Index

_

__add__() (refinegems.classes.medium.Medium method) (refinegems.classes.reports.MultiModelInfoReport method) __firstlineno__ (refinegems.classes.egcs.EGCSolver attribute) (refinegems.classes.egcs.GreedyEGCSolver attribute) (refinegems.classes.gapfill.BioCycGapFiller attribute) (refinegems.classes.gapfill.GapFiller attribute) (refinegems.classes.gapfill.GeneGapFiller attribute) (refinegems.classes.gapfill.KEGGapFiller attribute) (refinegems.classes.medium.Medium attribute) (refinegems.classes.reports.AuxotrophySimulationReport attribute) (refinegems.classes.reports.CorePanAnalysisReport attribute) (refinegems.classes.reports.GapFillerReport attribute) (refinegems.classes.reports.GrowthSimulationReport attribute) (refinegems.classes.reports.KEGGPathwayAnalysisReport attribute) (refinegems.classes.reports.ModelInfoReport attribute) (refinegems.classes.reports.MultiModelInfoReport attribute) (refinegems.classes.reports.MultiSBOTermReport attribute) (refinegems.classes.reports.Report attribute) (refinegems.classes.reports.SBOTermReport attribute) (refinegems.classes.reports.SingleGrowthSimulationReport attribute) (refinegems.classes.reports.SourceTestReport attribute) __init__() (refinegems.classes.egcs.EGCSolver method) (refinegems.classes.egcs.GreedyEGCSolver method) (refinegems.classes.gapfill.BioCycGapFiller method) (refinegems.classes.gapfill.GapFiller method) (refinegems.classes.gapfill.GeneGapFiller method) (refinegems.classes.gapfill.KEGGapFiller method) (refinegems.classes.medium.Medium method) (refinegems.classes.reports.AuxotrophySimulationReport method) (refinegems.classes.reports.CorePanAnalysisReport method) (refinegems.classes.reports.GapFillerReport method) (refinegems.classes.reports.GrowthSimulationReport method) (refinegems.classes.reports.KEGGPathwayAnalysisReport method) (refinegems.classes.reports.ModelInfoReport method) (refinegems.classes.reports.MultiModelInfoReport method) (refinegems.classes.reports.MultiSBOTermReport method) (refinegems.classes.reports.SBOTermReport method) (refinegems.classes.reports.SingleGrowthSimulationReport method) (refinegems.classes.reports.SourceTestReport method)

__static_attributes__ (refinegems.classes.egcs.EGCSolver attribute) (refinegems.classes.egcs.GreedyEGCSolver attribute) (refinegems.classes.gapfill.BioCycGapFiller attribute) (refinegems.classes.gapfill.GapFiller attribute) (refinegems.classes.gapfill.GeneGapFiller attribute) (refinegems.classes.gapfill.KEGGapFiller attribute) (refinegems.classes.medium.Medium attribute) (refinegems.classes.reports.AuxotrophySimulationReport attribute) (refinegems.classes.reports.CorePanAnalysisReport attribute) (refinegems.classes.reports.GapFillerReport attribute) (refinegems.classes.reports.GrowthSimulationReport attribute) (refinegems.classes.reports.KEGGPathwayAnalysisReport attribute) (refinegems.classes.reports.ModelInfoReport attribute) (refinegems.classes.reports.MultiModelInfoReport attribute) (refinegems.classes.reports.MultiSBOTermReport attribute) (refinegems.classes.reports.Report attribute) (refinegems.classes.reports.SBOTermReport attribute) (refinegems.classes.reports.SingleGrowthSimulationReport attribute) (refinegems.classes.reports.SourceTestReport attribute) __str__() (refinegems.classes.reports.GrowthSimulationReport method) (refinegems.classes.reports.SingleGrowthSimulationReport method) _add_annotations_from_bigg_reac_row() (in module refinegems.utility.db_access) _add_annotations_from_dict_cobra() (in module refinegems.utility.cvterms) _find_reac_in_model() (refinegems.classes.gapfill.GapFiller method) _search_ncbi_for_gp() (in module refinegems.utility.db_access)

