Ergatis: a web interface and scalable software system for bioinformatics workflows

被引：74

作者：

Orvis, Joshua ^{[1
]}

Crabtree, Jonathan ^{[1
]}

Galens, Kevin ^{[1
]}

Gussman, Aaron ^{[1
]}

Inman, Jason M. ^{[2
]}

Lee, Eduardo ^{[3
]}

Nampally, Sreenath ^{[2
]}

Riley, David ^{[1
]}

Sundaram, Jaideep P. ^{[2
,4
]}

Felix, Victor ^{[1
]}

Whitty, Brett ^{[5
]}

Mahurkar, Anup ^{[1
]}

Wortman, Jennifer ^{[1
]}

White, Owen ^{[1
]}

Angiuoli, Samuel V. ^{[1
,6
]}

机构：

[1] Univ Maryland, Sch Med, Inst Genome Sci, Baltimore, MD 21201 USA

[2] J Craig Venter Inst, Rockville, MD USA

[3] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA

[4] Georgetown Univ, Dept Biol, Computat Genom Lab, Washington, DC 20057 USA

[5] Michigan State Univ, Dept Plant Biol, E Lansing, MI 48824 USA

[6] Univ Maryland, Ctr Bioinformat & Computat Biol, College Pk, MD 20742 USA

来源：

BIOINFORMATICS | 2010年 / 26卷 / 12期

基金：

美国国家卫生研究院;

关键词：

COMPARATIVE GENOMICS; SEQUENCE; TOOL; UNIFICATION; FRAMEWORK; RESOURCE; ONTOLOGY;

D O I：

10.1093/bioinformatics/btq167

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. Software is also needed to simplify data management and make large-scale bioinformatics analysis accessible and reproducible to a wide class of target users. Results: We have developed a workflow management system named Ergatis that enables users to build, execute and monitor pipelines for computational analysis of genomics data. Ergatis contains preconfigured components and template pipelines for a number of common bioinformatics tasks such as prokaryotic genome annotation and genome comparisons. Outputs from many of these components can be loaded into a Chado relational database. Ergatis was designed to be accessible to a broad class of users and provides a user friendly, web-based interface. Ergatis supports high-throughput batch processing on distributed compute clusters and has been used for data management in a number of genome annotation and comparative genomics projects.

引用

页码：1488 / 1492

页数：5

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