Los Alamos National Laboratory

Los Alamos National Laboratory

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COVID-19 science updates

Los Alamos is focusing its scientific and technical capabilities in response to COVID-19 in several key areas: modeling, laboratory testing options, manufacturing, application of AI and machine learning, medical countermeasures, and high performance computing.

LANL's broad effort to fight COVID-19  

COVID-19 NEWS COVERAGE  

SCIENCE PAPERS ON COVID-19  

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New website supports genetic understanding of COVID-19  

Posted: Friday, May 1 11:30 a.m.

LOS ALAMOS, N.M., May 1—A new website to facilitate analysis and interpretation of SARS-CoV-2 genomic data is aimed at improving the global response to the COVID-19 pandemic by helping researchers to detect and identify the virus and to analyze its evolution and how mutations impact diagnostic assays.

The COVID-19 Genome Analytics site launched by the Los Alamos National Laboratory Bioscience Division comprises several tools, including a tailored bioinformatics workflow based on the fully open-source EDGE Bioinformatics platform developed at Los Alamos. This mini-version of EDGE consists of a user-friendly interface that accommodates multiple different types of raw genomic sequencing data from COVID-19 patient samples as input, such as data being generated by the CDC and public health labs around the world. If the virus is present within the sample, EDGE COVID-19 can generate a complete SARS-CoV-2 genome that is ready to be shared with public data repositories such as GenBank, the nation’s primary repository for genomic data.  

Currently, over 13,000 SARS-COV-2 genomes have been sequenced, and with every new sequence comes a more comprehensive understanding of the virus and its evolution. The COVID-19 Genome Analytics site not only facilitates the assembly and addition of more high-quality genomes, but it also helps scientists analyze how the virus is evolving and how these changes impact our ability to detect and identify the virus.

For instance, Los Alamos scientists are also computationally screening published diagnostic assays against the increasing number of SARS-CoV-2 sequences to determine the most reliable assays for diagnosis. This computational assay validation is also available on the COVID-19 Genome Analytics site, as well as information tracking both the growth in genomic data and in confirmed COVID-19 cases in the USA and around the globe.

Research was supported by the DOE Office of Science through the National Virtual Biotechnology Laboratory, a consortium of DOE national laboratories focused on response to COVID-19, with funding provided by the Coronavirus CARES Act.

Link to site: https://covid19.edgebioinformatics.org/#/home 

LA-UR-20-23280

 


Meeting the COVID-19 challenge head on

Posted: Monday, April 27 7:45 a.m.

By Thom Mason for the Santa Fe New Mexican

The COVID-19 pandemic has dramatically changed all of our lives — from how we work, to how we teach our children, to how we grocery shop. As we yearn to return to normal, we’re also called on to do what we can to protect ourselves, our loved ones and our communities.

Los Alamos National Laboratory is no different. We have responsibilities to the nation and to the communities where we live, and we take them very seriously. As one of the largest employers in Northern New Mexico, we’re doing what we can to answer the call to use our vast scientific and technical resources to help fight this disease, and protect our employees and the communities we call home.

To slow the spread of the virus, we took early and aggressive measures to get as much of our workforce as possible offsite, working from home. More than 85 percent of the laboratory’s workforce is teleworking.

The remaining employees are onsite because they are needed to assure the safety and security of our facilities or to perform essential national security work. For those onsite, measures are in place to keep them as safe as possible following CDC guidelines.

These measures are also helping to contain the spread of the virus in the communities where they live. About 75 percent of our employees live in Los Alamos, Rio Arriba and Santa Fe counties — where transmission rates have been lower than elsewhere in the state.

We are also bringing to bear our expertise, technology and materials to help the state combat COVID-19. By harnessing our capabilities in computer modeling, laboratory testing, manufacturing and medical countermeasures, we’re playing a crucial role in our country’s pandemic response.

For example, the laboratory’s HIV team, which designed an experimental HIV vaccine now in human trials, is deploying its expertise in genetic databases and bioinformatics against COVID-19. Specifically, we are developing a T-cell response vaccine approach, tracking the origin of the pathogen and building a robust bioinformatics pipeline to track the virus’s evolution, all of which are necessary for developing an effective vaccine.

