Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

NSF-funded Superhero Supercomputer Helps Battle Autism

27.03.2013
'Gordon,' a supercomputer with unique flash memory, helps identify gene-related paths to treating mental disorders
When it officially came online at the San Diego Supercomputer Center (SDSC) in early January 2012, Gordon was instantly impressive. In one demonstration, it sustained more than 35 million input/output operations per second--then, a world record.

Input/output operations are an important measure for data intensive computing, indicating the ability of a storage system to quickly communicate between an information processing system, such as a computer, and the outside world. Input/output operations specify how fast a system can retrieve randomly organized data common in large datasets and process it through data mining applications.

Supercomputer Gordon uses massive amounts of flash memory to retrieve randomly organized data.

The supercomputer's record-breaking feat wasn't a surprise; after all, Gordon is named after a comic strip superhero, Flash Gordon.

Gordon's new and unique architecture employs massive amounts of the type of flash memory common in cell phones and laptops--hence its name. The system is used by scientists whose research requires the mining, searching and/or creating of large databases for immediate or later use, including mapping genomes for applications in personalized medicine and examining computer automation of stock trading by investment firms on Wall Street.

Commissioned by the National Science Foundation (NSF) in 2009 for $20 million, Gordon is part of NSF's Extreme Science and Engineering Discovery Environment, or XSEDE program, a nationwide partnership comprising 16 high-performance computers and high-end visualization and data analysis resources.

"Gordon is a unique machine in NSF's Advanced Cyberinfrastructure/XSEDE portfolio," said Barry Schneider, NSF program director for advanced cyberinfrastructure. "It was designed to handle scientific problems involving the manipulation of very large data. It is differentiated from most other resources we support in having a large solid-state memory, 4 GB per core, and the capability of simulating a very large shared memory system with software."

Last month, a team of researchers from SDSC, the United States and the Institute Pasteur in France reported in the journal Genes, Brain and Behavior that they used Gordon to devise a novel way to describe a time-dependent gene-expression process in the brain that can be used to guide the development of treatments for mental disorders such as autism-spectrum disorders and schizophrenia.

The researchers identified the hierarchical tree of coherent gene groups and transcription-factor networks that determine the patterns of genes expressed during brain development. They found that some "master transcription factors" at the top level of the hierarchy regulated the expression of a significant number of gene groups.

The scientists' findings can be used for selection of transcription factors that could be targeted in the treatment of specific mental disorders.

"We live in the unique time when huge amounts of data related to genes, DNA, RNA, proteins, and other biological objects have been extracted and stored," said lead author Igor Tsigelny, a research scientist with SDSC as well as with UC San Diego's Moores Cancer Center and its Department of Neurosciences.

"I can compare this time to a situation when the iron ore would be extracted from the soil and stored as piles on the ground. All we need is to transform the data to knowledge, as ore to steel. Only the supercomputers and people who know what to do with them will make such a transformation possible," he said.

This research is one of a number of high-value projects being conducted at SDSC with Gordon. More information is available in the attached video.

Media Contacts
Bobbie Mixon, NSF (703) 292-8485 bmixon@nsf.gov
Lisa-Joy Zgorski, NSF (703) 292-8311 lzgorski@nsf.gov
Warren Froelich, San Diego Supercomputer Center (619) 534-8564 froelich@sdsc.edu
Program Contacts
Barry I. Schneider, NSF (703) 292-7383 bschneid@nsf.gov
Principal Investigators
Igor Tsigelny, San Diego Supercomputer Center (858) 822-0953 itsigelny@ucsd.edu
Related Websites
Gordon Achieves World Record for Input/output Operations: http://www.sdsc.edu/Gallery/vd_GordonDebut.html
SDSC’s Gordon Supercomputer Used in 61-Million-Person Facebook Experiment: http://www.sdsc.edu/News%20Items/PR092012_fb_vote.html

Researchers Use Gordon to Reveal Behaviors of the Tiniest Water Droplets: http://www.sdsc.edu/News%20Items/PR081512_water_behavior.html


The National Science Foundation (NSF) is an independent federal agency that supports fundamental research and education across all fields of science and engineering. In fiscal year (FY) 2012, its budget is $7.0 billion. NSF funds reach all 50 states through grants to nearly 2,000 colleges, universities and other institutions. Each year, NSF receives over 50,000 competitive requests for funding, and makes about 11,000 new funding awards. NSF also awards nearly $420 million in professional and service contracts yearly.

