New digital laboratory helps get COVID-19 analyses up and running quickly

Data analysis and visualization are helping answer a variety of questions about COVID-19 such as who is most at risk, how is the disease spreading, and what approaches might work best for treatments. However, setting up a computer environment to analyze the large amounts of data needed to answer such questions is no easy task. It requires selecting data libraries, software, and hardware and estimating how much memory and computing power will be needed. This process is time consuming and few individuals have the complex skill set needed to accomplish it.

RENCI scientists have developed a new digital data science laboratory called Blackbalsam that can help significantly shorten the planning stage for these efforts with a standardized environment housing computational and data sets for COVID-19 analytics.  

“As COVID-19 progressed, I saw that researchers were conducting analyses and visualization on an increasingly varied set of COVID-19 data,” said Blackbalsam co-author Steven Cox, assistant director of software systems architecture at RENCI. “I realized that it would be very helpful to have an environment that overcomes well-known technological and skill barriers by providing an interface that researchers with statistical, analytical, and visualization skills could use.”

The best tools, all in one place

Blackbalsam eliminates the need for each user to assemble all the required computational and data instruments from scratch by bringing together the best and newest technology for cluster computing, artificial intelligence, and visualization in a cloud-ready and open-source environment.

The creation of Blackbalsam draws on RENCI’s previous experience in bringing analytical tools to data scientists. “We’ve worked with communities at the National Science Foundation and National Institutes of Health in the areas of imaging, artificial intelligence, and knowledge graphs,” said Cox. “This has given us a wide and varied exposure to the kinds of tools scientists use and also the kinds of challenges that they face.”

Rather than selecting a specific tool to perform each function, the developers decided that the interface should provide a suite of artificial intelligence analysis capabilities and visualization environments so that users can use what works best for them. The platform also provides built-in tools for sharing and scaling up analyses.

The fact that the Blackbalsam infrastructure is cloud-ready will allow a scientist performing an unusually large analysis to move it to the cloud without changing any fundamental processes. It was also important for the tools available on Blackbalsam to be open source because using proprietary software for analytics can be expensive and can create a significant barrier for researchers to reproduce and build on each other’s work.

Air pollution and COVID-19

RENCI researchers plan to use Blackbalsam to examine COVID-19 and fine particulate matter pollution in North Carolina. “We’ve been involved in an ongoing project that has collected data on this type of air pollution in the state,” said Cox. “When we saw the research about higher mortality rates for COVID-19 in the presence of particulate matter, it created the opportunity to investigate the impact of COVID-19 in communities based on pollution levels.”

Although COVID-19 is the current focus of Blackbalsam, the design process accounts for the continuing need for unified analytics platforms that allow scientists to get started quickly. “We don’t want to be in the situation again where something happens that requires many people to quickly begin analyzing data, but we don’t have a consolidated environment ready for it,” said Cox.

Blackbalsam can be accessed at https://github.com/helxplatform/blackbalsam.

By Anne Johnson, Lead Science Writer at Creative Science Writing

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Professor learns new lessons while teaching during a pandemic

When UNC students left for spring break on March 9, the COVID-19 public health crisis was just heating up. Soon after, UNC administrators made the decision to move to remote teaching and extended the break by a week to give instructors time to prepare. RENCI Deputy Director Ashok Krishnamurthy was one of many UNC professors who made the quick transition to teaching via video conferencing on Zoom.

What course were you teaching when you received notice that classes would all be moved online?

I was teaching a computer science course called Introduction to Scientific Programming that is designed for non-computer science majors. Most of the students take the class to learn programming skills for their day-to-day work or research. My section of the course had about 160 students enrolled.

How easily were you able to convert this class to a virtual format?

Fortunately, the course was relatively easy to adapt to virtual teaching. The UNC Computer Science department, and my colleague John Majikes who was teaching another section of the same course, have set up this course in such a way that taking it online was quite straightforward.

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Beyond data: Supporting community during a pandemic

Families showing off their new face masks, donated by Sarah Davis.

When COVID-19 cases began to appear across the country, many RENCI employees felt a call to action. While several took it upon themselves to develop new data science technologies or to adapt existing ones to process COVID-19 data, others have contributed to communities in need by creating face masks, assisting food banks, connecting researchers to projects, and supporting foster youth.

