학술논문
Genome Modeling System: A Knowledge Management Platform for Genomics.
Document Type
Academic Journal
Author
Griffith M; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.; Griffith OL; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.; Smith SM; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Ramu A; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Callaway MB; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Brummett AM; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Kiwala MJ; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Coffman AC; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Regier AA; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Oberkfell BJ; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Sanderson GE; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Mooney TP; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Nutter NG; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Belter EA; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Du F; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Long RL; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Abbott TE; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Ferguson IT; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Morton DL; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Burnett MM; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Weible JV; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Peck JB; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Dukes A; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; McMichael JF; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Lolofie JT; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Derickson BR; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Hundal J; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Skidmore ZL; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Ainscough BJ; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Dees ND; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Schierding WS; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Kandoth C; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Kim KH; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Lu C; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Harris CC; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Maher N; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.; Maher CA; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America.; Magrini VJ; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.; Abbott BS; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Chen K; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Clark E; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Das I; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Fan X; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Hawkins AE; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Hepler TG; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Wylie TN; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Leonard SM; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Schroeder WE; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Shi X; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Carmichael LK; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Weil MR; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Wohlstadter RW; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Stiehr G; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; McLellan MD; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Pohl CS; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Miller CA; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Koboldt DC; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Walker JR; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Eldred JM; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Larson DE; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.; Dooling DJ; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.; Ding L; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America.; Mardis ER; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America.; Wilson RK; The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Source
Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE
Subject
Language
English
Abstract
In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.