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Abstract Detail



Conference Wide

Mckay, Sheldon [1], Williams, Jason [2].

iPlant Collaborative:A Unified Cyberinfrastructure for a Unified Research Paradigm.

Research in biology increasingly depends on data-intensive methods and complex computational analyses that span a range of investigational domains - from genomics and transcriptomics, to phenotyping and ecology. The iPlant Collaborative (NSF #DBI-0735191)presents a comprehensive cyberinfrastructure that services a broad range of biological research questions by providing a unified platform for the storage,sharing, and analyses of large data sets - from genomes to image data, and beyond. Additionally, the variety of iPlant tools and access points cater to every level of user, from bench-biologists to bioinformaticians; removing many of the barriers researchers face in managing and sharing large data sets and conducting sophisticated computational analyses. This hands-on workshop will use interesting phylogenetic (building and visualizing large trees) and genomics (RNA-Seq and transcriptome assembly) questions to introduce several iPlant technologies: Discovery Environment: iPlant's web-based platform for managing data, and running analyses. The Discovery Environment is a scalable and extensible platform that provides easy access to high-powered computing. Hundreds of commonly used bioinformatics tools are accessible through a simple, sleek interface. Researchers can easily integrate and share their own tools and workflows; the equivalent of a biology "app store." Atmosphere: iPlant offers cloud services for harnessing on-demand computational power; 1-click access to a custom computing environment. Atmosphere allows users to easily compile, launch and manage instances of Linux-based servers to tackle complex and compute-intense analysis routines. Data Store: iPlant's data storage system furnishes great flexibility and control over your data. The Data Store encompasses a variety of interfaces, from web services to mountable file systems to high speed command line transfers; all integrated with Atmosphere and the Discovery Environment. Fast uploads/downloads and interruptible file transfers mean you have reliable access to your initial 100GB storage allocation. PhytoBisque: iPlant's integration of the BISQUE image analysis software system enables researchers to conduct quantitative,image-based phenotype studies. An example of the Powered by iPlant program (use iPlant resources to serve your tools and services), the longer-term vision is to integrate PhytoBisque outputs with genotype data to build true multidimensional quantitative representations of the genotype-to-phenotype relationship.

Broader Impacts:


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Related Links:
Plant Ontology
Plant Ontology Wiki
iPlant Collaborative Homepage


1 - Cold Spring Harbor Laboratory, DNA Learning Center, 1 Bungtown Rd, Cold Spring Harbor Laboratory, NY, 11724, USA, 516-367-5185
2 - Cold Spring Harbor Laboratory, 1 Bungtown Rd., Cold Spring Harbor, NY, 11724, USA, 516-367-5186

Keywords:
high throughput data
next generation sequencing
data analysis
data management
data visualization
genotype to phenotype
Phylogenetics
cloud computing
iplant
iplant collaborative.

Presentation Type: Array
Session: WS02
Location: Marlborough B/Riverside Hilton
Date: Sunday, July 28th, 2013
Time: 8:00 AM
Number: WS02001
Abstract ID:31
Candidate for Awards:None


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