2018 Plant and Animal Genome Meeting (PAG XXVI)
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
Speakers
Time | Speaker/Affiliation | Abstract ID/Title |
|---|---|---|
08:10 | Carolina Sempertegui, Truman State University, Kirksville, MO | Next Generation RNA Sequencing: Facilitating Undergraduate Research |
| 08:40 | Victoria Hernandez, William Floyd High School, Mastic Beach, NY | Integrating Bioinformatics Tools in the High School Classroom |
| 09:10 | Oliver Hyman, Elizabeth Doyle, Andrea Pesce and Ray A. Enke, James Madison University, Harrisonburg, VA | CURE-All: Large Scale Implementation of Authentic DNA Barcoding Research into a Freshman Biology Curriculum |
| 09:40 | Nicola Anthony, University of New Orleans | Building Capacity for Genomics Data Analysis in Resource-Limited Environments |
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
Speakers
| Time | Speaker/Affiliation | Abstract ID/Title |
|---|---|---|
| 10:40 | Konstantinos Krampis, CUNY Weil-Cornel Medical College | |
| 10:57 | Carolyn Lawrence-Dill, Iowa State Univ. | |
| 11:14 | Brian Lee, UCSC | Benefits of Track Hubs and Byte-Range Requests |
| 11:31 | Hadi Quesneville, URGI, INRA, Université Paris-Saclay | An E-Infrastructure Model for the Plant Research Communities |
| 11:48 | Monica Poelchau, USDA/Agricultural Research Service/National Agricultural Library | |
| 12:05 | Sam Hokin, NCGR | Employ a Task List (AKA “Scavenger Hunt”) to Engage your Audience when Presenting your Software |
| 12:22 | Asher K Haug-Baltzell, 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
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
Speakers
Time | Speaker/Affiliation | Abstract ID/Title |
|---|---|---|
6:10 | Parker Antin, University of Arizona, Tucson, AZ | |
| 6:20 | Benjamin 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 | |
| 6:40 | Sarah 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, WI | A 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, WI | TIPS: A System for Automated Image-Based Phenotyping of Maize Tassels |
| 7:00 | Celeste Marie Falcon, University of Wisconsin-Madison, Madison, WI | Genetic Study of Maize Yield-Component Traits Measured by Automated Image Analysis |
| 7:10 | Cory D. Hirsch, University of Minnesota, St. Paul, MN | Machine Vision Phenotyping of Seedling Growth and Morphology |
| 7:30 | Paul C. Bailey, Earlham Institute, Norwich, United Kingdom | Development of a Gene Family Toolkit for Exploring Diversity in New Sequence Data |
| 7:45 | Alice Minotto1, Erik Van Den Bergh2 and Robert P. Davey1, (1)Earlham Institute, Norwich, United Kingdom, (2)EMBL-EBI, Hinxton, United Kingdom | CyVerse UK: Widening the Scope to the UK and Beyond |
| 8:00 | Brian Lee, UCSC, Santa Cruz, CA | Viewing 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.
Day | Time | Event |
|---|---|---|
Sunday | 3:00-8:30 | Booth Open |
Monday | 9:30-5:00 | Booth Open |
Tuesday | 9:30-3:00 | 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 - info@CyVerse.org
Social Media
Stay in touch with us throughout the event!
Twitter: @CyVerseOrg
Facebook: facebook.com/CyVerse.org
CyVerse is funded by the National Science Foundation under Grant No. DBI-0735191 and DBI-1265383.