Genome Modeling System: A Knowledge Management Platform for Genomics

被引：59

作者：

Griffith, Malachi ^{[1
,2
]}

Griffith, Obi L. ^{[1
,3
]}

Smith, Scott M. ^{[1
]}

Ramu, Avinash ^{[1
]}

Callaway, Matthew B. ^{[1
]}

Brummett, Anthony M. ^{[1
]}

Kiwala, Michael J. ^{[1
]}

Coffman, Adam C. ^{[1
]}

Regier, Allison A. ^{[1
]}

Oberkfell, Ben J. ^{[1
]}

Sanderson, Gabriel E. ^{[1
]}

Mooney, Thomas P. ^{[1
]}

Nutter, Nathaniel G. ^{[1
]}

Belter, Edward A. ^{[1
]}

Du, Feiyu ^{[1
]}

Long, Robert L. ^{[1
]}

Abbott, Travis E. ^{[1
]}

Ferguson, Ian T. ^{[1
]}

Morton, David L. ^{[1
]}

Burnett, Mark M. ^{[1
]}

Weible, James V. ^{[1
]}

Peck, Joshua B. ^{[1
]}

Dukes, Adam ^{[1
]}

McMichael, Joshua F. ^{[1
]}

Lolofie, Justin T. ^{[1
]}

Derickson, Brian R. ^{[1
]}

Hundal, Jasreet ^{[1
]}

Skidmore, Zachary L. ^{[1
]}

Ainscough, Benjamin J. ^{[1
]}

Dees, Nathan D. ^{[1
]}

Schierding, William S. ^{[1
]}

Kandoth, Cyriac ^{[1
]}

Kim, Kyung H. ^{[1
]}

Lu, Charles ^{[1
]}

Harris, Christopher C. ^{[1
]}

Maher, Nicole ^{[3
]}

Maher, Christopher A. ^{[1
,3
,4
]}

Magrini, Vincent J. ^{[1
,2
]}

Abbott, Benjamin S. ^{[1
]}

Chen, Ken ^{[1
]}

Clark, Eric ^{[1
]}

Das, Indraniel ^{[1
]}

Fan, Xian ^{[1
]}

Hawkins, Amy E. ^{[1
]}

Hepler, Todd G. ^{[1
]}

Wylie, Todd N. ^{[1
]}

Leonard, Shawn M. ^{[1
]}

Schroeder, William E. ^{[1
]}

Shi, Xiaoqi ^{[1
]}

Carmichael, Lynn K. ^{[1
]}

机构：

[1] Washington Univ, Genome Inst, St Louis, MO 63130 USA

[2] Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA

[3] Washington Univ, Sch Med, Dept Med, St Louis, MO 63110 USA

[4] Washington Univ, Sch Med, Siteman Canc Ctr, St Louis, MO USA

[5] Washington Univ, Sch Med, Dept Mol Microbiol, St Louis, MO 63110 USA

来源：

PLOS COMPUTATIONAL BIOLOGY | 2015年 / 11卷 / 07期

关键词：

EXPRESSION ANALYSIS; CANCER; MUTATIONS; SEQUENCE; GENE; ALIGNMENT; FORMAT; TOPHAT; TUMOR; TOOL;

D O I：

10.1371/journal.pcbi.1004274

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

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