Newsletters

to our monthly email newsletter, IMPACT by XSEDE, to receive the most up-to-date science outcomes, program news, and community events,

Key Points
Stay up to date with XSEDE Newsletters
« Back

XSEDE IMPACT MARCH 2022

 

 

 
March 2022 | Science Highlights, Announcements & Upcoming Events
 
XSEDE helps the nation's most creative minds discover breakthroughs and solutions for some of the world's greatest scientific challenges. Through free, customized access to the National Science Foundation's advanced digital resources, consulting, training, and mentorship opportunities, XSEDE enables you to Discover More. Get started here.
 
Science Highlights
 
Electrical Charge of Vaccine Particles May Lead to Blood-Clot Side Effect
 
XSEDE-powered simulations suggest complication may stem from oppositely charged clot-forming protein sticking to engineered adenovirus
 
 
Despite the lifesaving success of the COVID-19 vaccines, a very rare side effect of blood clots has appeared with those based on engineered adenovirus. Simulations on the XSEDE-allocated Bridges-2 system suggest that simple electrical charge may make adenovirus stick to a protein involved in blood clot formation stick to particles of the AstraZeneca vaccine. The discovery will be the foundation of an effort to explain how the side effect happens and how the vaccine can be re-engineered to prevent it.
 
 
Positively charged PF4 proteins (colored) stick to the negatively charged surface of the vaccine particle (gray), in some patients starting blood clot formation.
 
College Students Learn Molecular Simulation on Bridges-2
 
XSEDE educational allocation gives students taste of computational field, tools for science careers
 
 
Advanced computing has transformed the sciences, particularly biology. But college students often get no experience in wielding the supercomputers used in modern scientific research. That can make for a difficult transition from college to more advanced study. Using an XSEDE educational allocation on the Bridges-2 system at PSC, a class at Westminster College gave biology and chemistry students hands-on experience with molecular simulation. The class gave them tools valuable for their ongoing education, as well as a taste of the field that led many to choose careers likely to involve computational biology.
 
 
Graphical abstract from Riana Smith's project studying the serine-aspartate-repeat-containing protein G in the Westminster College class.
 
Experimental Statistics Theory Advanced Thanks to XSEDE Allocations
 
Comet and Bridges-2 put Mirzakhani Theorem to the test
 
 
Researchers used XSEDE allocations to conduct complex calculations that helped to resolve a discrepancy between two mathematics theorems: Mirzakhani's Theorem and DGZZ research. The team used Comet at the San Diego Supercomputer Center and Bridges-2 at the Pittsburgh Supercomputing Center. The study was published in Experimental Mathematics and they confirm and correct a numerical error in Mirzakhani's widely touted mathematics example.
 
 
The difference between a non-separating loop (shown in blue) and a separating loop (shown in red). Credit: Mark Bell
 
Supercomputers Provide Single Model of Both Inner and Outer Solar System
 
XSEDE allocations lend insight into the formation of multiple planets
 
 
While attempting to better understand the relationship between Earth and Mars, postdoctoral fellow Matt Clement (Carnegie Institution of Washington's Earth and Planets Laboratory) and his colleagues used XSEDE allocations on Comet at SDSC and Bridges at PSC to illustrate the formation of both the inner and outer solar system in a single model. Their work was recently published in the journal Icarus
 
 
 
Pioneering Simulations Focus on HIV-1 Virus
 
First computer models developed through XSEDE allocations and training for deadly virus's envelope and genome capsid
 
 
Thanks in part to supercomputer allocations and training by XSEDE, scientists have completed the first-ever biologically authentic computer model of the HIV-1 virus liposome, its complete spherical lipid bilayer. What's more, this study comes fresh off the heels of a new atomistic model of the HIV-1 capsid, which contains its genetic material. The scientists are hopeful this basic research into viral envelopes can help efforts to develop new HIV-1 therapeutics, as well as lie a foundation for study of other enveloped viruses such as the novel coronavirus.
 
 
Full-scale model of a realistic HIV-1 lipid vesicle at united atom resolution (MARTINI force-field) has been developed using XSEDE resources.Credit: Bryer et al.
 
Program Announcements
 
Advance to Access: Making a Successful Transition from XSEDE
 
XSEDE operations are ending in August
 
 
 
The XSEDE project is scheduled to end operations on August 31, 2022, giving way to a new National Science Foundation program, Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS), set to launch September 1, 2022.
 
