iPlant at PAG2015 Planning

Public URL

We have a wikipage that will ultimately have all iPlant events here: http://www.iplantc.org/pag2015

iPlant Staff Attending PAG XXIII (2015)

(thumbnail shows room cost for designated lodging)

iPlant Booth (231) Schedule

Saturday: DNA Subway: Genomics, DNA Barcoding, and RNA-Seq Made Easy for the Undergraduate Classroom (10:30 AM, California Room: Session XXX)

Date: Saturday, January 10th, 2015

Time: 10:30 AM - 12:40 PM

Location: California Rm

Workshop Description: This workshop introduces DNA Subway (dnasubway.iplantcollaborative.org), an educational bioinformatics platform developed by the NSF-sponsored iPlant Collaborative. DNA Subway bundles research-grade bioinformatics tools and databases into intuitive workflows - presenting them in an appealing interface modeled on the metaphor of a subway map. “Riding” on different DNA Subway lines, students can predict and annotate genes in up to 150 kb of DNA (Red Line), identify homologs in sequenced genomes (Yellow Line), analyze DNA barcodes and construct phylogenetic trees (Blue Line), and analyze RNA-Seq datasets (Green Line). With support for plant and animal genomes, DNA Subway engages students in their own learning by bringing to life key concepts of gene structure and function, genome
organization and complexity, and evolutionary biology. An integrated experiment on DNA Barcoding illustrates the modern synthesis of in vitro biochemistry with in silico bioinformatics, and provides an opportunity to merge molecular genetics with ecology and conservation biology. Presenters from a variety of undergraduate institutions will show how they are using DNA Subway to support novel, course-based and independent student research.

Organizer: Dave Micklos

Saturday: Genome Management and Analysis with CoGe (4:00 PM California Room: Session XXX)

Date: Saturday, January 10th, 2015

Time: 4:00 - 6:10 PM

Location: California Room

Workshop Description: CoGe/EPIC-CoGe: What to do after you a genome sequenced and assembled? With over 23,000 genomes from 17,000 different organisms, CoGe is where most people are managing and analyzing their genomic data. This two hour workshop will provide in-depth, hands-on training: 1) Managing your genome in CoGe: How to add your own genome to CoGe, add structural and functional annotations, keep it private, share it with collaborators, and make it fully public (http://genomevolution.org/r/8kzz) 2) Integrating functional and diversity data: The EPIC-CoGe addition enables researchers to integrate RNASeq, BS-Seq, ChIP-Seq, DNA resequencing data, microarrays, and any other type of quantitative genomic measurements to any genome in CoGe (http://genomevolution.org/wiki/index.php/EPIC-CoGe_Tutorial) 3) Map NGS reads to a genome: EPIC-CoGe’s RNASeq processing and SNP discovery pipelines make it easy to transform you read data into quantitative measurements. (https://www.youtube.com/watch?v=3fNyHGB02dM) 4) Visualizing your genomic data: The EPIC-CoGe genome browser, based on JBrowse, is instantly available for any genome and associated data loaded into CoGe (http://genomevolution.org/r/9xjy) 5) Whole genome comparisons: Identify and classify orthologous and paralogous genes, identify whole genome duplications, use synteny to order and orient contigs and scaffolds against any reference genome to create pseudo-assemblies 6) Micro-synteny analyses: Identify gene model errors, conserved non-coding sequences, tandem gene duplications, and changes in local genome structure 7) Multiple whole genome synteny analyses: Given a gene in one genome, find syntenic regions across multiple genomes, even if that specific gene is not present. CoGe offers a multitude of advanced on-the-fly analyses. To accomplish these, CoGe is part of the Powered by iPlant Program and leverages iPlant’s Cyberinfrastructure for computational scalability. Learn more about this program at: http://www.iplantcollaborative.org/discover/powered-by-iplant

Speaker: Eric Lyons, University of Arizona/CoGe PI/iPlant Co-PI

Monday: iPlant Workshop: Why a Biology Cyberinfrastructure is the Best Way to Meet the Challenges of Large Datasets (6:10 PM, California Room: Session 2663)

Date: Monday, January 12th, 2015

Time: 6:10 PM - 8:20 PM

Location: California Rm

Workshop Description: This workshop is for biologists who are working with large datasets. It will feature talks, tutorials, and demos that will help you use free, NSF-funded resources (#DBI-1265383) for a variety of data-intensive analyses (e.g. genome assembly and annotation, RNA-Seq, image analysis, GWAS, geospatial etc.). Users with limited bioinformatics experience, or experienced users who need access to greater HPC capacity will both benefit from attending. Whether you’re just getting started with high-throughput sequencing, or have been working with biological big data for years - data analysis and management are usually the most challenging aspects of investigation. Some challenges are obvious up front (“my files are too large to share”); some challenges appear later on (“I can’t replicate because metadata is missing or my previous software has disappeared”) – working with cyberinfrastructure can help solve these challenges and more. In this workshop we’ll cover the platforms, tools, and services developed by the iPlant Collaborative and demonstrate how research communities studying arthropods, microbes, animals are using them. The workshop is targeted at anyone working with large datasets and will • Overview of available resources (data storage/sharing, web interfaces, cloud computing) • “Get started” demos on tools, platforms, and intro to RNA-Seq analysis • Presentations by researchers who have used used these tools to solve problems • How tool developers can make their tools and pipelines more accessible to the research community For more information on related presentations and hand-on bioinformatics and developer tutorials at this year’s PAG, please visit www.iplantc.org/pag2015

*Organizer:  *Jason Williams

Speakers:

Computer Demonstration: Managing complex computations using clouds and containers in iPlant Atmosphere (Time/Date still to be determined)

Date: Tuesday, January 13, 2015

Time: at XX:YY during the 10:30 AM - 12:40 PM Session

Location: California Rm

Event Description: This computer demonstration will show you how to use Atmosphere, iPlant's cloud compute platform, to create, share, and publish virtual appliances (machine images) with your own software or your own customized analyses. Learn to use Atmosphere as a gateway to access iPlant's core infrastructure resources, including high performance computing (HPC) environments and the iPlant Data Store. We will demonstrate how you can extend this environment using Docker-based containers and how to add more applications to an existing virtual appliance. We will also build a ready-to-use appliance during the demo, from start to finish, and share it with attendees.

Presenter: Nirav Merchant

iPlant User-Group Meetings (Content TBD)

All meetings to be held in Stratford

Date(s): Saturday, January 10 - Tuesday, January 13, 2015

Time: 5:00 - 7:00 PM

Location: TBD/Jason

Event Description:

Related workshops, presentations, and posters