XSEDE in the News
XSEDE: More Than Just Supercomputers — It’s How To Use Them, Too!
To many familiar with the world of high-performance computing, the Extreme Science and Engineering Discovery Environment (XSEDE) means ‘supercomputers’ and not much more. Often, success stories involve a research team using XSEDE-allocated supercomputers like Stampede at the Texas Advanced Computing Center (TACC) or Comet at the San Diego Supercomputer Center. But what good are supercomputers without the expertise throughout the community to properly use them? Even worse, what good is training if the community is not aware of it? XSEDE is preparing the current and next generation of computational scientists by providing a full slate of training opportunities across the country. XSEDE’s outreach efforts and ability to give users tools to enhance their science are important steps toward breakthrough learning systems coming in the near future. Fully integrated, established training environments like CI-Tutor (est. 2000) and the Cornell Virtual Workshop (est. 1995) have long been part of the XSEDE landscape. To read more, please visit http://www.isgtw.org/spotlight/xsede-more-just-supercomputers-%E2%80%94-it%E2%80%99s-how-use-them-too
San Diego Supercomputer Center, University of California, San Diego
NSF and SDSC Give Trestles Supercomputer to U of Arkansas
A workhorse of a supercomputer is coming to the University of Arkansas.The National Science Foundation and the San Diego Supercomputer Center at the University of California, San Diego, have agreed to transfer ownership of the computer cluster known as “Trestles” to the Arkansas High Performance Computing Center. Once installed, the new supercomputer will more than double the center’s computational capacity and allow it to run three times the amount of jobs for campus researchers, said David Chaffin and Jeff Pummill, interim co-directors of the center. “We are thrilled to acquire a prominent national resource for high performance computing,” Pummill said. “Researchers at the University of Arkansas are in a perpetual state of evolution and advancement in their computational needs, and Trestles is known throughout the national high-performance computing community as a ‘high-productivity workhorse.’” The Arkansas High Performance Computing Center, founded in 2008, supports research for about 260 users in about 30 academic areas across the campus, including bioinformatics, physics, integrated nanoscience, computational chemistry, computational biomagnetics, materials science and spatial science, among others. To read more, please visit http://www.sdsc.edu.
WoRDS Center Workflow Hackathon
November 4, 2015 – San Diego, California
WorDS Center Workflow Hackathons are made for you and your application! Come and taste the spirit of collaborative development while you focus on the workflows for your applications. Centered around your individual usecases, we will help you hack workflow-driven applications from building a prototype of your workflows from scratch, running your workflows on HPC/cloud/cluster resources, making your workflow products reproducible through provenance tracking, and wrapping your workflows as web applications. The day will start with a crash course on workflow concepts and workflow systems. Each attendee will then focus on building the workflow for an application of his/her choice. Attendees without predefined usecases will be provided a list of workflows to choose from at varying complexity levels of basic, moderate and advanced. For more information, please visit http://words.sdsc.edu/h/2.
Texas Advanced Supercomputing Center, University of Texas, Austin
UT Austin Researchers Use Supercomputing to Assess the Impact of Climate Change on the Country's Growing Season
Malawi, a small landlocked country in southeast Africa, is home to 13 million people and is one of the least-developed countries in the world. As a nation that relies on subsistence farming, its security is highly dependent on rain-fed agriculture, including the crops maize, rice, and sweet potatoes. Changes in rainfall patterns associated with climate change can be devastating to people living in the country, leading to food crises, famines, and loss of life. Two researchers at The University of Texas at Austin, Kerry Cook and Edward (Ned) Vizy, are dedicated to understanding how climate change and climate variability will impact Malawi and other regions throughout Africa. By running regional climate models, Cook and Vizy are examining Africa's diverse climate zones, ranging from the monsoon regions in West Africa and the Horn of Africa to the central tropics to the desert region in the north. Cook and Vizy's findings on how climate change will impact Malawi's agricultural growing season were recently published in the journal Climate Dynamics. To read more, please visit https://www.tacc.utexas.edu/-/simulating-seasons.