Los Alamos has also partnered with Sandia and other national laboratories to develop an integrated COVID-19 pandemic monitoring, modeling and analysis capability. The goal is to support decision-makers at the federal and state level, including New Mexico. This should help our government leaders make informed decisions about preparedness for our health care system. It will also provide us with a deeper understanding of the disease. More information can be found at cdc.gov/coronavirus/2019-ncov/covid-data/forecasting-us.html.

In addition to providing disease forecasts, we are also working hard on testing and manufacturing lifesaving ventilators. In fact, we are leading a Department of Energy-wide laboratory group on testing and participating in assessments of lab capabilities for near- and long-term testing requirements, both for public health and for the lab’s workforce. And we are evaluating the potential of advanced manufacturing, specifically 3D printing, to produce scarce medical equipment that is so badly needed.

Equally as important as all this scientific research and technological support is supporting the communities in which we live. Los Alamos employees and Triad National Security, the laboratory’s management and operations contractor, recently contributed more than $60,000 to the Food Depot to help serve hungry families during this difficult time.

And because the crisis continues to take a toll on the economy, we have redoubled efforts to work with community partners to develop our region’s workforce. Just last week, we — together with Santa Fe Community College — announced a new machinist training program to provide residents with the skills they need to get such jobs at the laboratory. This program, together with Northern New Mexico College’s radiation control technicians program and a new mechanical engineering program at UNM-LA, is part of our long-term commitment to create well-paying and secure jobs for New Mexicans — something that has always been a top priority for Northern New Mexico and will take on even greater importance in the coming months.

The laboratory is committed to helping our state and nation during this global crisis. Since World War II, we have demonstrated our ability to quickly and adeptly apply our scientific and technological capabilities to respond to national emergencies. This time is no exception. We are determined to meet this challenge head-on, while doing our part to keep our workforce and our communities safe.

Thom Mason is director of Los Alamos National Laboratory.

 


Battling COVID-19 with expertise, technology, and materials

Updated: Monday, April 13 1:45 p.m.

A multidisciplinary effort

LOS ALAMOS, NM, April 8, 2020—Los Alamos National Laboratory, like many of the Department of Energy national laboratories, is drawing on its rich history in the biological sciences to actively engage in the national effort to study, understand, and answer important questions about the COVID-19 outbreak. Areas covered include disease detection and diagnostics, epidemic modeling, disease prediction and forecasting, decision support, data collection and integration, and medical measures.

“Over the last several weeks, the Laboratory has taken extraordinary steps to preserve the ability to execute our mission while assisting our surrounding communities, the state, and our nation during this demanding national emergency,” said Los Alamos Director Thom Mason. “Many are looking to the Laboratory for resources including our expertise, technology, and materials to help combat the COVID-19 virus.”

Los Alamos is providing decision-support for business and government, according to Mason.

“We are also collaborating with other national laboratories in the Department of Energy complex to develop an alternative COVID-19 testing method and are evaluating the potential of advanced manufacturing, specifically 3-D printing, to produce scarce medical equipment,” Mason said.

Los Alamos’ work in detection and diagnostics is being leveraged to optimize assays for detecting COVID-19 and bioinformaticians are looking at its close genetic relatives to analyze the virus’ evolutionary relationships to other viruses that have been studied. Epidemiological modeling centers are focusing on predicting disease spread to support decision making by government and health agencies. The modeling efforts relies on data collection, data integration, and experienced researchers who can answer questions for decision makers. Medical therapeutics efforts are focusing on ways to leverage our expertise in vaccine optimization, small-molecule discovery, and toxicity testing.

A rich history in biological sciences

Los Alamos has decades of experience integrating expertise across biology, chemistry, theory, and engineering. This multi-directorate focus of the Laboratory started in 1945 with studies of radiation health effects, expanded to the impact of radiation on DNA, and went on to include the Human Genome Project in Los Alamos. The Laboratory started GenBank, which is now the repository of DNA used in COVID-19 research.