A

add_annotations_from_BiGG_metabs() (in module refinegems.utility.db_access) add_compartment_structure_specs() (in module refinegems.curation.curate) add_cv_term_genes() (in module refinegems.utility.cvterms) add_cv_term_metabolites() (in module refinegems.utility.cvterms) add_cv_term_pathways() (in module refinegems.utility.cvterms) add_cv_term_pathways_to_entity() (in module refinegems.utility.cvterms) add_cv_term_reactions() (in module refinegems.utility.cvterms) add_cv_term_units() (in module refinegems.utility.cvterms) add_DISSIPATIONRXNS() (refinegems.classes.egcs.EGCSolver method) add_gene_reac_associations_from_table() (refinegems.classes.gapfill.GapFiller method) add_genes_from_table() (refinegems.classes.gapfill.GapFiller method) add_info_from_ChEBI_BiGG() (in module refinegems.utility.db_access) add_kegg_pathways() (in module refinegems.curation.pathways) add_reactions_from_table() (refinegems.classes.gapfill.GapFiller method)

add_report() (refinegems.classes.reports.MultiSBOTermReport method) add_sim_results() (refinegems.classes.reports.GrowthSimulationReport method) add_single_report() (refinegems.classes.reports.MultiModelInfoReport method) add_subset() (refinegems.classes.medium.Medium method) add_subset_to_db() (in module refinegems.classes.medium) add_substance_from_db() (refinegems.classes.medium.Medium method) adjust_BOF() (in module refinegems.utility.connections) ALL_BIGG_COMPARTMENTS_ONE_LETTER (in module refinegems.utility.db_access) ALL_BIGG_COMPARTMENTS_TWO_LETTER (in module refinegems.utility.db_access) ALLOWED_DATABASE_LINKS (in module refinegems.classes.medium) analyse() (in module refinegems.cmd_access) annot() (in module refinegems.cmd_access) apply_modifications() (refinegems.classes.egcs.GreedyEGCSolver method) are_compartment_names_valid() (in module refinegems.utility.entities) AuxotrophySimulationReport (class in refinegems.classes.reports)

B

BIGG (refinegems.utility.databases.ValidationCodes attribute) BIGG_MEDIA (refinegems.utility.databases.ValidationCodes attribute) BIGG_METABOLITES_URL (in module refinegems.utility.db_access) BIGG_MSEED_COMPOUNDS (refinegems.utility.databases.ValidationCodes attribute) biocyc_rxn_tbl (refinegems.classes.gapfill.BioCycGapFiller property) BIOCYC_TIER1_DATABASES_PREFIXES (in module refinegems.utility.db_access) BioCycGapFiller (class in refinegems.classes.gapfill) build_metabolite_bigg() (in module refinegems.utility.entities)

build_metabolite_kegg() (in module refinegems.utility.entities) build_metabolite_mnx() (in module refinegems.utility.entities) build_metabolite_xxx() (in module refinegems.utility.entities) build_reaction() (in module refinegems.utility.entities) build_reaction_bigg() (in module refinegems.utility.entities) build_reaction_kegg() (in module refinegems.utility.entities) build_reaction_mnx() (in module refinegems.utility.entities) build_reaction_xxx() (in module refinegems.utility.entities)

C

check_direction() (in module refinegems.curation.curate) check_egc_growth() (refinegems.classes.egcs.GreedyEGCSolver method) check_metab_integration() (refinegems.classes.egcs.EGCSolver method) check_normalise_biomass() (in module refinegems.curation.biomass) cobra_gapfill_wrapper() (in module refinegems.classes.gapfill) collect_reacs_from_model() (in module refinegems.analysis.core_pan) combine() (refinegems.classes.medium.Medium method) COMP_MAPPING (in module refinegems.utility.util) compare_gene_lists() (in module refinegems.utility.entities) compare_model_modelseed() (in module refinegems.utility.db_access) compare_to_core_pan() (in module refinegems.analysis.core_pan) compare_to_modelseed() (in module refinegems.utility.db_access) COMPLETE (refinegems.utility.databases.ValidationCodes attribute) CorePanAnalysisReport (class in refinegems.classes.reports)

correct_charges_from_db() (in module refinegems.curation.charges) correct_charges_modelseed() (in module refinegems.curation.charges) create_fba_units() (in module refinegems.utility.entities) create_gp() (in module refinegems.utility.entities) create_gpr() (in module refinegems.utility.entities) create_media_database() (in module refinegems.utility.databases) create_missing_genes_protein_fasta() (in module refinegems.utility.io) create_pathway_groups() (in module refinegems.curation.pathways) create_random_id() (in module refinegems.utility.entities) create_reaction() (in module refinegems.utility.entities) create_species() (in module refinegems.utility.entities) create_unit() (in module refinegems.utility.entities) create_unit_definition() (in module refinegems.utility.entities) curate() (in module refinegems.cmd_access)