Code @ TACC: Summer High School Stem Program
Session I: June 15-26, 2015 – Austin, Texas
Session II: July 13-24, 2015 – Austin, Texas
Application Deadline – May 31, 2015
Notification – June 7, 2015
Code @ TACC is an innovative and exciting summer program that incorporates a project based learning approach to expose students to Science, Technology, Engineering, and Math (STEM) careers. Students will foster their talent and creativity by being introduced to the principles of high performance computing, life sciences, networking, robotics, and electronics. All students are welcome to apply. We encourage the participation of underrepresented students in the experience, especially those with limited access to technology. We believe that everyone has an opportunity to contribute to the technological economy because we all bring unique perspectives and abilities to the table. Free of cost for selected participants! For more information, please visit https://www.tacc.utexas.edu/education/stem-programs/code-at-tacc.
Pittsburgh Supercomputing Center
PSC Helps Power Human-AI Poker Match-Up
First, Deep Blue came for Kasparov, besting the world’s top-ranked chess player in 1997. Then Watson beat Jeopardy!’s best and brightest in 2011. Now Claudico, a program developed at Carnegie Mellon University using high performance computing thanks to an XSEDE allocation on Pittsburgh Supercomputing Center’s Blacklight system, will take on the next great challenge in machine learning: facing off against four of the world’s top 10 players at no-limit, heads-up Texas hold ’em poker. Read the CMU press release https://www.cs.cmu.edu/brains-vs-ai. The two-week “Brains vs. Artificial Intelligence” tournament begins today at Rivers Casino in Pittsburgh, with poker pros Doug Polk, Dong Kim, Bjorn Li and Jason Les facing off against Claudico. Unlike earlier human-machine poker matches involving bid-limited Texas hold ’em, this competition will involve the vastly more complex unlimited version, which offers 10161 (1 followed by 161 zeroes) possible game situations. To read more, please visit https://www.psc.edu/index.php/news-and-media/press-releases/1944-blacklight-helps-power-human-ai-poker-match-up.
Study Suggests Vial Size Can Have Large Impact on Vaccine Supply Chain
Vaccine vial size – the total number of doses a single vaccine vial contains – can have a significant impact on vaccine distribution, costs and use, according to a new study by researchers at the Pittsburgh Supercomputing Center (PSC) and the Johns Hopkins Bloomberg School of Public Health. In a computer model of the vaccine supply chain of the West African nation of Benin, vial-size decisions had far-reaching and reverberating effects throughout the vaccine supply chain. Vial size greatly impacted supply chain logistics, increasing and decreasing constraints and bottlenecks depending on the combination of vial sizes used, with considerable effect on the availability of vaccines. The output of the model, generated by the HERMES software platform developed at Hopkins and PSC, holds great promise for improving the supply of vaccines and other medical tools in Benin, low-income nations and the entire world. To read more, please visit http://www.psc.edu/index.php/news-and-media/press-releases/1950-vial-size-impacts-vaccine-supply-chain.
Ohio Supercomputer Center
Large-Scale Systems Biology Research at OSC
Traditional molecular biology approach to study gene expression and gene regulation is based on an ad hoc individual analysis that is very laborious. Moreover, the data collected in this way is of isolated status and thus may not truly reflect the real characteristics of the cell or organism. With the advent of genome sequencing and high-throughput measurement technologies, comprehensive data can be collected at the system level or at the whole genome-scale. Particularly, gene expression microarray technology is revolutionizing many aspects of biological research as it allows monitoring many thousands of gene transcripts simultaneously. This provides powerful tools for the genome-wide correlation of gene transcript levels with physiological responses and alterations in physiological states to assess various biological models, including disease, therapy, or experimental manipulation. Recently, chromatin immunoprecipitation technology has been coupled with the high-throughput DNA microarray (CHIP-on-Chip) to study the protein-DNA binding assay at the genome-scale level. With the combined high-throughput data in both gene expression and bind assay, the gene regulatory network could be solidly constructed at the genome-wide level using sophisticated computer algorithms, such as GRAM, REDUCE, modified MOTIF REGRESSOR, etc. To continue reading, please visit https://www.osc.edu/research/bioinformatics/projects/gene_expression.
