Fall 2017: PSC News in Brief

by | Oct 20, 2017 | Science Highlights

PSC Interns Advance AI, Cybersecurity, System Administration

On two dates in July and August 2017, PSC’s summer interns—a central part of the center’s educational mission—reported the results of their projects to the PSC staff. The projects, which advanced artificial intelligence, cybersecurity, and high performance-computing system administration, also covered scientific topics ranging from physical chemistry to computer science to biology.

In an artificial intelligence (AI) project leveraging Bridges’ capabilities for deep learning, Ishtar Nyawĩra and Kristi Bushman, students at the University of Pittsburgh, expanded a 2016 intern project involving Nyawĩra as well as Annie Zhang and Iris Qian, both from Carnegie Mellon University, to help researchers create a 3D map of the connections of the zebrafish larva brain. (See the results of the larger zebra connectome project here.) Their aim was to use AI to automate the painstaking manual task of segmenting electron microscope images of ultra-thin slices of zebrafish brains, a necessary step in re-assembling those image slices into a 3D map. The ultimate goal is to speed the process by which neuroscientists create a 3D view of the brain’s connections so they can more rapidly begin asking scientific questions about what those connections mean for brain function.

Other projects undertaken by the 2017 interns include:

  • Generating reports and data that help PSC staff manage the center’s supercomputers, better serving users’ needs.
  • Creating better models for release and control of neurotransmitters at the junction between nerve and muscle cells in the frog, including a visualization of how the signal is transferred from the nervous system to movement.
  • Improving accuracy of the computation of interactions between the nucleus and core electrons in metal atoms.
  • Testing cybersecurity tools for authenticating users in electronic systems, identifying security vulnerabilities and backing up systems so that they are resistant to ransomware.
  • Automating the conversion of MRI scan images into an interactive 3D model of the brain, to aid in brain tumor diagnosis and surgical planning.
Bridges-Powered Research Wins PEARC17 Award

A project run on PSC’s Bridges system won the “Best Accelerating Discovery in Scholarly Research Paper” award at the inaugural PEARC17 supercomputing conference in New Orleans in July 2017. In “Extracting Meaningful Data from Decomposing Bodies,” a team led by the University of Pittsburgh’s Alison Langmead developed artificial intelligence programs to “read” hand-written prison records from the 1800s, including both numbers and written words. The effort used Bridges to produce preliminary results in using artificial intelligence to extract information for use by social scientists, historians, criminologists and any other digital researchers seeking to learn about society and history.

The “Decomposing Bodies” project, led by digital historian Langmead, was supported by computational experts from the NSF’s XSEDE supercomputing centers, of which PSC is a leading member. These were Alan Craig of the National Center for Supercomputing Applications (NCSA), Sandeep Puthanveetil Satheesan of NCSA and Paul Rodriguez of the San Diego Supercomputer Center. Langmead became an early user of Bridges, suggesting “Decomposing Bodies” as a good project for the system when queried by PSC’s Interim Director Nick Nystrom and Staff Computational Science Consultant Rick Costa.

PEARC17 stressed key objectives for those who manage, develop and use advanced research computing throughout the U.S. and the world. It was supported by a number of major participant institutions in the high performance-computing world, including XSEDE.

Early Successes on Anton 2

The new Anton 2 supercomputer at PSC is racking up successes in simulating the motion of large biomolecules at long timescales. New findings, some of which will be covered in future issues of PSC Science Highlights, include:

  • Revealing early events in the mis-folding of the beta amyloid peptide suspected of underlying Alzheimer’s disease.
  • Shedding light on how the tubulin protein interacts with the membranes surrounding the cell’s powerplants, the mitochondria. Tubulin, better known for its roles in cell division and nerve-cell growth, plays roles in healthy and diseased cells that are not yet fully understood.
  • Giving scientists their first look at how the massive insulin receptor protein sits astride the cell membrane—a first step in modeling how insulin commands the body’s cells to balance blood sugar and fat levels.

Anton 2, developed by D.E. Shaw Research (DESRES), enables life scientists to simulate much larger biomolecules for longer timescales than was previously feasible. Provided to PSC without cost by DESRES for use by the national biomedical research community and operationally funded by the National Institutes of Health, Anton 2 is the only such machine available at no charge to biomedical scientists carrying out non-commercial research.

WVU awarded $1 million grant from NSF for new HPC cluster at PSC

A three-year National Science Foundation grant totaling nearly $1 million will let West Virginia University (WVU) develop its next-generation high performance computing cluster to advance research in an array of fields, from drug delivery to genomics and astrophysics.

PSC will host and operate the cluster at its machine room in Monroeville, Pa. PSC will provide ongoing support, including hardware troubleshooting, on-site technical support and managing WVU’s network connection with the cluster.

The design and implementation of the new computing cluster will be funded by a $990,000 NSF Major Research Instrumentation Program (MRI) grant awarded to a group of 22 faculty and led by Blake Mertz of WVU’s C. Eugene Bennett Department of Chemistry. Co-investigators on this project include faculty at the WVU Blanchette Rockefeller Neurosciences Institute and the departments of Biology, Physics and Astronomy, and Mathematics, as well as the WVU Center for Gravitational Waves and Cosmology. The latter is part of the LIGO gravity wave project, three of whose leaders won the 2017 Nobel Prize in Physics.