D

database() (in module refinegems.cmd_access) DB2PREFIX_GENES (in module refinegems.utility.cvterms) DB2PREFIX_METABS (in module refinegems.utility.cvterms) DB2PREFIX_PATHWAYS (in module refinegems.utility.cvterms) DB2PREFIX_REACS (in module refinegems.utility.cvterms)

DB2REGEX (in module refinegems.utility.util) debug() (in module refinegems.developement.decorators) deprecate() (in module refinegems.developement.decorators) DISSIPATION_RXNS (in module refinegems.classes.egcs) download_config() (in module refinegems.utility.set_up) download_url() (in module refinegems.utility.set_up)

E

EGC_SCORING_MATRIX (in module refinegems.classes.egcs) egcs_removed() (refinegems.classes.egcs.EGCSolver method) EGCSolver (class in refinegems.classes.egcs) EMPTY (refinegems.utility.databases.ValidationCodes attribute) enter_db_single_entry() (in module refinegems.classes.medium) enter_m2s_row() (in module refinegems.classes.medium) enter_medium_into_db() (in module refinegems.classes.medium) enter_s2db_row() (in module refinegems.classes.medium)

enter_substance_row() (in module refinegems.classes.medium) export_to_cobra() (refinegems.classes.medium.Medium method) export_to_file() (refinegems.classes.medium.Medium method) extend_gp_annots_via_KEGG() (in module refinegems.curation.curate) extend_gp_annots_via_mapping_table() (in module refinegems.curation.curate) extend_metab_reac_annots_via_id() (in module refinegems.curation.curate) extend_metab_reac_annots_via_notes() (in module refinegems.curation.curate) extract_medium_info_from_model_bigg() (in module refinegems.classes.medium) extract_reactions_ids() (in module refinegems.analysis.core_pan)

F

fill_model() (refinegems.classes.gapfill.GapFiller method) filter_DIAMOND_blastp_results() (in module refinegems.utility.connections) find_additives_to_enable_growth() (in module refinegems.analysis.growth) find_core_reaction_ids() (in module refinegems.analysis.core_pan) find_egcs() (refinegems.classes.egcs.EGCSolver method) find_growth_enhancing_exchanges() (in module refinegems.analysis.growth) find_growth_essential_exchanges() (in module refinegems.analysis.growth) find_kegg_pathways() (in module refinegems.curation.pathways) find_missing_genes() (refinegems.classes.gapfill.BioCycGapFiller method) (refinegems.classes.gapfill.GapFiller method) (refinegems.classes.gapfill.GeneGapFiller method) (refinegems.classes.gapfill.KEGGapFiller method)

find_missing_reactions() (refinegems.classes.gapfill.BioCycGapFiller method) (refinegems.classes.gapfill.GapFiller method) (refinegems.classes.gapfill.GeneGapFiller method) (refinegems.classes.gapfill.KEGGapFiller method) find_mods_resolve_egcs_greedy() (refinegems.classes.egcs.GreedyEGCSolver method) find_pan_reactions() (in module refinegems.analysis.core_pan) find_solution_greedy() (refinegems.classes.egcs.GreedyEGCSolver method) FLOAT_REGEX (in module refinegems.classes.medium) format_table() (refinegems.classes.reports.ModelInfoReport method) full_gene_list (refinegems.classes.gapfill.BioCycGapFiller property)

G

GapFiller (class in refinegems.classes.gapfill) GapFillerReport (class in refinegems.classes.reports) GeneGapFiller (class in refinegems.classes.gapfill) generate_core_pan_model() (in module refinegems.analysis.core_pan) generate_cvterm() (in module refinegems.utility.cvterms) generate_docs_for_subset() (in module refinegems.classes.medium) generate_insert_query() (in module refinegems.classes.medium) generate_update_query() (in module refinegems.classes.medium) get_BiGG_metabs_annot_via_dbid() (in module refinegems.utility.db_access) get_charge_mismatch() (in module refinegems.utility.db_access) get_compared_formulae() (in module refinegems.utility.db_access) get_ec_from_ncbi() (in module refinegems.utility.db_access) get_ec_via_swissprot() (in module refinegems.utility.db_access) get_essential_exchanges_via_bounds() (in module refinegems.analysis.growth) get_essential_reactions_via_single_knockout() (in module refinegems.analysis.growth) get_formula_mismatch() (in module refinegems.utility.db_access) get_gpid_mapping() (in module refinegems.utility.entities) get_id_from_cv_term() (in module refinegems.utility.cvterms) get_kegg_genes() (in module refinegems.utility.db_access) get_last_idx_table() (in module refinegems.classes.medium) get_latest_bigg_databases() (in module refinegems.utility.databases) get_mass_charge_unbalanced() (in module refinegems.analysis.investigate) get_memote_score() (in module refinegems.utility.connections)

