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CyVerse Events at PAG XXV

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 14th

[4244] CyVerse Education: DNA Subway, Data Science, and Microbial Genomics

Time: 08:00AM - 10:10 AM

Location: California Room

PAG Online Program Link: Session 4244

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


Stacia E. Rodenbusch, University of Texas at Austin, Austin, TX

How does an early Course-based Undergraduate Research Experience (CURE) program affect students’ success and persistence in science?

08:40  Oliver Hyman and Ray A. Enke, James Madison University, Harrisonburg, VA  Large-Scale Implementation of DNA Barcoding in Freshman Biology
09:10Maria Brown, Sayville High School, Sayville, NY  Microbiome Studies in the High School Research in Science & Engineering Program: A Primer in Workforce Development
09:40Joslynn Lee, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY  Data Science Challenges and Solutions for Student Microbiome Research

[4249] Connecting Crop Phenotype Data

Workshop Time:10:30AM - 12:40 PM

Featured CyVerse Talk: W203 "CyVerse Data Commons" 

Time: 11:20AM - 11:50 AM

Presenter: Ramona Walls

Location: California Room

PAG Online Program Link: Session 4244


The Data Commons (DC) is a new service offered by CyVerse to support its vision of transforming science through data-driven discovery. The DC strives to build a space where data can live as a searchable, discoverable, and reusable resource. DC development builds on foundational CyVerse infrastructure such as the Data Store, APIs, and user interfaces like the Discovery Environment (DE), while expanding into new areas such as metadata and ontologies, data publication, and federation with external collaborators and repositories. Key components of the Data Commons are the data portal at, and newer functions within the DE such as metadata templates, permanent identifier requests, data submissions to NCBI, and a Projects Interface (under development). A key asset of the CyVerse DC is its co-location with CyVerse computational resources, which facilitates data re-use. This presentation will introduce you to features of the Data Commons that are available now and provide a preview of some features under development, with an eye toward how those features can support interoperability of crop phenotype data.

Sunday, January 15th


[4113] CyVerse User Meeting - Tools and Resources Demos

Time: 3:00PM - 5:00 PM

Location: Sheffield Room (See Sheffield Room on Map)

PAG Online Program Link: Session 4113


Workshop Description

CyVerse 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 and to gather feedback from our users. We will guide attendees through their choice of demos on our capabilities for 1) Data storage/sharing/management; 2)RNA-Seq, Genome Assembly, and other common genomics workflows including Methylation analysis and assembly of PacBio reads. Whether you are a long-time CyVerse/iPlant user, or are just getting introduced, we invite you to stop by, ask questions, or just say hello!

Organizer: Kapeel Chougule and Jason Williams

CyVerse Booth #502 (Open from 3:00PM - 8:30PM)

Monday, January 16th

[4198] CyVerse - Software, Tools, and Services for Data-Driven Discovery

Time: 6:10PM - 8:20 PM

Location: California Room

PAG Online Program Link: Session 4198

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

Overview of the CyVerse  

6:30Naser Alkhalifah, Iowa State University, Ames, IA

The Maize Genomes to Fields Initiative: Data Discovery and Reuse

6:50Zain A. Alvi, Seton Hall University, South Orange, NJ Genomic and Expression Analysis of Spermatid Nuclear Transition Proteins in Sequenced Drosophila Species
7:10  Matthew Vaughn, Texas Advanced Computing Center, Austin, TX Jetstream: On-Demand Cloud Computing for Life Sciences Research and Education
7:30Annemarie Eckes, Earlham Institute, Norwich, United Kingdom Cyverse for Brassica: Performing Associative Transcriptomics By Integrating with Sequence and Phenotype Repositories
7:50Liya Wang, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY A Cyverse Powered Data Coordination Center (DCC) for Maizecode
8:10Jawon Song, Texas Advanced Computing Center, Austin, TX Methylation Pipelines in CyVerse

Workshop Description

Calling all bioinformaticians and bioinformatics enthusiasts! CyVerse is hosting a small get together on a variety of topics relevant to making bioinformatics accessible and open to all communities. We will also have time to cover more questions on the new CyVerse project - specifically how developers can participate and how collaborative science projects can make use of CyVerse. If you are working on a collaborative science projects, 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.

Organizer: Jason Williams, Matt Vaughn

See Stratford Room on Map

Tuesday, January 17th

Visit our Booth (#502)

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

Related workshops, presentations, and posters  

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



Presenter/ Affiliation

Time/Location info

Workshop 4221

Interoperability and Federation Across Bioinformatic Platforms and Resources:

Eric Lyons, Organizer

Sat. Jan 14
10:30 AM - 12:40 PM


The Legume Information System ( and The Legume Federation ( Comparative Genomics and Genetics through Cooperative Resource Development

Andrew Farmer, National Center for Genome Resources (NCGR)

Mon, Jan 16

3:00 - 4:30 PM

Grand Exhibit Hall


Data Stewardship in the Life Sciences

Robert Davey, Earlham Institute

Sat. Jan 14

4:00 -4:15 PM

Pacific Salon 4-5

(2nd Floor)


RNA-Seq Analysis of Chicken Primordial Germ Cells (PGCs) for Identification of Sexually Dimorphic Gene Expression and Downstream Metabolic Pathways

Sohita Ojha, University of Arkansas, Fayetteville

Mon, Jan 16

3:00 - 4:30 PM

Grand Exhibit Hall



Fiona McCarthy, University of Arizona

Wed. Jan 18

12:12 - 12:30 PM

Pacific Salon 1


User-Friendly Whole Genome DNA Methylation Analysis With FlowGe

Jeffrey Grover, University of Arizona

Mon, Jan 16

3:00 - 4:30 PM

Grand Exhibit Hall


The Federated Plant Database Initiative for the Legumes

Steven Cannon, USDA-ARS CICGRU

Mon, Jan 16

3:00 - 4:30 PM

Grand Exhibit Hall


AgBioData: A Consortium of Agricultural Biological Databases

Jacqueline D. Campbell, Iowa State University

Mon, Jan 16

3:00 - 4:30 PM

Grand Exhibit Hall


COPO: A Data Stewardship Platform for Plant Scientists

Felix Shaw, Earlham Institute

Wed. Jan 18,

10:30 -10:45 AM



The Brassica Information Portal: Towards Integrating Phenotype and Genotype Data.

Annemarie Eckes, Earlham Institute

Mon, Jan 16

1:20 PM


W872The Importance of Making a Presence at Diversity-Focused ConferencesJoslynn Lee, Cold Spring Harbor Laboratory, DNA Learning Center

Tues, Jan 17

11:50 - 12:15PM

Esquire - Meeting House

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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