{"id":"W4391261909","doi":"10.1093/bioinformatics/btae051","title":"TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator","year":2024,"lang":"en","type":"article","venue":"Bioinformatics","topic":"RNA modifications and cancer","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; Simon Fraser University","funders":"Natural Sciences and Engineering Research Council of Canada; Michael Smith Health Research BC","keywords":"Computer science; Modular design; Scalability; Software; Human–computer interaction; Operating system; Computer architecture","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":[0.001123245,0.00109534,0.0007104618,0.0003391677,0.0004504141,0.0009704382,0.002720103,0.001352152,0.008926094],"category_scores_gemma":[0.002786624,0.0007305465,0.001440984,0.000495788,0.0005192002,0.0008428415,0.001082963,0.001824388,0.003672514],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009090101,"about_ca_system_score_gemma":0.00181703,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004077786,"about_ca_topic_score_gemma":0.003570029,"domain_scores_codex":[0.9995525,0.00009721237,0.00003973352,0.00009872121,0.0001506502,0.00006122215],"domain_scores_gemma":[0.9991672,0.0003786226,0.00005729712,0.0001227986,0.0001698522,0.000104233],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0007752174,0.0002317015,0.007475092,0.001157964,0.0002882092,0.0004102144,0.0004002378,0.8345887,0.06832699,0.01671964,0.03208549,0.03754055],"study_design_scores_gemma":[0.000124554,0.00009830479,0.0006908049,0.00003172565,0.0000432968,0.0000902246,0.00002849212,0.9449239,0.02209113,0.004705109,0.02711469,0.00005766372],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.05246961,0.0005812618,0.8097657,0.0004833003,0.0004268288,0.0004340234,0.008793229,0.1137022,0.01334386],"genre_scores_gemma":[0.4149503,0.001245214,0.5245814,0.0009534667,0.0001243401,0.00239844,0.02361464,0.02063471,0.01149744],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.008926094,"threshold_uncertainty_score":0.02986073,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0121096398317694,"score_gpt":0.2418908974974867,"score_spread":0.2297812576657173,"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."}}