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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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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Literature Cited

Literature Cited
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