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Interview: David Bader on Supercomputing the Human Condition

It may be hard to believe, but the ISC’13 conference kicks off in just eight days! To get you primed, we caught up with David Bader from Georgia Tech to discuss his upcoming ISC’13 session, Better Understanding Brains, Genomes & Life Using HPC Systems.

insideHPC: Can you tell me about your day job and the types of projects you are working on?

David Bader: Rich, thanks for taking the time to chat with me. As a professor and executive director of high performance computing at Georgia Tech, we’re in the leadership position for big solutions to big data problems! Our work in massive-scale streaming analytics has influenced the design of microprocessors and new data-centric supercomputers, as well as led to the advanced solutions for grand challenge problems. For example, in our STINGER project (STINGER stands for Spatio-Temporal Interaction Networks and Graphs, Extensible Representation), we have ingested massive unstructured social media data and made near real-time discoveries of important sources of information in breaking events. Our Big Data research has led to better and faster decisions for business analytic questions, helps us find insider threats within organizations, and protects us from cyber-based attacks. We are also developing new large-scale applications for important problems in computational biology and genomics, from understanding the evolution of multi-chromosome organisms, to assembling genomes from next-generation sequence data, and folding RNA sequences into their structure. The hallmark of our work is taking data and rapidly transforming it into information that is useful by a scientist, domain specialist, or even an end user wishing to make sense of it.

insideHPC: You will be chairing a session on life sciences at ISC’13. Who are your panelists and what topics will you focus on?

David Bader: Rich, supercomputers are one of the most amazing tools we’ve created to solve some of the most challenging problems facing the human condition. It’s an honor for me to chair a session at ISC’13 on the Better Understanding of Brains, Genomes, and Life, using the HPC systems discussed at the core of ISC. This is what it’s all about after all – how do we understand where life comes from, and how our genes determine our health and wellness, and how mysteries such as the brain function. We’re poised in the next few years to make some fantastic progress on these fronts using the exascale supercomputers previewed at ISC. I’ve assembled a panel of international experts for this session. Dr. BingQiang Wang from the Beijing Genome Institute in China will speak on accelerating scientific discovery using GPUs and other HPC systems to perform massive data mining from bioinformatics sequences now available from the rapid advancement of sequencing technologies that are producing truly massive volumes of diverse data. Dr. Rossen Apostolov, KTH Royal Institute of Technology in Sweden, and technical director of the EU-funded ScalaLife project, will tell us how HPC has enabled the efficient and scalable simulations from the life sciences. ScalaLife has tackled some of the previously unattainable problems in molecular dynamics, and has propelled the life sciences community ahead in these computationally challenging areas of bio-molecular simulation. Finally, Prof. Dr. Markus Diesmann, director of the Institute of Neuroscience and Medicine, Computational and Systems Neuroscience and the Institute for Advanced Simulation, Theoretical Neuroscience at the Jülich Research Centre and Professor for Computational Neuroscience at the Medical Faculty of RWTH Aachen University in Germany, will speak about brain-scale neuronal networks. Analyzing the structure and dynamics of the human brain is a grand-challenge, and he will discuss how the micro-circuits of a square millimeter of brain tissue are at the reach using high-performance computing software and infrastructure, leading to brain-scale networks at cellular and synaptic resolution.

Wouldn’t it be great if these supercomputers could help improve our lives, our health and wellness, cure diseases, and give us more effective and personalized medicines? Our supercomputing community is the enabling factor to turn these dreams into reality in our lifetimes!

insideHPC: President Obama recently announced a large-scale program human brain research. How do you think HPC might contribute to such an endeavor?

David Bader: HPC will be at the forefront of any large-scale research into the structure and dynamics of the human brain. From the number of neurons and synapses, to the complexity of understanding the signal processing within the brain, we are talking about a truly exascale simulation. Data collected today from the neurosciences is already a computational big data problem. HPC techniques will be required to rapidly make sense of these massive data sets, and to simulate the models developed by our brain researchers. Rich, you and I are getting older every year – and I hope our brains continue to work as they do today! So I’m glad we are making a concerted effort to apply HPC to understanding our how brains work, improve our memory, help those with traumatic brain injuries, and understand the connection between our brains and our mental health.

insideHPC: This is not your first time speaking at ISC. What do you like most about this particular conference?

David Bader: The International Supercomputing Conference (ISC) is a wonderful venue to get a glimpse of the international research and development community around high-performance computing, from system vendors to applications researchers. ISC provides a nice balance between a supercomputing industrial trade-show, to a high-quality technical program with some of the world’s foremost experts in HPC. This is the place to be each June in Germany if you want to know, with an international perspective, what’s happening in HPC, from Asia, to Europe, and to the Americas. I’m also at ISC to learn about the Top500 supercomputers in the world, and how they are accelerating scientific discovery, and I will be releasing its complementary list, called Graph500, for the most capable “Big Data” supercomputers in 2013.

I’m looking forward to seeing you and the HPC community in Leipzig!

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