W420 How to Use the iPlant's Discovery Environment for Your Research

Date: Tuesday, January 17, 2012
Time: 11:20 AM
Room: California
Sheldon McKay , Dolan DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
The iPlant Discovery Environment (DE) is a system for managing and running tools, analyses, and workflows. The DE connects various components of iPlant's cyberinfrastructure together to create a rich web-based system for analyzing data. The DE contains a growing list of integrated applications for scientific workflows and a mechanism for users to integrate their own applications. In this hands-on session, we will demonstrate how to use the iPlant DE by guiding users through an RNA-seq analysis workflow.  RNA-seq refers to whole transcriptome shotgun sequencing of cDNA, generally using an ultra-high-throughput ("next-generation") sequencing technology. The value of RNA-seq is the ability generate deep-coverage information about a sample's RNA. This can be used for a variety of purposes such as transcriptome assembly, gene discovery/annotation, and detecting differential transcript abundances between tissues, developmental stages, genetic backgrounds, and environmental conditions. In this example we will compare gene transcript abundance between wild type and mutant Arabidopsis strains.