Better storm surge modeling using high performance computing

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From left to right: RENCI’s Casey Averill, Brian Blanton and John McGee

When hurricanes or tropical storms head toward the North Carolina coast, RENCI’s Dell PowerEdge cluster, called Hatteras, springs into action, producing finely-detailed models of possible storm tracks and resulting coastal storm surge several times a day.

A recent upgrade to Hatteras means more capacity to produce  a large number of storm surge forecast ensembles and high-resolution models in less than three hours. The effort to upgrade Hatteras was documented in a recent case study developed by Dell.

Read the case study.

For more on RENCI’s coastal modeling work, see Coastal Hazards Modeling web page.

Software Skills for Scientists

Forty-five students from around the globe spent the last three weeks in classrooms at RENCI in Chapel Hill and at the National Center for Ecological Analysis and Synthesis (NCEAS) at the University of California, Santa Barbara, learning the software and technology skills needed for open, collaborative, and reproducible synthesis research.

Participants and instructors in the RENCI portion of the Open Science for Software course pose for a group photo on the final day of class.

Participants and instructors in the RENCI portion of the Open Science for Software course pose for a group photo on the final day of class.

The event was the Open Science for Synthesis (OSS) three-week workshop, held simultaneously on both coasts, with students and instructors at the two sites interacting using high-speed video collaboration tools. The workshop targeted early career scientists primarily in ecological, environmental and water science disciplines. According to Ray Idaszak, RENCI’s director of collaborative environments and lead coordinator of the RENCI portion of the workshop, the OSS workshop illustrates the value that a research institute can add to the educational offerings of a university.

“This course was an example of how a research institute can complement the educational infrastructure of a university,” Idaszak said. “It adds flexibility and deepens and enriches the educational experience for graduate students, post docs and early-career faculty. In the future, we hope the OSS can serve as a model for similar courses in other domains and that we can expand the participation and scope.”

Matt Jones, Director of Informatics Research and Development at NCEAS, said the multi-disciplinary course presents critical topics for early career ecological and environmental scientists that they aren’t getting through graduate education.

“Through OSS, we enrich participants understanding of data science, complementing their already strong subject area expertise and knowledge of statistics and analysis,” Jones said.  “These skills in data management, software design and development for science, and collaborative synthesis should be taught throughout graduate schools around the country.  OSS helps to fill that gap.”

The workshop weaved together several core themes using a mixture of instructive lectures, discussions, and exercises. These themes were reinforced—and injected into the real-time synthetic scientific research process—through daily work on group synthesis projects. Core themes included:

  • Collaboration modes and technologies, virtual collaboration
  • Data management, preservation, and sharing
  • Data manipulation, integration, and exploration
  • Scientific workflows and reproducible research
  • Agile and sustainable software practices
  • Data analysis and modeling
  • Communicating results to broad communities

The last day of the course was devoted to student teams reporting on their synthesis research projects. Topics included marine populations dynamics, land use intensity and its relationship to ecosystems, the drought that has affected California, the dimensions of biodiversity, plant community dynamics and multi-scale eco-hydrology.

Open Science for Synthesis was sponsored by the Institute for Sustainable Earth and Environmental Software (ISEES) at NCEAS and the Water Science Software Institute (WSSI) at RENCI, two National Science Foundation projects that are developing concepts for institutes for sustainable scientific software. The workshop collaboration was born out of the shared mission of the two sustainable software institute conceptualization efforts and was modeled after NCEAS’ successful Summer Institute 2013.

For more information, see http://www.nceas.ucsb.edu/OSS.

Putting data in its place

With many large data sets, place is an important component. From the emergency manager looking for the best evacuation route to the historian trying to understand urban development patterns over the years, people rely on geographically referenced data to meet a variety of research, business, and government needs.

RENCI’s Geoanalytics platform provides intuitive, map-based visualizations to help transform data into decisions. Among other applications, this free, open source software has been used to inform disaster response, study the spread of disease, and increase the accessibility of public records.

