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Turing Institute Engaging the Science of Big Data

Posted in Big Data, Intelligent Information Systems, tagged Analytical solutions, analytics, Archer, Big data, Cray Computing, Supercomputer on December 10, 2015| Leave a Comment »

Turing Institute Engaging the Science of Big Data

Larry H. Bernstein, MD, FCAP, Curator

LPBI

Alan Turing Institute Will Lead Research in Data Science

12/08/2015 – Duncan Roweth, Cray

http://www.scientificcomputing.com/sites/scientificcomputing.com/files/Alan_Turing_Institute_Will_Lead_Research_in_Data_Science_440.jpg

http://www.scientificcomputing.com/blogs/2015/12/alan-turing-institute-will-lead-research-data-science

Cray is partnering with the Alan Turing Institute, the new U.K. data science research organization in London, to help the U.K. as it increases research in data science to benefit research and industry.

Earlier this month Fiona Burgess, U.K. senior account manager, and I attended the launch of the institute. At the event, U.K. Minister for Science and Universities Jo Johnson paid tribute to Turing and his work. Institute director Professor Andrew Blake told the audience that the Turing Institute is about much more than just big data — it is about data science, analyzing that data and gaining a new understanding that leads to decisions and actions.

Alan Turing was a pioneering British computer scientist. He has become a household name in the U.K. following publicity surrounding his role in breaking the Enigma machine ciphers during the Second World War. This was a closely guarded secret until a few years ago, but has recently become the subject of numerous books and several films. Turing was highly influential in the development of computer science, providing a formalization of the concepts of algorithm and computation with the Turing machine. After the war, he worked at the National Physical Laboratory, where he designed ACE, one of the first stored-program computers.

The Alan Turing Institute is a joint venture between the universities of Cambridge, Edinburgh, Oxford, Warwick, University College London, and the U.K. Engineering and Physical Science Research Council (EPSRC). The Institute received initial funding in excess of £75 million ($110 million) from the U.K. government, the university partners and other business organizations, including the Lloyd’s Register Foundation.

The Turing Institute will, among other topics, research how knowledge and predictions can be extracted from large-scale and diverse digital data. It will bring together people, organizations and technologies in data science for the development of theory, methodologies and algorithms. The U.K. government is looking to this new Institute to enable the science community, commerce and industry to realize the value of big data for the U.K. economy.

Cray will be working with the Turing Institute and EPSRC to provide data analytics capability to the U.K.’s data sciences community. EPSRC’s ARCHER supercomputer, a Cray XC30 system based at the University of Edinburgh, has been chosen for this work. Much as we worked with NERSC to port Docker to Cray systems, we will be working with ATI to port analytics software to ARCHER and then XC systems generally.

ARCHER is currently the largest supercomputer for scientific research in the U.K. — with its recent upgrade ARCHER’s 118,080 cores can access in excess of 300 TB of memory. What sort of problem might need that amount of processing power? Genomics England is collecting around 200 GB of DNA sequence data from each of 100,000 people. Finding patterns in all this information will be a mammoth task!

ATI have put together a wide ranging programme of workshops and data science summits, details of which can be found on their Web site.

Duncan Roweth is a principal engineer in the Cray CTO Office in Bristol, U.K.

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Simulating the Human Heart Function requires World’s Fastest Supercomputer

Posted in Bio Instrumentation in Experimental Life Sciences Research, Biomarkers & Medical Diagnostics, Cardiovascular Pharmacogenomics, Cell Biology, Signaling & Cell Circuits, Chemical Genetics, Computational Biology/Systems and Bioinformatics, Genome Biology, Genomic Testing: Methodology for Diagnosis, Personalized and Precision Medicine & Genomic Research, Population Health Management, Genetics & Pharmaceutical, Statistical Methods for Research Evaluation, Technology Transfer: Biotech and Pharmaceutical, tagged IBM, Lawrence Livermore National Laboratory, LLNL, Los Alamos National Laboratory, Salt Lake City, Sandia National Laboratories, Sequoia, Supercomputer on October 29, 2012| Leave a Comment »

Reporter: Aviva Lev-Ari, PhD, RN

October 24, 2012

Sequoia Supercomputer Pumps Up Heart Research

Tiffany Trader

The Cardioid code developed by a team of Livermore and IBM scientists divides the heart into a large number of manageable pieces, or subdomains. The development team used two approaches, called Voronoi (left) and grid (right), to break the enormous computing challenge into much smaller individual tasks.Source: LLNLThe world’s fastest computer has created the fastest computer simulation of the human heart.

The Lawrence Livermore National Laboratory‘s Sequoia supercomputer, a TOP500 chart topper, was built to handle top secret nuclear weapons simulations, but before it goes behind the classified curtain, it is pumping out sophisticated cardiac simulations.

Earlier this month, Sequoia, which currently ranks number one on the TOP500 list of the world’s fastest computer systems, received a 2012 Breakthrough Award from Popular Mechanics magazine. Now the magazine is reporting on Sequoia’s ground-breaking heart simulations.

Clocking in at 16.32 sustained petaflops (20 PF peak), Sequoia is taking modeling and simulation to new heights, enabling researchers to capture greater complexity in a shorter time frame. With this advanced capability, LLNL scientists have been able to simulate the human heart down to the cellular level and use the resulting model to predict how the organ will respond to different drug compounds.

