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Computing Power at Our Fingertips

Computational sciences represent a strategic and transformative axis of development for UT, and our department is on the cutting edge in teaching and research in the field. Five research groups in the department specialize in computational biophysics and systems biology and virtually all BCMB research groups utilize these approaches for intradepartmental collaboration.

The supercomputers owned and operated by UT/ORNL computational scientists within the Joint Institute for Computational Sciences offer BCMB faculty and students a computing power that is, without question, unrivaled. Today, the TITAN supercomputer (#4 in the world), located in Oak Ridge, is available to our students and researchers and is one of the most powerful supercomputer in the world. TITAN debuted as number one in the world in 2012 and has maintained the top four position for the last five years.

Until a few years ago, UT also operated the Kraken supercomputer, the most powerful academic supercomputer on the planet at the time. Kraken is now replaced with a newer and more powerful machine, STAMPEDE2 (#12 in the world, located at University of Texas Supercomputer Center), which is accessible for our research. Supercomputing resource consortium XSEDE built and now manage both Kraken and STAMPEDE2. UT computer scientists at NICS are a part of it.

In order to grasp the power of a supercomputer, think of Neyland Stadium entirely filled with spectators. Even if each of these spectators had a computer on their knees, and if they were all working at the same time on the same task, it would still represent only about a fifth of the supercomputing power available to us.

With such computing power at our fingertips, we can address research questions and grand challenges within molecular and cellular biology that are far more complex and realistic than what was previously achievable. For instance, scientists led by BCMB Professor and Governor’s Chair Jeremy Smith and BCMB faculty member Jerome Baudry have used Titan to virtually test tens of millions of drug candidates as potential agents for protein targets associated with a wide variety of diseases and human pathologies, and also, remarkably, to test for potential unwanted side effects of these compounds.

“The supercomputer Deep Thought in the Hitchhiker’s Guide to the Galaxy was rumored to have predicted the existence of the baguette and the Archbishop of Lyon from the Big Bang in under a millisecond,” Smith says. “Buoyed by that concept, the BCMB computational scientists have thrown themselves onto TITAN at ORNL, the nation’s most powerful machine, which is capable of doing 19,000,000,000,000,000 (19 quadrillion) calculations a second. They use this monster to design drugs, understand bacterial membranes, and improve bioenergy. Predicting the genesis of the Archbishop of Lyon is on the list of future activities.”

In addition to these applications, BCMB scientists are using the power of petascale computing in systems biology inquiries, which integrate large complex datasets to simulate, understand, and predict the behavior of entire cells, organisms, and populations.

These research opportunities provide unique and powerful training experiences for BCMB graduate and undergraduate students and have spearheaded the development of computation laboratories within the evolving BCMB curriculum. There are not many departments in the nation that can offer their seniors a class with a lab project on “Top-10 in the world” supercomputers. It is, to paraphrase one student’s comment, like “using the Saturn V rocket to learn how to fly.”