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In early March, when experimental scientists released an important batch of information about the coronavirus, biophysicist Rommie Amaro sent an email to Dan Stanzione at Austin's Texas Advanced Computing Center (TACC). She asked for time on Frontera, the fifth most powerful supercomputer in the world.
She and a team from her computational biology lab at the University of California, San Diego, together with scientists from other labs, were creating a model of the virus. Their goals included simulating its movements, which would provide information about how the virus interacted with human cells and provide structural insights for drug development.
Amaro and her team previously modeled and analyzed an influenza virus. The project, which was finished in 2019, took six years. Now, amid a global pandemic, they were hoping to create the coronavirus model in a matter of weeks. This could only be possible with collaboration in the global community and the use of one of the world's most powerful supercomputers. So she contacted Stanzione, TACC's executive director.
"It took me one email to Dan Stanzione," she says. "He said, 'I know what you guys do. Just go for it.' It turned out to be so critical for this work. It's unprecedented and impressive."
As researchers race to provide important information about the coronavirus and its spread, organizations from the federal government, industry and academia have come together to quickly get researchers free access to supercomputers. They joined forces to create the COVID-19 High Performance Computing Consortium, which carries out a daily review of requests for computing capacity. When Amaro was modeling influenza, it took her a year to get her proposal for supercomputer time funded.
TACC is a member of the consortium. The Austin center is part of the University of Texas-Austin and is funded by the National Science Foundation. It has more than 10 supercomputers, and Frontera is the fastest academic computer in the world.
"We are supporting over 20 projects now that are in some way dealing with the coronavirus response," says Stanzione, "for probably a few hundred researchers around the country."
Some projects come in through the daily review process, while others have been green-lit even more quickly, using a discretionary process similar to that used in emergencies such as a hurricane threat in the Gulf of Mexico. The researchers now receiving this immediate approval are usually those who have worked with the center before. They are able to use elements of past projects to approach the new coronavirus threat.
"Existing capacity matters a lot," he says. "Software has been built. There are data sets you can use. The projects where we are already pushing out results that are helping come from existing relationships."
The supercomputers at TACC have hundreds of thousands of processors networked in such a way that the transmission time between the processors is extremely low. This allows for large, intricate calculations to be done. Stanzione says that in order to simulate the coronavirus over time, processors need to communicate with each other within fractions of a femtosecond, which is a millionth of a billionth of a second.
Amaro and her team, along with several groups from other labs, will create a three-dimensional model of the outside of the new coronavirus, SARS-CoV-2, as well as a simulation of its movements. This should give information about how it interacts with human cells and provide insights for drug and vaccine development. The researchers expect the model to contain about 200 million atoms.
So far, the team has built a three-dimensional model of the spike proteins (which are the red "knobs" seen on coronavirus images), the tether that connects the spikes to the membrane on the outside of the virus, and some of that membrane. They have also been able to model the sugar-like molecules found on the proteins, which may be camouflaging the virus from our immune system.
The team will now apply the laws of physics to model how the virus moves.
"You have to have to understand how it is moving in order to understand its function," she says.
Amaro says that simulations of other viruses have revealed hidden aspects of the coronavirus, such as drug targets, that could not be seen experimentally. Simulation data such as hers is used to augment data collected in experimental labs around the world. It is part of a fast-moving, global effort to conquer coronavirus.
"The sharing and collaboration has been surprising and incredible," says Amaro.
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The Austin City Council on Friday unanimously approved a measure to add to the November ballot the massive $7.1B "Project Connect," a 20-year overhaul of Austin's transit system that would include a new light rail and "rapid bus" lines.
The council plans to add it to the ballot in a formal order next week, members said. Then it's up to voters to decide whether to approve it.
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Life was so sweet for live music junkies living in the Live Music Capital of the World—up until the venues closed, the stages went dark, and the world of Austin music closed down.
Miss your places? Miss your people? Miss blowing all your money on music?
Jagtronica Wednedsays, Purple Bee TV<span style="display:block;position:relative;padding-top:56.25%;" class="rm-shortcode" data-rm-shortcode-id="9a2cab8a9562f05e4d4667d82dfca7bd"><iframe lazy-loadable="true" src="https://www.youtube.com/embed/KbeRftaXIZg?rel=0" width="100%" height="auto" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;"></iframe></span><p>Interstellar grooves and psychedelic explorations improvised by a full band - live in the <a href="http://purplebeetv.org" target="_blank">Purple Bee</a> studios. Wednesdays 8 p.m.</p>
