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Primeur weekly 2017-02-20

Focus

HPC expert Genias Benelux to show its skillful expertise in brandnew website ...

Are billion Euro Flagships the right way to finance innovative areas like graphene, human brain research and quantum computing? ...

Exascale supercomputing

Advanced fusion code led by PPPL selected to participate in Early Science Programmes on three new DOE Office of Science pre-exascale supercomputers ...

Focus on Europe

From robotics to particle physics: Data analytics gets the spotlight in Distinguished Talk series at ISC 2017 ...

A new spin on electronics ...

Data mining tools for personalized cancer treatment ...

Why host HPC in Iceland to tackle Big Data for life sciences at Earlham Insititute ...

Biological experiments become transparent - anywhere, any time ...

Middleware

IBM delivers new platform to help clients address storage challenges at massive scale ...

Hewlett Packard Enterprise unveils most significant 3PAR Flash storage innovations to date ...

Hardware

Tokyo Institute of Technology partners with DDN on Tsubame3.0 to build forward-looking AI and Big Data computing infrastructure ...

Mellanox demonstrates four times improvement in crypto performance with Innova IPsec 40G Ethernet network adapter ...

Supermicro launches BigTwin - the industry's highest performing Twin multi-node system supporting the full range of CPUs, maximum memory and all-flash NVMe ...

Applications

Researchers catch extreme waves with higher-resolution modelling ...

Researchers are creating software to 'clean' large datasets, making it easier for scientists and the public to use Big Data ...

Designing new materials from 'small' data ...

Success by deception ...

DNA computer brings 'intelligent drugs' a step closer ...

'Lossless' metamaterial could boost efficiency of lasers and other light-based devices ...

Perimeter Institute researchers apply machine learning to condensed matter physics ...

When treating brain aneurysms, two isn't always better than one ...

Real-time MRI analysis powered by supercomputers ...

Analyzing data for transportation systems using TACC's Rustler, XSEDE ECSS support ...

NCSA facilitates performance comparisons with China's nr. 1 supercomputer ...

IBM delivers Watson for cyber security to power cognitive security operations centres ...

The Cloud

Optimizing data centre placement and network design to strengthen Cloud computing ...

Dutch start-up solution impacts data centres ...

OpenFog Consortium releases landmark reference architecture for Fog computing ...

IBM brings machine learning to the private Cloud ...

IBM accelerates hybrid Cloud adoption by enabling channel partners to offer VMware solutions ...

Oracle launches Cloud service to help organisations integrate disparate data and drive real-time analytics ...

Real-time MRI analysis powered by supercomputers

Raw image data collected from dGEMRIC MRI protocol at an inversion time of 1600 milliseconds (left). The T1 map computed from seven different inversion times using the automated, real-time, quantitative magnetic resonance imaging pipeline (right).16 Feb 2017 Austin - One of the main tools doctors use to detect diseases and injuries in cases ranging from multiple sclerosis to broken bones is magnetic resonance imaging (MRI). However, the results of an MRI scan take hours or days to interpret and analyze. This means that if a more detailed investigation is needed, or there is a problem with the scan, the patient needs to return for a follow-up. A new, supercomputing-powered, real-time analysis system may change that.

Researchers from the Texas Advanced Computing Center (TACC), the University of Texas Health Science Center (UTHSC) and Philips Healthcare, have developed a new, automated platform capable of returning in-depth analyses of MRI scans in minutes, thereby minimizing patient callbacks, saving millions of dollars annually, and advancing precision medicine.

The team presented a proof-of-concept demonstration of the platform at the International Conference on Biomedical and Health Informatics in Orlando, Florida.

The platform they developed combines the imaging capabilities of the Philips MRI scanner with the processing power of the Stampede supercomputer - one of the fastest in the world - using the TACC-developed Agave API Platform infrastructure to facilitate communication, data transfer, and job control between the two.

An API, or Application Programme Interface, is a set of protocols and tools that specify how software components should interact. Agave manages the execution of the computing jobs and handles the flow of data from site to site. It has been used for a range of problems, from plant genomics to molecular simulations, and allows researchers to access cyberinfrastructure resources like Stampede via the web.

"The Agave Platform brings the power of high-performance computing into the clinic", stated William (Joe) Allen, a life science researcher for TACC and lead author on the paper. "This gives radiologists and other clinical staff the means to provide real-time quality control, precision medicine, and overall better care to the patient."

For their demonstration project, staff at UTHSC performed MRI scans on a patient with a cartilage disorder to assess the state of the disease. Data from the MRI was passed through a proxy server to Stampede where it ran the GRAPE - GRAphical Pipelines Environment - analysis tool. Created by researchers at UTHSC, GRAPE characterizes the scanned tissue and returns pertinent information that can be used to do adaptive scanning - essentially telling a clinician to look more closely at a region of interest, thus accelerating the discovery of pathologies.

