Summary: The Texas Advanced Computing Center (TACC) is part of the University of Texas at Austin. TACC designs and operates some of the world's most powerful computing resources. The center's mission is to enable discoveries that advance science and society through the application of advanced computing technologies.
John Fonner is part of the Life Sciences Computing Group at TACC, and Rion Dooley manages the web and cloud services group plus he leads the Agave API project. Fonner and Dooley present a hands-on four-hour workshop for South by Southwest Interactive on Tuesday, March 17th. It's called Science as a Service and other Lies: Hacking Big Data on the Web. In the podcast they discuss science-as-a-service. Rion Dooley: When we talk about science as a service, what we're really talking about is the ability to think about your science and interact with your data and with your experiments in a way that is thinking in terms of the problems you're trying to solve rather than the machines you're trying to solve them on. John Fonner: The domain field is a patchwork of individual codes out there that have very specific assumptions about the type of system that you're running them on. The types of algorithms might have very different hardware requirements. And the data volumes now for a lot of the next-generation sequencing questions are just huge. We want to talk about the tools that we have and the way that we've been tackling this problem and really taking it from a place that is inaccessible to most biologists and only accessible to the most technically savy scientists, and putting it in a place where pretty much anyone can have access to it.
Maytal Dahan is a research engineer and science associate at the Texas Advanced Computing Center. She presents a meet up for South by Southwest Interactive on Saturday, March 14. It's called Science and Tech Meet Up: Scientists and Geeks Unite!. In the podcast Dahan talks about some interesting intersections where science meets software development, and she predicts the next big thing at SXSW -- science! Maytal Dahan: It'd be really great if we could get developers of all kinds – user interface, web, application developers – who are interested to learn how science impacts the world we live in today, and how to engage and possibly contribute their skills to science projects…A developer at a start-up doesn't always get to meet a scientist creating an API for their application.
Host Jorge Salazar reports from the Texas Advanced Computing Center an interview with Klaus Schulten, professor of Physics at the University of Illinois at Urbana-Champaign.One of life's strongest bonds has been discovered by a science team doing research on biofuels with the help of supercomputers. The biomolecular interaction binds at about half the strength of a chemical covalent bond the pieces of a finger-like system of proteins called cellulosomes used by bacteria in cow stomachs to digest plants. The researchers published their results in the journal Nature Communications in December of 2014. Their find could boost efforts to develop catalysts for biofuel production from non-food waste plants.
Materials with novel electrical properties discovered using XSEDE computational resources Stampede and Lonestar supercomputers of TACC. This podcast features an interview with materials research scientist Xiaofeng Qian of Texas A&M University.
Scientists have used supercomputers to find what they say is the best evidence yet that a plant's genes sensitive to cold and drought will help it adapt to changes in its environment. What they studied in plants was gene expression, instructions coded in DNA that regulate how many proteins it makes. Gene expression gives rise to traits such as tolerance of cold or drought, and it can evolve through natural selection to help a plant cope with environments out of its comfort zone. The results of the computational biology study were published in the journal Molecular Biology and Evolution in September of 2014. In it scientists studied the flowering mustard weed Arabidopsis thaliana, known as a model plant in part because it has one of the smallest genomes, which was completely sequenced in 2000. The science team first took Arabidopsis genes found in the lab from a prior study that respond to cold and drought. They then compared those to reference genomic data from over a thousand strains collected throughout Europe and Asia. Finding associations was like finding a needle in a haystack, and to do that they enlisted the help of the iPlant collaborative and they used the Ranger and Lonestar supercomputers of the Texas Advanced Computing Center.The study was co-authored by Thomas Juenger, a faculty member in the Department of Integrative Biology of the University of Texas at Austin.
Astrophysicists have been puzzled by their observations since the 1970s that only a small fraction of matter in the cloud becomes a star and part of a galaxy. They found a lot less of the universe's mass than expected in the middle of galaxies. Things changed when a multi-university collaboration produced a set of new supercomputer models of galaxies called FIRE, The Feedback in Realistic Environments. FIRE simulations ran on the Stampede supercomputer at TACC, an XSEDE resource funded by the National Science Foundation. Theoretical astrophysicist Philip Hopkins of CalTech led a 2014 study of initial results that found that star activity - like supernova explosions or even just starlight - plays a big part in the formation of other stars and the growth of galaxies. Philip Hopkins spoke more about galaxies on FIRE.
