The Best Thing Since Sliced Bread?

Zebrafish Study Reveals First Fine Structure of a Complete Vertebrate Brain

May 10, 2017

Zebrafish larva head in cross-section. Note this isn’t a single electron microscope image, but many thousands of slices seen on edge. The large black circle is the eye, the big darker gray shape at top the brain. You can also see the nose (black crescent at right), the ear (black crescent near center) and several vertebrae (center bottom).

Why It’s Important

Every thought, every feeling, every sensation—and every behavioral illness—ultimately depends on how our brains work. Despite decades of stunning advances in imaging the brain and measuring its activity, though, we still don’t understand how even a simple vertebrate brain works.

Enter the zebrafish larva. Small and transparent—yet able to swim freely and even hunt small prey—these baby fish have long been studied by researchers to understand how their tiny brains generate behaviors. David Hildebrand, working in

the laboratories of Florian Engert and Jeff Lichtman at Harvard University, took this work a step farther, creating electron microscopic images of the zebrafish brain cut
into tens of thousands of slices.

With the help of co-author PSC’s Art Wetzel, they led an international collaboration that used these images to reconstruct specific nerve cells that spanned nearly the entire larval zebrafish brain. The hope is that this kind of thorough “nano-scale” imaging will make it possible to

extract the brain’s complete “wiring diagram.” While this work has only just begun, it may eventually shed new light on past studies of zebrafish behavior—and point the way toward a better understanding of more complex brains, such as ours.

Modest Increase in Kids' Exercise May Yield Outsized Benefits

May 2, 2017

Getting just a few more American kids to run and play for 25 minutes three times a week could have outsized benefits in reducing obesity and save tens of billions of dollars, according to researchers at the Global Obesity Prevention Center at Johns Hopkins Bloomberg School of Public Health and the Pittsburgh Supercomputing Center at Carnegie Mellon University.

The investigators used their computer simulation tool, called VPOP—Virtual Population for Obesity Prevention—to calculate how increasing the number of elementary school children participating in physical activity would play out in health benefits. Increasing the percent of kids who get thrice-weekly exercise from the current 32 percent to just 50 percent, they found, would result in 340,000 fewer obese or overweight kids and save $21.9 billion in lifetime medical costs and lost wages.

Read more.

Heat Stable Vaccines Could Save Lives, Money

April 26, 2017

Health care workers in low-income nations often have to deliver vaccines on rugged footpaths, via motorcycle or over river crossings. On top of this, vaccines need to be kept refrigerated or they may degrade and become useless, which can make getting vaccines to mothers and children that need them challenging.

That’s why researchers at Doctors Without Borders and the HERMES Logistics Team of the Global Obesity Prevention Center at the Johns Hopkins Bloomberg School of Public Health and the Pittsburgh Supercomputing Center at Carnegie Mellon University carried out the first computer simulation of the health and economic impacts of introducing heat-stable vaccines in India and in Benin and Niger in Africa. The simulation offered good news. Not only would vaccines that don’t require refrigeration help increase vaccination rates in these countries, the cost savings of decreased spoilage and improved health would more than cover the cost of making the vaccines stable, even at twice or three times the current cost per dose.

Read more.

Users Can Run Trinity RNA-Seq Assembly Jobs on XSEDE from Galaxy Main

Researchers preparing de novo transcriptome assemblies via the popular Galaxy platform for data-intensive analysis now have transparent access to a premier HPC resource ideal for rapid assembly of massive RNA sequence data. A high-performance Trinity tool has been installed on the public Galaxy Main instance at usegalaxy.org. All Trinity jobs in workflows run from usegalaxy.org will execute transparently on large memory nodes on the Bridges system at the Pittsburgh Supercomputing Center, without the need for users to obtain their own XSEDE allocation. These tools are free to use for open scientific research. Additional de novo assembly applications will be added to Galaxy Main in the future. For more information about Galaxy and Bridges see https://galaxyproject.org/ and http://www.psc.edu/index.php/bridges.

PSC System Powers Libratus, and More

Jan. 31, 2017

Watch the press conference at the Rivers Casino.

In the “Brains vs. AI” competition at the Rivers Casino in Pittsburgh, a CMU School of Computer Science artificial intelligence program—“AI”—called Libratus beat four of the world’s top players at heads-up, no-limit Texas hold’em poker. Libratus ran on a Pittsburgh Supercomputing Center (PSC) system named Bridges to provide the vast amounts of computing and data needed to achieve this milestone.

Upgrade of PSC’s Big Data System Now in Production

Jan. 9, 2017

The Phase 2 Upgrade of the Bridges supercomputer at the Pittsburgh Supercomputing Center (PSC) has been approved by the National Science Foundation (NSF), which funded the project. The approval makes new Bridges hardware, introduced as a technical upgrade, available for research allocations to the national scientific community.

The new upgrades increase the number of nodes available on the system and expand its data storage capacity. New nodes introduced in this upgrade include two with 12 TB (terabytes) of random-access memory (RAM), 34 with 3 TB of RAM, and 32 with two NVIDIA Tesla P100 GPUs. The configuration of Bridges, using different types of nodes optimized for different computational tasks, represents a new step to provide powerful “heterogeneous computing” to fields that are entirely new to high-performance computing (HPC) as well as to “traditional” HPC users.

Upping The Ante: Top Poker Pros Face Off With Artificial Intelligence

20-Day Contest at Rivers Casino in Pittsburgh Begins Jan. 11

Jan. 4, 2017

Four of the world’s best professional poker players will match wits with an artificial intelligence developed by Carnegie Mellon University and using PSC's Bridges system to formulate strategy. The epic rematch will determine whether a computer can beat humans playing one of the world’s toughest poker games.

In “Brains vs. Artificial Intelligence: Upping the Ante,” beginning Wednesday, Jan. 11, at the Rivers Casino in Pittsburgh, poker pros together will play Heads-Up No-Limit Texas Hold’em over 20 days with a CMU School of Computer Science computer program called Libratus.

Read the Carnegie Mellon School of Computer Science release.

Visit the Rivers Casino tournament Web page.

For more information, contact:

Ken Chiacchia
Pittsburgh Supercomputing Center
(412) 268-5869
chiacchi@psc.edu

Vivian Benton
Pittsburgh Supercomputing Center
(412) 268-6355

PSC Bridges and Brain Reconstruction Project Earn 2016 HPCwire Awards

Annual Awards Bestowed on Leaders in the Global High-Performance Computing Community

Nov. 14, 2016

The Pittsburgh Supercomputing Center (PSC) has received two international awards in high-performance computing. PSC was cited in the annual HPCwire Readers’ and Editors’ Choice Awards for two projects: Its new Bridges supercomputer won “Best Data-Intensive System (End User Focused);” and its ongoing collaboration to reconstruct the microscopic architecture of the brain with Harvard University and the Allen Institute for Brain Science won “Best Use of High Performance Data Analytics.”