Principal investigator Dave Richards couldn’t resist a little showboating: “Other labs are working on similar models for many body systems, including the heart,” he told Popular Mechanics. “But Lawrence Livermore’s model has one major advantage: It runs on Sequoia, the most powerful supercomputer in the world and a recent PM Breakthrough Award winner.”

The simulations were made possible by an advanced modeling program, calledCardioid, that was developed by a team of scientists from LLNL and the IBM T. J. Watson Research Center. The highly scalable code simulates the electrophysiology of the heart. It works by breaking down the heart into units; the smaller the unit, the more accurate the model.

Until now the best modeling programs could achieve 0.2 mm in each direction. Cardioid can get down to 0.1 mm. Where previously researchers could run the simulations for tens of heartbeats, Cardioid executing on Sequoia captures thousands of heartbeats.

Scientists are seeing 300-fold speedups. It used to take 45 minutes to simulate just one beat, but now researchers can simulate an hour of heart activity – several thousand heartbeats – in seven hours.

With the less sophisticated codes, it was impossible to model the heart’s response to a drug or perform an electrocardiogram trace for a particular heart disorder. That kind of testing requires longer run times, which just wasn’t possible before Cardioid.

The model could potentially test a range of drugs and devices like pacemakers to examine their affect on the heart, paving the way for safer and more effective human testing. But it is especially suited to studying arrhythmia, a disorder of the heart in which the organ does not pump blood efficiently. Arrhythmias can lead to congestive heart failure, an inability of the heart to supply sufficient blood flow to meet the needs of the body.

There are various types of medications that disrupt cardiac rhythms. Even those designed to prevent arrhythmias can be harmful to some patients, and researchers do not yet fully understand exactly what causes these negative side effects. Cardioid will enable LLNL scientists to examine heart function as an anti-arrhythmia drug enters the bloodstream. They’ll be able to identify when drug levels are highest and when they drop off.

“Observing the full range of effects produced by a particular drug takes many hours,” noted computational scientist Art Mirin of LLNL. “With Cardioid, heart simulations over this timeframe are now possible for the first time.”

The Livermore–IBM team is also working on a mechanical model that simulates the contraction of the heart and pumping of blood. The electrical and mechanical simulations will be allowed to interact with each other, adding more realism to the heart model.

It’s not entirely clear why a national defense lab took on this heart simulation work. Fred Streitz, director of the Institute for Scientific Computing Research at LLNL, would say only that “there are legitimate national security implications for understanding how drugs affect human organs,” adding that the project stretched the limits of supercomputing in a manner that is relatable to the American people.

The cardiac modeling work was performed during the system’s “shakedown period” – the set-up and testing phase – and the team had to hurry to finish in the allotted time span. Once Sequoia becomes classified, it’s unclear if it will still be available to run Cardioid and other unclassified programs, although access will certainly be more difficult since the machine’s principle mission is running nuclear weapons codes.

Sequoia is an integral part of the NNSA’s Advanced Simulation and Computing (ASC) program, which is run by partner organizations LLNL, Los Alamos National Laboratory and Sandia National Laboratories. With 96 racks, 98,304 compute nodes, 1.6 million cores, and 1.6 petabytes of memory, Sequoia will help the NNSA fulfill its mission to “maintain and enhance the safety, security, reliability and performance of the U.S. nuclear weapons stockpile without nuclear testing.”

The Cardioid simulation has been named as a finalist in the 2012 Gordon Bell Prize competition, awarded each year to recognize supercomputing’s crowning achievements. Research partners, Streitz, Richards, and Mirin, will reveal their results at the Supercomputing Conference in Salt Lake City, Utah, on November 13.

SOURCE:

http://www.hpcwire.com/hpcwire/2012-10-24/sequoia_supercomputer_pumps_up_heart_research.html

Human heart simulated on world’s fastest supercomputer

October 29, 2012 | By Ryan McBride

Before the U.S. government cloaks the operations of the Sequoia supercomputer for classified nuclear arms analyses, scientists have tapped the world’s fastest computer for an unprecedented simulation of the human heart. With the aid of the supercomputer, according to an HPC Wire report, researchers have been able to model the heart down to the cellular level and simulate how the organ would react to certain drugs.

The supercomputer has been performing simulations of the heart with a modeling program, Cardioid, from researchers at Lawrence Livermore National Laboratory (LLNL) and IBM’s T.J. Watson Research Center, HPC Wire reported. The computing power and capabilities of the modeling program have advanced heart modeling from simulations of a handful of heartbeats to thousands. It enables researchers to get closer to the real thing as they boost their capacity to capture activities in the heart at finer levels of detail and complexity.

Drugmakers have spent billions of dollars on studies to improve their understanding of the heart, and computer simulations offer a way for researchers to gauge the potential impacts of a compound before testing it in living subjects. Researchers believe that Cardioid could help them understand the activity and potential side effects of drugs for an inefficient heart-pumping condition known as an arrhythmia, which can trigger congestive heart failure and other medical problems.

“Observing the full range of effects produced by a particular drug takes many hours,” Art Mirin, an LLNL computational scientist, noted, as quoted by HPC Wire. “With Cardioid, heart simulations over this timeframe are now possible for the first time.”

SOURCE:

http://www.fiercebiotechit.com/story/human-heart-simulated-worlds-fastest-supercomputer/2012-10-29