title: Ergatis: a web interface and scalable software system for bioinformatics workflows.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  Ergatis is an open-source project and is freely available at http://ergatis.sourceforge.net.
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA. jorvis@users.sourceforge.net
authors.forename: Joshua
authors.initials: J
authors.lastname: Orvis
authors.forename: Jonathan
authors.initials: J
authors.lastname: Crabtree
authors.forename: Kevin
authors.initials: K
authors.lastname: Galens
authors.forename: Aaron
authors.initials: A
authors.lastname: Gussman
authors.forename: Jason M
authors.initials: JM
authors.lastname: Inman
authors.forename: Eduardo
authors.initials: E
authors.lastname: Lee
authors.forename: Sreenath
authors.initials: S
authors.lastname: Nampally
authors.forename: David
authors.initials: D
authors.lastname: Riley
authors.forename: Jaideep P
authors.initials: JP
authors.lastname: Sundaram
authors.forename: Victor
authors.initials: V
authors.lastname: Felix
authors.forename: Brett
authors.initials: B
authors.lastname: Whitty
authors.forename: Anup
authors.initials: A
authors.lastname: Mahurkar
authors.forename: Jennifer
authors.initials: J
authors.lastname: Wortman
authors.forename: Owen
authors.initials: O
authors.lastname: White
authors.forename: Samuel V
authors.initials: SV
authors.lastname: Angiuoli
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D030562:Databases, Protein; D020407:Internet; D012984:Software; D057188:Workflow