get_metabs_essential_for_growth_wrapper() (in module refinegems.analysis.growth) get_metabs_with_one_cvterm() (in module refinegems.analysis.investigate) get_model_charges() (in module refinegems.utility.db_access) get_model_reacs_or_metabs() (in module refinegems.utility.entities) get_modelseed_charges() (in module refinegems.utility.db_access) get_modelseed_compounds() (in module refinegems.utility.db_access) get_modelseed_compounds_database() (in module refinegems.utility.databases) get_orphans_deadends_disconnected() (in module refinegems.analysis.investigate) get_production() (in module refinegems.analysis.growth) get_reac_counts() (refinegems.classes.reports.CorePanAnalysisReport method) get_reac_with_gpr() (in module refinegems.analysis.investigate) get_reaction_annotation_dict() (in module refinegems.utility.entities) get_reactions_per_sbo() (in module refinegems.analysis.investigate) get_reversible() (in module refinegems.utility.entities) get_secretion() (in module refinegems.analysis.growth) get_source() (refinegems.classes.medium.Medium method) get_uptake() (in module refinegems.analysis.growth) GFF_COLS (refinegems.classes.gapfill.GeneGapFiller attribute) GreedyEGCSolver (class in refinegems.classes.egcs) growth() (in module refinegems.cmd_access) growth_analysis() (in module refinegems.analysis.growth) growth_sim_multi() (in module refinegems.analysis.growth) growth_sim_single() (in module refinegems.analysis.growth) GrowthSimulationReport (class in refinegems.classes.reports)

I

implement() (in module refinegems.developement.decorators) initialise() (in module refinegems.cmd_access) initialise_database() (in module refinegems.utility.databases) INTEGER_REGEX (in module refinegems.classes.medium)

is_aerobic() (refinegems.classes.medium.Medium method) is_stoichiometric_factor() (in module refinegems.utility.util) is_valid_database() (in module refinegems.utility.databases) isreaction_complete() (in module refinegems.utility.entities) isValid() (refinegems.classes.reports.CorePanAnalysisReport method)

K

KEGG_GLOBAL_PATHWAY (in module refinegems.classes.reports) KEGG_METABOLISM_PATHWAY (in module refinegems.classes.reports) KEGG_METABOLISM_PATHWAY_DATE (in module refinegems.classes.reports) KEGG_OVERVIEW_PATHWAY (in module refinegems.classes.reports)

kegg_pathway_analysis() (in module refinegems.curation.pathways) kegg_reaction_parser() (in module refinegems.utility.db_access) KEGGapFiller (class in refinegems.classes.gapfill) KEGGPathwayAnalysisReport (class in refinegems.classes.reports)

L

limit_bounds() (refinegems.classes.egcs.EGCSolver method) load_a_table_from_database() (in module refinegems.utility.io) load_document_libsbml() (in module refinegems.utility.io) load_external_medium() (in module refinegems.classes.medium) load_media() (in module refinegems.classes.medium)

load_medium_from_db() (in module refinegems.classes.medium) load_model() (in module refinegems.utility.io) load_model_enable_groups() (in module refinegems.curation.pathways) load_subset_from_db() (in module refinegems.utility.io) load_substance_table_from_db() (in module refinegems.utility.io)

