Posts tagged supercomputers
Articles and news from the latest research reports.
Alzheimer’s and Cancer Link Found
A team led by Houston Methodist Research Institute (HMRI) scientists has found that Alzheimer’s disease and cancer share a pathway in gene transcription, a process essential for cell reproduction and growth. They published their findings in December 2013 in the open access journal Scientific Reports by the Nature Publishing Group.
The scientists used the Lonestar and Stampede supercomputers at the Texas Advanced Computing Center (TACC) at The University of Texas at Austin to analyze and compare data from thousands of genes and to narrow the search for common cell signaling pathways of the two diseases. The Lonestar and Stampede systems are part of the Extreme Science and Engineering Discovery Environment (XSEDE), a single virtual system that scientists use to interactively share computing resources, data and expertise. The research is supported by a gift from the T.T. and W.F. Chao Foundation, and by grants from the National Institutes of Health (NIH).
Lead investigator Stephen Wong, a medical researcher and bioengineer with HMRI, said his study showed a new link between Alzheimer’s disease, the most prevalent form of neurodegenerative disease, and glioblastoma multiform (GBM), the most aggressive form of brain cancer.
"This is the first time people have found that at the molecular mechanism level there are linkages between the two diseases," Wong said.
A 2012 study in Taiwan and a 2013 study in Italy of public health data had shown an inverse association between Alzheimer’s disease, a severe degeneration of the brain’s nerve cells, and with cancer, where cells grow out of control.
"No one understands why this link is there, in a biological sense," Wong said. "And that’s the reason we did this study. I think we are among the first to study it this way."
Neuroscience to Benefit from Hybrid Supercomputer Memory
To handle large amounts of data from detailed brain models, IBM, EPFL, and ETH Zürich are collaborating on a new hybrid memory strategy for supercomputers. This will help the Blue Brain Project and the Human Brain Project achieve their goals.
Motivated by extraordinary requirements for neuroscience, IBM Research, EPFL, and ETH Zürich through the Swiss National Supercomputing Center CSCS, are exploring how to combine different types of memory – DRAM, which is standard for computer memory, and flash memory that is akin to USB sticks – for less expensive and optimal supercomputing performance.
The Blue Brain Project, for example, is building detailed models of the rodent brain based on vast amounts of information – incorporating experimental data and a large number of parameters – to describe each and every neuron and how they connect to each other. The building blocks of the simulation consist of realistic representations of individual neurons, including characteristics like shape, size, and electrical behavior.
Given the roughly 70 million neurons in the brain of a mouse, a huge amount of data needs to be accessed for the simulation to run efficiently.
“Data-intensive research has supercomputer requirements that go well beyond high computational power,” says EPFL professor Felix Schürmann of the Blue Brain Project in Lausanne. “Here, we investigate different types of memory and how it is used, which is crucial to build detailed models of the brain. But the applications for this technology are much broader.”
70 Million Neurons for the New IBM Blue Gene/Q
The Blue Brain Project has acquired a new IBM Blue Gene/Q supercomputer to be installed at CSCS in Lugano, Switzerland. This machine has four times the memory of the supercomputer used by the Blue Brain Project up to now, but this still may not be enough to model the mouse brain at the desired level of detail.
The challenge for scientists is to modify the supercomputer so that it can model not only more neurons—as many as the 70 million in the mouse brain—but with even more detail while using fewer resources. The researchers aspire to do just that by engineering different types of memory. The Blue Gene/Q comes equipped with 64 terabytes of DRAM memory. But this type of memory, which is ubiquitous in personal computers, loses data almost instantaneously when the power is turned off.
The scientists plan to boost the supercomputer’s capacity by combining DRAM with another type of memory that has made its way into everyday devices, from cameras to mobile phones: flash memory. Unlike DRAM, flash memory can retain information, even without power, and is much more affordable. The Blue Brain Project’s new supercomputer efficiently integrates 128 terabytes of flash memory with the 64 terabytes of DRAM memory.
“These technological advancements will not only help scientists model the brain, but they will also contribute to future evidence-based systems,” says IBM Research computational scientist Alessandro Curioni, who is based in Zurich.
To take full advantage of this novel mix of memory, IBM has been developing a scalable memory system architecture, while EPFL and ETH Zürich researchers are working on high-level software to optimize this hybrid memory for large-scale simulations and interactive supercomputing.
“The resulting machine may not necessarily be the fastest supercomputer in the world, but it will certainly open up new avenues for data-intensive science,” says ETH Zürich professor and CSCS director Thomas Schulthess. “The results of this collaboration will support scientific investigations across all types of data intensive applications including astronomy, geosciences and healthcare.”
Towards the Human Brain
The Blue Brain Project has recently become the core of an even more ambitious project, the European Flagship Human Brain Project, also coordinated by EPFL. The Human Brain Project faces the daunting task of providing the technical tools to integrate as much data as possible into detailed models of the human brain by 2023. Estimated at 90 billion neurons, the human brain compared to that of a mouse contains roughly a thousand times more neurons. The new strategy to use hybrid memory is an important step towards helping the Human Brain Project meet its 10-year goal.
As it goes with research and innovation, a scientific pursuit is pushing the boundaries of technology, leading to new and more powerful tools. The Blue Brain and Human Brain Projects have brought into perspective the need to deal with complex and unusual calculations, requiring supercomputer technology where speed is simply not enough.
(Source: actu.epfl.ch)