To learn more, read the RENCI Geoanalytics White Paper or visit the Geoanalytics@RENCI website.

Participants from around the world to participate in bicoastal Open Science for Synthesis course

CHAPEL HILL, NC and SANTA BARBARA, CA – A unique training course that will take place simultaneously on both U.S. coasts will get underway July 21 at RENCI headquarters in Chapel Hill, NC, and at the National Center for Ecological Analysis and Synthesis (NCEAS) at the University of California, Santa Barbara.

Open Science for Synthesis (OSS) is aimed at early career scientists who want to learn new software and technology skills needed for open, collaborative, and reproducible synthesis research. The three-week intensive program will run through August 8, with 45 participants who completed a competitive application process participating in the program.

During the three-week, bicoastal training, OSS participants will receive hands-on guided experience from a dynamic group of instructors assembled to provide a mixture of instructive lectures, discussions forums, exercises, and real-world application of skills to collaborative group synthesis research projects.

Participants who complete the program will gain direct experience and a greater understanding of best practices in the technical aspects that underlie successful open science and synthesis—from data discovery and integration to analysis and visualization. They will also learn techniques for collaborative scientific research, including virtual collaboration over the Internet.

Congratulations to all participants, who will travel to both course locations from sites around the globe.

RENCI Participants

  • Annie Adelson, Stanford University
  • Olivia Burge, University of Canterbury
  • Benjamin Carr, Boston University
  • Tony Chang, Montana State University
  • Jonathan Duncan, University of North Carolina at Chapel Hill
  • Emma Fuller, Princeton University
  • Tian Gan, Utah State University
  • Kelly Garbach, Loyola University Chicago
  • Edgar Gonzalez, Universidad Nacional Autonoma de Mexico
  • Monica Granados, McGill University
  • Elizabeth Kalies, University of Missouri/NC Museum of Natural Sciences
  • Ingrid Knapp, University of Hawaii, Manoa
  • Nina Lany, Dartmouth College
  • Marissa Lee, Duke University
  • Silvia Lomascolo, Universidad Nacional de Tucuman
  • John Lovette, University of North Carolina at Chapel Hill
  • Vanessa Michelou, University of Hawaii, Manoa
  • Pamela Reynolds, University of California, Davis
  • Zahra Samadi, University of South Carolina
  • Kes Schroer, Dartmouth College
  • Michael Treglia, Texas A&M University
  • Tyson Wepprich, North Carolina State University

 NCEAS Participants

  • Georgina Adams, Imperial College London
  • Timothy Assal, USGS/Colorado State University
  • Leah Bremer, Stanford University
  • Julia Buck, Sam Houston State University
  • Mary Donovan, University of Hawaii
  • Debora Drucker, EMBRAPA
  • Vicken Hillis, University of California, Davis
  • Megan Jennings, San Diego State University
  • Suzanne Langridge, University of California, Santa Cruz
  • Sparkle Malone, Rocky Mountain Research Station
  • Rachael Orben, University of California, Santa Cruz
  • Antonio Jesús Pérez Luque, University of Granada
  • Katherine Renwick, Colorado State University
  • Annie Schmidt, Point Blue Conservation Science
  • Paul Selmants, University of Hawaii, Manoa
  • Diego Sotomayor, York University
  • Brian Stock, Scripps Institution of Oceanography, University of California, San Diego
  • Lynn Sweet, University of California, Santa Barbara
  • Christopher Trisos, South African Environmental Observation Network
  • Mirela Tulbure, University of New South Wales
  • Sara Varela, Charles University
  • Lynn Waterhouse, Scripps Institution for Oceanography, University of California, San Diego
  • Jennifer Weaver, University of California, Berkeley
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REACH NC Resource Finder expands capabilities of successful statewide researcher portal

reachnc-logoCHAPEL HILL, NC – REACH NC, a Web portal that connects businesses, developers, government officials, other researchers and citizens to thousands of experts working in higher education and research institutions throughout North Carolina now helps users find university assets and resources across the state through a new tool called the REACH NC Resource Finder.