Bobbie Mixon | EurekAlert!
Further information:
http://www.nsf.gov

More articles from Interdisciplinary Research:

nachricht A new method for the 3-D printing of living tissues
16.08.2017 | University of Oxford

nachricht Bergamotene - alluring and lethal for Manduca sexta
21.04.2017 | Max-Planck-Institut für chemische Ökologie

All articles from Interdisciplinary Research >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: The pyrenoid is a carbon-fixing liquid droplet

Plants and algae use the enzyme Rubisco to fix carbon dioxide, removing it from the atmosphere and converting it into biomass. Algae have figured out a way to increase the efficiency of carbon fixation. They gather most of their Rubisco into a ball-shaped microcompartment called the pyrenoid, which they flood with a high local concentration of carbon dioxide. A team of scientists at Princeton University, the Carnegie Institution for Science, Stanford University and the Max Plank Institute of Biochemistry have unravelled the mysteries of how the pyrenoid is assembled. These insights can help to engineer crops that remove more carbon dioxide from the atmosphere while producing more food.

A warming planet

Im Focus: Highly precise wiring in the Cerebral Cortex

Our brains house extremely complex neuronal circuits, whose detailed structures are still largely unknown. This is especially true for the so-called cerebral cortex of mammals, where among other things vision, thoughts or spatial orientation are being computed. Here the rules by which nerve cells are connected to each other are only partly understood. A team of scientists around Moritz Helmstaedter at the Frankfiurt Max Planck Institute for Brain Research and Helene Schmidt (Humboldt University in Berlin) have now discovered a surprisingly precise nerve cell connectivity pattern in the part of the cerebral cortex that is responsible for orienting the individual animal or human in space.

The researchers report online in Nature (Schmidt et al., 2017. Axonal synapse sorting in medial entorhinal cortex, DOI: 10.1038/nature24005) that synapses in...

Im Focus: Tiny lasers from a gallery of whispers

New technique promises tunable laser devices

Whispering gallery mode (WGM) resonators are used to make tiny micro-lasers, sensors, switches, routers and other devices. These tiny structures rely on a...

Im Focus: Ultrafast snapshots of relaxing electrons in solids

Using ultrafast flashes of laser and x-ray radiation, scientists at the Max Planck Institute of Quantum Optics (Garching, Germany) took snapshots of the briefest electron motion inside a solid material to date. The electron motion lasted only 750 billionths of the billionth of a second before it fainted, setting a new record of human capability to capture ultrafast processes inside solids!

When x-rays shine onto solid materials or large molecules, an electron is pushed away from its original place near the nucleus of the atom, leaving a hole...

Im Focus: Quantum Sensors Decipher Magnetic Ordering in a New Semiconducting Material

For the first time, physicists have successfully imaged spiral magnetic ordering in a multiferroic material. These materials are considered highly promising candidates for future data storage media. The researchers were able to prove their findings using unique quantum sensors that were developed at Basel University and that can analyze electromagnetic fields on the nanometer scale. The results – obtained by scientists from the University of Basel’s Department of Physics, the Swiss Nanoscience Institute, the University of Montpellier and several laboratories from University Paris-Saclay – were recently published in the journal Nature.

Multiferroics are materials that simultaneously react to electric and magnetic fields. These two properties are rarely found together, and their combined...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

“Lasers in Composites Symposium” in Aachen – from Science to Application

19.09.2017 | Event News

I-ESA 2018 – Call for Papers

12.09.2017 | Event News

EMBO at Basel Life, a new conference on current and emerging life science research

06.09.2017 | Event News

 
Latest News

Rainbow colors reveal cell history: Uncovering β-cell heterogeneity

22.09.2017 | Life Sciences

Penn first in world to treat patient with new radiation technology

22.09.2017 | Medical Engineering

Calculating quietness

22.09.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>