Sathoshi Matsuoka came to the supercomputing conference SC14 and received the 2014 IEEE Computer Society Sidney Fernbach Award for innovation in the application of high performance computers. Dr. Matsuoka is a professor and leader of the Tsubame project, one of the world's fastest and most efficient supercomputing grid clusters. Tsubame is at the Global Scientific Information and Computing Center, hosted by the Tokyo Institute of Technology. We spoke with Sathoshi Matsuoka on the opening night of a busy convention floor at SC14.
Thomas Sterling spoke on a couple of panels at the supercomputing conference SC14 that looked at the promises and pitfalls on the path to developing exascale supercomputers, the next-generation of the world's fastest computers. Dr. Sterling is the executive associate director and chief scientist at the Center for Research in Extreme Scale Technologies at Indiana University, Bloomington. He's won the Gordon Bell Prize for innovations in high performance computing, and he laid the foundation for the current paradigm of supercomputers by co-developing the Beowulf cluster of commodity Linux cluster computing. Sterling's latest project is the ParalleX execution model being tested in part on XSEDE resources here at TACC with the Stampede supercomputer.
Best-selling author and physicist Brian Greene of Columbia University gave the keynote address at the SC14 conference. His latest book is The Hidden Reality: Parallel Universes and the Deep Laws of the Cosmos. In it Greene describes the hypothesis of multiple universes, and in particular that of a computer simulated multiverse. Brian Greene spoke with me by phone about the possibilities and future of supercomputing.
Computer scientists from the University of Texas at Austin's Institute for Computational Engineering and Sciences, or ICES, teamed up with researchers at the University of Illinois at Urbana-Champaign to present work at the technical program of the supercomputing conference SC14. It's titled "Parallelization of Reordering Algorithms for Bandwidth and Wavefront Reduction." Here to explain the work and to talk a little about SC14 is Keshav Pingali, a professor in the computer science department at UT Austin and a member of ICES.
Larry Smarr was an invited speaker at SC14, where he shared his experience studying the ecology of microbes inside his body using the XSEDE cluster Gordon of the San Diego Supercomputer Center. Dr. Smarr is the director of the California Institute for Telecommunications and Information Technology, and he holds the Harry E. Gruber professorship in Computer Science and Engineering at the Jacobs School of Engineering of the University of California in San Diego. Larry Smarr's spent his early career as an astrophysicist computing the dynamics of black holes. In the mid-1980s he led the proposal to the National Science Foundation that created the first national supercomputing center specifically for university researchers, the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign. His work there led to the creation of Mosaic, the world's first widely used graphical Web browser.
Two graduate students from UT Austin, Dhairya Malhotra and Amir Gholami, are up for Best Student Paper at the supercomputing conference SC14. They've co-authored the work with George Biros, a professor in mechanical engineering and computer science at UT Austin's Institute for Computational Engineering and Science. Dr. Biros is a two-time winner of the Gordon Bell Prize for innovation in high performance computing. In this podcast he spoke more about the paper he and his students are presenting for SC14.
Larry Smarr is the founding Director of the California Institute for Telecommunications and Information Technology (Calit2), a UC San Diego/UC Irvine partnership, and holds the Harry E. Gruber professorship in the Department of Computer Science and Engineering (CSE) of UCSD’s Jacobs School of Engineering. At Calit2, he has continued to drive major developments in information infrastructure-- including the Internet, Web, scientific visualization, virtual reality, and global telepresence--begun during his previous 15 years as founding Director of the National Center for Supercomputing Applications (NCSA).
George Biros is the W. A. "Tex" Moncrief Chair in Simulation-Based Engineering Sciences in the Institute for Computational Engineering and Sciences and has Full Professor appointments with the departments of Mechanical Engineering and Computer Science at the University of Texas at Austin. This clip is from an interview released mid-November as part of coverage of the SC14 conference.
A group of scientists peered thousands of years back into Europe's murky past and found a mysterious ancestor. Researchers used the Stampede supercomputer, supported by the National Science Foundation, to analyze and compare genomes from modern Europeans to ancient genomes from bones seven, eight, and twenty-four thousand years old.