Sunday, March 31, 2013

Autism: 'Gordon,' a supercomputer with unique flash memory

Gordon, a completely new kind of supercomputer that uses massive amounts of flash memory, helps researchers study transcription factors that can be targeted for treatment of mental disorders. 

Credit: UC San Diego Publications/Erik Jepsen 

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.

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.

"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 Behaviour 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.


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