Tacc Podcasts

Paleoanthropologist Denne Reed of UT Austin is interviewed by host Jorge Salazar about making connections in big data from fossils of human origins. New discoveries might lie buried deep in the data of human fossils. That's according to Denné Reed, an associate professor in the Department of Anthropology at The University of Texas at Austin (UT Austin). Reed is the principal investigator of PaleoCore, an informatics initiative funded by the National Science Foundation (NSF). The PaleoCore project aims to get researchers of human origins worldwide all on the same page with their fossil data. Reed said PaleoCore is doing this by implementing data standards; making a place to store all data of human fossils; and developing new tools to collect the data. What he hopes to come out of this are deeper insights into our origins from better integration and sharing between different research projects in paleoanthropology and paleontology. "We've tried to take advantage of some of the geo-processing and database capabil

Computer scientist Joshua New of the Oak Ridge National Laboratory speaks with host Jorge Salazar on how to optimize buildings to save energy using computer models. Saving energy saves money. Scientists at Oak Ridge National Laboratory (ORNL) are using supercomputers to do just that by making virtual versions of millions of buildings in the U.S. The Wrangler data-intensive supercomputer is working jointly with ORNL's Titan in a project called Autotune that trims the energy bills of buildings. Computer scientist Joshua New of the ORNL Building Technology Research and Integration Center is the principal investigator of the Autotune project, funded by the U.S. Department of Energy. Autotune takes a simple software model of a building's energy use and optimizes it to match reality. "What we're trying to do is create a crude model from publicly available data," New said. "Then the Autotune project takes utility bill data, whether it's monthly electrical utility bills, or hourly bills from advanced metering infrast

UT Austin biologist Rebecca Young discuss her work with host Jorge Salazar about how she traces the genes behind monogamous behavior using the Wrangler supercomputer at the Texas Advanced Computing Center. Scientists at the Hofmann Lab of UT Austin are using the Wrangler data-intensive supercomputer to find orthologs — genes common to different species. They'll search for them in each of the major lineages of vertebrates — mammals, birds, reptiles, amphibians and fishes. "What we want to know is, even though they've evolved independently, whether it's possible that some of the same genes are important in regulating this behavior, in particular expression of these genes in the brain while monogamous males are reproductively active," said Rebecca Young. Young is a research associate in the Department of Integrative Biology and at the Center for Computational Biology and Bioinformatics, UT Austin. Music Credits: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Scientists and engineers at TACC have created a new kind of supercomputer to handle big data.Featured on the podcast is Niall Gaffney, Director of Data Intensive Computing at the Texas Advanced Computing Center. Gaffney leads efforts at TACC to bring online a new data-intensive supercomputing system called Wrangler.The National Science Foundation's Division of Advanced Cyberinfrastructure awarded TACC and its collaborators 11.2 million dollars in November of 2013 to build and operate the Wrangler supercomputer. Indiana University, TACC, and the University of Chicago worked together on the project.In April of 2015, Wrangler began early operations for the open science community, where results are made freely available to the public. Wrangler will augment the Stampede supercomputer, one of the most powerful in the world. And Wrangler will join the cyberinfrastructure of NSF-funded XSEDE, the eXtreme Science and Engineering Discovery Environment.Niall Gaffney:We went to propose to build Wrangler with (the data wo

The 2015 ACM Gordon Bell Prize, given in recognition of outstanding achievement in high-performance computing, was awarded to researchers Johann Rudi and Omar Ghattas of the Institute for Computational Engineering and Sciences at the University of Texas at Austin. They share the award with their study co-authors, who utilized the Stampede supercomputer of the Texas Advanced Computing Center and the IBM Sequoia supercomputer at Lawrence Livermore National Laboratory. The award-winning study modeled the flow thousands of kilometers deep in the mantle, which moves Earth's plates and triggers unpredictable events like volcanic eruptions and massive earthquakes. The SC15 supercomputing conference took place in Austin, November 15-20, 2015. SC showcases the latest in high performance computing, networking, storage and analysis to advance scientific discovery, research, education and commerce. The study, "An Extreme-Scale Implicit Solver for Complex PDEs: Highly Heterogeneous Flow in Earth's Mantle," was funded in p

