Updated: Tue, 06 Dec 2011 21:49:38 +0000
TACC Offers New, Broader Computational Biology Software Stack to Open Science Community
AUSTIN, Texas, Nov. 10, 2011 — One of the fastest growing areas in science is comparative genomics, which is driven by advances in next-generation sequencing technology. To meet the needs of scientists in this rapidly expanding field, the Texas Advanced Computing Center (TACC) today announced a significantly improved software set of more than 30 new and updated applications (full list: www.tacc.utexas.edu/compbio/applications
) for life science researchers across the country.
"TACC's goal is to provide a core software set for tackling the most challenging biological questions using advanced computing technologies," said John Fonner, computational biology research associate. "The newly deployed software set reflects TACC's current focus on genomics, bioinformatics and molecular simulation. In the future this will expand into other disciplines as well."
Complex biological systems range from the molecular and cellular to the organismal and ecosystem level. Understanding these systems and their interactions requires the development of algorithms, methods, and software for the accumulation, manipulation, and modeling of biological data. The need for advanced computing resources to address these questions is evident in the fact that approximately a quarter of all TACC's computing cycles are devoted to life science research.
"Today's biological research increasingly involves computationally-intensive modeling and analysis of very large data sets," said Stanley J. Watowich, associate professor in the Department of Biochemistry & Molecular Biology at The University of Texas Medical Branch in Galveston.
In many cases it is difficult for individual labs to maintain the advanced computing resources necessary to carry out the most demanding calculations. "Access to TACC's software and cutting-edge resources enables us to greatly accelerate our efforts to discover novel drugs to combat infectious diseases," Watowich said.
TACC is home to some of the world's most powerful computing systems including the Lonestar and Ranger supercomputers. In January 2013, TACC will be deploying Stampede, an even larger system for enabling large-scale computational research. These high performance computing (HPC) systems are part of the Extreme Science and Engineering Discovery Environment, the most advanced, powerful, and robust collection of integrated digital resources and services in the world (www.xsede.org). Any researcher who uses TACC's HPC resources will now have access to this new, optimized software stack for life science research.
"We have attempted to aggregate the most widely requested applications for life science research on our systems," said Michael Gonzales, TACC's computational biology program director. "And to ensure these applications take full advantage of our architecture, we've completed compiler-level optimizations for these applications so our users can better make use of TACC's large-scale systems. This will enable our users to do things they would not be able to do with these same applications elsewhere."
One optimized molecular modeling package, Amber 11, can now take advantage of Lonestar's GPU compute nodes. "Using a few of Lonestar's GPUs, we have been able to reach simulation speeds that exceed more than a hundred traditional computer cores," says Miguel Elizondo Riojas, postdoctoral fellow in the Institute of Molecular Medicine, Centers for Proteomics and Systems Biology at The University of Texas Health Science Center at Houston. "It's another way to push the frontiers of what we can learn from molecular simulations."
Lindsay G. Cowell's research group focuses on host genetic susceptibility to infectious diseases and the role of antibodies and lymphocyte antigen receptors in infectious and autoimmune diseases. "We rely heavily on TACC's bioinformatics tool stack and have already begun using tools in the new stack, such as NCBI BLAST, mpiBLAST, BioPerl, and R," said Cowell, who is a researcher in the Department of Clinical Sciences at The University of Texas Southwestern Medical Center at Dallas.
This new software stack is an important component of TACC's computational biology program that also includes training and a team of individuals at the center devoted to this growing area. "In addition to providing a robust software stack, TACC's Computational Biology Program has a group of scientists that can assist users with running the applications," said Karl W. Schulz, associate director and leader of TACC's Application Collaboration group.
TACC will continue to support the life science research community by continually updating and extending its software offering to support the evolving needs of its users.