{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001684611,0.001521718,0.0009899111,0.002324196,0.000577018,0.002492894,0.00234296,0.001458459,0.02637807],"category_scores_gemma":[0.00273159,0.001502297,0.001119521,0.001633685,0.0003535419,0.00191184,0.002487601,0.002667842,0.01574167],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003898184,"about_ca_system_score_gemma":0.001175927,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003931236,"about_ca_topic_score_gemma":0.005656346,"domain_scores_codex":[0.9992495,0.0001284802,0.00006774038,0.0001742226,0.0002974114,0.00008256533],"domain_scores_gemma":[0.9989987,0.0002759634,0.00008298607,0.0002662609,0.0002060053,0.0001700772],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.001763459,0.000344506,0.006172161,0.001762911,0.0003923349,0.001142233,0.0008942161,0.008142028,0.2237607,0.01637788,0.5424268,0.1968208],"study_design_scores_gemma":[0.0005404259,0.00009940744,0.006477628,0.0003998418,0.0001065597,0.00132738,0.0002117919,0.0522941,0.09952346,0.01502915,0.8236108,0.000379421],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.01623174,0.00154577,0.5507821,0.0008863894,0.0004686447,0.0002334371,0.0632866,0.3569977,0.009567617],"genre_scores_gemma":[0.06950221,0.001724149,0.7015529,0.0007884983,0.0001713109,0.0008250638,0.1378949,0.06558339,0.02195762],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.02637807,"threshold_uncertainty_score":0.08824342,"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."}}