June 2021 | Science Highlights, Announcements & Upcoming Events
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Science Highlights
XSEDE Systems Power Discovery of Two-X-Chromosome Male Voles
The way this rodent species determines sex differs from all other mammals known
Sex can be complicated. In creeping voles, a small rodent in the Pacific Northwest, it's even more so. Scientists using the XSEDE-allocated Bridges and Bridges-2 advanced research computers at the Pittsburgh Supercomputing Center to assemble DNA sequences discovered that, rather than the XX sex chromosomes that determine genetic females and XY that determine genetic males in mammals, this species has been doing just fine with only a single X chromosome in females and a strange combination of an X and another, different X in males. The work, which earned a cover image in the prestigious journal Science, raises important questions on how early sexual development works.

In most mammals (top), the father (left) contributes an X or a Y chromosome and the mother (right) two Xs. When the sperm and egg merge, XY makes a genetic male offspring, XX female (center). To avoid double-strength X genes, in females one X chromosome is silenced (wiggly line). Leaping voles turn this convention on its head (bottom), with the father contributing only an XP chromosome. A second, XM, chromosome is mostly or all silenced in most of the male's cells, again shown by a wiggly line. That XM is lost when sperm cells form (center). The female in turn only contributes XM chromosomes (right). Offspring that get no sex chromosome from their father and the XM from their mother are genetically female; those that get an XM from mom and XP from dad are genetically male (center). Credit: AAAS.
Stickiness of COVID Particles Reduces Airborne Concentration in Supermarkets
XSEDE-allocated supercomputer simulates how pathogens travel, land in grocery store space
No one likes a sticky public surface, but when it comes to shopping for groceries during a pandemic, stickiness might not be all that bad — as long as you use hand sanitizer. A team of environmental engineers recently used XSEDE-allocated Comet at the San Diego Supercomputer Center at the University of California San Diego to simulate how the virus' airborne pathogens travel and land in the familiar setting of the supermarket. The research findings, published in the Journal of Environmental Engineering, revealed that the attachment of virus-laden particles on the shelves, floor, and ceiling of the supermarket reduces the maximum concentration of suspended particles in the air by as much as 50%.
Using XSEDE allocations on Comet, this image illustrates virus-laden particles in a supermarket five minutes after release. Dark blue indicates particles suspended in air, orange shows particles stuck on the ceiling, light blue represents particles attached to shelves, and yellow shows particles on the floor. Credit: New Jersey Institute of Technology.
XSEDE Systems Power DNA-Based Identification of Surface, Airborne Microbes Worldwide
Samples from 60 cities reveal previously unknown microbes, diversity of antibiotic resistance genes
Dangerous microbes can emerge with little warning, a harsh lesson COVID-19 bestowed upon the world. Using XSEDE's advanced research computers, a team of scientists has undertaken a vast analysis of microbial DNA in thousands of urban air and surface samples worldwide. The results, recently published as a cover story in the journal Cell, revealed city-specific "fingerprints" of bacteria and viruses. They also gave us a first look at the population of dangerous antibiotic-resistance-conveying genes across the globe, as well as thousands of previously undiscovered species in the urban microbial world.
The fingerprint of the microbial species in a given city's public transit surfaces (coded by color) changed over time (samples from 2016 shown as circles, 2017 triangles), but cities remained distinct from each other. Credit: Danko D, Bezdan D et al.
Program Announcements
XSEDE Cyberinfrastructure Integration (XCI) Updates
The XSEDE Cyberinfrastructure Integration (XCI) team continues to provide cyberinfrastructure consulting to support teaching and research at institutions around the state of Oklahoma. Most recently, the team has engaged with Southwest Oklahoma State University to coordinate cyberinfrastructure implementation at that institution.
XSEDE EMPOWER Now Accepting Applications for Fall Internships
XSEDE EMPOWER (Expert Mentoring Producing Opportunities for Work, Education, and Research) provides undergraduate students with the opportunity to work on a variety of XSEDE projects, such as computational and/or data analytics research and education in all fields of study, networking, system maintenance and support, visualization, and more. The EMPOWER program aims to enable a diverse group of students to participate in the actual work of XSEDE. Those interested can find more information at the link below and should apply for Fall 2021 positions by June 25, 2021.
Check out this video to learn more about XSEDE EMPOWER and what two interns have to say about the program.
Encourage Undergraduates to Apply for C4C!
Do you know an undergraduate who wants to learn data science skills to create a positive change in their community? All undergraduate students are invited to apply for the Computing4Change (C4C) Competition, a social action-themed experience during SC21! All majors are welcome. No prior coding experience required. The program will take place during SC21, November 12-19, 2021. The deadline to apply for C4C is August 2, 2021.
Community Announcements
TACC Celebrates 20 Years
Happy 20th Anniversary, TACC! On June 1, 2001, the center began its journey to become one of the leading academic supercomputing centers in the world. TACC looks forward to formally celebrating with an event later this year. In the meantime, check out their highlights and accomplishments from the past two decades below. #TACC20
Register by June 8 (early) or June 25 (full) for Galaxy Community Conference
Galaxy is a data integration and analysis platform that makes HPC resources accessible to scientists through a web browser interface. If you are doing or supporting data-intensive science, then please join us for the three-day meeting, a week of training, and a CollaborationFest, starting June 28. All events will take place online. Find more information and register at the link below.
Register by June 9 for Gateway Focus Week
Gateway Focus Week, offered by the Science Gateways Community Institute (SGCI), is an intensive workshop designed for innovative research teams to work together on producing a strong sustainability plan. The full Focus Week curriculum is now offered in a new format: online, over the course of two weeks. Register by June 9 to join the next session, taking place June 14-24, 2021. Attendees may choose to either attend the full workshop or attend sessions "a la carte."
Upcoming Dates and Deadlines