{"id":"W2564755845","doi":"10.1128/msystems.00127-16","title":"Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research","year":2017,"lang":"en","type":"article","venue":"mSystems","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":711,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Dalhousie University","keywords":"Microbiome; Workflow; Scripting language; Metagenomics; Computer science; Human Microbiome Project; Data science; Resource (disambiguation); Field (mathematics); Computational biology; World Wide Web; Biology; Bioinformatics; Human microbiome; Genetics; Database","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":[0.007645259,0.002979759,0.002420307,0.003491241,0.002356331,0.003287663,0.004376155,0.001940779,0.05213759],"category_scores_gemma":[0.01357197,0.003285704,0.00233869,0.001958949,0.000988392,0.003969352,0.006727822,0.004553441,0.06583611],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00112898,"about_ca_system_score_gemma":0.004085941,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002659245,"about_ca_topic_score_gemma":0.004705219,"domain_scores_codex":[0.9959336,0.0006518557,0.0004397274,0.001304431,0.001204148,0.0004662287],"domain_scores_gemma":[0.9932857,0.002335061,0.0005687801,0.001644912,0.001257079,0.0009084193],"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":[0.003140431,0.0003615562,0.006395289,0.003986122,0.0005576164,0.0009924124,0.002287572,0.002556144,0.2025272,0.005632268,0.5684142,0.2031493],"study_design_scores_gemma":[0.0004476506,0.0002627182,0.005826153,0.0005188522,0.0001436009,0.001248084,0.0003046977,0.01571831,0.1581193,0.01194203,0.8048586,0.0006099777],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.005392153,0.0008029991,0.438532,0.0005137464,0.0006615295,0.0009752435,0.04546244,0.5028365,0.004823196],"genre_scores_gemma":[0.01454965,0.0006333147,0.7718562,0.001232649,0.0002091845,0.003631651,0.09584314,0.10048,0.01156419],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.05213759,"threshold_uncertainty_score":0.1744176,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05488475493851853,"score_gpt":0.3453655676219921,"score_spread":0.2904808126834735,"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."}}