Over the years, Los Alamos has also developed deep expertise in bioinformatics—the information science side of biology.

Detection

Detection and modeling begin with understanding historical outbreaks. A Los Alamos database catalogues historic information for key outbreaks of nearly 40 different diseases. That information helps responders select the historic similarities to each new situation, even as an outbreak evolves over the first hours and days. 

“When an outbreak occurs, we can look at these tools and see if it’s matching what we’ve seen historically,” said Kirsten Taylor-McCabe, a biochemist and national security and defense program manager at Los Alamos. “If it’s not matching, it alerts us that something might be different. It also shows us what happened in the past that people used for mitigative actions, such as contact tracing, vaccination and therapeutic campaigns, and social distancing. Did they work well? What lessons learned can we take away from actions taken in past outbreaks?”

Los Alamos has a long history in computational design assays, which assess or measure the presence of pathogens. Bacteria and viruses evolve over time and researchers learn more about their genomes on a daily basis. This information is utilized to optimize assays.

“They erode over time,” Taylor-McCabe said. “We need to keep pace with that and deliver assays that will be functional for COVID-19 or for future outbreaks. For diagnostics, we’re trying to leverage ways that we understand the host’s innate immune system. How can we triage what’s going on in the field? How can we understand if you have a bacterial or a viral infection? At Los Alamos, these are the techniques we are trying to leverage for this COVID-19 outbreak.”

Testing

Los Alamos is leading a Department of Energy–wide laboratory working group on COVID-19 testing and participating in assessments of lab capabilities for near- and long-term testing requirements, both for public health and for the Los Alamos enterprise.

COVID-19 modeling

“Modeling the epidemic sheds light on its growth rate, time of origin, future case counts, and the effectiveness of mitigation strategies,” said Nick Hengartner, leader of the Theoretical Biology and Biophysics group at Los Alamos. “Realistic epidemic models enable decision makers to validate data quality and play what-if scenarios.”

Virus spread

“For modeling, we’re looking at the spread of disease. We’re looking at it globally, all the way down to the county level,” said Kirsten Taylor-McCabe. “So in New Mexico we’re looking at the county level, we’re looking at how the disease is spreading, what the forecasts are for when we will see a peak in cases, how many people might be hospitalized, how many people may be in the ICU, how many might need ventilators, both from no intervention scenarios all the way through to high intervention scenarios.”

“Because we have those physical models that are reasonably realistic and we can model them at low levels of geographic aggregation, it allows us to actually validate the data,” said Nick Hengartner. “One of the things that comes out is that we believe that we don’t see everyone who is sick at this time. That is something that our model is able to tell us. It’s also able to tell us if the mitigation strategies that we are implementing are working because we can compare what the models predict with the actual data that we are collecting.”

Genetic research

“Part of the modeling also uses the basic law of biology—evolution,” Hengartner said. “Things evolve, and by looking at how viruses evolve and putting them in context of related organisms, which is what a phylogenetic tree shows, we can make several conclusions. For example, we know now that COVID-19 is related to but not the same as the SARS virus. We can also see that COVID-19 evolves relatively slowly, which is good news.”

The phylogenetic tree also shows close genetic neighbors or related viruses that have been found in bats and pangolins.

“When we look at genetic-sequence similarity and we compare it to others, we see that this particular virus not only made use of point mutation, or very small genetic mutations, but it also rearranges its genome a little bit,” Hengartner said. “And looking at the patterns and how it has been rearranged and point mutations, we are very confident to say that this follows what we would expect from a naturally emerging and evolving organism.”

Medical measures

“One of the interesting proteins of the coronavirus is the crown—it’s those spikes,” Hengartner said, referring to the spiky protuberances that can be seen in microscopic images of the virus. “Those spikes matter because they attach themselves to the surface of a cell and then somehow inject the virus’s RNA into the cell and that’s how the infection happens. For that to happen, this attaching to the cell membrane, there are two receptors. It turns out that having two ways for the virus attach to itself to the membrane is actually not common, and one of these receptors is in the upper lung and the other one is in the lower lung,” Hengartner said.

