Tyler O'Neal, Staff Editor APPLICATIONS

UCSC genome browser posts the coronavirus genome

Researchers can now use the Browser's features to see genetic code at any scale and add annotations for global collaboration

Research into the novel Wuhan seafood market pneumonia virus, the deadly "coronavirus" that has forced the Chinese government to quarantine more than 50 million people in the country's dense industrial heartland, will be facilitated by the UC Santa Cruz Genomics Institute. The Genomics Institute's Genome Browser team has posted the complete biomolecular code of the virus for researchers all over the world to use.

"When we display coronavirus data in the UCSC Genome Browser, it lets researchers look at the virus' structure and more importantly work with it so they can research how they want to attack it," said UCSC Genome Browser Engineer Hiram Clawson.

Samples of the virus have been processed in labs all over the world, and the raw information about its genetic code has been sent to the worldwide repository of genomic information at the National Institutes of Health's National Center for Bioinformatics (NCBI) in Bethesda, Maryland. CAPTION The virus structure is made up of at least three viral proteins, the spike protein, the membrane protein and the envelope protein. CREDIT From Mechanisms of Coronavirus Cell Entry Mediated by the Viral Spike Protein Belouzard et al, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3397359/{module INSIDE STORY}

"The NCBI is a worldwide repository established in the very early days of genomics," said Clawson. "When people find novel viruses, they send them to the NCBI, and the NCBI assigns them a name and number so everyone can refer to an exact specimen. Once they've processed the genomic information, it's made available to the world from the database."

From there, the UC Santa Cruz Genome Browser processes the information into a visual display of the virus.

The NCBI named the Wuhan seafood market pneumonia virus 2019-nCoV, which stands for novel coronavirus discovered in 2019.

UC Santa Cruz retrieved the information, consisting of 29,903 nucleotides -- the base pairs that make up the DNA and RNA molecules that encode all life on earth.

"When we obtain this data from NCBI, it's a single file with the letters in it from the DNA or RNA (A, C, G, and T)," Clawson said. "This one happens to be single-stranded RNA, a relatively simple structure.

This information is processed and placed into a database, where the Genome Browser can access the material and display it in a web browser in a much more useful format.

"What makes the Genome Browser so valuable is that it is so visual," Clawson said. "It makes it very clear where everything is, so when people make interesting measurements about the genome in the virus, they can see what they're looking at," Clawson said.

Researchers can zoom in and out of the genome. This allows them to see base pairs at the most detailed level. Or, they zoom all the way out and see the 10 individual genes that the 29,903 base pairs comprise.

The Browser also contains a CRISPR track, which allows researchers to see where they can splice genetic material and how they can cut it. With CRISPR, researchers can edit the genetic material, a tremendously valuable tool for determining which genes do what.

"In the case of this virus," Clawson said, "there are approximately ten genes and the largest is its spike protein," referring to the chemical spine which the virus uses to snag onto human cells and hijack their cellular machinery to reproduce themselves. "So they might make a change to see if it makes the spike protein more or less virulent."

Formulus Black shows how Forsa allows applications to benefit from high-performance memory-based storage at SC19

Tyler O'Neal, Staff Editor APPLICATIONS

Company’s revolutionary software stack enables any application to leverage memory-based storage, without modification

Venture-backed startup Formulus Black is showcasing how its Forsa solution enables memory to be provisioned and managed as a high-performance, low-latency storage media for the most demanding workloads at the supercomputing show SC19 in Booth No. 296 of the Colorado Convention Center in Denver next week.

Forsa enables any application or filesystem to utilize DRAM or Intel Optane DC persistent memory as a memory-based POSIX compliant block storage. Because of this, no application modifications are needed on the application side to supercharge the performance of I/O intensive HPC processes such as checkpointing. 

Forsa brings a suite of memory-management features that are not available for standard persistent memory devices such as the ability to increase the size of persistent memory block devices that are at full capacity, create clones and snapshots, and manage persistent memory resources on multiple nodes from one management console.  Supporting both legacy and new application environments, Forsa is ideally suited to solving the needs of enterprises in the financial services, automotive, telecom, energy, university, gaming, and healthcare industries. {module INSIDE STORY}

“In the same way that Tesla disrupted the automobile market by demonstrating how batteries could be used for more than just starting a car and keeping the radio on, Formulus Black is disrupting the server market by elevating the role of memory on servers as both a caching layer and a tier 1 low latency storage media for I/O intensive processes” said Jing Xie, Chief Operating Officer at Formulus Black.  “Forsa works with servers powered by Intel Optane DC Persistent Memory Modules and older generation Intel servers with DRAM to deliver memory-accelerated I/O performance for data-intensive applications while providing the manageability, data protection, and usability features typically found in peripheral storage solutions such as snapshots, clones, block resize, backup/restore, and high availability.”