Powered by the eagle-i open-source tool from Harvard University (funded by Harvard Catalyst, The Harvard Clinical and Translational Science Center [grant number 1UL1 TR001102-01]), the Resource Finder allows users to locate facilities such as wet labs and service labs, and resources such as scientific instruments, clinical trial participation opportunities, and open source software. The Resource Finder is the first statewide implementation of its kind and was developed through a partnership with UNC General Administration, the North Carolina Biotechnology Center, the Renaissance Computing Institute (RENCI) and The North Carolina Translational and Clinical Sciences (NC TraCS) Institute at The University of North Carolina at Chapel Hill.

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Data visualization to fine-tune healthcare

RENCI teams up with Duke University researcher to use visualization to understand disease risk factors and symptoms.

The age of big data presents both great opportunities for new knowledge as well as challenges in figuring out how to interpret, organize and use such large quantities of data. Data analysis and management are especially important hurdles to overcome in medicine, where data can help physicians better understand and treat disease.

RENCI Senior Visualization Researcher David Borland, Ph.D., works with Ed Hammond, Ph.D, director of the Duke University Center for Health Informatics, to develop ways to improve physicians’ access to, and comprehension of, large sets of medical information by transforming the data into easy-to-understand visual formats.

This image shows results of a query of the Duke Medical Center Electronic Health Record (HER) system. The squares represent the top two users of the system and circles represent the queries they initiated—the bigger the circle the more the term was queried. Light red lines connecting query terms show the strength of the relationship between those terms. The green section shows terms used by both users. This visualization was used on existing data to better understand the kinds of queries made by users and see how queries relate to each other so that future visualizations could aggregate data in meaningful ways.

This image shows results of a query of the Duke Medical Center Electronic Health Record (HER) system. The squares represent the top two users of the system and circles represent the queries they initiated—the bigger the circle the more the term was queried. Light red lines connecting query terms show the strength of the relationship between those terms. The green section shows terms used by both users. This visualization was used on existing data to better understand the kinds of queries made by users and see how queries relate to each other so that future visualizations could aggregate data in meaningful ways.

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North Carolina researchers to demonstrate distributed computing as a defense against power grid cyber attacks

logoA nationwide team that includes researchers from RENCI (Renaissance Computing Institute at UNC Chapel Hill) and North Carolina State University will demonstrate how innovative cyber-physical systems can be used to prevent cyber attacks on power grids as part of the SmartAmerica Challenge and Expo, June 11 in Washington, D.C.

The event will showcase how cyber-physical systems and the “Internet of things” can boost American competitiveness, create new business opportunities and jobs, and improve the quality of life. Twenty-four teams, including the NC State-RENCI team, will show the potential benefits of integrated systems of cyber and physical technologies: for example, vehicles that can make their own way through a battlefield to pick up the wounded, or disaster response systems that can coordinate human first responders, robots and dogs.

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Data Matters summer short courses to focus on data issues in business and research

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Business managers, data analytics specialists, academic researchers, data center administrators and anyone else who grapples with big data are the target audience for a weeklong workshop series on data issues sponsored by the National Consortium for Data Science (NCDS), the Odum Institute for Social Science Research at UNC Chapel Hill, and the Renaissance Computing Institute (RENCI). Read more

Big data means big career opportunities, UNC students learn at NCDS career event

A full house for the NCDS Big Data Career Event

As a leader in the growing and evolving field of data science, the National Consortium for Data Science (NCDS) works to share knowledge and recruit a new generation of data researchers to innovate and solve challenges in organizing and managing data. Read more

iRODS 4.0 release brings popular data management tool to wider audience

iRODS-Consortium-Logo-DarkChapel Hill, NC, April 2, 2014 – The iRODS Consortium today announced the release of iRODS 4.0, a sustainable and production-oriented version of the iRODS (integrated Rule-Oriented Data System) data management platform. Read more