M

make_aerobic() (refinegems.classes.medium.Medium method) make_anaerobic() (refinegems.classes.medium.Medium method) make_html() (refinegems.classes.reports.ModelInfoReport method) map_biocyc_to_reac() (in module refinegems.classes.gapfill) map_dmnd_res_to_sp_ec_brenda() (in module refinegems.utility.db_access) map_ec_to_reac() (in module refinegems.classes.gapfill) map_to_homologs() (in module refinegems.utility.db_access) match_id_to_namespace() (in module refinegems.utility.entities) MEDIA (refinegems.utility.databases.ValidationCodes attribute) media() (in module refinegems.cmd_access) MEDIA_MSEED_COMPOUNDS (refinegems.utility.databases.ValidationCodes attribute) Medium (class in refinegems.classes.medium) medium_to_model() (in module refinegems.classes.medium) MIN_GROWTH_THRESHOLD (in module refinegems.utility.util) MIRIAM (in module refinegems.utility.cvterms) model_minimal_medium() (in module refinegems.analysis.growth) ModelInfoReport (class in refinegems.classes.reports) MODELSEED_COMPOUNDS (refinegems.utility.databases.ValidationCodes attribute) module refinegems.analysis.comparison refinegems.analysis.core_pan refinegems.analysis.growth refinegems.analysis.investigate refinegems.classes.egcs refinegems.classes.gapfill refinegems.classes.medium refinegems.classes.reports refinegems.cmd_access refinegems.curation.biomass refinegems.curation.charges refinegems.curation.curate refinegems.curation.pathways refinegems.developement.decorators refinegems.utility.connections refinegems.utility.cvterms refinegems.utility.databases refinegems.utility.db_access refinegems.utility.entities refinegems.utility.io refinegems.utility.set_up refinegems.utility.util

MultiModelInfoReport (class in refinegems.classes.reports) multiple_cobra_gapfill() (in module refinegems.classes.gapfill) MultiSBOTermReport (class in refinegems.classes.reports)

N

NH_PATTERN (in module refinegems.curation.curate)

O

OLD_MIRIAM (in module refinegems.utility.cvterms)

P

parse_dict_to_dataframe() (in module refinegems.utility.io) parse_gbff_for_cds() (in module refinegems.utility.io) parse_gff_for_cds() (in module refinegems.utility.io) parse_KEGG_ec() (in module refinegems.utility.db_access) parse_KEGG_gene() (in module refinegems.utility.db_access) parse_reac_str() (in module refinegems.utility.entities) PATH_MEDIA_CONFIG (in module refinegems.utility.set_up) PATH_TO_DB (in module refinegems.utility.databases) PATH_TO_DB_FOLDER (in module refinegems.utility.databases) perform_mcc() (in module refinegems.utility.connections) plot_growth() (refinegems.classes.reports.GrowthSimulationReport method)

plot_venn() (in module refinegems.analysis.comparison) polish_entity_conditions() (in module refinegems.curation.curate) polish_model() (in module refinegems.curation.curate) polish_model_units() (in module refinegems.curation.curate) PREFIX2DB_GENES (in module refinegems.utility.cvterms) PREFIX2DB_METABS (in module refinegems.utility.cvterms) PREFIX2DB_PATHWAYS (in module refinegems.utility.cvterms) PREFIX2DB_REACS (in module refinegems.utility.cvterms) print_cvterm() (in module refinegems.utility.cvterms) print_UnitDefinitions() (in module refinegems.utility.entities) produce_medium_docs_table() (refinegems.classes.medium.Medium method)

R

reaction_equation_to_dict() (in module refinegems.utility.entities) read_from_cobra_model() (in module refinegems.classes.medium) read_substances_from_file() (in module refinegems.classes.medium) reannotate_sbo_memote() (in module refinegems.utility.util) REF_COL_GF_GENE_MAP (in module refinegems.utility.entities) refine() (in module refinegems.cmd_access) refinegems.analysis.comparison module refinegems.analysis.core_pan module refinegems.analysis.growth module refinegems.analysis.investigate module refinegems.classes.egcs module refinegems.classes.gapfill module refinegems.classes.medium module refinegems.classes.reports module refinegems.cmd_access module refinegems.curation.biomass module refinegems.curation.charges module refinegems.curation.curate module refinegems.curation.pathways module

refinegems.developement.decorators module refinegems.utility.connections module refinegems.utility.cvterms module refinegems.utility.databases module refinegems.utility.db_access module refinegems.utility.entities module refinegems.utility.io module refinegems.utility.set_up module refinegems.utility.util module remove_non_essential_genes() (in module refinegems.utility.entities) remove_substance() (refinegems.classes.medium.Medium method) Report (class in refinegems.classes.reports) report() (refinegems.classes.gapfill.GapFiller method) REQUIRED_SUBSTANCE_ATTRIBUTES (in module refinegems.classes.medium) reset() (in module refinegems.cmd_access) reset_database() (in module refinegems.utility.databases) resolve_compartment_names() (in module refinegems.utility.entities) resolve_duplicate_metabolites() (in module refinegems.curation.curate) resolve_duplicate_reactions() (in module refinegems.curation.curate) resolve_duplicates() (in module refinegems.curation.curate) run_DIAMOND_blastp() (in module refinegems.utility.connections) run_memote() (in module refinegems.utility.connections) run_SBOannotator() (in module refinegems.utility.connections)

