Cloud Computing with iPlant Atmosphere
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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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PDF or HTML at Wiley Online LibraryTable 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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Figure 9.15.1 The Web interface for Atmosphere. A list of running Atmosphere instances in shown on the left panel. Resource usage, instance information, and shell and VNC access are in the right panel. View Image -
Figure 9.15.2 The virtual desktop for the iPlant base cloud instance. Atmosphere images are preloaded with VNC server, which allows remote, graphical access to the running instance's Gnome desktop software. View Image -
Figure 9.15.3 The virtual desktop accessed through mobile computing platforms. The desktop shown is an instance of Atmosphere NGS (Next Generation Sequence) Viewers image. (A ) The desktop accessed iOS VNC viewer App on an iPad mini. (B ) The desktop accessed on the Android VNC Viewer App on a Samsung Galaxy Note smartphone. View Image -
Figure 9.15.4 Atmosphere shell interface. View Image -
Figure 9.15.5 This error message is a security feature to prevent IP address spoofing by malicious third parties. View Image -
Figure 9.15.6 The iDrop user interface. The right panel shows the user's iPlant Data Store home directory. The left panel shows the directory tree for the Atmosphere instance's local file system. View Image -
Figure 9.15.7 The Generic Genome Browser on an instance of the Atmosphere Ubuntu image. The data shown are default yeast data that are included in the GBrowse distribution. View Image -
Figure 9.15.8 TopHat alignment data, mapped to the Arabidopsis thaliana TAIR 10 genome assembly and displayed in the Integrated Genome Viewer on an instance of the Atmosphere RNA‐Seq Visualization image. The gene shown is AT1G67090 ( RBCS1A; ribulose bisphosphate carboxylase small chain 1A ). View Image -
Figure 9.15.9 A cummeRbund scatter plot comparing transcript abundance levels from RNA‐Seq data from wild‐type and hy5 mutant seedlings. The units used on the x and y axes are fpkm values (fragments per kilobase per million reads), which are normalized transcript abundance levels measured by the Cufflinks package. Density of transcripts at particular fpkm value is summarized in heat maps along the axes. View Image
Videos
Literature Cited
| Literature Cited | |
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