{"id":"W2123246614","doi":"10.1101/gr.1890304","title":"Sockeye: A 3D Environment for Comparative Genomics","year":2004,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":39,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre","funders":"BC Cancer Agency; Michael Smith Health Research BC; Genome British Columbia; Genome Canada; Canada's Michael Smith Genome Sciences Centre; BC Cancer Foundation","keywords":"Annotation; Ensembl; Genomics; Visualization; Biology; Comparative genomics; Software; Java; Computational biology; Sequence (biology); Structural genomics; Suite; Computer science; Genome; Bioinformatics; Data mining; Genetics","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":[0.0004750518,0.0001309798,0.0001549423,0.00005693861,0.0002958504,0.00002756519,0.0002550721,0.00009017525,0.00002001367],"category_scores_gemma":[0.00002086032,0.0001280775,0.00008280904,0.00005986565,0.0002003861,3.534029e-7,0.000276352,0.0001056444,0.00006583212],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009766818,"about_ca_system_score_gemma":0.0001537212,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002890519,"about_ca_topic_score_gemma":0.00002770812,"domain_scores_codex":[0.998714,0.00004739917,0.0001607986,0.0004035138,0.0001772134,0.0004970877],"domain_scores_gemma":[0.9993944,0.00002546959,0.00003093503,0.0003418354,0.0001048327,0.0001025151],"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":[0.0000970788,0.00008385167,0.00008658454,0.00001581565,0.0001111248,0.0000011353,0.0005421365,0.002639602,0.9950265,0.0002909915,0.0002923163,0.0008129155],"study_design_scores_gemma":[0.001409763,0.001052365,0.004091286,0.000003786775,0.00001280301,0.000006869688,0.0006191563,0.00002235752,0.1209674,0.002345127,0.8691828,0.0002862503],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9895213,0.004065395,0.003703195,0.0003944051,0.00005876065,0.0007822356,0.0001650348,0.000002127293,0.001307495],"genre_scores_gemma":[0.9856717,0.001400644,0.01144278,0.00007344464,0.000369994,0.0002320721,0.0000898569,0.00002552706,0.0006939981],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.874059,"threshold_uncertainty_score":0.5222847,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.09813126836767501,"score_gpt":0.3602772481688281,"score_spread":0.2621459798011531,"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."}}