aarondubrow writes "Metagenomics makes it possible to investigate microbes in their natural environments and in the complex communities in which they normally live, but requires massive computing power. Researchers from the J. Craig Ventor Institute used the Ranger supercomputer at TACC to determine the bacterial and viral diversity of the Indian Ocean as part of the Global Ocean Sampling Expedition. They reported their results in PLOS One in October 2012. They are now applying a metagenomic approach to the human esophagus and the microbial imbalances there that may play a role in certain kinds of gastric acid reflux and esophageal cancer." top
aarondubrow writes "Researchers reported results in Nature Communications on a new way of sculpting tailor-made fluid flows by placing tiny pillars in microfluidic channels. The method could allow clinicians to better separate white blood cells in a sample, increase mixing in industrial applications, and more quickly perform lab-on-a-chip-type operation. Using the Ranger and Stampede supercomputers, the researchers ran more than 1,000 simulations representing combinations of speeds, thicknesses, heights or offsets that produce unique flows. This library of transformations will help the broader community design and use sculpted fluid flows." top
aarondubrow writes "Researchers recently created OpenfMRI, a web-based, supercomputer-powered tool that makes it easier for researchers to process, share, compare and rapidly analyze fMRI brain scans from many different studies. Applying supercomputing to the fMRI analysis allows researchers to conduct larger studies, test more hypotheses, and accommodate the growing spatial and time resolution of brain scans. The ultimate goal is to collect enough brain data to develop a bottom-up understanding of brain function." top
aarondubrow writes "Using supercomputers and gene sequencers, researchers are answering a number of basic questions about the evolution of single-celled diatoms: What were the earliest diatoms like? How has the organism moved from a single site to every body of water in the world? And how have some species developed the ability to produce prodigious amounts of snot?" top
aarondubrow writes "You hear it before you see it — a roar like a factory in full production. But instead of cars or washing machines, this factory produces scientific knowledge.
Stampede, the newest supercomputer at the Texas Advanced Computing Center (TACC) and one of the most advanced scientific research instruments in the world, fills aisle after aisle of a new 11,000-square-foot data center on the J.J. Pickle Research Campus of The University of Texas at Austin. Over the past year TACC staff designed, built and deployed Stampede, working closely with Dell and Intel engineers and university researchers.
aarondubrow writes "2011 Nobel Prize Winner, Bruce Beutler, is using the Ranger supercomputer at The University of Texas at Austin for an ambitious new project to discover all of the genes involved in the mammalian immune response – the so-called "resistome." Over several years, Beutler's lab will sequence the protein coding portions of genes in 8,000 mice to detect the impact of mutations on immunity. This means scanning, enriching and sequencing 500 billion base pairs every week. The project represents a "Big Data" problem of the highest order." Link to Original Source top
aarondubrow writes "Researchers from UC Santa Barbara used the Ranger supercomputer to simulate small forms of amyloid peptides that are believed to be a primary cause of toxicity in Alzheimer's disease. They found that hairpin-shaped forms of the peptide initiated the aggregation of oligomers that ultimately led to the formation of a fibril. The simulations are leading to new diagnostic and treatment options they may stop the disease." Link to Original Source top
aarondubrow writes "For millennia, mankind has discovered new drugs either through educated guesswork or blind luck. But with the proliferation of advanced computing, a new paradigm has emerged whereby one can find drug targets through simulation and modeling...As a consequence of improvements to the image reconstruction and modeling algorithms, researchers can now identify secondary structures of molecules, like individual side-chains — floppy but crucial limbs that extend from the central spine of molecule. This level of detail is required to accurately predict binding." Link to Original Source top
aarondubrow writes "In their paper, Ceder and his team describe the creation of Li9M3(P2O7)3(PO4)2 or lithium pyrophosphate — a material that never existed before — by means of artificial intelligence calculations performed on local clusters at MIT. They then turned to the Ranger supercomputer at TACC to perform diffusion calculations on the new material. The simulations led the scientists to understand why the material worked better than its less-complex relatives, and how it can be improved further." Link to Original Source top
aarondubrow writes "Researchers used the Ranger supercomputer to test a new, high-resolution hurricane forecasting system that incorporates Doppler radar data from planes flying into the storm. The forecasts were shown to improve intensity predictions by an average of 20 to 40 percent over the official forecasts of the National Hurricane Center (NHC). The prediction system is being hailed as a breakthrough and is one of a handful being assessed by the NHC to become part of the operational forecasting system used in emergency situations." Link to Original Source top
Convert 10 million TIFFs in a few days? No Problem
aarondubrow writes "A chance investigation in Guatemala City in 2005 led to the discovery of nearly 80 million pages of police records dating from 1882 to 1996 documenting human rights abuses. The Guatemalan researchers partnered with The University of Texas at Austin and the Texas Advanced Computing Center to make the Archive available online. The Ranger supercomputer was used to create reference files for the first 10 million documents in just a few days. By speeding up the process, UT and the AHPN researchers were able to get the archive online in time for the Guatemalan elections." Link to Original Source top