title: cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud.
abstract: : One of the solutions proposed for addressing the challenge of the overwhelming abundance of genomic sequence and other biological data is the use of the Hadoop computing framework. Appropriate tools are needed to set up computational environments that facilitate research of novel bioinformatics methodology using Hadoop. Here, we present cl-dash, a complete starter kit for setting up such an environment. Configuring and deploying new Hadoop clusters can be done in minutes. Use of Amazon Web Services ensures no initial investment and minimal operation costs. Two sample bioinformatics applications help the researcher understand and learn the principles of implementing an algorithm using the MapReduce programming pattern.
  
  
  METHODS
  Source code is available at https://bitbucket.org/booz-allen-sci-comp-team/cl-dash.git.
  
  
  BACKGROUND
  hodor_paul@bah.com.
authors.affiliation: Booz Allen Hamilton, Rockville, MD 20852, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Hodor
authors.affiliation: Booz Allen Hamilton, Rockville, MD 20852, USA.
authors.forename: Amandeep
authors.initials: A
authors.lastname: Chawla
authors.affiliation: Booz Allen Hamilton, Rockville, MD 20852, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Clark
authors.affiliation: Booz Allen Hamilton, Rockville, MD 20852, USA.
authors.forename: Lauren
authors.initials: L
authors.lastname: Neal
mesh_terms: D000465:Algorithms; D035843:Biomedical Research; D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016247:Information Storage and Retrieval; D011381:Programming Languages; D057386:Search Engine; D017422:Sequence Analysis, DNA; D012984:Software