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NIMBioS Tutorial

Join instructors from NIMBioS, iPlant, NICS and other national institutions to learn how to use TeraGrid, the CIPRES Portal, the iPlant Discovery environment, university clusters, and other typically free high performance computing (HPC) resources for phylogenetic analysis.

A lack of treatment, cure, or vaccine for both AIDS and its precursor, HIV, is largely the result of a limited understanding of how all the components of the HIV-1 infection pathway operate. Despite the nearly three decades of study since both afflictions entered the public consciousness in the early 1980s, the most successful treatments currently available consist of antiretroviral drug therapies which, at best, merely slow the infection or disease’s progression.

More than 33 million people worldwide are infected with HIV — roughly four times the population of New York City. Using Kraken, Carlos Simmerling is studying the dynamics of HIV-1 protease.

The Top500 list of the world’s fastest supercomputers places University of Tennessee supercomputer Kraken in third place.
University of Tennessee Press Release

Using the world's fastest supercomputer managed by academia, a Cray XT5 known as Kraken located at the National Institute for Computational Sciences (NICS), a group of scientists has performed simulations that help explain how atomic-scale interactions ultimately result in a functioning biological assembly.

The number of transistors that will fit onto a modern computer chip may soon reach the limit, and the usual materials have been pushed to their performance peak. If Moore’s Law is to continue to hold true, a technological revolution of some sort is necessary. Supercomputers are preparing engineers for battle.

KNOXVILLE – Add one more top ten finish to the list of accomplishments at the University of Tennessee–Knoxville, home to the world's most powerful academic supercomputer.

The computer, called Kraken, has made the ten best in the most recent edition of the Top500 list of the world’s most powerful computers, announced today at the International Supercomputing Conference in Hamburg, Germany.

Kraken in the Press:

The push for alternative energy sources worldwide is leading to more advanced research in biofuels. Searching for new materials from which to produce such fuels is keeping researchers at Oak Ridge National Laboratory (ORNL) and the University of Tennessee (UT) busy.

A team led by Jeremy Smith, director of the ORNL Center for Molecular Biophysics and the UT-ORNL Governor’s Chair, will use UT’s Kraken supercomputer to run simulations that will help reveal the detailed workings of cellulose, a potential biofuel material.

Despite the comfort and confidence of the nightly weatherman, accurately predicting future forecasts is a difficult, and very important, task. Reliable weather information is critical to a number of government agencies and objectives, from the Department of Energy to the United States Air Force. When it comes to our military’s strategic, weather-dependent decisions, getting it wrong is not an option. And in order to get it right, you need computers—big ones.

Chains of amino acids called peptides move, jump, twist, and change shape, all of which add to the myriad difficulties involved in peptide research. Yet understanding them is instrumental in putting them to good use—for example, in the treatment of diabetes. To better understand one such peptide’s properties and strengthen its effectiveness in combating this disease, a team led by Adrian Roitberg of the University of Florida has used approximately 500,000 hours on Kraken at NICS.

One area in which Kraken’s presence will surely be felt is climate change. With the consensus that carbon dioxide is altering the Earth’s climate, the Fifth Assessment Report of the Intergovernmental Panel on Climate Change has asked climate modelers to perform a new type of short-term climate simulation.