Computational Biology at the Texas Advanced Computing Center

Life scientists, including biologists, physicians, and biochemists, are increasingly using advanced computing to model life's basic processes, interpret massive amounts of data, and improve human health.

Over the past three years, the Texas Advanced Computing Center, already a leader in high-performance computing, has broadened its computational biology programming, adding software, support and expertise to multiply the number of cutting-edge research projects in this field carried out on Ranger and other HPC systems. In doing so, TACC supported the creation of the first 3D model of the H1N1 virus's active protein; helped release the potential of 3D electron microscopes; drove the development of realistic models of the human lung; and performed laser cancer surgery on a canine.

In April, we highlight four projects that illustrate the breadth of biological research taking place on TACC systems. Each project, briefly described here, has the capacity to significantly forward our understanding of many of life's basic processes and improve society. Come back each week to read about these groundbreaking projects.

In Search of Tomorrow's Cures
PI: Pengyu Ren, The University of Texas at Austin

Omar GhattasDespite massive financial and intellectual investments, computational drug discovery has failed to live up to its potential. Current docking programs have missed many of the most effective drug compounds, while promoting ineffective ones as candidates. Yet more accurate methods have been too expensive or complicated to employ. The emergence of powerful supercomputers is finally opening the door to more accurate drug discovery methods. Pengyu Ren, from The University of Texas at Austin, is using the Ranger supercomputer to more fully utilize robust molecular dynamics methods and to predict effective drug candidates for proteins involved in cancer and heart disease.


Catching Evolution in Action
PI: Mikhail Matz, The University of Texas at Austin — 4/12

Klaus SchultenIn 2005, the first of the next-generation gene sequencers arrived on the market. With the ability to decode full genomes at a fraction of the cost and time of previous efforts, the tool has a profound ability to change the study and practice of human health. It has also allowed researchers to study non-model organisms and sample across populations.

Biologist Mikhail Matz is using the supercomputers at the Texas Advanced Computing Center to analyze the genome of corals impacted by climate change, in the hope of better understanding the mechanisms driving their evolution.

Blueprint for the Affordable Genome
PI: Aleksei Aksimentiev, University of Illinois Urbana-Champaign — 4/19

Gabriele JostScientists believe the $1,000 genome is close at hand and that it will transform medicine. Aleksei Aksimentiev, a computational physicist at the University of Illinois Urbana-Champaign, is on one of the leading teams rushing to develop Generation 4 sequencers that "read" DNA directly by measuring the charges of the bases as they pass through a nanopore.

Using the Ranger supercomputer, Aksimentiev has been rapidly prototyping atomistic models to explain the behavior of these nanopore sequencers and to optimize their functionality.


Cyberinfrastructure for Plant Biologists
PI: Dan Stanzione, Texas Advanced Computing Center, The University of Texas at Austin

Edward WalkerIn January 2008, the National Science Foundation initiated a $50 million, 5-year project — the "iPlant Collaborative" — to create the cyberinfrastructure needed to tackle grand challenge questions in plant biology. TACC is an active collaborator in iPlant, applying the computational resources as well as the talent of the center's staff, to help empower scientists with the tools to address the most demanding questions in plant sciences and ultimately discover solutions to some of the world's most pressing issues such as food shortages.

Read an interview with Dan Stanzione, TACC's deputy director and co-PI on iPlant, to learn more about this important initiative.

 


Stay tuned throughout the month as we bring you news about these and other exciting projects and initiatives.