COVID-19 has transformed life around the globe. In NYC, where I work for the Mount Sinai Health System, we were at the center of the epidemic in the United States in March. At this time, our clinicians and researchers leveraged their domain expertise to focus solely on better understanding and treating this new disease. The spotlight on COVID-19 created new interdisciplinary teams that have already been fruitful: the discovery that the first COVID-19 cases in NYC came from Europe in March¹, the first to use AI to detect COVID-related lung disease in CT scans² and the identification of inflammatory markers to help guide treatment for severe COVID-19 cases³. These advances were made possible through a team science approach that brought together experts in diverse domains, including cancer, computational science and infectious disease. Bridging disciplines is an essential tenet to productive modern science.

We have shared this same interdisciplinary approach for the design of the Computational Approaches for Cancer Workshop, now in its sixth year, at SC20. Experts in the computational, computer, basic and data sciences from the National Cancer Institute (NCI), National Institutes of Health (NIH), U.S. Department of Energy (DOE), Frederick National Laboratory for Cancer Research (FNL), National Science Foundation (NSF), academia and industry have gathered to discuss innovations and best practices on a wide array of topics from drug design, machine learning and data sharing. This workshop has enabled new human connections, facilitated a common language across disciplines, and improved understanding of biomedical opportunities and challenges in the high performance computing community.

With the bridges that have already been built over the last five years, and with the pandemic continuing to rage, this workshop comes at a critical time: never before has the intersection of computational, data and biomedical sciences been more crucial. We look forward to seeing you at the workshop.

¹ https://www.mountsinai.org/about/newsroom/2020/mount-sinai-study-finds-first-cases-of-covid-19-in-new-york-city-are-primarily-from-european-and-us-sources-pr

² https://www.mountsinai.org/about/newsroom/2020/mount-sinai-first-in-us-to-use-artificial-intelligence-to-analyze-coronavirus-covid19-patients-pr

³ https://pubmed.ncbi.nlm.nih.gov/32511562/

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Patricia Kovatch is the Senior Associate Dean for Scientific Computing and Data Science at the Icahn School of Medicine at Mount Sinai (ISMMS), founding the division in October 2011. She is also an Associate Professor for the Department of Genetics and Genomic Sciences, the Icahn Institute for Data Science and Genomic Technology and Pharmalogical Sciences. Kovatch is on the Organizing Committee for the CAFCW20.

Planning each SC conference is a three-year journey. By the time we are in the final year of planning, the shape of the conference is well-determined, as are the known unknowns. The events of 2020 have upended all of that, and have made for the most challenging final year for any SC planning committee yet.

The vast majority of the more than 700 people on the SC planning committee are volunteers from the HPC community. All of us share your concerns regarding the challenges of remaining healthy and safe while continuing with our daily routines. Many of us are also subject to institutional and governmental travel guidance and restrictions — as are our attendees and participants — and much like everything else today, they change frequently.

Over my twenty years of involvement on the SC committee many of our team members have become lifelong friends and family to me; I hold their safety, and yours, as the utmost concern for the conference.

Still, there is the business of ensuring the HPC community can continue to exchange ideas and achievements on a broad scale in a normal rhythm. The SC20 committee began planning for both in-person and virtual attendance — a first for SC — within a month of the United States COVID-related shutdowns. We are fortunate in that we have a longer runway with which to plan than did most conferences this spring and summer. That allows us to not only draw from lessons learned across a wide range of experiences in many fields, but also to carefully plan for the most robust conference experience possible for our participants and attendees.

In a normal year, the most-often heard characterization of our conference is that there is too much content from which to choose. It’s a good problem to have, and we’re working to provide abundant content again this year.

We recently held the first ever completely virtual SC paper review meeting, and it was a tremendous success due to the planning of many, most of all that of our Technical Papers Chair Franck Cappello and Co-Chair Rudolf Eigenmann. The SC20 committee is continually finding ways to accomplish the usual planning tasks from all corners of the earth. The events of this year have us re-examining nearly every aspect of the conference, and while we can and are addressing some of those this year, others require steady, longer-term approaches from the SC conference series, the SC Steering Committee and the HPC community as a whole.

