{"id":"W2168281812","doi":"10.1186/1752-0509-1-36","title":"Facile: a command-line network compiler for systems biology","year":2007,"lang":"en","type":"article","venue":"BMC Systems Biology","topic":"Gene Regulatory Network Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":21,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"Natural Sciences and Engineering Research Council of Canada; Mitacs","keywords":"Computer science; Scripting language; Compiler; Perl; Systems biology; Modelling biological systems; Line (geometry); Bifurcation; Simple (philosophy); MATLAB; Programming language; Theoretical computer science; Bioinformatics; Biology; Nonlinear system; Mathematics; Physics","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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.001827172,0.0004198786,0.0008109765,0.0001273316,0.0002324162,0.0000349539,0.000484425,0.0008472247,0.0000110429],"category_scores_gemma":[0.00009347911,0.0003665816,0.0003320842,0.0002588484,0.0002309301,0.000003110369,0.0001848662,0.00013028,0.00003723682],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005159287,"about_ca_system_score_gemma":0.0001014874,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001434291,"about_ca_topic_score_gemma":0.0003767797,"domain_scores_codex":[0.9966332,0.0004454526,0.0009358622,0.0008470836,0.0000912343,0.001047185],"domain_scores_gemma":[0.9979936,0.0002080556,0.0004249315,0.0008797296,0.0002818339,0.000211791],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"not_applicable","study_design_scores_codex":[0.001387516,0.0002789707,0.4315229,0.0006638908,0.002023789,0.000008053489,0.0000610257,0.07112841,0.396569,0.02415984,0.07012047,0.002076121],"study_design_scores_gemma":[0.002329334,0.001306755,0.00249551,0.00006415438,0.0002020208,0.0001490211,0.0002326924,0.009400994,0.003621544,0.0001939902,0.9790534,0.0009506007],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.4947713,0.02786318,0.4693958,0.00004660854,0.004663177,0.001850373,0.000272166,0.000109145,0.001028217],"genre_scores_gemma":[0.9906499,0.0001080121,0.001064647,0.0001295151,0.004529768,0.0002132592,0.001738648,0.00005924566,0.001506993],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9089329,"threshold_uncertainty_score":0.9998786,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02887046295059158,"score_gpt":0.2911497765064473,"score_spread":0.2622793135558557,"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."}}