Statewide User's Group Meeting
June 4, 2015 – Columbus, Ohio
Abstract Deadline – May 13, 2015
Notification Deadline – May 15, 2015
The purposes of the SUG meeting are to highlight new scientific developments produced using OSC resources, foster connections between OSC staff and the SUG members, and get constructive feedback as to the future of OSC and its role in supporting science across Ohio. During the meeting in the morning (starting at 10:30 a.m.), there will be a ‘Face OSCHelp’ session, enabling interactions between the current/potential OSC clients and OSC staff. In the afternoon, we will host two half-hour keynotes on areas of interest to OSC clients. Free lunch and snacks will be provided. After the SUG meeting, we will reconvene in one of the active social neighborhoods of Columbus for drinks, dinner and networking. To register, please visit https://www.osc.edu/calendar/events/statewide_users_group_meeting_0.
Oak Ridge National Laboratory
Technology That Overcomes Movement During Imaging
Jefferson Lab, in collaboration with Oak Ridge National Laboratory and Johns Hopkins University, has been developing a system for imaging in un-anesthetized, unrestrained mice. Basic research into human disease states and pharmaceutical development depend heavily on biomedical investigations involving animal models. But studies are limited by the necessity of using anesthetic and/or physical restraint during imaging. Jefferson Lab technology has been used in an awake animal study. Unique mouse brain studies of gamma-ray emitting molecules are now underway at JHU with this never before available technology. This methodology is now being extended to explore new ways to facilitate radioisotope imaging for plant biologists involved in bio-fuel and environmental research. Free-electron lasers (FELs) offer substantial cost and capability advantages—including advantages for high-volume materials processing—over other manufacturing tools. FELs based on Jefferson Lab’s superconducting electron-accelerating technology are being developed to process plastics, synthetic fibers, advanced materials, and metals as well as components for electronics, microtechnology, and nanotechnology. To continue reading, please visit http://www3.sura.org/~suraorg/programs/jefferson-lab/research-in-action-2/.
UT KNOXVILLE Presents National Instruments Engineering Technology Road Show
May 19, 2015 – Knoxville, Tennessee
See the latest technologies and trends in data acquisition, embedded control and monitoring and test. Join us for in-depth technical presentations, live product demonstrations and consultations with NI field engineers on your application needs. In this session, explore measurement, control and test system challenges that often stretch the limits of configuration-based design. Learn the key considerations when configuring your next system to meet your application needs and minimize development time. For more information, please visit http://www.utk.edu/events/index.php?com=detail&eID=59102.
Shodor Education Foundation
SUCCEED Apprenticeship Program for High School Students
October, 2015 – August, 2016 – Durham, North Carolina
Applications – Open August 1, 2015
The SUCCEED Apprenticeship Program seeks to develop and evaluate activities and support mechanisms that move students from an excitement for computational science and information technology (IT) to having experience and developing expertise. Students learn one or more areas of computational science and associated use of technologies, techniques, and tools of IT, within the context of STEM. The program has made significant progress in developing and evaluating a methodology for bridging this excitement-expertise gap for upper-middle and high school students. The SUCCEED Apprenticeship Program draws students from diverse backgrounds to STEM fields through its dynamic, hands-on learning experience. For more information, and to apply, please visit https://www.shodor.org/succeed/apprenticeships/.
LittleFe Curriculum Module Buildout
July 7-10, 2015 - Durham, North Carolina
Notification – June 7, 2015
Teams from past LittleFe Buildout events will bring their LittleFe/BCCD units to a workshop to share ideas and best practices for developing new curriculum in a "Buildout-style" assembly of new curriculum modules. We would like you and a colleague or student working directly with you on LittleFe/BCCD curriculum or classroom use to attend as a team, but this is not a requirement. For more information, please visit http://www.computationalscience.org/workshops/9980.