Every day brings new information that more sharply hones the shape of SC20 and the conferences that follow. Every day there are more decisions to be made with that brand new information. We know that this ever-changing professional and personal environment is the case for many of you and your employers, and as such we have made adjustments in numerous areas of the SC20 experience:

• We will open registration for the conference on August 14, 2020.
• We are working with our exhibitors, attendees, and content authors to provide as much flexibility as possible for in-person and virtual attendance and participation.
• We will provide flexible cancellation and rebate policies where possible.

More information regarding all of that, and the SC20 program itself, will come in the next several weeks. Please continue to check the SC20 website’s Coronavirus & SC page for conference status.

SC20 won’t be the same as SC conferences of the past. But it will be an event that brings the HPC community together to further our field, our connections to each other and the world around us, and our desire to be more than HPC.

Warm Regards,
Christine E. Cuicchi
SC20 General Chair

HPC has been a tremendous enabler of advances in healthcare and medical research for many years. And as you’d expect, HPC is helping scientists get a lead on the coronavirus and its impacts on human health.

Japanese Researchers Use Fugaku, the World’s Fastest Supercomputer, to Simulate Air Particle Movement Resulting in Recommended Procedures for Reducing COVID-19 Spread

Via DailyMail.com

World’s fastest supercomputer that has been running simulations to determine how best to reduce the spread of COVID-19 recommends open train windows and limiting passengers as well we using floor-to-ceiling curtains around hospital beds. Read full article

Fighting COVID with Computing: Fermilab, Brookhaven, and Open Science Grid Dedicate Computational Power to COVID-19 Research

Via Brookhaven National Laboratory

During the times that select Fermilab and Brookhaven computers get a break from particle collision analysis, they’re free to crunch data outside particle physics. That’s where the Open Science Grid comes in. Among other tasks, the OSG evaluates research proposals to determine which are a good fit for its networks. In offering its resources to COVID-19 proposals, it provided the kind of vetting that the labs wouldn’t have been able to assume on their own. Read full article

ORNL Team Enlists World’s Fastest Supercomputer to Combat the Coronavirus

Via Oak Ridge National Laboratory

Simulations of more than 8000 small-molecule drug compounds to screen for those that could bind to a protein in coronaviruses and disable it from infecting host cells have been performed on the Summit supercomputer at Oak Ridge National Laboratory. The S-protein spike is present in both the virus responsible for the SARS epidemic of 2003 and the COVID-19 disease. The systematic screening of compounds reduced the original set of 8000 down to a more reasonable 77 small-molecule drug compounds that can potentially undergo experimental testing. Thanks to Summit, the simulations took only a day or two, saving valuable time that can be used by experimental researchers to focus on a manageable number of options for stopping the coronavirus. Read full article

Supercomputers Playing a Significant Role in COVID-19 Research

Via TechRepublic

Initiatives are underway to predict where the virus will spread and analyze how effective preventive measures are, according to the National Center for Supercomputing Applications. Read full article

Researchers Tackle the Flu with Breakthrough Virus Simulations

Via UC San Diego News Center

Supercomputing power applied to records of historical pandemics, such as the 2009 H1N1 flu pandemic which killed more than 200,000 people, can help us fight new diseases. A team from the University of California at San Diego built an all-atom, solvated, and experimentally based integrative model of pH1N1 (the H1N1 flu virus) on the Blue Waters supercomputer hosted by the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign. Using this model of the entire viral envelope, which consisted of more than 160 million atoms, they examined two binding sites on the flu’s viral proteins. For the first time they were able to understand how flu proteins on the surface of the virus interact with each other. From this research, new anti-influenza therapeutics may be developed. Read full article

