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IMPACT SEPTEMBER 2018

September 2018 | Science Highlights, Announcements & Upcoming Events
The Extreme Science and Engineering Discovery Environment (XSEDE) is an NSF-funded single virtual organization which connects scientists with advanced digital resources. People around the world use these resources and services — things like supercomputers, collections of data, expert staff and new tools — to improve our planet. Learn how XSEDE can enable your research here.
Science Highlights
Putting Neutrinos on Ice

Microscope images of a cell trying to get a foothold on a soft (A) and hard (B) substrate. The cell puts out a lamellipodium that grips the hard substrate, but only tests the soft one.

Identification of cosmic-ray source by IceCube Neutrino Observatory depended on global collaboration, XSEDE resources

Thanks to multiple XSEDE-allocated GPU and CPU resources, scientists running the IceCube Neutrino Observatory in Antartica and their international partners have answered a hundred-year-old scientific mystery: Where do cosmic rays come from?

Function Follows Form

View from the inside of a nerve cell. The synapse and the muscle cell are not pictured, but would be below the nerve cell's cell membrane, at the bottom. In the frog NMJ (A), neurotransmitter-containing packets (vesicles) waiting to be dumped into the synapse are arranged in two rows. (Vesicles are in red, calcium channels below the vesicles are small red dots, and the calcium ions diffusing in the nerve terminal are represented as small blue or yellow dots.) In the mouse (B), the vesicles are organized in clusters that each contain two vesicles. Simulations on Bridges showed that the frog system, when rearranged in clusters like the mouse, began to behave like the mouse NMJ.

Simulations on XSEDE-allocated resource plus lab work on frog neuromuscular junction sheds light on human diseases
When a nerve cell passes a message to its neighbors, it must do so via chemicals sent across the synapse—a small space between the cells. Early researchers studied a synapse called the frog neuromuscular junction (NMJ) because it is large and easy to work with. But its different organization and behavior compared to mammalian synapses led many scientists to dismiss it as not relevant to human biology. A team of University of Pittsburgh and XSEDE Extended Collaborative Support Services (ECSS) scientists performed simulations on the XSEDE-allocated Bridges supercomputer at the Pittsburgh Supercomputing Center (PSC) and parallel lab experiments on the frog and mouse NMJ. They showed that, when reorganized into the same geometric pattern as in the mouse, the components of the frog NMJ act like those in the mouse. Lessons from the work are already being used to design candidate drugs to treat human neuromuscular diseases.
XSEDE Researchers Visualize Massive Joplin, Missouri Tornado
Using XSEDE services and resources and the power of NCSA's Data Analysis and Visualization group, a pair of Illinois researchers were able to accurately simulate an EF-5 tornado in Joplin, MO from 2011.

What if we could peer into the formation of a tornado in hopes of better understanding it? Better yet, what if we could look into one of the deadliest and most unpredictable storm cells in recent memory? Thanks to XSEDE, visualization expert David Bock (National Center for Supercomputing Applications) and atmospheric science researcher Brian Jewett (University of Illinois) are doing just that, by working together to visualize a unique tornado that wreaked havoc on Joplin, Missouri in 2011.

Testing the Footing

Microscope images of a cell trying to get a foothold on a soft (A) and hard (B) substrate. The cell puts out a lamellipodium that grips the hard substrate, but only tests the soft one.

XSEDE-allocated resources help University of Chicago team simulate cell movement, upending scientific expectations

The movement of white blood cells to fight infections and the spread of cancer cells both rely on the same natural process. The cell reaches out to a new surface with a lamellipodium—a kind of tiny foot that tests the surface like we'd test ice before stepping onto it. As part of a multi-institutional collaboration, a team from the University of Chicago simulated how the lamellipodium works, using XSEDE-allocated resources and online training tools in concert with laboratory experiments. Their virtual cells duplicated their lab findings perfectly, showing how integrin and fibronectin—two proteins scientists had previously not expected to play a role—tug on the surface before the cell commits to moving onto it. The discovery points to possible ways for doctors to encourage good cell movement and discourage bad cell movement.

Program Announcements
Significant XSEDE resources granted extensions from NSF

SDSC's Comet supercomputer and PSC's Bridges supercomputer have both been awarded an additional year of operational funding from the NSF, pushing their end of service dates to March 2021 and November 2020, respectively. Both will continue to be allocated as XSEDE resources throughout this time. Read more about Comet's extension here and Bridge's extension here.

XSEDE Cyberinfrastructure Integration (XCI) Updates
 

The XSEDE Cyberinfrastructure Integration (XCI) team recently provided a new debugging tool for XSEDE Web Single Sign-on, XSEDE Globus ID Explorer, that can help users and support staff resolve login issues with applications that use the XSEDE Web SSO feature. XCI has also published a second major version of its Community Infrastructure use cases that detail a series of specific community needs that enable participation in the development of the XSEDE system and a third major verison of its Campus Bridging use cases. Finally, the XCI team has established a new internal repository to gather and retain long-term XSEDE integrated software usage data and have instrumented several central services so far; XCI is also offering community software and service providers assistance in instrumenting and tracking the long term use of their components.

Upcoming Events
Writing a Successful XSEDE Allocation Proposal Webinar next Wednesday, September 12

The XSEDE Resource Allocations Committee will host a short webinar next Wednesday, September 12 with tips for submitting a successful XSEDE allocation proposal. The webinar will introduce users to the process of writing an XSEDE allocation proposal and cover the elements that make a proposal successful. This webinar is recommended for users making the jump from a startup allocation to a research allocation, and new Campus Champions. Click the link below to register and share with colleagues who may be interested!

Last Day to Register for Gateways 2018!

Registration for Gateways 2018 closes Friday, September 7. Use the following hyperlinks to check out the conference program, or reserve a space at the Resource Expo.

Questions? Email help@sciencegateways.org.