This may give a hint about how COVID-19 progresses as a respiratory disease.

“Now that we know that it binds with those receptors, this provides us with an opportunity to say ‘well, are there any therapeutics that could mitigate or disrupt this kind of behavior?’” Hengartner said. “Just looking at the structure of the molecule gives us an idea about what kind of molecules or drugs we should be looking for.”

Developing artificial human organs for drug testing

“When we have these drug candidates, it would be fantastic to be able to test them rapidly in a human-based system, something that’s clinically relevant to the human,” said Taylor-McCabe. “Right now, drugs go through animal testing. At Los Alamos, we’re trying to bridge that gap with a human organoid platform that would better mimic what would happen within the human host. Our project includes an artificial human heart, lung, and liver. These are systems that would be able to screen some of the drug candidates that are out there.”

Supporting vaccine development

“People are feverishly trying to develop a vaccine and have already designed vaccines that are in testing phase, but at Los Alamos, we also want to look into the future,” said Hengartner. “One of the risks that we’ve recognized with this coronavirus is that there is an immense pool of other coronaviruses hiding in bats and pangolins and snakes and what not. We would like to come up with a strategy to protect us, not just against this particular strain, but maybe next year’s jump, too.”

Los Alamos’ research in this area draws on its experience designing an HIV vaccine, which recently underwent human trials. HIV mutates extremely quickly, giving it a broad diversity that is difficult to address with a single vaccine. Los Alamos addressed that problem by creating a “mosaic” vaccine that is a patchwork of HIV genomes.

With COVID-19, Hengartner said, “it doesn’t mutate that fast but we have a broad diversity, so if we can use similar mosaic strategies, we can start thinking about designing a vaccine that will protect us from future infections and outbreaks—and nip this one in the bud at the get-go.”

Manufacturing

“On the manufacturing side of the house, Los Alamos has been working in a DOE-wide working group, participating in assessments of how the labs can support the need for ventilators, masks, face-shields, and consumable parts for lab testing,” said Kirsten Taylor-McCabe. “We’re in the deep dive phase, trying to figure out how we can help and what is the best way that we can work with the commercial sector.”

Research Collaborations with Los Alamos

The Biosurveillance Gateway is a Los Alamos website housing data about the pandemic and giving outside researchers an entry point for accessing Laboratory expertise in COVID-19 modeling, diagnosis, and decision support.

“You can also look at who to contact for some of these efforts and submit questions, which we will triage and try to link you up to the scientists that are working in this area,” Taylor-McCabe said.

Kirsten Taylor-McCabe is a biochemist and national security and defense program manager, and Nicolas Hengartner is leader of the Theoretical Biology and Biophysics group at Los Alamos National Laboratory.

LA-UR-20-22777

 


Lab leverages existing infrastructure to create new HPC system for COVID-19 research

Posted: Wednesday, April 29 10:25 a.m.

LOS ALAMOS, N.M., April 29, 2020—Los Alamos National Laboratory, partnering with Hewlett-Packard Enterprises, is building on existing infrastructure at Los Alamos to create a new high-performance computing system dedicated to COVID-19 researchers and applications.

“As part of its COVID-19 effort, the Laboratory is increasing its computational capabilities to support a variety of related research problems,” said Irene Qualters, Associate Laboratory Director for Simulation and Computation. “This is a unique opportunity to provide a broad range of researchers with the versatile, next-generation computing capabilities they need in the battle against COVID-19.”

As the Department of Energy continues to expand its efforts to fight COVID-19, the Laboratory is participating in a number of activities in concert with other DOE labs, federal and state agencies, universities, and industry partners.

The new HPC system will be a 500+ AMD Rome nodes or more than 64,000 cores occupying two HPE/Cray racks. It will be one of the most powerful machines that Los Alamos has dedicated to the COVID-19 High Performance Computing Consortium.