How Supercomputers Are Getting Us Closer to a COVID-19 Vaccine

Via The Hill

The global scientific community has joined forces in an unprecedented effort to understand, track, forecast, test for, and find a cure for the current coronavirus pandemic. But in a crisis where every second lost means more loss of lives, solidarity alone isn’t enough. Supercomputers are enabling a vastly accelerated pace by which scientists can conduct research and collect and analyze data. Never have they proven their value to society more than during this COVID-19 pandemic. Read full article

Researcher Say Spread of Coronavirus Extends Far Beyond China’s Quarantine Zone

Via Texas Advanced Computing Center (TACC)

Epidemiologists have been using the Wrangler supercomputer at UT Austin’s Texas Advanced Computing Center to model the spread of the coronavirus. The team used historical travel data for the busy Spring Festival season to chart movements between 371 Chinese cities, yielding a more accurate model than could be created on a desktop computer. Read full article

Share Your Research News

If you or your organization is involved in virus- or pandemic-related research, please share your news with the SC20 Communications Team so we can highlight how HPC is making a positive impact in the world. 

—

Christine E. Cuicchi, SC20 General Chair

Monitoring the Situation

As the impact of COVID-19 and the worldwide response to the virus grows, I want to express the SC20 team’s heartfelt concern for our friends, colleagues, and families around the world. So, you may be wondering: is SC20 still on? The short answer is, yes.

Because there is extreme fluidity with this situation, we are continuing to plan to hold SC20 as scheduled in November while monitoring the situation.  We encourage you to continue to submit to our various Technical Program, Students@SC Program, and SCinet Program events.

Call for Participation

Submission Deadlines

Out of concern for the health and well-being of stakeholders, many employers have implemented travel restrictions; NVIDIA transformed GTC into an online-only format; and the American Physical Society and SXSW have canceled their March events. As of this writing, other conferences and large gatherings, like ISC in Frankfurt and the 2020 Olympics, are in wait-and-see mode.

Coronavirus & SC Guidelines & Policy

HPC & Coronavirus

HPC has been a tremendous enabler of advances in healthcare and medical research for many years. And as you’d expect, HPC is helping scientists get a lead on the coronavirus and its impacts on human health.

• Epidemiologists have been using the Wrangler supercomputer at UT Austin’s Texas Advanced Computing Center to model the spread of the coronavirus. The team used historical travel data for the busy Spring Festival season to chart movements between 371 Chinese cities, yielding a more accurate model than could be created on a desktop computer. Learn more
• Supercomputing power applied to records of historical pandemics, such as the 2009 H1N1 flu pandemic which killed more than 200,000 people, can help us fight new diseases. A team from the University of California at San Diego built an all-atom, solvated, and experimentally based integrative model of pH1N1 (the H1N1 flu virus) on the Blue Waters supercomputer hosted by the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign. Using this model of the entire viral envelope, which consisted of more than 160 million atoms, they examined two binding sites on the flu’s viral proteins. For the first time they were able to understand how flu proteins on the surface of the virus interact with each other. From this research, new anti-influenza therapeutics may be developed. Learn more
• Simulations of more than 8000 small-molecule drug compounds to screen for those that could bind to a protein in coronaviruses and disable it from infecting host cells have been performed on the Summit supercomputer at Oak Ridge National Laboratory. The S-protein spike is present in both the virus responsible for the SARS epidemic of 2003 and the COVID-19 disease. The systematic screening of compounds reduced the original set of 8000 down to a more reasonable 77 small-molecule drug compounds that can potentially undergo experimental testing. Thanks to Summit, the simulations took only a day or two, saving valuable time that can be used by experimental researchers to focus on a manageable number of options for stopping the coronavirus. Learn more

Share Your Research News

If you or your organization is involved in virus- or pandemic-related research, please share your news with the SC20 Communications Team so we can highlight how HPC is making a positive impact in the world.

We hope to see all of you in Atlanta in November, and wish you all the best in these trying times.

—

Christine E. Cuicchi, SC20 General Chair