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
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 | |
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 | |
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
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)
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 | |
8:00 | Brian Lee, UCSC, Santa Cruz, CA |