Using the iPlant Collaborative Discovery Environment

Shannon L. Oliver1, Andrew J. Lenards1, Roger A. Barthelson1, Nirav Merchant1, Sheldon J. McKay2

1 The University of Arizona, Tucson, Arizona, 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.22
DOI:  10.1002/0471250953.bi0122s42
Online Posting Date:  June, 2013
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Abstract

The iPlant Collaborative is an academic consortium whose mission is to develop an informatics and social infrastructure to address the “grand challenges” in plant biology. Its cyberinfrastructure supports the computational needs of the research community and facilitates solving major challenges in plant science. The Discovery Environment provides a powerful and rich graphical interface to the iPlant Collaborative cyberinfrastructure by creating an accessible virtual workbench that enables all levels of expertise, ranging from students to traditional biology researchers and computational experts, to explore, analyze, and share their data. By providing access to iPlant's robust data‐management system and high‐performance computing resources, the Discovery Environment also creates a unified space in which researchers can access scalable tools. Researchers can use available Applications (Apps) to execute analyses on their data, as well as customize or integrate their own tools to better meet the specific needs of their research. These Apps can also be used in workflows that automate more complicated analyses. This module describes how to use the main features of the Discovery Environment, using bioinformatics workflows for high‐throughput sequence data as examples. Curr. Protoc. Bioinform. 42:1.22.1‐1.22.26. © 2013 by John Wiley & Sons, Inc.

Keywords: cyberinfrastructure; science gateways; bioinformatics; plant sciences; plant biology; computational biology; RNA‐Seq

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Entering Data Into the Discovery Environment
  • Alternate Protocol 1: Bulk Data Upload Using iDrop Lite
  • Basic Protocol 2: Running an Application in the Discovery Environment
  • Basic Protocol 3: Processing Bar‐Coded Sequence Read Data with Sabre, Scythe, and Sickle
  • Basic Protocol 4: Creating an Automated Workflow
  • Basic Protocol 5: RNA‐Seq Analysis with the Tuxedo Workflow
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

   Conway, M., Rajasekar, A., and Moore, R. 2010. iDROP: A Graphical User Interface for Community Remote Sensing. 2010 GSA Denver Annual Meeting. Geological Society of America, Boulder, Colo.
   Goff, S.A. Vaughn, M., McKay, S., 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.
   Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. 2012. Ultrafast and memory‐efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
   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.
   Pennisi, E. 2011. Human genome 10th anniversary. Will computers crash genomics? Science 331:666‐668.
   Stanzione, D. 2011. The iPlant collaborative: Cyberinfrastructure to feed the world. IEEE Computer 44:44‐52.
   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.
   Zhang, H., He, H., Wang, X., Wang, X., Yang, X., Li, L., and Deng X.W. 2011. Genome‐wide mapping of the HY5‐mediated gene networks in Arabidopsis that involve both transcriptional and post‐transcriptional regulation. Plant J. 65:346‐358.
Internet Resources
   http://user.iplantcollaborative.org
  iPlant Collaborative's user management portal.
   http://de.iplantcollaborative.org
  iPlant Collaborative's Discovery Environment home page.
   http://ask.iplantcollaborative.org
  iPlant Collaborative's user help forum.
   http://iplantcollaborative.org/CPB2012_apps
  iPlant Collaborative's Discovery Environment App documentation pages.
   http://www.iplantcollaborative.org/DEManual
  iPlant Collaborative's Discovery Environment manual.
   http://iplantcollaborative.org/CPB2012_table1
  iPlant Collaborative's documentation page describing uploading and importing data.
   http://iplant.co/ScytheDoc
  iPlant Collaborative's documentation page for the Scythe App.
   http://www.java.com/en
  Java's home page, where Java downloads and documentation are available.
   http://www.bioinformatics.babraham.ac.uk/projects/fastqc
  The Babraham Bioinformatics group is the developer of FastQC.
   http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
  Cuffdiff's documentation Web site.
   http://www.irods.org
  iRODS is the core storage infrastructure for the iPlant Collaborative.
  http://www.xsede.org
  XSEDE is a high‐performance computing resource utilized by the Discovery Environment.
  http://www.samtools.sourceforge.net/
  Available source code for SAMtools
  http://www.github.com/najoshi/sabre
  Available source code page for the Sabre application.
  http://github.com/vsbuffalo/scythe
  Available source code page for the Scythe application.
  http://www.github.com/najoshi/sickle
  Available source code page for the Sickle application.
  http://hannonlab.cshl.edu/fastx_toolkit
  FASTX‐Toolkit documentation Web site.
  http://www.tophat.cbcb.umd.edu
  TopHat documentation Web site.
   http://compbio.mit.edu/cummeRbund/manual_2_0.html
  CummeRbund documentation Web site.
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