This November 2015 marks 100 years of Einstein's field equations that describe space and time as one interwoven continuum - and predict the existence of black holes and more. Manuela Campanelli is a professor at the Rochester Institute of Technology and the Director of the Center for Computational Relativity and Gravitation. Dr. Campanelli was invited to give a presentation at SC15 titled "Revealing the Hidden Universe with Supercomputer Simulations of Black Hole Mergers." Dr. Campanelli uses the computational resources of XSEDE, the Extreme Science and Engineering Discovery Environment, to probe the mysteries of black holes. She spoke by Skype to talk about that and about the 100th anniversary of Einstein's field equations and about her work that takes on the complexity of accurately describing black hole mergers. The SC15 supercomputing conference takes place in Austin, November 15-20, 2015. SC15 showcases the latest in high performance computing, networking, storage and analysis to advance scientific disco

Thomas Jordan is a professor of Earth Sciences at University of Southern California and the Director of the Southern California Earthquake Center. It's a big national collaboration of over a thousand earthquake experts and 70 institutions. Dr. Jordan uses the computational resources of XSEDE, the Extreme Science and Engineering Discovery Environment, to model earthquakes and help reduce their risk to life and property. Dr. Jordan was invited to speak at SC15 on the Societal Impact of Earthquake Simulations at Extreme Scale. The SC15 supercomputing conference takes place in Austin, November 15-20, 2015. SC15 showcases the latest in high performance computing, networking, storage and analysis to advance scientific discovery, research, education and commerce. Thomas Jordan: One thing people need to understand is we need a lot of supercomputer time in order to be able to do these calculations. Some of our simulation models that are based on the simulation of earthquake physics can take hundreds of millions of hou

Alan Alda, actor, director and writer, has had a lifelong interest in science. He hosted the PBS program Scientific American Frontiers from 1993 to 2005, an experience he called "the best thing I ever did in front of a camera." Perhaps best known as surgeon 'Hawkeye' Pierce on the TV series MASH, Alda has won seven Emmys, six Golden Globes, and three Directors Guild of America awards for directing. His two memoires are both New York Times bestsellers. A recipient of the National Science Board's Public Service Award, Alda is a visiting professor at and founding member of Stony Brook University's Alan Alda Center for Communicating Science, where he helps develop innovative programs on how scientists communicate with the public. He is also on the Board of Directors of the World Science Festival. SC15 is the 27th annual International Conference for High Performance Computing, Networking, Storage and Analysis. The event showcases the latest in supercomputing to advance scientific discovery, research, education and

Robert McLay manages the software tools group in high performance computing at the Texas Advanced Computing Center. Dr. McLay is one of the developers of XALT, a software tool developed with funding by the National Science Foundation. XALT tracks user codes and environments on a computer cluster. Robert McLay and Mark Fahey of the Argonne National Laboratory will be co-leading a session called "Understanding User-Level Activity on Today's Supercomputers with XALT" at SC15. The SC15 supercomputing conference takes place in Austin, November 15-20, 2015. SC15 showcases the latest in high performance computing, networking, storage and analysis to advance scientific discovery, research, education and commerce. Robert McLay: XALT is a tool that me and my colleague, Dr. Mark Fahey, put together to help people try and use our systems. We run the system. We manage the system. We develop software for the system and install software for our users. We want to know what's used and what's not. XALT gives us a way to find o

This podcast features an interview with biologist Mikhail Matz, Department of Integrative Biology, College of Natural Sciences, The University of Texas at Austin. Matz was part of a study funded by the National Science Foundation and the Australian Institute of Marine Science. In June of 2015 they published results in the journal Science that found the first evidence that corals can genetically adapt to warmer waters from climate change. Podast host Jorge Salazar interviewed Matz about his computationally-based findings and about open source tools other scientists can freely use to analyze genomes of plants and animals.