The researchers demonstrated the system's effectiveness using a T1 mapping process, which converts raw data to useful imagery. The transformation involves computationally-intensive data analyses and is therefore a reasonable demonstration of a typical workflow for real-time, quantitative MRI.

A full circuit, from MRI scan to supercomputer and back, took approximately five minutes to complete and was accomplished without any additional inputs or interventions. The system is designed to alert the scanner operator to redo a corrupted scan if the patient moves, or initiate additional scans as needed, while adding only minimal time to the overall scanning process.

"We are very excited by this fruitful collaboration with TACC", stated Refaat Gabr, an assistant professor of Diagnostic and Interventional Imaging at UTHSC and the lead researcher on the project. "By integrating the computational power of TACC, we plan to build a completely adaptive scan environment to study multiple sclerosis and other diseases."

Ponnada Narayana, Refaat Gabr's co-principal investigator and the director of Magnetic Resonance Research at the University of Texas Medical School at Houston, elaborated: "Another potential of this technology is the extraction of quantitative, information-based texture analysis of MRI. There are a few thousand textures that can be quantified on MRI. These textures can be combined using appropriate mathematical models for radiomics. Combining radiomics with genetic profiles, referred to as radiogenomics, has the potential to predict outcomes in a number diseases, including cancer, and is a cornerstone of precision medicine."

According to William Allen, "science as a service" platforms like Agave will enable doctors to capture many kinds of biomedical data in real time and turn them into actionable insights.

"Here, we demonstrated this is possible for MRI. But this same idea could be extended to virtually any medical device that gathers patient data", he stated. "In a world of big health data and an almost limitless capacity to compute, there is little reason not to leverage high-performance computing resources in the clinic."

The research is supported in part by National Science Foundation (NSF) award ACI-1450459, by the Clinical Translational Science Award (CTSA) Grant UL1-TR000371 from the National Institutes of Health (NIH) National Center for Advancing Translational Sciences, and by the Chair in Biomedical Engineering Endowment Fund. Stampede was generously funded by the NSF through award ACI-1134872.
Source: University of Texas at Austin, Texas Advanced Computing Center - TACC

Back to Table of contents

Primeur weekly 2017-02-20

Focus

HPC expert Genias Benelux to show its skillful expertise in brandnew website ...

Are billion Euro Flagships the right way to finance innovative areas like graphene, human brain research and quantum computing? ...

Exascale supercomputing

Advanced fusion code led by PPPL selected to participate in Early Science Programmes on three new DOE Office of Science pre-exascale supercomputers ...

Focus on Europe

From robotics to particle physics: Data analytics gets the spotlight in Distinguished Talk series at ISC 2017 ...

A new spin on electronics ...

Data mining tools for personalized cancer treatment ...

Why host HPC in Iceland to tackle Big Data for life sciences at Earlham Insititute ...

Biological experiments become transparent - anywhere, any time ...

Middleware

IBM delivers new platform to help clients address storage challenges at massive scale ...

Hewlett Packard Enterprise unveils most significant 3PAR Flash storage innovations to date ...

Hardware

Tokyo Institute of Technology partners with DDN on Tsubame3.0 to build forward-looking AI and Big Data computing infrastructure ...

Mellanox demonstrates four times improvement in crypto performance with Innova IPsec 40G Ethernet network adapter ...

Supermicro launches BigTwin - the industry's highest performing Twin multi-node system supporting the full range of CPUs, maximum memory and all-flash NVMe ...

Applications

Researchers catch extreme waves with higher-resolution modelling ...

Researchers are creating software to 'clean' large datasets, making it easier for scientists and the public to use Big Data ...

Designing new materials from 'small' data ...

Success by deception ...

DNA computer brings 'intelligent drugs' a step closer ...

'Lossless' metamaterial could boost efficiency of lasers and other light-based devices ...

Perimeter Institute researchers apply machine learning to condensed matter physics ...

When treating brain aneurysms, two isn't always better than one ...

Real-time MRI analysis powered by supercomputers ...

Analyzing data for transportation systems using TACC's Rustler, XSEDE ECSS support ...

NCSA facilitates performance comparisons with China's nr. 1 supercomputer ...

IBM delivers Watson for cyber security to power cognitive security operations centres ...

The Cloud

Optimizing data centre placement and network design to strengthen Cloud computing ...

Dutch start-up solution impacts data centres ...

OpenFog Consortium releases landmark reference architecture for Fog computing ...

IBM brings machine learning to the private Cloud ...

IBM accelerates hybrid Cloud adoption by enabling channel partners to offer VMware solutions ...

Oracle launches Cloud service to help organisations integrate disparate data and drive real-time analytics ...