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CyVerse Events at PAG XXVI

CyVerse 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 13th

[4772] CyVerse Education: Scaling Genomics and Data Science for the Biology Classroom

Time: 08:00AM - 10:10 AM

Location: California Room

PAG Online Program Link: Session 4772

Workshop Description

Course-based undergraduate research experiences (CUREs) scale research methods to allow large numbers of students to explore open-ended problems. CUREs typically use a common set of biochemical and bioinformatics tools to allow students to obtain novel results within the time-frame of a one or two semester course. This workshop will present practical reports of CUREs in action in different institutional and class settings, as well as data on how CUREs improve student attitudes toward science and retention in STEM disciplines. Projects on DNA barcoding on microbiome analysis use DNA Subway and other computational resources provided by CyVerse, an NSF-funded cyber-infrastructure for biological research (DBI-0735191 and DBI-1265383).

Organizers:  Dave Micklos, Jason Williams - CSHL DNA Learning Center/ CyVerse




Abstract ID/Title


Carolina Sempertegui, Truman State University, Kirksville, MO Next Generation RNA Sequencing: Facilitating Undergraduate Research
08:40  Victoria Hernandez, William Floyd High School, Mastic Beach, NYIntegrating Bioinformatics Tools in the High School Classroom
09:10Oliver Hyman, Elizabeth Doyle, Andrea Pesce and Ray A. Enke, James Madison University, Harrisonburg, VACURE-All: Large Scale Implementation of Authentic DNA Barcoding Research into a Freshman Biology Curriculum
09:40Nicola Anthony, University of New OrleansBuilding Capacity for Genomics Data Analysis in Resource-Limited Environments

Time: 10:30AM - 12:40 PM

Location: California Room

PAG Online Program Link: Session 4820

Workshop Description

As the wealth of data increases across the life sciences, so does the complexity for managing and analyzing those data. A new class of bioinformatic platforms are emerging that provide web-enabled user interfaces as well as application programming interfaces. This has enabled developers of these platforms to more easily share their computational resources and use those developed by others. The goal of this workshop is to share experience, ideas, technology, and best-practices on developing and using bioinformatic platforms that share data and computational services.

Organizers:  Eric Lyons, University of Arizona/ CyVerse, Haibao Tang, University of Arizona



Sunday, January 14th


  • CyVerse Booth #613 (Open from 3:00PM - 8:30PM)

Monday, January 15th

Pragmatic solutions for scaling your analysis: Machine Learning, Imaging, Containers, Clouds and APIs

Time: 4:00PM - 5:30 PM

Location: TOWNE

PAG Online Program Link: Workshop


Workshop Description

With ever growing volume of data, the need to effectively utilize multiple computational platforms (clouds, HPC) and contemporary analysis techniques (Machine Learning, Large Scale Visualization, Containers) are key for rapidly building solutions that provide reproducibility, scalability, ease of sharing for research teams and communities with the ability to extend and customize these (using API's) for your own projects. This BoF is an informal discussion about challenges, learning opportunities and technology landscape (commercial, academic and hybrid) for building tools, platforms and analysis pipelines. 

Organizer: Nirav Merchant and Jason Williams

  • CyVerse Booth #613  (Open from 9:30AM - 5:00PM)


[4771] CyVerse - Software, Tools, and Services for Data-Driven Discovery

Time: 6:10PM - 8:20 PM

Location: California Room

PAG Online Program Link: Session 4771

Workshop Description

CyVerse (the successor to iPlant Collaborative) serves the entire life science community by delivering the platforms, tools, and datasets that enable data-driven discovery. This session updates the community on the project's activities including new features and services. Presentations by exemplar users illustrate ways CyVerse is being used by individual investigators and as platform for entire projects. CyVerse provides resources and support for every level of user - from bench-biologists working on their first RNA-Seq project, to collaborations who need the computational support to deliver high-impact science and datasets. CyVerse is funded by the National Science Foundation (DBI-0735191 and DBI-1265383) and provides free, user-friendly access to data storage/management platforms, cloud computing, and high-performance computing. We also provide learning materials, training, and support, including serving open-source developers who want to deliver tools and pipelines to the research community.