The system will align with Los Alamos’ and other DOE labs’ next generation machines, and will be made available on the Laboratory’s open network, which provides remote and local users with access to ultra-high-bandwidth connectivity.

By leveraging the space, power, cooling, hardware, networking infrastructure, systems management, and user support already available at Los Alamos, the new system will be quickly deployed and could be online before September.

The Laboratory has already dedicated a number of high performance computers to examine areas such as how artificial intelligence might apply in analyzing the spread of COVID-19, and in developing a path to a vaccine. Other important areas of study include optimizing the medical infrastructure to manage the anticipated number of patients and understanding the mitigating or correlating factors of COVID-19’s spread.

The research was supported by the DOE Office of Science through the National Virtual Biotechnology Laboratory, a consortium of DOE national laboratories focused on response to COVID-19, with funding provided by the Coronavirus CARES Act.

LA-UR-20-23205

  


Los Alamos bringing broad experience to COVID-19 Supercomputing Consortium

Posted: Thursday, March 26 9:21 a.m.

Following Department of Energy leadership, Los Alamos is supporting the consortium by providing access to supercomputers and support for researchers.

“We have been working with Sandia National Laboratories and Lawrence Livermore National Laboratory, along with DOE Office of Science laboratories, to be ready to accommodate a variety of research problems at scale,” said Irene Qualters, Associate Laboratory Director for Simulation and Computation. “We are also working in areas where artificial intelligence might apply in analyzing the spread of COVID-19 and in developing a path to a vaccine. Other important areas of study include optimizing the medical infrastructure to manage the anticipated number of patients and understanding the mitigating or correlating factors of COVID-19’s spread.”

Read full Albuquerque Journal story:

Sandia, LANL help hunt for vaccine

By Scott Turner
Wednesday, March 25, 2020 at 9:38pm

ALBUQUERQUE, NM — Sandia National Laboratories and Los Alamos National Laboratory are playing roles in the search for a vaccine and other medications to halt the spread of COVID-19.

The two New Mexico facilities are part of a network of government and private laboratories providing computing resources and personnel to scientists involved in the hunt for a vaccine and treatments for coronavirus.

Their efforts could mean the difference in finding medications and vaccines in the next few weeks or months as opposed to years, Argonne National Laboratory Associate Director Rick Stevens said during a teleconference with representatives from the five national laboratories that are part of the effort.

“Our national laboratories house the top supercomputers in the country,” Department of Energy Under Secretary for Science Paul Dabbar said. Also involved in the effort are Lawrence Livermore and Oak Ridge national labs.

Although the labs are known more for their nuclear energy and nuclear weapons research, they’ve already been involved in the design of medications. Los Alamos has been involved with cancer research.

“This taps into an effort already underway in the industry and academia,” said Irene Qualters, Los Alamos associate director for simulation and computation.

The computing system being made available through the network will be able to process numbers of calculations related to bioinformatics, epidemiology and molecular modeling, Dabbar said.

“It will help scientists develop complex scientific questions about COVID-19 in hours or days,” he said.

But Qualters said providing computing space and data storage “was not enough.”

To that end, the labs will provide scientists and researchers who know how the systems work, Scott Collins of Sandia National Laboratories said.

He said both facilities and research talent would be made available.

The network of labs is part of the COVID-19 High Performance Computing Consortium launched by the Trump administration this week. The consortium also includes Amazon, IBM, Google, Microsoft, Hewlett Packard and NASA.

Researchers are invited to submit COVID-19-related proposals to the consortium, which will then be reviewed and matched with computing resources from one of the partner institutions, the DOE said.

 


HIV vaccine-research team shifts to SARS-CoV-2

Posted: Monday, April 20 6:45 a.m.

LOS ALAMOS, N.M., April 20, 2020—Building on previous work designing an experimental HIV vaccine being tested in two human vaccine efficacy trials, Los Alamos National Laboratory’s HIV team is now deploying its expertise in genetic databases and bioinformatics against the novel coronavirus SARS-CoV-2.

