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PLoS Comput Biol. 2015 Jul 9;11(7):e1004274. doi: 10.1371/journal.pcbi.1004274. eCollection 2015 Jul.

Genome Modeling System: A Knowledge Management Platform for Genomics.

Author information

1
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.
2
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.
3
The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
4
Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.
5
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.
6
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.
7
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.

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.

PMID:
26158448
PMCID:
PMC4497734
DOI:
10.1371/journal.pcbi.1004274
[Indexed for MEDLINE]
Free PMC Article

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