While access to XSEDE-allocated resources will continue under the ACCESS program, there will be changes in how the new program is managed.
 
XSEDE leadership has created a website to provide information about this transition as it becomes available. Please visit it at the link below.
 
 
XSEDE Cyberinfrastructure Integration (XCI) Updates
 
 
A new feature of XSEDE's Globus data management service, "Timers," makes synchronizing research data easy. StonyBrook University's Ookami system, as well as Texas A&M's FASTER system, are continuing work to integrate into the XSEDE ecosystem and are expected to begin accepting early user allocations in mid to late spring. 
 
 
Community Announcements
 
NSF Extends Lifespan of TACC's Stampede2 Supercomputer through June 2023
The NSF has extended operational funding for TACC's XSEDE-allocated Stampede2 supercomputer through June 2023. Prior to the extension, the life of the system was expected to end in September 2022. This extension will allow the system to continue supporting world-class science for an additional nine months.
 
 
Ookami Allocations Available
Ookami (NSF grant OAC 1927880) provides researchers with access to the A64FX processor developed by Riken and Fujitsu for the Japanese path to exascale computing and is currently deployed in the fastest computer in the world, Fugaku.
 
Ookami is an XSEDE level 2 service provider with allocations starting in October 2022. Selected XSEDE users can get access sooner. Currently, allocations are handled through Stony Brook University.
 
 
Introducing the SGCI Storybook!
For over five years, the Science Gateways Community Institute (an XSEDE L2 service provider) has worked with the gateways community to improve access to essential resources and services. We have helped more than 150 gateways reach their goals so, we thought, why not collect all the great feedback into a storybook that could illustrate the many ways that the community has benefited from our existence? Behold, the SGCI Storybook! In this collection, we have compiled synopses of individual gateway clients and how their engagements with SGCI contributed to their success. Check it out at the link below.
 
 
Call for LCI Host Sites
The Linux Clusters Institute (LCI) is currently seeking applications from institutions interested in hosting an on-site LCI Introductory OR Intermediate Workshop in 2022 or early 2023. These workshops provide education and technical training for the deployment and use of computing clusters to the high-performance computing community worldwide. 
 
The deadline to submit your host site letter of interest form is March 15, 2022. You can access the letter of interest form at the link below.  
 
Feel free to forward this to anyone who may be interested and appropriate. PLEASE NOTE: the LCI website is currently under construction and not currently functioning. Should you have questions or need further information, please reach out to Leslie Froeschl at lfroesch@illinois.edu.
 
 
Mini Gateways 2022 Call for Community Participation
Mini Gateways 2022 will be online April 5-7. The mini-conference is planned as a free opportunity to learn about technologies and communities and to build connections for today and tomorrow.
 
The conference invites the submission of abstracts (500 words) related to science gateways. All contributions will be subject to standard peer review on quality and relevance, which will decide acceptance of a lightning talk, panel, or tutorial. Open forum topic abstracts are limited to 200 words. All submissions due March 7, 2022.
 
 
News from Globus
Navigating Cloud Storage with Globus
There are varying reasons for mass migration, from security concerns to cost. Regardless of the reason, there are common barriers to success that can make these data transfers difficult. The good news is that Globus has a connector for nearly every popular cloud storage out there. 
 
 
New Globus Timer Feature Simplifies Data Synchronization
 
Some research projects—particularly those with team members at multiple campuses—need to maintain copies of the project's data on a campus system and on an XSEDE system. Keeping these copies synchronized is important, but it shouldn't be time-consuming for researchers. A new feature of XSEDE's Globus data management service, "Timers," makes synchronizing research data easy. Researchers can now create a timer task in Globus to run a synchronization transfer (synchronization transfers only transfers files that are newer or different on the source) at a frequency you specify. You can set up unidirectional or bidirectional synchronization, and you can configure an end date or a maximum number of synchronization runs. With this new feature, you can keep copies of your project's data—on XSEDE and one or more campuses—up-to-date as your team adds to or updates the data. XSEDE's description of this feature and instructions for use with XSEDE are on the Data Management page in the XSEDE User Portal. (Look under "Data Synchronization" at the end of the page for details.)
 
GlobusWorld 2022 – Call for Proposals – Due by March 19
 
It is not too late to submit your proposal for GlobusWorld 2022. Come and share your solution, and hear from others how Globus is helping to simplify and streamline research data management. Register for the conference today!
 
 
Upcoming Dates and Deadlines