Organizers |
Jason Williams, 411 |
iPlant Attendees/Trainers |
Jason Williams, Sheldon McKay, Uwe Hilgert |
Location |
Riverside Hilton, New Orleans, LA |
Dates |
July 24 - Aug 1, 2013 |
Agenda
Conference Website
Conference Schedule (not yet available)
Date |
Time |
Event |
Location |
Jul 28th |
8:00-5:00 |
DNA Subway: Genomics, DNA Barcoding, and RNA-Seq - Bringing Cutting-Edge Biology into the Classroom.
Workshop Wiki Page
Educators looking to teach modern molecular biology & genomics will benefit from this 1 day workshop introducing DNA Subway; iPlant's educational platform for gene annotation, phylogenetics, and transcriptomeanalysis. DNA Subway bundlesresearch-grade bioinformatics tools and databases into intuitive workflows - presentingthem in an appealing interface modeled on the metaphor of a subway map.“Riding� on any of four different DNA Subway lines, users can predict and annotate genesin up to 150 kb of DNA (Red Line), identify homologs in sequenced genomes(Yellow Line), analyze DNA barcodes and construct phylogenetic trees(BlueLine), and analyze RNA-Seq data (Green Line). DNA Subway is a freeweb-platform developed by the NSF-Funded iPlant Collaborative (www.iplantcollaborative.org).Workshop participants will use DNA Subway to analyze sequence data and learn how tointegrate genome analysis into their own teaching. In addition, workshopparticipants will learn about a novel DNA barcoding lab, an open-ended inquirybased lab in which students identify plants by amplifying, sequencing andanalyzing their DNA. Participants will also see how they can use their own (or providedexample) transcriptome datasets to introduce and examine RNA-Seq experimentsand data. |
Marlborough A/Riverside Hilton |
Jul 28th |
8:00-5:00 |
iPlant Collaborative: A Unified Cyberinfrastructure for a Unified Research Paradigm.
Workshop Wiki Page
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 visualizinglarge trees) and genomics (RNA-Seq and transcriptome assembly) questions tointroduce 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 toolsand 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. |
Marlborough B/Riverside Hilton |