Three main thrusts are underway from the HIV team: developing a T-cell response vaccine approach, tracking the origin of the pathogen, and building a robust bioinformatics pipeline to track the virus’s evolution. While this work focuses on attacking the virus itself, other bioinformatics and modeling efforts across the lab aim at predicting disease spread to support decision making by government and health agencies.

Developing a T-cell response vaccine approach

Bette Korber, a computational biologist and the driving force behind the “mosaic” vaccine concept for HIV, together with fellow scientists Will Fischer and Sandrasegaram Gnanakaran, is shifting her attention from HIV, ebola, and influenza vaccines to developing a T-cell based vaccine design for the SARS CoV-2 coronavirus.

Traditional antibody vaccines are primarily intended to reduce rates of infection. Korber says they hope that vaccine-elicited T-cell responses could help ameliorate disease severity if people do get infected, and so this approach could be used to complement antibody-based vaccines. Korber and the HIV team members are in the Laboratory’s Theoretical Biology and Biophysics group.

Tracking the origin of the pathogen

Elena Giorgi, also of the Theoretical Biology and Biophysics group, recently published a pre-print paper on the origins of the virus,“Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection.”

“Our team demonstrated, by looking at the genetic sequence of the virus and comparing it to other known coronaviruses, that it originated from animals,” said Giorgi. “More specifically, it most likely came from a family of bat viruses that acquired the ability to infect human cells from another family of coronaviruses found in pangolins.”

Coauthors are Xiaojun Li, Manukumar Honnayakanahalli Marichann, Brian Foley, Chuan Xiao, Xiang-peng Kong, Yue Chen, Bette Korber, Feng Gao, all of Los Alamos National Laboratory. The paper is on bioRxiv.org (doi: https://doi.org/10.1101/2020.03.20.000885).

Developing a robust bioinformatics pipeline

The LANL HIV database team led by Korber is now developing a real-time bioinformatics pipeline to track the evolution of the SARS Cov-2 spike protein, the target of the antibody-based vaccine approaches that are currently under development by many different groups worldwide. The implementation of this pipeline is being led by Will Fischer, Hyejin Yoon, and Werner Abfalterer.

The team is working to ensure that the evolving SARS Cov-2 variants that will be circulating when the vaccine is ready for delivery will remain sensitive to vaccine responses elicited using a spike protein based on the original strain that seeded the pandemic. As part of this effort, Gnanakaran will be modeling the molecular dynamics of the SARS Cov-2 spike protein and the sugars on its surface, to better understand the impact of the mutations that are beginning to accumulate in the circulating population.

They will also be adapting vaccine strategies they developed for HIV, which is a very diverse virus, to attempt to design vaccines that could work not only against the current pandemic virus, which is quite conserved, but also against highly diverse reservoir of coronaviruses that circulate in bats and other animals.

“One of the risks that we’ve recognized with this coronavirus is that there is an immense pool of other coronaviruses hiding in bats and pangolins and snakes and whatnot. We would like to come up with a strategy to protect us, not just against this particular strain, but maybe next year’s jump, too,” said Nick Hengartner, leader of the Theoretical Biology and Biophysics group.

Here's more information about previous LANL work in the HIV vaccine field.

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RETRO Rx web tools aid public health organizations

Posted: Wednesday, April 8 3:33 p.m.

Los Alamos National Laboratory has years of experience developing tools that can now be applied to the battle against COVID-19, including the Rapid, Easy Tools for Responding to Outbreaks and Re-emergence Events (RETRO Rx), designed for disease forecasting and response.

RETRO Rx is actually two tools, Analytics for Investigation of Disease Outbreaks (AIDO), and Re-emerging Infectious Disease (RED) Alert. These tools put disease outbreak data into context to provide situational awareness and actionable information.

Read full story.

 


Outbreak analysis tool online at Los Alamos

Posted: Wednesday, April 8 2:21 p.m.

