelTreeNode (class in biggr_models.queries.model_queries) module biggr_models biggr_models.handlers biggr_models.handlers.advanced_search_handlers biggr_models.handlers.compartment_handlers biggr_models.handlers.data_access_handlers biggr_models.handlers.db_interop_handlers biggr_models.handlers.download_handlers biggr_models.handlers.escher_handlers biggr_models.handlers.gene_handlers biggr_models.handlers.genome_handlers biggr_models.handlers.home_handlers biggr_models.handlers.identifiers_handlers biggr_models.handlers.metabolite_handlers biggr_models.handlers.model_handlers biggr_models.handlers.object_handlers biggr_models.handlers.reaction_handlers biggr_models.handlers.utils biggr_models.queries biggr_models.queries.compartment_queries biggr_models.queries.download_queries biggr_models.queries.escher_map_queries biggr_models.queries.escher_queries biggr_models.queries.gene_queries biggr_models.queries.genome_queries biggr_models.queries.memote_queries biggr_models.queries.metabolite_queries biggr_models.queries.model_queries biggr_models.queries.object_queries biggr_models.queries.reaction_queries biggr_models.queries.summary_queries biggr_models.queries.utils biggr_models.routes biggr_models.server biggr_models.version N name (biggr_models.handlers.escher_handlers.EscherHandler attribute) (biggr_models.handlers.utils.DataColumnSpec attribute) (biggr_models.handlers.utils.DataHandler attribute) (biggr_models.queries.model_queries.TreeNode attribute) node_type (biggr_models.queries.model_queries.TreeNode property) NON_LINK_SOURCES (in module biggr_models.queries.gene_queries) NotFoundError O OBJECT_DEFAULT_LOAD (in module biggr_models.queries.object_queries) object_property_variant() (in module biggr_models.handlers.object_handlers) object_type_variant() (in module biggr_models.handlers.object_handlers) ObjectHandler (class in biggr_models.handlers.object_handlers) OptStr (in module biggr_models.queries.utils) order_asc (biggr_models.handlers.utils.DataColumn attribute) order_priority (biggr_models.handlers.utils.DataColumn attribute) orderable (biggr_models.handlers.utils.DataColumn attribute) P page_data (biggr_models.handlers.compartment_handlers.ModelsWithCompartmentListViewHandler attribute) (biggr_models.handlers.gene_handlers.GeneListViewHandler attribute) (biggr_models.handlers.gene_handlers.GenesInGenomeListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteInModelsListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteInReactionsListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.UniversalMetaboliteListViewHandler attribute) (biggr_models.handlers.model_handlers.ModelCollectionHandler attribute) (biggr_models.handlers.model_handlers.ModelsListViewHandler attribute) (biggr_models.handlers.reaction_handlers.UniversalReactionListViewHandler attribute) (biggr_models.handlers.utils.DataHandler attribute) parse_id_type() (in module biggr_models.handlers.object_handlers) parse_inchi_key() (biggr_models.handlers.advanced_search_handlers.MetaboliteInChIKeySearchHandler method) parse_optstr() (in module biggr_models.handlers.object_handlers) parse_strlist() (in module biggr_models.handlers.object_handlers) post() (biggr_models.handlers.db_interop_handlers.QueryByGeneHandler method) (biggr_models.handlers.db_interop_handlers.QueryByPairHandler method) (biggr_models.handlers.db_interop_handlers.QueryByStrainHandler method) (biggr_models.handlers.identifiers_handlers.IdentifiersHandler method) (biggr_models.handlers.object_handlers.ObjectHandler method) (biggr_models.handlers.utils.DataHandler method) post_filter() (biggr_models.handlers.advanced_search_handlers.GeneSearchHandler method) (biggr_models.handlers.advanced_search_handlers.GenomeSearchHandler method) (biggr_models.handlers.advanced_search_handlers.MetaboliteAnnotationSearchHandler method) (biggr_models.handlers.advanced_search_handlers.MetaboliteInChIKeySearchHandler method) (biggr_models.handlers.advanced_search_handlers.MetaboliteReferenceSearchHandler method) (biggr_models.handlers.advanced_search_handlers.ModelSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalMetaboliteSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionAnnotationSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionECSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionReferenceSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionSearchHandler method) (biggr_models.handlers.model_handlers.ModelsListViewHandler method) (biggr_models.handlers.utils.DataHandler method) pre_filter() (biggr_models.handlers.advanced_search_handlers.MetaboliteAnnotationSearchHandler method) (biggr_models.handlers.advanced_search_handlers.MetaboliteInChIKeySearchHandler method) (biggr_models.handlers.advanced_search_handlers.MetaboliteReferenceSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalMetaboliteSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionAnnotationSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionECSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionReferenceSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionSearchHandler method) (biggr_models.handlers.compartment_handlers.ModelsWithCompartmentListViewHandler