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iPlant Events at PAG XXIV

iPlant invites you to take part in user-oriented events taking place across several days at this year's Plant and Animal Genome Meeting.

Saturday, January 9th

[3082] iPlant and Education: DNA Subway, Data Science, and Microbial Genomics

Time: 10:30AM - 12:40 PM

Location: California Room

PAG Online Program Link: Session 3082

Workshop Description

Cyberinfrastructure developed by iPlant Collaborative makes it possible for large numbers of students and educators to effectively use computation in research and teaching. This session showcases ways iPlant has advanced learning from high school to post-graduate contexts. Talks on DNA Subway (www.dnasubway.org) demonstrate how thousands of students have been able to use wet-lab and bioinformatics activities to explore species identification through DNA barcoding (Blue Line) as well as differential gene expression through RNA-Seq (Green Line). Metagenomics has exciting potential for student learning and course-based research (CUREs); we will cover classroom examples using iPlant’s Discovery Environment which will serve as the basis for new DNA Subway-style microbial/metagenomics workflows. Data Science is a tremendously important skill for genomics and iPlant’s collaboration with Data Carpentry (www.datacarpentry.org) has produced new lesson materials for Next-generation sequence data. Finally, iPlant is centered on democratizing access to resources – we discuss a vision for broadening participation and impacts that focus on reaching Native American / American Indian / Alaskan Native communities.

Organizer: Jason Williams, Dave Micklos - CSHL DNA Learning Center/ iPlant

Speakers

Time

Speaker/Affiliation

Abstract ID/Title

10:30

Dave Micklos, DNA Learning Center/ iPlant

22292: Introductory Remarks

10:40Stephen Harris, Graduate Center - City University of New York21871: Using DNA barcoding and educational bioinformatics to create authentic research experiences for science students
11:05Carrie Thurber, Abraham Baldwin Agricultural College21870: RNA-Seq in the Classroom: Pathways to Undergraduate Research
11:30Carlos Goller, North Carolina State University21872: Sifting through metagenomes using the iPlant Discovery Environment
11:55Tracy Teal, Data Carpentry

21881: Data Carpentry: Data Skills Training to Enable More Effective Research

12:20Joslynn Lee, Cold Spring Harbor Laboratory22088: Creating a positive space to train Native Americans / American Indians in genomics

[3882] iPlant User Meeting - Tools and Resources Demos

Time: 5:30PM - 7:00 PM

Location: Stratford Room

PAG Online Program Link: Session 3882

 

Workshop Description

iPlant Collaborative has developed cyberinfrastructure (access to software and data management tools, HPC, and support) that enables data-intensive biology. This informal user meeting is designed to get you informed and using the most recent capabilities of the platform. Particular highlights of this session will include the latest work on the iPlant Data Commons and its role reproducibility and discoverability, iPlant’s SRA submission pipeline. We will also have demos  on data sharing and management, and popular products for genome assembly, annotation, and RNA-Seq. Whether you are a long-time iPlant user, or are just getting introduced, we invite you to stop by, ask questions, or just say hello!

Organizer: Jason Williams


See Stratford Room on Map

Sunday, January 10th

  • iPlant Booth #503 (Open from 3:00PM - 8:30PM)


[3883] iPlant User Meeting - Getting Started with Docker, APIs, and Phenotyping

Time: 4:00PM - 6:00 PM

Location: Stratford Room

PAG Online Program Link: Session 3883

Workshop Description

At this iPlant user meeting, we will cover some of resources for bringing your own tools and workflows to iPlant platforms. We will have several informal presentations as well as hands on guidance and demos. The session focus will be on tool installation as well as working with image/phenotype data, however we will provide help for all iPlant related questions.

Organizer: Nirav Merchant, Matthew Vaughn, Jason Williams

Talks:

Time

Speaker/Affiliation

Abstract ID/Title

04:00

Nirav Merchant, University of Arizona/ iPlant

22363: Bringing your favorite analysis applications to iPlant using Docker containers

04:30Matthew Vaughn, Texas Advanced Computing Center/ iPlant22363: Deploying simple-to-use scalable workflows using the Agave API
05:00Ramona Walls, University of Arizona/ iPlant22290: Phenotyping with BISQUE
05:30Open Discussion/Questions/Demos 

 


See Stratford Room on Map

Monday, January 11th

  • iPlant Booth #503 (Open from 9:30AM - 5:00PM)

[3121] Cyberinfrastructure for Life Science and Beyond – Scaling your science with iPlant

Time: 6:10PM - 8:20 PM

Location: California Room

PAG Online Program Link: Session 3121

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 developed by the iPlant Collaborative (#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. The workshop will feature an overview of available resources (data storage/sharing, web interfaces, cloud computing), presentations by researchers who have used these tools to solve problems, and how tool developers can make their tools and pipelines more accessible to the research community.