A Los Alamos project focused on situations such as the world now faces with COVID-19 is being put to the test. The web-based disease-outbreak tool is a quick analysis resource called AIDO (“I-do”) for Analytics for Investigation of Disease Outbreaks. The tool does not yet have a category for SARS-CoV2, but related coronavirus libraries (MERS and SARS) are included and can show the mitigation strategies found valuable for those diseases.

Read full Albuquerque Journal story. 

 


The COVID-19 Outbreak: Delivering Science and Technology to Protect Our Nation

Posted: Thursday, April 2 7:01 a.m.

Los Alamos National Laboratory is drawing on its rich history in the biological sciences to actively engage in the national effort to study, understand, and answer important questions about the COVID-19 outbreak.

In this video, Kirsten Taylor-McCabe, a biochemist and national defense and security program manager, and Nicolas Hengartner, group leader of the Theoretical Biology and Biophysics group at Los Alamos, discuss the Laboratory’s important contributions. Areas covered include disease detection and diagnostics, epidemic modeling, disease prediction and forecasting, decision support, data collection and integration, and medical countermeasures.


Fighting COVID-19 with computer modeling

Posted: Tuesday, March 31 11:15 a.m.

For at least the next three months, Los Alamos, Sandia, Argonne, and Oak Ridge national laboratories will collaborate to develop an integrated COVID-19 pandemic monitoring, modeling, and analysis capability.

"The work builds on existing spatial demography and human dynamics research, agent-based modeling systems, infrastructure-, and economic- and risk-modeling capabilities," said Kirsten Taylor-McCabe, a biochemist and National Defense and Security Program manager. "Integrating these components with scalable data and computing capabilities, the four laboratories will work together to rapidly develop a COVID-19 analysis framework and multiscale modeling system. They will also develop a scalable COVID-19 data collection process and integrated team that will respond to the near real-time needs of supporting U.S. policy makers."

The goal is to provide routine and frequent modeling and analysis deliverables to DOE and federal government leadership, and to revise the analysis and modeling goals on demand. This joint framework will answer questions about alternative options for interventions and preparedness for our healthcare system. It will also track the ongoing, deepening understanding of the disease and the risks to various demographic and age groups.

"In addition, the COVID-19 analysis framework will give U.S. government leadership improved situational awareness, offering improved insight into what is happening in different regions of the country, exploring how different areas and populations are responding and reacting to changing conditions and varied intervention strategies," Taylor-McCabe said.

 


Roles national labs in New Mexico have to help combat coronavirus

Posted: Thursday, March 26 7:32 a.m.

Read full KRQE news story and see video:

By Rachel Knapp
Posted:  Updated: 

ALBUQUERQUE, NM (KRQE)—Gov. Michelle Lujan Grisham is grabbing national attention for New Mexico’s coronavirus response. She also mentioned getting help from the state’s two national labs. So what exactly is their role?

On MSNBC’s ‘The 11th Hour Show’ Monday night, Governor Lujan Grisham told a national audience that part of New Mexico’s success in processing hundreds of COVID-19 tests quickly is because of the equipment at the state lab and Tricore. She also gave credit to something New Mexico has that other states don’t.

“The position that New Mexico is in is a bit different,” said Gov. Lujan Grisham on MSNBC. “Is that we are a state that has two of the five national laboratories.”

She’s referring to Sandia National Laboratories and Los Alamos National Laboratory, which are under the U.S. Department of Energy. KRQE News 13 asked the governor to clarify how the labs help in test processing but she declined an interview.

So we looked into what role the labs have in the fight against the coronavirus.

For Sandia, their supercomputers will help the government figure out how and where the government should put their resources.

“Where one should put test sites, where are we going to run out of medical supplies, doing those kind of predictions to help decision-makers how to best understand how to adapt and anticipate to mitigate the disease,” said Sandia National Labs Director of Computing Research, Scott Collis.

President Trump said they’ll also turn to LANL’s supercomputers to help make a vaccine.

“They’re going to be contributing a lot of different things but primarily computing resources to help researchers discover new treatments along with vaccines,” said President Trump.

That’s not all.

“Are looking at things like advanced manufacturing, how we could help make, rapidly make more masks for our medical professionals and other personal protective equipment,” said Collis.

