{"id":"W4385894309","doi":"10.25080/gerudo-f2bc6f59-00f","title":"aPhyloGeo-Covid: A Web Interface for Reproducible Phylogeographic Analysis of SARS-CoV-2 Variation using Neo4j and Snakemake","year":2023,"lang":"en","type":"article","venue":"Proceedings of the Python in Science Conferences","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Sherbrooke","funders":"Natural Sciences and Engineering Research Council of Canada; Université de Sherbrooke","keywords":"Computer science; Phylogeography; Data science; Coronavirus disease 2019 (COVID-19); Context (archaeology); Workflow; Phylogenetic tree; Database; Geography; Biology; Infectious disease (medical specialty)","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":[0.002551358,0.002186667,0.001476776,0.002369478,0.0008831518,0.002415739,0.002678826,0.001133603,0.04454064],"category_scores_gemma":[0.005105727,0.001412804,0.002556855,0.001373232,0.0007019931,0.003285816,0.005443211,0.002470493,0.01772085],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007446142,"about_ca_system_score_gemma":0.001788077,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003205495,"about_ca_topic_score_gemma":0.005143214,"domain_scores_codex":[0.9992372,0.0001041794,0.00008801869,0.0002311472,0.0002434758,0.000096044],"domain_scores_gemma":[0.9986249,0.0006206044,0.0001316373,0.0002692861,0.0001827307,0.0001708283],"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":[0.003280171,0.0004816481,0.02418825,0.00396502,0.001078453,0.001514878,0.002087937,0.009237194,0.03697075,0.01373089,0.7733051,0.1301598],"study_design_scores_gemma":[0.001695134,0.0002990718,0.0362328,0.001003327,0.0004036158,0.001312452,0.0006556649,0.1993876,0.03870655,0.05923271,0.6602517,0.0008194079],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.01560676,0.0004080926,0.162303,0.0004726694,0.0004339248,0.0005253841,0.127568,0.683959,0.008723203],"genre_scores_gemma":[0.09850132,0.0008120465,0.3834136,0.001788355,0.0002110501,0.00371774,0.2744471,0.225134,0.01197489],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.04454064,"threshold_uncertainty_score":0.1490033,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05797028395049003,"score_gpt":0.3319342107216462,"score_spread":0.2739639267711562,"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."}}