Podcast host Jorge Salazar interviews scientists Michael Sacks, Institute for Computational Engineering and Sciences at the University of Texas at Austin; and Ming-Chen Hsu, Department of Mechanical Engineering at Iowa State University. New supercomputer simulations have come closer than ever to capturing real behavior of human heart valves. The studies focused on how heart valve tissue realistically responds to blood flow. And to be clear this is ongoing research, meaning they don't have all the answers yet, but they do say they've made progress on a really tough problem that potentially affects hundreds of thousands of people each year with hearth disease. The scientists say their new supercomputer models can potentially help doctors make more durable repair and replacement of heart valves.

Host Jorge Salazar interviews scientists Karen Vasquez and Albino Bacolla of the University of Texas at Austin. Supercomputers have helped scientists find a surprising link between cross-shaped pieces of DNA and human cancer, according to a study at The University of Texas at Austin. DNA naturally folds itself into cross-shaped structures called cruciforms that jut out along the sprawling length of its double helix. The DNA cruciforms typically aren't anything to worry about. In fact, previous evidence show that DNA cruciforms are essential to life. They enable DNA replication, part of how cells make copies of themselves. And they help initiate gene expression, which makes proteins. What's more small DNA cruciforms are commonly found inside our bodies. Scientists estimate as many as 500,000 cruciform-forming sequences of DNA can exist on average in a normal human genome. What the UT scientists are doing is investigating the origins of human cancer. And what they've found is that these tiny cruciforms - just a

Host Jorge Salazar interviews scientists Min Chen of Rice University and Jeroen Tromp of Princeton University. An international science team reported a discovery of gigantic rock structures hidden deep under East Asia, centered on the Tibetan Plateau. Scientists used supercomputers to process earthquake data and make images in 3-D down to depths of about 900 kilometers, or about 560 miles below ground. Scientists from China, Canada, and the U.S. worked together to publish their results March of 2015 in the American Geophysical Union Journal of Geophysical Research, Solid Earth. The study area is a hotspot for earthquakes. And it's surrounded by networks of seismographic stations, 1869 stations in all. That's where scientists got their data to take cat scans of the Earth using the supercomputer model they developed. The science team says their research could potentially help discover hidden pockets of hydrocarbon resources like oil and gas. More broadly they say their work will help explore the Earth hidden mi

Host Jorge Salazar reports from the Texas Advanced Computing Center an interview with Michael Grabe, an associate professor in the Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute at the University of California, San Francisco. For the first time ever, scientists designed completely from scratch a protein molecule that behaves like a slice of life. It mimics a natural protein found in living cells that transports ions across a cell membrane. The cell membrane surrounds living   cells like an envelope. And ion transport through the membrane helps keep us alive. It lets nutrients in and waste out of cells, and it also transmits signals between nerve cells of the brain and spinal cord. Scientists used the Stampede supercomputer at TACC to model the stability and dynamics of the designed protein. They did this with an allocation through XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation. The researchers published their result

Matthew Hanlon manages the Web and Mobile Applications Group at the Texas Advanced Computing Center. And Matt Vaughn directs the Life Sciences Computing Group at TACC. Vaughn and Hanlon present a one-hour core conversation for South by Southwest Interactive on Monday, March 16. It's called A Next Generation Platform for Open Data. In the podcast they discuss their work on the Arabidopsis Information Portal, a new online resource for plant biology research. Matthew Hanlon: We're looking to attract both data scientists and portal developers, anyone who has experienced developing, hosting, running or trying to market an open data portal to the community. Matthew Vaughn: The Arabidopsis Information Portal, Araport for short, serves two purposes. It's a clearinghouse for genetic, genomic, protein and gene expression information for the model plant Arabidopsis thaliana… But it's also a resource for people who build portals.

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 sequenci

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 AM 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 E