Discover

Discovery Environment

The Discovery Environment (DE) is one of the ways users can interact with iPlant cyberinfrastructure. Rather than managing computing resource details, or learning new software for every type of analysis, the DE allows you to handle all aspects of your bioinformatics workflow (e.g., data management, analysis, sharing large datasets, etc.) in one space.

Overview & Tutorials
Discovery Environment Overview

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Documentation

The primary graphical interface to iPlant is the Discovery Environment (DE). The DE provides a web interface and a platform to access the computing, data storage, and analysis application resources provided by iPlant. The DE is designed to facilitate data exploration and scientific discovery by integrating analytical tools as modular components that may be used individually or in workflows, accessing iPlant’s Data Store, and seamlessly running tools on local or high-performance computing nodes, depending on the throughput and resource needs of the analysis. In addition, the DE will employ provenance tracking of both primary and derived files to track and reproduce experiments, and collaboration tools that enable users to share data, workflows, analysis results, and data visualizations.

 

The DE is integrated with iPlant's data management system and compute resources, creating a unified environment in which researchers can access tools and data with an unprecedented degree of scalability. It features easy integration of new tools and data by any user, resulting in an ever-expanding set of analytical tools.

 

Tool Integration by Users One of the most exciting features of the DE is how simple it is for any user to add a new tool into the DE and create a new interface for the tool in just three steps:

  1. Deploy the tool on iPlant's compute nodes using a simple web form to describe the tool and where it may be obtained. iPlant's Core Services team then installs it on iPlant's cluster computing resources.
  2. Create a graphical user interface (GUI) for using the tool using the DE's intuitive web-based integration system.
  3. Define how to use the tool, what the various options do, and how to find additional information.

 

If the analysis tool being integrated is intended to be used for very computationally intensive analyses, the tool integrator works with the iPlant team located at the Texas Advanced Computing Center (TACC) to ensure the tool is well suited for running on a supercomputer. The programming resources provided by iPlant's Foundation API make such tool integration straightforward.

 

Expanded Analytical Capabilities Thanks to the simplified tool integration process, the DE has a total of about 90 command line analytical tools, with more being added all the time. They support data analyses in the following research areas:

  • Clustering and network analysis
  • QTL mapping and genome-wide association studies
  • Sequence alignments and phylogenetic tree building
  • Next Generation Sequencing
  • Phylogenetic comparative methods and trait evolution

 

A number of utility tools and scripts are also available. A full, up-to-date list of applications available in the DE may be found in the online documentation. This apps list is growing rapidly as community members integrate additional tools and new interfaces for those tools.

 

iPlant's Data Store A unified system through which all of iPlant's resources can store, retrieve, and manage data. This scalable, distributed system for storing data files is built upon highly redundant, high-performance storage arrays that are geographically replicated between The University of Arizona and TACC in Austin.

More on iPlant's Data Store.

 

Computational Power Analyses in the DE can run on iPlant's clusters or, for appropriately designed analytical tools, on the TACC supercomputers.

 

We invite you to explore iPlant's Discovery Environment. While extensive documentation and tutorials exist for using the DE and other iPlant resources, please feel free to contact the iPlant team via Ask iPlant with any questions you may have, or for help with integrating new tools, learning how to access iPlant's Data Store, and any problems you find in the system.

Development Team

Name Role Institution
Sriram Srinivasan
Software Engineer/Team Lead iPlant Collaborative, The University of Arizona
Dennis Roberts Senior Software Engineer iPlant Collaborative, The University of Arizona
Tony Edgin Software Engineer iPlant Collaborative, The University of Arizona
Paul Sarando Software Engineer iPlant Collaborative, The University of Arizona
Jonathan Strootman Software Engineer iPlant Collaborative, The University of Arizona
John Wregglesworth Software Engineer iPlant Collaborative, The University of Arizona
Jerry Schneider QA Manager iPlant Collaborative, The University of Arizona
Rob Bovill QA Test Engineer iPlant Collaborative, The University of Arizona
Victor Cordero Performance Test Engineer iPlant Collaborative, The University of Arizona
Kathleen Kennedy Documentation Coordinator/QA Analyst iPlant Collaborative, The University of Arizona