method) (biggr_models.handlers.gene_handlers.GeneListViewHandler method) (biggr_models.handlers.gene_handlers.GenesInGenomeListViewHandler method) (biggr_models.handlers.metabolite_handlers.MetaboliteInModelsListViewHandler method) (biggr_models.handlers.metabolite_handlers.MetaboliteInReactionsListViewHandler method) (biggr_models.handlers.metabolite_handlers.MetaboliteListViewHandler method) (biggr_models.handlers.metabolite_handlers.UniversalMetaboliteListViewHandler method) (biggr_models.handlers.model_handlers.ModelCollectionHandler method) (biggr_models.handlers.reaction_handlers.ReactionListViewHandler method) (biggr_models.handlers.reaction_handlers.UniversalReactionListViewHandler method) (biggr_models.handlers.utils.DataHandler method) prepare() (biggr_models.handlers.escher_handlers.EscherHandler method) (biggr_models.handlers.utils.DataHandler method) priority (biggr_models.handlers.utils.DataColumnSpec attribute) process_annotation_for_template() (in module biggr_models.queries.metabolite_queries) process_string_array() (in module biggr_models.handlers.advanced_search_handlers) prop (biggr_models.handlers.utils.DataColumnSpec attribute) Q QueryByGeneHandler (class in biggr_models.handlers.db_interop_handlers) QueryByPairHandler (class in biggr_models.handlers.db_interop_handlers) QueryByStrainHandler (class in biggr_models.handlers.db_interop_handlers) R rank_id (biggr_models.queries.model_queries.TaxonTreeNode attribute) REACTION_ANNOTATIONS_SUBQ (in module biggr_models.queries.reaction_queries) REACTION_TESTS (in module biggr_models.queries.memote_queries) ReactionHandler (class in biggr_models.handlers.reaction_handlers) ReactionListViewHandler (class in biggr_models.handlers.reaction_handlers) ReactionsDownloadHandler (class in biggr_models.handlers.download_handlers) ReactionWithStoichHandler (class in biggr_models.handlers.reaction_handlers) recursive_collapse() (biggr_models.queries.model_queries.CollectionTreeNode method) (biggr_models.queries.model_queries.TaxonTreeNode method) (biggr_models.queries.model_queries.TreeNode method) RedirectError REF_ANNOTATIONS_SUBQ (in module biggr_models.queries.metabolite_queries) (in module biggr_models.queries.reaction_queries) REFERENCE_COMPOUND_TYPES (in module biggr_models.queries.metabolite_queries) REGEX_COL_NUMBER_1 (in module biggr_models.handlers.utils) REGEX_COL_NUMBER_2 (in module biggr_models.handlers.utils) REQUEST_PARAMETER_TYPES (in module biggr_models.handlers.object_handlers) requires (biggr_models.handlers.utils.DataColumnSpec attribute) return_data() (biggr_models.handlers.advanced_search_handlers.GeneSearchHandler method) (biggr_models.handlers.advanced_search_handlers.GenomeSearchHandler method) (biggr_models.handlers.advanced_search_handlers.MetaboliteAnnotationSearchHandler method) (biggr_models.handlers.advanced_search_handlers.MetaboliteInChIKeySearchHandler method) (biggr_models.handlers.advanced_search_handlers.MetaboliteReferenceSearchHandler method) (biggr_models.handlers.advanced_search_handlers.ModelSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalMetaboliteSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionAnnotationSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionECSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionReferenceSearchHandler method) (biggr_models.handlers.advanced_search_handlers.UniversalReactionSearchHandler method) (biggr_models.handlers.utils.DataHandler method) return_page() (biggr_models.handlers.utils.DataHandler method) return_result() (biggr_models.handlers.utils.BaseHandler method) root_directory (in module biggr_models.queries.utils) run() (in module biggr_models.server) run_server() (in module biggr_models.server) S S_API (in module biggr_models.handlers.advanced_search_handlers) safe_query() (in module biggr_models.handlers.utils) score_modes (biggr_models.handlers.utils.DataColumnSpec attribute) search() (biggr_models.handlers.utils.DataColumn method) search_query (biggr_models.handlers.advanced_search_handlers.GeneSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.GenomeSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.MetaboliteAnnotationSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.MetaboliteInChIKeySearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.MetaboliteReferenceSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.ModelSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalMetaboliteSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionAnnotationSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionECSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionReferenceSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionSearchHandler attribute) search_query_remove_namespace (biggr_models.handlers.utils.DataColumnSpec attribute) search_regex (biggr_models.handlers.utils.DataColumn attribute) (biggr_models.handlers.utils.DataHandler attribute) search_type (biggr_models.handlers.utils.DataColumnSpec attribute) search_value (biggr_models.handlers.utils.DataColumn attribute) (biggr_models.handlers.utils.DataHandler attribute) searchable (biggr_models.handlers.utils.DataColumn attribute) SearchResultsHandler (class in