{"id":"W4401482693","doi":"10.1002/cpz1.1120","title":"Setting Up the JBrowse 2 Genome Browser","year":2024,"lang":"en","type":"article","venue":"Current Protocols","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Institute for Cancer Research","funders":"National Institute of General Medical Sciences; National Cancer Institute; National Human Genome Research Institute; National Institutes of Health","keywords":"Computational biology; Genome; Computer science; Biology; Genetics; Gene","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0002280005,0.0001510037,0.00009252095,0.00002071728,0.0001372696,0.0001089104,0.0002573582,0.00005144207,0.00002803343],"category_scores_gemma":[0.00003210113,0.0001012959,0.0001087428,0.00007926361,0.00006935324,8.901178e-7,0.0002134404,0.0001217783,0.00006356204],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001034592,"about_ca_system_score_gemma":0.00007597205,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000141756,"about_ca_topic_score_gemma":0.000002450257,"domain_scores_codex":[0.9991059,0.00004400599,0.0001778679,0.0003283276,0.0001004812,0.0002433949],"domain_scores_gemma":[0.9995179,0.00001564756,0.00003374823,0.0003419966,0.00004504763,0.00004562927],"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":[0.00005494481,0.00007279215,0.002245157,0.0004468422,0.0002008719,0.000003974689,0.0006223082,0.00009752531,0.8625602,0.001460795,0.02945883,0.1027758],"study_design_scores_gemma":[0.0001597371,0.00008493501,0.00229589,0.00005598009,0.0000127102,0.000007387688,0.00003357633,0.0000607259,0.01639548,0.0003673094,0.9803699,0.0001563108],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7034362,0.07321047,0.005505225,0.003722904,0.005597024,0.1955543,0.0003642391,0.0001546579,0.01245497],"genre_scores_gemma":[0.8997774,0.0002810437,0.0002138831,0.0002497736,0.002129895,0.09513633,0.00005647421,0.00006278083,0.002092444],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9509111,"threshold_uncertainty_score":0.4130729,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03264182508206101,"score_gpt":0.3384350446391596,"score_spread":0.3057932195570986,"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."}}