Indiana University
IU Wins Nearly $9 Million to Manage, Improve International Research Networks
Two new National Science Foundation grants to Indiana University -- totaling $8.6 million -- call on long-standing expertise to manage and analyze the networks that power the agency's international research and education collaborations. IU has now earned more than $13 million in NSF international networking awards this year. The IU Global Research Network Operations Center, or GlobalNOC, won a $3.6 million award to manage the Network Operations Center for the NSF's International Research Network Connections-funded infrastructure projects. The program supports the continuous high-performance network connectivity required by today’s researchers to analyze and share vast amounts of data with colleagues around the world. To read more, please visit http://news.iu.edu/releases/iu/2015/05/nsf-networking-awards.shtml.
Long-Term Study on Ticks Reveals Shifting Migration Patterns, Disease Risks
Over nearly 15 years spent studying ticks, Indiana University's Keith Clay has found southern Indiana to be an oasis free from Lyme disease, the condition most associated with these arachnids that are the second most common parasitic disease vector on Earth. He has also seen signs that this low-risk environment is changing, both in Indiana and in other regions of the U.S.A Distinguished Professor in the IU Bloomington College of Arts and Sciences' Department of Biology, Clay has received support for his research on ticks from over $2.7 million in grants from the National Science Foundation-National Institutes of Health's Ecology and Evolution of Infectious Diseases Program and others. Clay's lab has found relatively few pathogens in southern Indiana ticks that cause common tick-borne diseases compared to the Northeast and states like Wisconsin and Minnesota. To read more, please visit http://news.indiana.edu/releases/iu/2015/05/tick-microbiome.shtml.
Michigan State University
Tortoise Approach Works Best – Even For Evolution
When it comes to winning evolutionary fitness races, the tortoise once again prevails over the hare. In the current issue of Proceedings of the National Academy of Sciences, a team of BEACON scientists centered at Michigan State University found that limiting migrations among populations of bacteria produced better adaptations. The cost, however, was that the bacteria evolved slower. Taking your time, however, isn’t always a bad thing, said Joshua Nahum, MSU biocomputational research associate. All living organisms rely on evolution by natural selection to better adapt to their environment. This adaptation requires mutations, or changes in DNA, that improve reproductive success, referred to as fitness. Rather than a racetrack, though, these tortoises and hares are competing on a landscape riddled with hills, elevations that represent populations with the highest level of fitness. To read more, please visit http://msutoday.msu.edu/news/2015/tortoise-approach-works-best-even-for-evolution/?utm_campaign=standard-promo&utm_source=msuedu-news-links&utm_medium=msuhome.
Certification in College Teaching Institute
May 14-15, 2015 - East Lansing, Michigan
The Graduate School invites you to an intensive program that will help fulfill the workshop portion of the requirements for the MSU Certification in College Teaching (CCTP). Over the course of two days, featured speakers will focus on teaching with technology, assessing student learning outcomes, creating effective learning environments through writing, and developing teaching portfolios for different kinds of academic institutions. Through a combination of interactive group sessions and focused breakouts, you will gain skills in core competency areas of the Certification, plan a mentored teaching project, and develop the template for your final portfolio. The Certification is designed for doctoral students and postdocs preparing to become faculty members in a college or university. The CCTP culminates in an e-portfolio that will help students prepare for academic job interviews and plan for their professional development as early career faculty. Doctoral students who successfully complete all requirements will receive a designation of the Certification on their MSU transcript. For more information, please visit http://grad.msu.edu/workshops/workshops.aspx?id=131.