biggr_models.handlers.advanced_search_handlers) set_default_headers() (biggr_models.handlers.utils.BaseHandler method) (biggr_models.handlers.utils.HealthHandler method) set_extra_headers() (biggr_models.handlers.utils.StaticFileDownloadHandler method) spec (biggr_models.handlers.utils.DataColumn attribute) start (biggr_models.handlers.utils.DataHandler attribute) start_debug_server() (in module biggr_models.server) start_production_server() (in module biggr_models.server) static_model_dir (in module biggr_models.handlers.utils) StaticFileDownloadHandler (class in biggr_models.handlers.utils) StaticFileHandlerWithEncoding (class in biggr_models.handlers.utils) StatisticsHandler (class in biggr_models.handlers.home_handlers) StrainListHandler (class in biggr_models.handlers.db_interop_handlers) StrList (in module biggr_models.queries.utils) SUMMARY_ENTITY_TYPES (in module biggr_models.queries.summary_queries) T tax_id (biggr_models.queries.model_queries.TaxonTreeNode attribute) TaxonTreeNode (class in biggr_models.queries.model_queries) template (biggr_models.handlers.advanced_search_handlers.SearchResultsHandler attribute) (biggr_models.handlers.compartment_handlers.CompartmentHandler attribute) (biggr_models.handlers.data_access_handlers.DataAccessPageHandler attribute) (biggr_models.handlers.gene_handlers.GeneHandler attribute) (biggr_models.handlers.gene_handlers.GenomeGeneHandler attribute) (biggr_models.handlers.genome_handlers.GenomeHandler attribute) (biggr_models.handlers.home_handlers.HomeHandler attribute) (biggr_models.handlers.home_handlers.StatisticsHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteHandler attribute) (biggr_models.handlers.metabolite_handlers.UniversalMetaboliteHandler attribute) (biggr_models.handlers.model_handlers.ModelCollectionsTreeViewHandler attribute) (biggr_models.handlers.model_handlers.ModelHandler attribute) (biggr_models.handlers.reaction_handlers.ReactionHandler attribute) (biggr_models.handlers.reaction_handlers.UniversalReactionHandler attribute) (biggr_models.handlers.utils.DataHandler attribute) TemplateHandler (class in biggr_models.handlers.utils) title (biggr_models.handlers.advanced_search_handlers.GeneSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.GenomeSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.MetaboliteAnnotationSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.MetaboliteInChIKeySearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.MetaboliteReferenceSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.ModelSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalMetaboliteSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionAnnotationSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionECSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionReferenceSearchHandler attribute) (biggr_models.handlers.advanced_search_handlers.UniversalReactionSearchHandler attribute) (biggr_models.handlers.compartment_handlers.CompartmentListViewHandler attribute) (biggr_models.handlers.compartment_handlers.ModelsWithCompartmentListViewHandler attribute) (biggr_models.handlers.gene_handlers.GeneListViewHandler attribute) (biggr_models.handlers.gene_handlers.GenesInGenomeListViewHandler attribute) (biggr_models.handlers.genome_handlers.GenomeListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteInModelsListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteInReactionsListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.MetaboliteListViewHandler attribute) (biggr_models.handlers.metabolite_handlers.UniversalMetaboliteListViewHandler attribute) (biggr_models.handlers.model_handlers.ModelCollectionHandler attribute) (biggr_models.handlers.model_handlers.ModelsListViewHandler attribute) (biggr_models.handlers.reaction_handlers.ReactionListViewHandler attribute) (biggr_models.handlers.reaction_handlers.UniversalReactionListViewHandler attribute) (biggr_models.handlers.utils.DataHandler attribute) TreeNode (class in biggr_models.queries.model_queries) U UniversalMetaboliteHandler (class in biggr_models.handlers.metabolite_handlers) UniversalMetaboliteListViewHandler (class in biggr_models.handlers.metabolite_handlers) UniversalMetaboliteSearchHandler (class in biggr_models.handlers.advanced_search_handlers) UniversalReactionAnnotationSearchHandler (class in biggr_models.handlers.advanced_search_handlers) UniversalReactionECSearchHandler (class in biggr_models.handlers.advanced_search_handlers) UniversalReactionHandler (class in biggr_models.handlers.reaction_handlers) UniversalReactionListViewHandler (class in biggr_models.handlers.reaction_handlers) UniversalReactionReferenceSearchHandler (class in biggr_models.handlers.advanced_search_handlers) UniversalReactionSearchHandler (class in biggr_models.handlers.advanced_search_handlers) url() (in module biggr_models.routes) V visible (biggr_models.handlers.utils.DataColumnSpec attribute) W write() (biggr_models.handlers.utils.BaseHandler method) write_data() (biggr_models.handlers.utils.DataHandler method) write_error() (biggr_models.handlers.db_interop_handlers.BaseInteropQueryHandler method) write_map() (biggr_models.handlers.escher_handlers.EscherHandler method)