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UNIT 11.9 Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy

  1. Enis Afgan1,5,
  2. Brad Chapman2,
  3. Margita Jadan3,
  4. Vedran Franke4,
  5. James Taylor5

Published Online: 1 JUN 2012

DOI: 10.1002/0471250953.bi1109s38

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Afgan, E., Chapman, B., Jadan, M., Franke, V. and Taylor, J. 2012. Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy. Current Protocols in Bioinformatics. 38:11.9:11.9.1–11.9.20.

Author Information

  1. 1

    Center for Informatics and Computing, Ruder Bošković Institute (RBI), Zagreb, Croatia

  2. 2

    Harvard School of Public Health, Boston, Massachusetts

  3. 3

    Division of Materials Chemistry, Laboratory for Ichthyopathology–Biological Materials, Ruder Bošković Institute (RBI), Zagreb, Croatia

  4. 4

    Department of Biology, University of Zagreb, Zagreb, Croatia

  5. 5

    Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia

Publication History

  1. Published Online: 1 JUN 2012

Abstract

Cloud computing has revolutionized availability and access to computing and storage resources, making it possible to provision a large computational infrastructure with only a few clicks in a Web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this unit, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatic analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy, into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to set up the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command-line interface, and the Web-based Galaxy interface. Curr. Protoc. Bioinform. 38:11.9.1-11.9.20. © 2012 by John Wiley & Sons, Inc.

Keywords:

  • accessible cloud computing;
  • enabling bioinformatics analyses;
  • turnkey computing system