Creating Face Masks

Like many across the nation, some RENCI employees have started sewing face masks to donate to medical workers, neighbors, and people in need.

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FABRIC and iRODS events shift to virtual venues

Due to the current COVID-19 situation, many previously scheduled in-person events are moving to virtual spaces. Events associated with RENCI projects and with consortium and partner institutions are making decisions daily about whether to postpone, transition to virtual, or potentially proceed in the late summer and fall. We will keep our events calendar updated, so check back regularly for announcements. 

Two major events that have made the choice to transition to virtual are the FABRIC Community Workshop and the iRODS User Group Meeting. Although this change is unprecedented, both teams are adjusting their sessions to accommodate the virtual atmosphere and provide a memorable experience for attendees.

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From the Director: RENCI responds to the COVID-19 crisis

The past few weeks have presented unique challenges to how we work, how we enjoy ourselves, and how we live our everyday lives. We are all worried about the uncertainties and about how this will affect us and our loved ones in the coming weeks. 

That being said, I am proud to work at RENCI and UNC-Chapel Hill, and blessed to be confronting the current challenges in a region where we are so fortunate to have skilled personnel and resources to bring to bear.

We can gather data and compute. We can volunteer. We can serve. We can encourage each other. We can broadcast. With relatively limited risk through working remotely, we can use our brains, our team spirit, our good will, our tools, and our machines to do science and serve.

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A Radical New Tack: True Collaboration

Data Commons Pilot Phase teams plan how a rising tide of data and tools can float all research boats

Last November the National Institutes of Health announced $9 million in pilot funding to explore feasibility and best practices for a new approach to advancing biomedical research. The initiative, known as Data Commons, is focused on making digital objects—that is, the data, models, and analytical tools that constitute the engine behind the modern research enterprise—available through collaborative platforms.

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RENCI Provides Insight on Data Science in Courtrooms

Stan Ahalt, Director, and Sarah Davis, Research Project Manager, attended the Science in the Courtroom Seminar for Resource Judges, held August 29-31, 2018, at the U.S. Court of Appeals for the Federal Circuit in Washington, DC. The seminar – organized by Franklin Zweig, Esq., of the National Courts and Sciences Institute and Dr. James Evans of the UNC Department of Genetics and Bryson Center for Judicial Science Education – is part of an ongoing science training program for state and federal judges from around the country, educating the judges to become resources on scientific issues for judges in their jurisdictions.

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RENCI participates in NSF Cyber Carpentry workshop to prepare early-career researchers

Teacher and students discuss an issue with their team project.
From left: Andres Espindola-Camacho from Oklahoma State University, Jeremy Thorpe from Johns Hopkins University School of Medicine, Gaurav Kandoi from Iowa State University, and Yingru Xu from Duke University discuss an issue with their team project.

Big data is only getting bigger, and that can cause big problems for researchers who need to store and share their data. Twenty doctoral students and post-doctoral associates from across the county learned the tools and techniques to solve these problems at the inaugural Cyber Carpentry Workshop at the University of North Carolina at Chapel Hill. Sponsored by the National Science Foundation (NSF) and hosted by the UNC School of Information and Library Science (SILS), the two-week workshop in late July introduced students to a variety of applications, platforms, and processes for data life-cycle management and data-intensive computation. The Renaissance Computing Institute (RENCI) provided support for the workshop in the form of instructors and project management staff.

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Strategies for hiring and maintaining a diverse data scientists workforce

RTI’s Kristina Brunelle (left) moderates a panel discussion with Amy Roussel, RTI (center); Gracie Johnson-Lopez, Diversity and HR Solutions (right); and Sackeena Gordon-Jones, Transformation Edge and NC State University (on screen).

Data science is hot. That’s good news for workers with data science skills. It also means organizations competing to hire data scientists need to understand how to recruit talent that will solve their data science challenges and contribute to creating a productive and diverse workforce.  Read more…

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Winston-Salem State University students visit RENCI, UNC-Chapel Hill

A group of undergraduate Winston-Salem State University (WSSU) students majoring in math recently visited Chapel Hill for an educational tour of RENCI and to make connections with peers and educators in the UNC-Chapel Hill math department.

John Hutchens and Felicia Griffin, assistant professors in the mathematics department at WSSU, arranged the visit as part of a series for their students to highlight the types of jobs available to math and computer science graduates. Read more…