{"id":"W4316926479","doi":"10.1093/bioinformatics/btad032","title":"JBrowse Jupyter: a Python interface to JBrowse 2","year":2023,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Institute for Cancer Research","funders":"National Institute of General Medical Sciences; National Human Genome Research Institute; National Institutes of Health","keywords":"Python (programming language); Computer science; Programming language; Interface (matter); Operating system","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":[0.0001587927,0.0001634593,0.0001405307,0.00008318116,0.0000890071,0.00003849352,0.0002345897,0.00008927615,0.00001024935],"category_scores_gemma":[0.0000804937,0.0001505265,0.00007676167,0.0002119844,0.00003573199,0.000001379343,0.0003760812,0.00005028486,0.0006847112],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001146883,"about_ca_system_score_gemma":0.00003541608,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006198192,"about_ca_topic_score_gemma":0.00001549872,"domain_scores_codex":[0.999108,0.0000123879,0.0002765113,0.0001634683,0.0001172102,0.0003223993],"domain_scores_gemma":[0.9993628,0.00001086833,0.00005963806,0.0003832878,0.0000621767,0.0001212253],"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":[0.0001577027,0.0000747357,0.003223735,0.0002031099,0.0002590553,0.000006674325,0.005479773,0.002294838,0.6726219,0.0002379075,0.2756955,0.03974505],"study_design_scores_gemma":[0.0006685582,0.0006572076,0.007112324,0.00003440572,0.00002838227,0.00001953412,0.001713286,0.002420566,0.1362716,0.0001316422,0.8503463,0.0005961658],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9908715,0.0002178661,0.00220686,0.0004184923,0.0004346949,0.0002821353,0.00006130578,0.00003515928,0.005471976],"genre_scores_gemma":[0.9882278,0.0003207813,0.007629695,0.0008325441,0.0002151553,0.00004047388,0.00005965505,0.00003219354,0.00264166],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5746508,"threshold_uncertainty_score":0.8800805,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01484453589691458,"score_gpt":0.26097935467307,"score_spread":0.2461348187761554,"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."}}