{"id":"W2160219419","doi":"10.1093/nar/gkt394","title":"IslandViewer update: improved genomic island discovery and visualization","year":2013,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":109,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University; Dalhousie University","funders":"Genome Canada; Canadian Institutes of Health Research; Genome British Columbia; SFU Community Trust Endowment Fund; Simon Fraser University; Michael Smith Health Research BC","keywords":"Genome; Biology; Upload; Annotation; Computational biology; ENCODE; Visualization; Genome browser; Virulence; Gene; Genomic island; Genomics; Genetics; Computer science; Data mining; World Wide Web","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002834104,0.0001263805,0.0001268547,0.0000646105,0.0001972252,0.0001552646,0.0001750505,0.0001147865,0.0001601925],"category_scores_gemma":[0.00007416435,0.0001072958,0.00003715445,0.00009694472,0.0001847069,0.000003182728,0.0003833125,0.000110318,0.00007526269],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001470319,"about_ca_system_score_gemma":0.00003058786,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009748963,"about_ca_topic_score_gemma":0.00007972539,"domain_scores_codex":[0.9988696,0.00009492924,0.0001569748,0.0003676399,0.0001507973,0.0003600683],"domain_scores_gemma":[0.9993903,0.00001565073,0.00002998753,0.0003016478,0.0001796408,0.00008277301],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00002239833,0.00003249306,0.009844784,0.0000201729,0.00004901053,5.402496e-7,0.0001325341,0.000001794317,0.9706947,0.0002064618,0.01474272,0.004252436],"study_design_scores_gemma":[0.003867189,0.002110865,0.2742223,0.00004436335,0.00005409978,0.00004966891,0.001559665,0.005827359,0.09466107,0.004946368,0.6112276,0.001429375],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9943044,0.002724471,0.000237149,0.0003628141,0.00007554095,0.0003592073,0.0000325845,0.000002745233,0.001901079],"genre_scores_gemma":[0.9938914,0.003137384,0.0002064554,0.0001705546,0.0002341426,0.00006174566,0.00004265158,0.00002971557,0.002225959],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8760336,"threshold_uncertainty_score":0.4375398,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01763936832012315,"score_gpt":0.3007132121858329,"score_spread":0.2830738438657097,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}