{"id":"W4289131647","doi":"10.1101/2022.07.28.501447","title":"JBrowse 2: A modular genome browser with views of synteny and structural variation","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":31,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Institute for Cancer Research","funders":"National Institutes of Health; Hospital for Sick Children; Johns Hopkins University","keywords":"Genome browser; Computer science; JavaScript; Synteny; Visualization; Plug-in; World Wide Web; Genome; Annotation; Modular design; Software; Debugging; Web application; Variation (astronomy); Genomics; Programming language; Biology; Data mining; Genetics; Artificial intelligence; Gene","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002512875,0.0003828405,0.0004338043,0.00009001245,0.0001347912,0.00004313442,0.0003074409,0.0002321548,0.00002384764],"category_scores_gemma":[0.00004560255,0.0003674636,0.00009398835,0.0001262382,0.000120921,0.000001941025,0.0007910684,0.0002426286,8.504165e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004081494,"about_ca_system_score_gemma":0.0002141982,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005377797,"about_ca_topic_score_gemma":0.000005827702,"domain_scores_codex":[0.9982917,0.00009624819,0.0003566664,0.0007684376,0.0002016115,0.0002853645],"domain_scores_gemma":[0.9984332,0.00001075482,0.0003668285,0.0008343727,0.0002493267,0.0001054703],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00006827947,0.00002699826,0.008201834,0.0001850511,0.0003361622,0.000005269257,0.00002281218,0.0007365121,0.9903085,0.00009541323,0.00001189721,0.000001293746],"study_design_scores_gemma":[0.0007788068,0.0004108216,0.8169549,0.00006355505,0.0002505471,1.25434e-7,0.00001247599,0.0002646024,0.1726287,0.000007725323,0.007755003,0.000872847],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9917842,0.006419004,0.0005898898,0.00004462606,0.0002476162,0.0005120612,0.0003818636,0.00001165864,0.000009082773],"genre_scores_gemma":[0.9939903,0.0008523429,0.004665069,0.00007968779,0.0001974945,0.0001301397,0.000001997797,0.00007578466,0.000007188632],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8176798,"threshold_uncertainty_score":0.9998778,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009958762718597261,"score_gpt":0.2039011507182873,"score_spread":0.19394238799969,"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."}}