Cloud Computing with iPlant Atmosphere

Sheldon J. McKay1, Edwin J. Skidmore2, Christopher J. LaRose2, Andre W. Mercer2, Christos Noutsos1

1 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2 The University of Arizona, Tucson, Arizona
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 9.15
DOI:  10.1002/0471250953.bi0915s43
Online Posting Date:  October, 2013
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Abstract

Cloud Computing refers to distributed computing platforms that use virtualization software to provide easy access to physical computing infrastructure and data storage, typically administered through a Web interface. Cloud‐based computing provides access to powerful servers, with specific software and virtual hardware configurations, while eliminating the initial capital cost of expensive computers and reducing the ongoing operating costs of system administration, maintenance contracts, power consumption, and cooling. This eliminates a significant barrier to entry into bioinformatics and high‐performance computing for many researchers. This is especially true of free or modestly priced cloud computing services. The iPlant Collaborative offers a free cloud computing service, Atmosphere, which allows users to easily create and use instances on virtual servers preconfigured for their analytical needs. Atmosphere is a self‐service, on‐demand platform for scientific computing. This unit demonstrates how to set up, access and use cloud computing in Atmosphere. Curr. Protoc. Bioinform. 43:9.15.1‐9.15.20. © 2013 by John Wiley & Sons, Inc.

Keywords: iPlant; cloud computing; virtualization; cloud storage

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Launching an Atmosphere Server Instance
  • Basic Protocol 2: Logging into an Atmosphere Cloud Instance Using Web VNC
  • Alternate Protocol 1: Connecting to an Atmosphere Cloud Instance Using VNC Viewer in MAC OS X or Mobile Computing Platforms
  • Basic Protocol 3: Connecting to an Atmosphere Instance Using the Web Shell
  • Alternate Protocol 2: Connecting to an Atmosphere Instance Using an External Secure Shell Client
  • Basic Protocol 4: Mounting Your Home Directory from the iPlant Data Store
  • Alternate Protocol 3: Accessing the iPlant Data Store with the iDrop Interface
  • Basic Protocol 5: Terminating a Cloud Server Instance
  • Alternate Protocol 4: Creating a GBrowse Server in Atmosphere (For Advanced Users)
  • Alternate Protocol 5: Visual Analytics of RNA‐SEQ Data from the Tuxedo Protocol (For Advanced Users)
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
  Goecks, J., Nekrutenko, A., Taylor, J. and The Galaxy Team. 2010. Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11:R86.
  Goff, L. and Trapnell, C. 2011. cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high‐throughput sequencing data. R package version 1.2.0. http://www.bioconductor.org/packages/2.12/bioc/html/cummeRbund.html.
  Goff, S.A., Vaughn, M., McKay, S.J., Lyons, E., Stapleton, A.E., Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M., Jordan, C., Skidmore, E., Dooley, R., Cazes, J., McLay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W.H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S.J., Kvilekval, K., Manjunath, B.S., Tannen, V., Stamatakis, A., Sanderson, M., Welch, S.M., Cranston, K.A., Soltis, P., Soltis, D., O'Meara, B., Ane, C., Brutnell, T., Kleibenstein, D.J., White, J.W., Leebens‐Mack, J., Donoghue, M.J., Spalding, E.P., Vision, T.J., Myers, C.R., Lowenthal, D., Enquist, B.J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., and Stanzione, D. 2011. The iPlant Collaborative: Cyberinfrastructure for plant biology. Front. Plant Sci. 2:34.
  Lenards, A.J., Merchant, N., and Stanzione, D. 2011. Building an environment to facilitate discoveries for plant sciences. Proceedings from Gateway Computing Environments 2011 at Supercomputing 11, Seattle. IEEE Computer Society, Washington D.C.
  Nicol, J.W., Helt, G.A., Blanchard, S.G. Jr., Raja, A., and Loraine, A.E. 2009. The Integrated Genome Browser: Free software for distribution and exploration of genome‐scale dataset. Bioinformatics 25:2730‐2731.
  Nurmi, D., Wolski, R., Grzegorczyk, C., Obertelli, G., Soman, S., Youseff, L., and Zagoodnov, D. 2009. The Eucalyptus open‐source cloud‐computing system. Cluster Computing and the Grid, 2009. CCGRID '09. 9th IEEE/ACM International Symposium. J. Phys.:Conf. Ser. 180 012051 doi: 10.1088/1742‐6596/180/1/012051.
  R Core Team. 2012. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
  Stanzione, D. 2011. The iPlant Collaborative: Cyberinfrastructure to Feed the World. IEEE Computer 44:44‐52.
  Stein, L.D. 2010. The case for cloud computing in genome informatics. Genome Biol. 11:207.
  Stein, L.D. 2013. Using GBrowse 2.0 to visualize and share next‐generation sequence data. Brief. Bioinform. 14:162‐171.
  Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., and Lewis, S. 2002. The generic genome browser: A building block for a model organism system database. Genome Res. 12:1599‐1610.
  Trapnell, C., Pachter, L., and Salzberg, S.L. 2009. TopHat: Discovering splice junctions with RNA‐Seq. Bioinformatics 25:1105‐1111.
  Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., and Pachter, L. 2010. Transcript assembly and quantification by RNA‐Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28:511‐515.
  Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., and Pachter, L. 2012. Differential gene and transcript expression analysis of RNA‐seq experiments with TopHat and Cufflinks. Nat. Protoc. 7:562‐578.
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