Patrice Pike Band Keep the Faith Livestream<div class="rm-shortcode" data-rm-shortcode-id="a94897344c627ae7362202afe441fa05"><div class="fb-video" data-href="https://www.facebook.com/PatricePikeBand/videos/324002002065701" data-allowfullscreen="true"></div></div><p>Iconic hard rock favorite unplugs in her home space. Thursdays at 8 p.m. and Sundays at 7 p.m. </p>
Afro Jazz Saturdays at the Sahara Lounge<div class="rm-shortcode" data-rm-shortcode-id="d5519cfcd8eee1dc9add8a63b3c1b66f"><div class="fb-video" data-href="https://www.facebook.com/SaharaLoungeATX/videos/217338429591881" data-allowfullscreen="true"></div></div><p>Join this East Austin gem of a bar for regular virtual live shows from the stage, including a regular online residency by African jazz musicians Ibrahim Aminou and Aboubacar Sylla. Saturdays 8 p.m. https://www.facebook.com/SaharaLoungeATX</p>
KUTX Livestreams<span style="display:block;position:relative;padding-top:56.25%;" class="rm-shortcode" data-rm-shortcode-id="950f84e2286e0dc0304d59aa99edfbc1"><iframe lazy-loadable="true" src="https://www.youtube.com/embed/QNVfbrr_v0M?rel=0" width="100%" height="auto" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;"></iframe></span><p>This local Austin-centric arm of KUT hosts various performance livestreams nearly every day of the week. Find their schedule here. </p>
Live in the Virtual Gallery with Bonnie Whitmore<img lazy-loadable="true" src="https://assets.rebelmouse.io/eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpbWFnZSI6Imh0dHBzOi8vbWVkaWEucmJsLm1zL2ltYWdlP3U9JTJGY29udGVudCUyRjU2ZTVkNGU4MWQwN2MwNzQzZDI4MWQ2MyUyRjE1OTYxNDgzMjQ1MjctTlQ2VlFQM1ZNM0daR0VMNTQ1OEElMkZCVyUyQmF1Z3VzdC5wbmclM0Zmb3JtYXQlM0QxNTAwdyUyNmNvbnRlbnQtdHlwZSUzRGltYWdlJTJGcG5nJmhvPWh0dHBzJTNBJTJGJTJGaW1hZ2VzLnNxdWFyZXNwYWNlLWNkbi5jb20mcz00OCZoPWQ0YmY4MjkzMTA2OTRkNjdjNzQ1ZmNhODhjNGQ3ZDI4YWY3YTE2ZDgyZjM3OTI4MjVkOGJmY2U3MTk0NjU2YWYmc2l6ZT05ODB4JmM9MTI2MDUxNzQxNiIsImV4cGlyZXNfYXQiOjE2NDg3MTY2NzJ9.J2ntaGHE00UZvxWETyI9XZ3xC3iC1nAAo8bk38ILkyA/img.jpg" id="72e14" class="rm-shortcode" data-rm-shortcode-id="dc34d23c5508b20dfea2642717052bfd" />August 2020 — Bonnie Whitmore
BettySoo's Nobody's Happy (Online and Isolated) Hour<img lazy-loadable="true" src="https://assets.rebelmouse.io/eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.gaEmnDK5F-J8rgXWUIAnXGHJOveE-ub3wm8UUPTLrhA/img.jpg" id="82829" class="rm-shortcode" data-rm-shortcode-id="d4fa34ac0fa355da87c02e8572d3fe46" />BettySoo's Nobody's Happy Hour - Summer 2020
DJ Mel's Living Room Dance Party<div class="rm-shortcode" data-rm-shortcode-id="45581c8bb0ae6cf0ddbe03e775d6825f"><div class="fb-video" data-href="https://www.facebook.com/video.php?v=3446714958713944" data-allowfullscreen="true"></div></div><p>A streaming staple practically since the day the venues shut down, DJ Mel Cavaricci (aka DJ Mel) spins from his living room. Saturdays 6-10p.m.</p>
Dreadneck Wednesdays from the Flamingo Cantina<img lazy-loadable="true" src="https://assets.rebelmouse.io/eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.Txy1LrSKsTPNG0dDU0xjlU2KkBu5cmcE8txaOdO8I_M/img.jpg" id="7c376" class="rm-shortcode" data-rm-shortcode-id="ebccf8a39ef46845384013bb233d0747" />Dreadneck Wednesdays Live Stream w/ Mau Mau Chaplains
James McMurtry's Wednesday residency<div class="rm-shortcode" data-rm-shortcode-id="46c8760066753cce717a6a3335d5f43d"><div class="fb-video" data-href="https://www.facebook.com/8637988681/videos/608632053134073" data-allowfullscreen="true"></div></div><p>A fixture on the alt-country music scene in Austin and beyond, McMurtry brings his weekly residency at Continental Club home to you (from his place) with opening acts. Wednesdays 8 p.m. </p>
Not at Donn's Depot<div class="rm-shortcode" data-rm-shortcode-id="b8a0b32db58eccac4a2695a8eb2f4747"><div class="fb-video" data-href="https://www.facebook.com/chrisgageaustin/videos/10159892023859008" data-allowfullscreen="true"></div></div><p>The slightly obvious but oh-so-telling title for pianist Chris Gage's Monday livestream, where he tickles the ivories from his home studio, joined occasionally by wife Christine Albert, and recreates his popular and long-running Monday residency at Donn's. Mondays 8 p.m. </p>
Jackie Venson<span style="display:block;position:relative;padding-top:56.25%;" class="rm-shortcode" data-rm-shortcode-id="d41a9251d5c15ad731ae31c77455a79a"><iframe lazy-loadable="true" src="https://www.youtube.com/embed/43xotR5fRNM?rel=0" width="100%" height="auto" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;"></iframe></span><p>Austin born-and-bred singer songwriter, brings her guitar and her truth-telling music to her live-streaming page. Wednesdays, Thursdays, Fridays at 9 p.m. and Sundays at 1 p.m. <a href="https://jackievenson.com/livestream/" target="_blank">https://jackievenson.com/livestream/</a></p>
The Austin Justice Coalition is clearly frustrated with city leadership, which has not responded to its request to cut $100 million in funding from the Austin Police Department and remove Chief Brian Manley (or make him resign).
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The Austin Independent School Board delayed the school year to Sept. 8 in an early-Friday vote, giving teachers three more weeks to prepare for online learning and the community more time to see a drop in COVID-19 cases before students, faculty and staff return to the classroom.
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The group behind a petition to put a citywide public-camping ban on the November ballot in Austin said Thursday that they were "engaging a highly respected local Democratic litigator" in their efforts to fight a city ruling earlier in the week that their petition did not enough valid signatures.
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David Frost, 22, had never attended a protest before the Black Lives Matter demonstrations in May. Then the cell phone-wielding Austinite became a key player in a series of events that touched off major change in the Austin Police Department.
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