 

Organizer: Jason Williams - Cold Spring Harbor Laboratory / iPlant

Speakers

Time

Speaker/Affiliation

Abstract ID/Title

6:10

Parker Antin, University of Arizona/ iPlant

21734: Introducing CyVerse

6:30Ming Cheng Luo, UC Davis

21777: Integrated approach towards sequencing a large and complex genome - iPlant Portal Facilitates Management of Big Data

6:50Andrew Nelson, University of Arizona, Tucson22209: Evolinc: A Pipeline for Comparative Genomic and Transcriptomic Analyses of Long Non-Coding RNAs
7:10Eric Fritz-Waters, Iowa State University21735: The iPlant Agave Application Program Interface, High Performance Computing, and You (the Computationally Competent)
7:30Jeremy DeBarry, University of Arizona/ iPlant21738: How to do Big-Data Science - Data Management for Genomics
7:50Ryan Joynson, University of Liverpool21937: "We liked the shaver so much we bought the company": Federating iPlant to the UK and beyond!  

[3884] Bioinformatics Ice Cream Social - Collaborating and Networking Across Complex Projects

Time: 8:30PM - 10:30 PM

Location: Stratford Room

PAG Online Program Link: Session 3884

Workshop Description

Calling all bioinformaticians and bioinformatics enthusiasts! We're hosting a small get together on a variety of topics relevant to making bioinformatics accessible and open to all communities. If you have ever contributed code to an open source project, helped with documentation, or trained students and colleagues we'd like to invite you down to this late-night event. Our goal is to gather feedback on how we can all leverage cyberinfrastructure investments and support open source bioinformatics that works for every investigator and student. We will talk about projects such as Data Carpentry (http://datacarpentry.org/) and how you can get involved.

Organizer: Jason Williams, Matt Vaughn


See Stratford Room on Map

Tuesday, January 12th

  • iPlant Booth #530 (Open from 9:30AM - 3:00PM)

Visit our Booth (#503)

Come meet with members of the iPlant team! This is our chance to get to meet our users, reconnect with people who have been to our workshops. See demos of iPlant tools and services and get your questions answered.

Day

Time

Event

Sunday

3:00-8:30

Booth Open

Monday

9:30-5:00

Booth Open

Tuesday

9:30-3:00

Booth Open


See Booth Location

Related workshops, presentations, and posters  

See the work of our friends, colleagues, and collaborators. Is your presentation/poster missing? Email info@iplantcollaborative.org

Poster/Session

Title

Presenter/ Affiliation

Time/Location info

3084iMicrobe: Extending the iPlant Cyberinfrastructure for Metagenomic Analysis in Microbial EcologyBonnie Hurwitz, University of Arizona 
3183Reference Sequence of the Genome of Aegilops tauschii, the Progenitor of the Wheat D GenomeJan Dvorak, University of California Davis,  
3102Next-Gen Sequence Analysis in CoGe: Read Alignment, Expression Analysis, SNP Identification, and What's to ComeMatthew Bomhoff,

University of Arizona, Tucson

 
3536Teaching Bioinformatics Data Analysis Using Cloud Computing TechnologyVivek Krishnakumar, J. Craig Venter Institute 
3732A pragmatic path forward for integrating phenotype and trait data using ontologiesRamona Walls,  iPlant Collaborative 
C12Integrated, Accurate and Multi-Environment Structural Variation Discovery from Whole Genome Sequencing Data with NGSEPJorge A. Duitama Castellanos, International Center for Tropical Agriculture (CIAT) 
P1278The DOE Systems Biology Knowledgebase (KBase): Introduction to a System for Collaborative and Reproducible Inference and Modeling of Biological FunctionRobert W. Cottingham, Oak Ridge National Laboratory 
P0358fRNAkenseq: a Powered-by-iPlant RNA Sequencing Analysis PlatformAllen Hubbard, University of Delaware 
P0720Exploring and Comparing Plant Genomes Using the Gramene/Ensembl Plants BrowserJoshua Stein, Cold Spring Harbor Laboratory 
P0319Data Management and Analysis Solutions for Maize Predictive Phenomics: A Partnership with the GxE Subgroup of the Genomes to Fields (G2F) InitiativeJack Gardiner, University of Iowa 
P0217Evolinc: A Pipeline for Comparative Genomic and Transcriptomic Analyses of Long Non-Coding RNAsAndrew D Nelson, University of Arizona 
C18The Legume Information System and The Legume Federation: Working Together for the Legume-Fed WorldAndrew D. Farmer, National Center for Genome Resources (NCGR) 
3110Exploring and Comparing Plant Genomes Using the Gramene/Ensembl Plants BrowserJoshua Stein, Cold Spring Harbor Laboratory 

Social Media

Stay in touch with us throughout the event!

Twitter: @iPlantCollab #iPlantPAG, AND @CyVerseOrg

Facebook: facebook.com/iPlantCollab OR facebook.com/CyVerse.org

LinkedIn: iplant.co/iPlantCollabLinkedIn OR CyVerse LinkedIn

Google+: iplant.co/iPlantGooglePlus OR CyVerse Google+

iPlant is funded by the National Science Foundation (#DBI - 1265383)


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