UVA tapped to create graduate course that advances public interest technology

Tyler O'Neal, Staff Editor APPLICATIONS

Cyber Innovation and Society Institute receives inaugural 'Network Challenge' grant

A multidisciplinary team of computer science, law, and public policy faculty at the University of Virginia have earned a national grant to establish a course aimed at teaching graduate students to deeply examine the complex ethical, legal, and policy implications of new technologies.

The Public Interest Technology University Network, which is part of Washington, D.C.-based think tank New America, awarded the grant as a way to cultivate academic initiatives that prepare the next generation of lawyers, policymakers, and technologists to design, build, and govern new technologies that advance the public interest.

UVA, through the Office of the Provost, is the only Virginia university that is a founding partner of the Public Interest Technology University Network. The $90,000 grant, one of 27 awarded across the country, will be led by Jack Davidson, a professor of computer science and an internationally renowned cybersecurity researcher at UVA's School of Engineering who also leads the University's Cyber Innovation and Society Institute. Davidson is collaborating with Thomas Nachbar, UVA law professor and senior fellow at the Law School's Center for National Security Law, and Philip Potter, UVA associate professor of politics and public policy and director of the National Security Policy Center. {module In-article}

The graduate course they are creating will be called Innovation in the Public Interest. The course will be offered for the first time in the spring of 2020.

"I am so pleased that a UVA team was recognized with one of the inaugural awards from the network," said Louis P. Nelson, vice provost for academic outreach at the University of Virginia. "Our faculty recognize the need for cross-disciplinary partnerships between policy specialists, technologists, and experts in the humanities for solving global technological challenges. The collaborations we see at UVA -- not to mention our mission --position us to be leaders in using technology to benefit society, with the team's course development as an ideal example."

The award highlights a long-standing strength at UVA for research and teaching that analyzes the implications of technology for society, particularly through UVA Engineering's Department of Engineering and Society. The Cyber Innovation and Society Institute, which UVA launched in 2018, brings faculty together from technical and humanities fields across the University to understand the impact of cyber systems on society, especially how they affect human values such as privacy, freedom, democracy, and individual autonomy.

The institute adopts an anticipatory approach, addressing political, ethical, and data ramifications before they emerge. In the process, the institute carries out multidisciplinary research and education initiatives that focus on the complex technical, social, and policy challenges posed by emerging cyber innovations to ensure that cyber technology benefits all of society equally, fairly, and dependably.

"As cyber technologies become pervasive, anticipating the impact these technologies have on society and developing policies that guide their interaction with society becomes critical," Davidson said. "A major focus of this new public interest technology course is on creating cyber innovations that are in the public interest and ensure an ethical evolution."

Innovation in the Public Interest will provide students with a structured experience in the development of public interest technology. The course will be offered through UVA's schools of engineering, law, and politics. It will create hands-on, real-world, problem-solving challenges across each week of the course.

Davidson, Nachbar, and Potter are working with government and industry partners who have posed the problems. Teams of diverse students from the different schools will be assigned those problems. They then will conduct team "sprints" designed to quickly engineer a solution that incorporates ongoing stakeholder input throughout the process. Each team also will make a formal presentation of its designed solution to the stakeholders.

This interactive class structure is intended to emulate the process of "agile development." Used by large corporations and start-ups alike, the agile process accelerates timelines on the delivery of better technology products. But the process can fall short in the age of big data, with so many social implications involved due to the ubiquitous nature of technology and the amount of information being gathered.

Unfortunately, agile development does not commonly consider legal requirements, policy ramifications or social implications of the new technologies. "That can result in serious problems down the road," Davidson said. "The idea of the course is to introduce a new mindset about the current process and how it can work better with regards to the public interest. Better social outcomes can be reached by including diverse viewpoints from the very first stages of development."

As the first course of its kind in UVA Engineering's Department of Computer Science, the curriculum also reflects the Engineering School's focus on diversity and multidisciplinary initiatives for better research outcomes. "Studies have shown that diverse groups come up with better solutions," Davidson said. "In alignment with UVA's 2030 strategic plan, a major impetus for offering the course is to expose our students to the rewarding possibilities of harnessing technology for the public good."

Nachbar said, "By integrating technology, policy, and law in our course, we are matching how this area is developing. There is not a single discipline that determines how public sector innovation takes place and affects our society. Our course, which brings together faculty and students from the three disciplines to solve actual problems that are provided by public agency sponsors, reflects that reality."

"Policy students need to learn to operate in multidisciplinary spaces," Potter added. "The really hard national security policy problems facing the United States are nearly always also technical and legal problems. By bringing together three UVA schools, we are preparing students to face that reality."

Innovation in the Public Interest course materials -- the syllabus, lectures, readings, assignments, and project descriptions -- will also be made publicly available for other universities that are interested in building a similar pipeline of public interest technology students.