National Center for Atmospheric Research
2015 Gsi/Enkf Community Tutorial
August 11-14, 2015 – Boulder, Colorado
The combined Gridpoint Statistical Interpolation and Ensemble Kalman Filter (GSI/EnKF) Community Data Assimilation System Tutorial will be offered at the NCAR Foothills Laboratory, in Boulder, Colorado on August 11-14, 2015. This will be the sixth Community GSI tutorial, but the first time EnKF will be included. GSI is the operational data assimilation (DA) system being used by various national operational and research centers, including NOAA and the National Aeronautics and Space Administration (NASA). It is traditionally a three-dimensional variational DA system and has been extended to run with advanced features, including the hybrid ensemble-variational data assimilation technique and the four dimensional EnVAR technique. The EnKF system is a Monte-Carlo algorithm for data assimilation that uses an ensemble of short-term forecasts to estimate the background-error covariance in the Kalman Filter. For more information, please visit http://www.dtcenter.org/com-GSI/users/tutorials/2015.php.
Hao Colloquium Series Maxim Kramar (Nasa/Catholic University Of America)
May 27, 2015 - 1:30pm MDT
Measurement of the coronal magnetic field is a crucial ingredient in understanding the nature of solar coronal phenomena at all scales. A significant progress has been recently achieved here with deployment of the Coronal Multichannel Polarimeter (CoMP) of the High Altitude Observatory (HAO). The instrument provides polarization measurements of Fe xiii 10747 A forbidden line emission. The observed polarization are the result of a line-of-sight (LOS) integration through a nonuniform temperature, density and magnetic field distribution. In order resolve the LOS problem and utilize this type of data, the vector tomography method has been developed for 3D reconstruction of the coronal magnetic field. The 3D electron density and temperature, needed as additional input, have been reconstructed by tomography method based on STEREO/EUVI data. We will present the 3D coronal magnetic field and associated 3D curl B, density, and temperature resulted from these inversions. To watch, please visit https://ucarconnect.ucar.edu/live?room=cg12126&_ga=1.256970882.827280332.1431029351.
National Center for Supercomputing Applications - University of Illinois at Urbana-Champaign
Tiny Silicone Spheres Come Out Of the Mist
Technology in common household humidifiers could enable the next wave of high-tech medical imaging and targeted medicine, thanks to a new method for making tiny silicone microspheres developed by chemists at the University of Illinois. Led by chemistry professor Kenneth Suslick, the researchers published their results in the journal Advanced Science. Microspheres, tiny spheres as small as a red blood cell, have shown promise as agents for targeted drug delivery to tissues, as contrast agents for medical imaging, and in industrial applications. One prime contender as a material for microspheres is silicone, the rubbery plastic found in everything from bathtub caulk to kitchenware to medical implants, but a method of making silicone into microspheres has eluded scientists. Silicone owes its versatility to its unique combination of properties: It is biocompatible, heat resistant, chemically stable, waterproof and environmentally benign. To read more, please visit http://news.illinois.edu/news/15/0506Silicone_Microspheres_KennethSuslick.html.
Report: Brain-Injured Patients Need Therapies Based On Cognitive Neuroscience
Patients with traumatic brain injuries are not benefiting from recent advances in cognitive neuroscience research – and they should be, scientists report in a special issue of Current Opinion in Behavioral Sciences. Those who treat brain-injured patients rarely make use of new scientific discoveries about the workings of the brain. Instead, doctors, nurses and emergency personnel rely on a decades-old tool, the Glasgow coma scale, to categorize brain injuries as mild, moderate or severe. Brain scans are sometimes performed to help identify damaged regions, and then most patients receive one or more of the following four diagnoses: coma (no response to sensory stimulation), delirium (impaired ability to sustain attention), amnesia (impaired memory) and dysexecutive syndrome (impaired ability to engage in goal-directed thought). To read more, please visit http://news.illinois.edu/news/15/0429braintrauma_aronbarbey.html.
National Institute for Computational Sciences
Earth, Wind, & Fire: A Computer Model Combination Could Unravel the Mysteries of Sudden Firestorms
The thought of a wildfire evokes images of firefighting crews, airplanes, and helicopters battling the blaze. But fire analysts and managers have other weapons in their arsenal to plan the attack before sending resources out. Among those are computer-model wildfire forecasts. For many years, Smith has been involved with teams strategizing to suppress some of the biggest wildfires across Texas and the nation, and so he’s familiar with the important questions that wildfire computer model forecasts can help answer: What do we need to do with our resources? How long will the battle take? What are the chances of success? What is the potential for the fire to move into values at risk, whether a community, homestead, or something else? Smith sees the models as another important input in decision support, along with first-hand accounts, reports from a network of weather stations, reports on vegetation (fuels to the fire), maps, or other data. To read more, please visit https://www.nics.tennessee.edu/wildfire-modeling.