S

save() (refinegems.classes.reports.AuxotrophySimulationReport method) (refinegems.classes.reports.CorePanAnalysisReport method) (refinegems.classes.reports.GapFillerReport method) (refinegems.classes.reports.GrowthSimulationReport method) (refinegems.classes.reports.KEGGPathwayAnalysisReport method) (refinegems.classes.reports.ModelInfoReport method) (refinegems.classes.reports.MultiModelInfoReport method) (refinegems.classes.reports.MultiSBOTermReport method) (refinegems.classes.reports.SBOTermReport method) (refinegems.classes.reports.SourceTestReport method) SBO_BIOCHEM_TERMS (in module refinegems.utility.util) sbo_terms() (in module refinegems.analysis.comparison) SBO_TRANSPORT_TERMS (in module refinegems.utility.util) SBOTermReport (class in refinegems.classes.reports) search_sbo_label() (in module refinegems.utility.io)

set_bounds_to_default() (in module refinegems.analysis.growth) set_default_flux() (refinegems.classes.medium.Medium method) set_initial_amount_metabs() (in module refinegems.curation.curate) set_kegg_pathways() (in module refinegems.curation.pathways) set_model_default_units() (in module refinegems.curation.curate) set_oxygen_percentage() (refinegems.classes.medium.Medium method) set_source() (refinegems.classes.medium.Medium method) set_units_of_parameters() (in module refinegems.curation.curate) setup() (in module refinegems.cmd_access) single_cobra_gapfill() (in module refinegems.classes.gapfill) SingleGrowthSimulationReport (class in refinegems.classes.reports) solve_egcs() (refinegems.classes.egcs.GreedyEGCSolver method) SourceTestReport (class in refinegems.classes.reports) statistics (refinegems.classes.reports.GapFillerReport property) sum_biomass_weight() (in module refinegems.utility.util)

T

template() (in module refinegems.developement.decorators) test_auxotrophies() (in module refinegems.analysis.growth) test_biomass_consistency() (in module refinegems.utility.util) test_biomass_presence() (in module refinegems.utility.util)

test_growth_with_source() (in module refinegems.analysis.growth) test_modifications() (refinegems.classes.egcs.GreedyEGCSolver method) to_dict() (refinegems.classes.reports.SingleGrowthSimulationReport method) to_table() (refinegems.classes.reports.GrowthSimulationReport method)

U

update_annotations_from_others() (in module refinegems.curation.curate) update_bigg_db() (in module refinegems.utility.databases) update_db_entry_single() (in module refinegems.classes.medium)

update_db_multi() (in module refinegems.classes.medium) update_mnx_namespaces() (in module refinegems.utility.databases) updated_db_to_schema() (in module refinegems.classes.medium)

V

VALID_COMPARTMENTS (in module refinegems.utility.util) validate_libsbml_model() (in module refinegems.utility.io) validate_reaction_compartment_bigg() (in module refinegems.utility.entities) ValidationCodes (class in refinegems.utility.databases) VERSION_FILE (in module refinegems.utility.databases) VERSION_URL (in module refinegems.utility.databases) visualise() (refinegems.classes.reports.GapFillerReport method) (refinegems.classes.reports.ModelInfoReport method) (refinegems.classes.reports.MultiModelInfoReport method) (refinegems.classes.reports.MultiSBOTermReport method) (refinegems.classes.reports.SBOTermReport method) (refinegems.classes.reports.SourceTestReport method)

visualise_auxotrophies() (refinegems.classes.reports.AuxotrophySimulationReport method) visualise_kegg_counts() (refinegems.classes.reports.KEGGPathwayAnalysisReport method) visualise_kegg_pathway() (refinegems.classes.reports.KEGGPathwayAnalysisReport method) visualise_reactions() (refinegems.classes.reports.CorePanAnalysisReport method)

W

write_model_to_file() (in module refinegems.utility.io)