Organizer: Jason Williams - Cold Spring Harbor Laboratory / CyVerse




Abstract ID/Title


Parker Antin, University of Arizona, Tucson, AZ

 CyVerse: Looking Towards the Future

6:20Benjamin Bolduc1, Ken Youens-Clark2, Simon Roux3, Bonnie L. Hurwitz2 and Matthew B Sullivan1, (1)The Ohio State University, Columbus, OH, (2)University of Arizona, Tucson, AZ, (3)Joint Genome Institute, Walnut Creek, CA

iVirus: Facilitating New Insights in Viral Ecology with Software and Community Data Sets Imbedded in a Cyberinfrastructure

6:40Sarah D. Turner1, Shelby Ellison2, Douglas Senalik3, Philipp W. Simon3, Edgar Spalding4 and Nathan Miller4, (1)Division of Biological Sciences, University of Missouri, Columbia, MO, (2)USDA-ARS, Madison, WI, (3)USDA-Agricultural Research Service, Vegetable Crops Unit, University of Wisconsin-Madison, Madison, WI, (4)University of Wisconsin-Madison, Madison, WIA High-Throughput Image Analysis Pipeline to Quantify Carrot Shoot and Root Morphology
6:50 Joseph Gage1, Nathan Miller1, Edgar Spalding1, Shawn Kaeppler2 and Natalia de Leon1, (1)University of Wisconsin-Madison, Madison, WI, (2)Department of Agronomy and Wisconsin Crop Innovation Center, Madison, WITIPS: A System for Automated Image-Based Phenotyping of Maize Tassels
7:00Celeste Marie Falcon, University of Wisconsin-Madison, Madison, WIGenetic Study of Maize Yield-Component Traits Measured by Automated Image Analysis
7:10Cory D. Hirsch, University of Minnesota, St. Paul, MNMachine Vision Phenotyping of Seedling Growth and Morphology
7:30Paul C. Bailey, Earlham Institute, Norwich, United Kingdom Development of a Gene Family Toolkit for Exploring Diversity in New Sequence Data
7:45Alice Minotto1, Erik Van Den Bergh2 and Robert P. Davey1, (1)Earlham Institute, Norwich, United Kingdom, (2)EMBL-EBI, Hinxton, United KingdomCyVerse UK: Widening the Scope to the UK and Beyond
8:00Brian Lee, UCSC, Santa Cruz, CAViewing Data Hosted at CyVerse on the UCSC Genome Browser

Tuesday, January 16th

  • CyVerse Booth #613 (Open from 9:30AM - 3:00PM)

Visit our Booth (#613)

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






Booth Open



Booth Open



Booth Open

Wednesday, January 17th

Plenary: "Challenges and Opportunities for Agriculture in the Era of Big Data"

CyVerse Co-PI: Dr. Doreen Ware

Time: 08:45AM

Related workshops, presentations, and posters  (coming soon)

See the work of our friends, colleagues, and collaborators. Is your presentation/poster missing? Email -



Presenter/ Affiliation

Time/Location info

Connecting Crop Phenotype and Genotype DataIdentifier Services for Distributed Data ManagementRamona Walls, Univ of Ariz./CyVerseSaturday, Jan 13 12:20 PM (Golden Ballroom)
Arabidopsis InformaticsHelping the Community Transform High-Throughput Imaging Data into Phenotype InformationEdgar Spalding, U. Wisc, MadisonMonday, Jan 15 2:35 PM (Pacific Salon 6-7 - 2nd Floor)
Galaxy: An Open Platform for Data Analysis and IntegrationG-OnRamp: Visualizing and Annotating Eukaryotic Genomes with GalaxyJeremey Goecks, Oregon Health Sci. Cntr.Tuesday, Jan 16 4:20 PM (California)
Gramene: Unifying Comparative Genomics and Pathway Resources for Plant CommunitiesFunctional Curation - How Do We Prioritize and Scale up?Pankaj, JaiswalTuesday, Jan 16 3:10 PM (California)

Resources and Programs for Undergraduate Education in Genomics

Educational Workflows in Metagenomics: Microbiomes and Environmental (e)DNA

David Micklos, CSHL/CyVerse 

Sunday, Jan 14 8:30 AM (Towne)

The U.S. National Plant Genome Initiative—The Next 20 YearsCyberinfrastructure, Community Development, Capacity BuildingEric Lyons, Univ of Ariz./CyVerse Sunday, Jan 14 2:15 PM (California)
P0739The Federated Plant Database Initiative for the LegumesAndrew Farmer, NCGR 
P0112SciApps: A Web-Based Platform for Reproducible Bioinformatics WorkflowsZhenyuan Lu, CSHL 
P0064Development of a Gene Family Toolkit for Exploring Diversity in New Sequence DataPaul Bailey, Earlham Institute 
P0054G-OnRamp: Create Genome Browsers for Collaborative Eukaryotic Genome AnnotationsYating Liu, Wash. Univ. St. Louis 
P0238AgBioData: Identifying and Meeting Common Goals in the Management of Agricultural Biological DataRamona Walls, Univ of Ariz./CyVerse 

Social Media

Stay in touch with us throughout the event!

Twitter:  @CyVerseOrg


CyVerse is funded by the National Science Foundation under Grant No. DBI-0735191 and DBI-1265383.

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