Taking R Training to the World: Tutorial Resonates with People Eager to Know More About a Popular Research Tool
R, the free open-source software environment for statistical computing and graphics, brings out a crowd. In fact, so much so that a recent online and in-person tutorial on the subject broke training participation records for the event's organizers—the National Institute for Computational Sciences (NICS), the Extreme Science and Engineering Discovery Environment (XSEDE), and the National Institute for Mathematical and Biological Synthesis (NIMBioS). Approximately 800 people worldwide signed up for the four-hour, online and in-person tutorial on “Using R for HPC [High-performance Computing].” More than 420 logged in to watch online, and thirty of the participants were on site at the venue for the event, the NIMBioS presentation room in the Claxton Education Building at the University of Tennessee, Knoxville. To read more, please visit https://www.nics.tennessee.edu/r-tutorial-worldwide-2015.
Purdue University
Studies: Science-Based Response Lacking In Chemical Disasters
Three new studies suggest that when communities are hit with disasters that contaminate drinking water the official decision-making and response often lack scientific basis. The result has been an inability to fully anticipate public health risks and effectively rid plumbing systems of contaminants, sometimes exposing residents to toxic chemicals, said Andrew Whelton, an assistant professor in Purdue University's Division of Environmental and Ecological Engineering and Lyles School of Civil Engineering. Since 2014 more than 1.5 million people across the nation have received drinking water tainted with crude oil, diesel fuel, algal toxins and coal-washing chemicals. His team has been examining recent disasters in which tainted drinking water was distributed to homes. To read more, please visit http://www.purdue.edu/newsroom/releases/2015/Q2/studies-science-based-response-lacking-in-chemical-disasters.html.
Southeastern Universities Research Association
Technology That Overcomes Movement During Imaging
Jefferson Lab, in collaboration with Oak Ridge National Laboratory and Johns Hopkins University, has been developing a system for imaging in un-anesthetized, unrestrained mice. Basic research into human disease states and pharmaceutical development depend heavily on biomedical investigations involving animal models. But studies are limited by the necessity of using anesthetic and/or physical restraint during imaging. Jefferson Lab technology has been used in an awake animal study. Unique mouse brain studies of gamma-ray emitting molecules are now underway at JHU with this never before available technology. This methodology is now being extended to explore new ways to facilitate radioisotope imaging for plant biologists involved in bio-fuel and environmental research. To read more about developing technology at SURA, please visit http://www3.sura.org/~suraorg/programs/jefferson-lab/research-in-action-2/.
XSEDE Friends and Their Research
Biting Back: Scientists Aim to Forecast West Nile Outbreaks
New research has identified correlations between weather conditions and the occurrence of West Nile virus disease in the United States, raising the possibility of being able to better predict outbreaks. The study, by researchers with the National Center for Atmospheric Research (NCAR) and the Centers for Disease Control and Prevention (CDC), finds strong correlations across much of the country between an increased occurrence of West Nile virus disease and above average temperatures in the preceding year. The scientists also find that precipitation influences subsequent disease outbreaks, although the impacts vary by region. The weather may influence West Nile virus activity by affecting the breeding habitats and abundance of Culex species mosquitoes, which transmit the virus. The weather may also have other impacts, such as affecting populations of infected birds that pass on the virus to mosquitoes. The study appears this week in the American Journal of Tropical Medicine and Hygiene. It was funded by CDC and the National Science Foundation, which is NCAR’s sponsor. To continue reading, please visit https://www2.ucar.edu/atmosnews/news/15431/biting-back-scientists-aim-forecast-west-nile-outbreaks.