There is still no explanation from the state for why New Mexico has the ability to process so many more tests than other states.

 


President Trump Announces New Effort to Unleash U.S. Supercomputing Resources to Fight COVID-19

Posted: Tuesday, March 24 7:32 p.m.

As part of the Department of Energy’s efforts to combat COVID-19, Los Alamos National Laboratory is making available to the broader research community its vast supercomputing capabilities,” said Laboratory Director Thom Mason. “This should accelerate the work of researchers studying the origins and development of COVID-19, as well help in the effort to develop urgently needed treatments and vaccines.

Read full DOE news release:

WASHINGTON, D.C.—President Donald J. Trump announced a new, unique public-private consortium, spearheaded by the White House Office of Science and Technology Policy (OSTP), the U.S. Department of Energy (DOE), and IBM, including government, industry, and academic leaders to unleash the power of America’s supercomputing resources to combat COVID-19.The launch of the COVID-19 High Performance Computing Consortium will provide COVID-19 researchers with access to the world’s most powerful high performance computing resources that can significantly advance the pace of scientific discovery in the fight to stop the virus.

Researchers are invited to submit COVID-19 related research proposals to the consortium via the online portal which will then be reviewed and matched with computing resources from one of the partner institutions. An expert panel of top scientists and computing researchers will work with proposers to quickly assess the public health benefit of the work and coordinate the allocation of the group’s powerful computing assets.

The COVID-19 High Performance Computing Consortium currently pools 16 systems that together offer over 330 petaflops of supercomputing capacity. Additional capacity, including cloud computing resources, will be added through present and future partners. The sophisticated computing systems available through this Consortium can process massive numbers of calculations related to bioinformatics, epidemiology, molecular modeling, and healthcare system response, helping scientists develop answers to complex scientific questions about COVID-19 in hours or days versus weeks or months.

“Under the Trump Administration, the United States has regained its position as the dominant global force in Supercomputing technology. The Department of Energy is home to the world’s fastest and most powerful supercomputers, and we are eager to partner with leaders across industry and the scientific community who will use our world class innovation and technology to combat COVID-19,” said U.S. Secretary of Energy Dan Brouillette.

“America is coming together to fight COVID-19, and that means unleashing the full capacity of our world-class supercomputers to rapidly advance scientific research for treatments and a vaccine. We thank the private sector and academic leaders who are joining the federal government as part of the Trump Administration’s whole-of-America response,” said Michael Kratsios, U.S. Chief Technology Officer.

“The Department of Energy’s National Labs have made profound advancements towards combatting COVID-19,” said DOE Under Secretary for Science Paul Dabbar. “By providing researchers access to world leading technology here in our own backyard, we take an additional leap towards ending this pandemic. We look forward to collaborating with scientists and researchers to bring an end to COVID-19.”

“DOE’s National Nuclear Security Administration is eagerly lending its world-class supercomputing resources to combat COVID-19 in collaboration with OSTP and other agencies,” said Lisa E. Gordon-Hagerty, DOE Under Secretary for Nuclear Security and NNSA Administrator. “NNSA supercomputers will be available, empowering researchers to understand the COVID-19 virus, develop treatments and vaccines, and ultimately bring an end to this pandemic.”

“Accelerating the process of discovery to unlock treatments and a cure for COVID-19 is of vital importance to us all. By bringing together the world's most advanced supercomputers and matching them with the best ideas and expertise, this consortium can drive real progress in this global fight. IBM is proud to have helped kick-start this important effort," said Dario Gil, Director of IBM Research.

Participants in this consortium will include:

Industry
IBM
Amazon Web Services
Google Cloud
Microsoft

Academia
Massachusetts Institute of Technology
Rensselaer Polytechnic Institute

U.S. Department of Energy National Laboratories
Argonne National Laboratory
Lawrence Livermore National Laboratory
Los Alamos National Laboratory
Oak Ridge National Laboratory
Sandia National Laboratories
Federal Agencies National Science Foundation
NASA