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[Arabidopsis] iPlant Collaborative is now CyVerse; Upcoming events; Learning opps

Joanna Friesner via arab-gen%40net.bio.net (by jdfriesner from ucdavis.edu)
Wed Jan 13 11:04:26 EST 2016


Dear Community- 

I'd like to draw your attention to the new name and emphasis of the iPlant Collaborative, which is now CyVerse (www.cyverse.org). Subscribe to CyVerse newsletter for updates on events, resources and tools: http://www.cyverse.org/newsletter

Below some learning options I've listed is notation of an *upcoming CyVerse digital imaging of roots webinar* and a *US training opportunity for faculty* who wish to integrate biology and bioinformatics, essential for plant scientists in the 21st century. For all events see: http://www.cyverse.org/events

Additional CyVerse Learning Opportunities: 
 (1) Attend a one hour CyVerse orientation webinar, held monthly, usually the first Wednesday of the month. For January, it will be held at the end of the month. Newly registered users of CyVerse will be sent information on joining an orientation webinar. (2) Access the CyVerse Learning Center which includes tutorials for major CyVerse components and learn on your own time- e.g.  using RNA-Seq, GWAS, etc. http://www.cyverse.org/learning-center (3) Check out the CyVerse wiki for how-to instructions: https://pods.iplantcollaborative.org/wiki/dashboard.action.
(4) Use CyVerse Training Modules- slides and guides: https://pods.iplantcollaborative.org/wiki/pages/viewpage.action?pageId=8391124 (5) Subscribe to CyVerse newsletter to stay up to date on things: http://www.cyverse.org/newsletter 

***1 hour Webinar: Digital Imaging of Root Traits, with Alexander Bucksch, Georgia Inst. of Technology.***
 Jan. 29; 12 noon EST/11 am CST/ 10 a,m MST/ 9 am PST: http://www.cyverse.org/blog/events/webinar-digital-imaging-root-traits (register here)
This webinar will feature the Digital Imaging of Root Traits (DIRT) platform. DIRT is an online tool that enables plant scientists to obtain quantitative phenotype information on the root systems of plants imaged in the field. The program automatically provides dozens of phenotype measurements from images of plants. More information about DIRT is available at http://dirt.iplantcollaborative.org/welcome. 
This webinar is open to people who are using CyVerse resources and want to learn more about the specific topic. Users are encouraged to post questions and problems encountered to the Ask Forum for discussion during the webinar.
Alexander Bucksch received his PhD from the University of Technology in Delft, The Netherlands, for research focused on developing algorithms to extract tree crown parameters from laser scanning data. He obtained his Bachelor and Master's degrees for algorithmic research on plants at the Brandenburg University of Technology in Germany. At Georgia Institute of Technology he has been working to develop mathematical and computational approaches to describe plant architecture. DIRT is one such approach, allowing field scientists to do experiments with ten-thousands of samples to achieve highly significant results. In future, Bucksch plans to continue in the field of computational plant science doing ongoing phenomics research in linking individual plant morphology to the ecology level with novel computational methods.

**2 day educator workshop: GENOMICS IN EDUCATION WORKSHOP - UNIVERSITY OF DELAWARE** Feb 1-2, register at: http://www.cyverse.org/blog/events/genomics-education-workshop-university-delaware- This free workshop empowers college faculty to integrate modern methods for genome analysis into courses and student research projects. The workshop is for: Biology educators working with undergraduate students are our primary focus. However, educators working with advanced high school students, or graduate students and post-docs with teaching responsibilities will also benefit from attending. The majority of the workshop will focus on using the DNA Subway website to analyze DNA sequence with a variety of outcomes. We will understand how to determine the structure and function of genes, and learn more about the genomes of organisms around us. We will also do a hands-on DNA extraction (bring a leaf from your favorite plant) and use DNA Subway to identify the organism by DNA sequencing.

*CyVerse Press Release*
The National Science Foundation's premier data management platform for the life sciences has rebranded, shedding the project's original label of iPlant Collaborative and donning the new name CyVerse. The rebrand emphasizes the project's capacity to provide data management services beyond plant sciences, and across scientific disciplines.

"The CyVerse name reflects and communicates our expanded mission of enabling data-driven discovery across all of the life sciences," said Parker Antin, CyVerse's principal investigator as well as professor at the University of Arizona(UA)'s College of Medicine and associate dean for research of the UA College of Agriculture and Life Sciences, President of the Federation of American Societies for Experimental Biology (FASEB), and affiliate of the UA's BIO5 Institute.

The official launch of the new branding includes a new homepage at www.cyverse.org with a new look and layout, and updated logo, symbolizing the fluid momentum of data streams that are transforming modern science.
The vision for the new CyVerse brand, "transforming science through data-driven discovery," invokes the transformative power of big data, computational technology, and human intellect - all combined to enable scientific discovery.

"Given the UA's proud tradition of encouraging interdisciplinary work, it's not surprising that iPlant is expanding," said Kimberly Andrews Espy, UA senior vice president for research. "One of our main themes at the UA is to 'boundlessly collaborate,' and that is exactly what CyVerse is doing: breaking boundaries of data science and transforming how we do research."

The iPlant Collaborative was launched in 2008 with a $50 million grant from the National Science Foundation (NSF) to provide computational infrastructure for plant sciences. The project's early success led to a renewal grant in 2013, also worth $50 million, but with the expanded directive to serve all life sciences' data management needs.

"We are delighted the scientific research community has embraced iPlant and found new and exciting ways to make use of the platform, integrating it into forward-looking plans for data management and analysis," said Jane Silverthorne, deputy assistant director for NSF's Biological Sciences Directorate, which funds iPlant.

CyVerse is a continuing federation of four institutions led by the University of Arizona. Partner sites are the Texas Advanced Computing Center, Cold Spring Harbor Laboratory, and the University of North Carolina Wilmington.

"Over the past several years we have attracted thousands of users in all areas of biology, ecology, environmental sciences, geography, climate and even space sciences," Antin explained. "As more fields of science become driven by the acquisition and analysis of very large data sets, the need for ways to store, share, analyze and archive data and results are becoming critical requirements for scientific advancement. CyVerse provides a comprehensive platform for researchers to realize their goals."

"The work from iPlant has been a great benefit to plant scientists across the globe, but the computational infrastructure it provides goes far beyond that specific field," said Espy. "CyVerse really reflects those expanded capabilities, handling the computational infrastructure for everything from astronomy to zoology."

CyVerse aims to push boundaries continually and challenge the "convention" in conventional ways of doing science.

"We are guided by several future-focused goals," said Antin. "These include enabling data-driven discovery by providing deep data integration and analysis capabilities, fostering a growing ecosystem of interoperability across computational resources and platforms, and developing a sophisticated workforce through training of data scientists."

"I am honored to have the opportunity to lead a project with the potential to transform how science is conducted and accelerate scientific discovery across all areas of science," Antin added.
CyVerse is funded by NSF award numbers DBI-0735191 and DBI-1265383. 

Co-principal investigators include Eric Lyons and Nirav Merchant of the University of Arizona, Matthew Vaughn of Texas Advanced Computing Center, and Doreen Ware of Cold Spring Harbor Laboratory.
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Joanna Friesner, PhD
jdfriesner from ucdavis.edu
Coordinator
North American Arabidopsis Steering Committee (NAASC)




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