title: Genome Modeling System: A Knowledge Management Platform for Genomics.
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.affiliation: 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.
authors.forename: Malachi
authors.initials: M
authors.lastname: Griffith
authors.affiliation: 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.
authors.forename: Obi L
authors.initials: OL
authors.lastname: Griffith
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Scott M
authors.initials: SM
authors.lastname: Smith
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Avinash
authors.initials: A
authors.lastname: Ramu
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Callaway
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Anthony M
authors.initials: AM
authors.lastname: Brummett
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Michael J
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authors.lastname: Kiwala
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Adam C
authors.initials: AC
authors.lastname: Coffman
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Allison A
authors.initials: AA
authors.lastname: Regier
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Oberkfell
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Gabriel E
authors.initials: GE
authors.lastname: Sanderson
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Mooney
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Nathaniel G
authors.initials: NG
authors.lastname: Nutter
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Edward A
authors.initials: EA
authors.lastname: Belter
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Feiyu
authors.initials: F
authors.lastname: Du
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Long
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Travis E
authors.initials: TE
authors.lastname: Abbott
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Ian T
authors.initials: IT
authors.lastname: Ferguson
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: David L
authors.initials: DL
authors.lastname: Morton
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Mark M
authors.initials: MM
authors.lastname: Burnett
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: James V
authors.initials: JV
authors.lastname: Weible
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Joshua B
authors.initials: JB
authors.lastname: Peck
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Adam
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authors.lastname: Dukes
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Joshua F
authors.initials: JF
authors.lastname: McMichael
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Justin T
authors.initials: JT
authors.lastname: Lolofie
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Brian R
authors.initials: BR
authors.lastname: Derickson
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Jasreet
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authors.lastname: Hundal
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Zachary L
authors.initials: ZL
authors.lastname: Skidmore
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Ainscough
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Dees
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: William S
authors.initials: WS
authors.lastname: Schierding
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Cyriac
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authors.lastname: Kandoth
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Kyung H
authors.initials: KH
authors.lastname: Kim
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Charles
authors.initials: C
authors.lastname: Lu
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Christopher C
authors.initials: CC
authors.lastname: Harris
authors.affiliation: Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors.forename: Nicole
authors.initials: N
authors.lastname: Maher
authors.affiliation: 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.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Maher
authors.affiliation: 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.
authors.forename: Vincent J
authors.initials: VJ
authors.lastname: Magrini
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Benjamin S
authors.initials: BS
authors.lastname: Abbott
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Ken
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authors.lastname: Chen
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Eric
authors.initials: E
authors.lastname: Clark
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Indraniel
authors.initials: I
authors.lastname: Das
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Xian
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authors.lastname: Fan
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Amy E
authors.initials: AE
authors.lastname: Hawkins
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Todd G
authors.initials: TG
authors.lastname: Hepler
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Todd N
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authors.lastname: Wylie
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Leonard
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: William E
authors.initials: WE
authors.lastname: Schroeder
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Xiaoqi
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authors.lastname: Shi
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Lynn K
authors.initials: LK
authors.lastname: Carmichael
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Weil
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Richard W
authors.initials: RW
authors.lastname: Wohlstadter
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Gary
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authors.lastname: Stiehr
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Michael D
authors.initials: MD
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authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Craig S
authors.initials: CS
authors.lastname: Pohl
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Christopher A
authors.initials: CA
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authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Daniel C
authors.initials: DC
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authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Jason R
authors.initials: JR
authors.lastname: Walker
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: James M
authors.initials: JM
authors.lastname: Eldred
authors.affiliation: 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.
authors.forename: David E
authors.initials: DE
authors.lastname: Larson
authors.affiliation: The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
authors.forename: David J
authors.initials: DJ
authors.lastname: Dooling
authors.affiliation: 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.
authors.forename: Li
authors.initials: L
authors.lastname: Ding
authors.affiliation: 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.
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.affiliation: 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.
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D003628:Database Management Systems; D030541:Databases, Genetic; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D051188:Knowledge Bases; D008957:Models, Genetic; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D014584:User-Computer Interface