Genome Modeling System: A Knowledge Management Platform for Genomics.

Journal: PLoS computational biology
Published Date: Jul 1, 2015

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.

Authors

  • Malachi Griffith
    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.
  • Obi L Griffith
    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.
  • Scott M Smith
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Avinash Ramu
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Matthew B Callaway
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Anthony M Brummett
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Michael J Kiwala
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Adam C Coffman
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Allison A Regier
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Ben J Oberkfell
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Gabriel E Sanderson
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Thomas P Mooney
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Nathaniel G Nutter
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Edward A Belter
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Feiyu Du
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Robert L Long
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Travis E Abbott
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Ian T Ferguson
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • David L Morton
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Mark M Burnett
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • James V Weible
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Joshua B Peck
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Adam Dukes
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Joshua F McMichael
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Justin T Lolofie
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Brian R Derickson
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Jasreet Hundal
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Zachary L Skidmore
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Benjamin J Ainscough
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Nathan D Dees
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • William S Schierding
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Cyriac Kandoth
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Kyung H Kim
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Charles Lu
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Christopher C Harris
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Nicole Maher
    Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.
  • Christopher A Maher
    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.
  • Vincent J Magrini
    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.
  • Benjamin S Abbott
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Ken Chen
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Eric Clark
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Indraniel Das
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Xian Fan
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Amy E Hawkins
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Todd G Hepler
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Todd N Wylie
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Shawn M Leonard
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • William E Schroeder
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Xiaoqi Shi
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Lynn K Carmichael
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Matthew R Weil
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Richard W Wohlstadter
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Gary Stiehr
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Michael D McLellan
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Craig S Pohl
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Christopher A Miller
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Daniel C Koboldt
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Jason R Walker
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • James M Eldred
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • David E Larson
    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.
  • David J Dooling
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Li Ding
    College of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410014, China.
  • Elaine R Mardis
    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.
  • Richard K Wilson
    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.

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