title: Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE.
abstract: BACKGROUND
  Funded by the National Institutes of Health (NIH), the aim of the Model Organism ENCyclopedia of DNA Elements (modENCODE) project is to provide the biological research community with a comprehensive encyclopedia of functional genomic elements for both model organisms C. elegans (worm) and D. melanogaster (fly). With a total size of just under 10 terabytes of data collected and released to the public, one of the challenges faced by researchers is to extract biologically meaningful knowledge from this large data set. While the basic quality control, pre-processing, and analysis of the data has already been performed by members of the modENCODE consortium, many researchers will wish to reinterpret the data set using modifications and enhancements of the original protocols, or combine modENCODE data with other data sets. Unfortunately this can be a time consuming and logistically challenging proposition.
  
  
  RESULTS
  In recognition of this challenge, the modENCODE DCC has released uniform computing resources for analyzing modENCODE data on Galaxy (https://github.com/modENCODE-DCC/Galaxy), on the public Amazon Cloud (http://aws.amazon.com), and on the private Bionimbus Cloud for genomic research (http://www.bionimbus.org). In particular, we have released Galaxy workflows for interpreting ChIP-seq data which use the same quality control (QC) and peak calling standards adopted by the modENCODE and ENCODE communities. For convenience of use, we have created Amazon and Bionimbus Cloud machine images containing Galaxy along with all the modENCODE data, software and other dependencies.
  
  
  CONCLUSIONS
  Using these resources provides a framework for running consistent and reproducible analyses on modENCODE data, ultimately allowing researchers to use more of their time using modENCODE data, and less time moving it around.
authors.affiliation: Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON, M5G 0A3, Canada.
authors.forename: Quang M
authors.initials: QM
authors.lastname: Trinh
authors.forename: Fei-Yang Arthur
authors.initials: FY
authors.lastname: Jen
authors.forename: Ziru
authors.initials: Z
authors.lastname: Zhou
authors.forename: Kar Ming
authors.initials: KM
authors.lastname: Chu
authors.forename: Marc D
authors.initials: MD
authors.lastname: Perry
authors.forename: Ellen T
authors.initials: ET
authors.lastname: Kephart
authors.forename: Sergio
authors.initials: S
authors.lastname: Contrino
authors.forename: Peter
authors.initials: P
authors.lastname: Ruzanov
authors.forename: Lincoln D
authors.initials: LD
authors.lastname: Stein
mesh_terms: D047369:Chromatin Immunoprecipitation; D012984:Software