HPC and Data Applications for Increased Impact on Research
Dr Phil Mjwara
Director General, Department of Science and Technology, RSA
Opening Keynote Address
Dr Phil Mjwara has served as the Director General of the Department of Science and Technology (DST) since April 2006. In this capacity he is responsible for all policy development in the science and technology sector in South Africa, as well as the portfolio management and governance of South Africa’s systems of government laboratories. His responsibilities further include the management of South African science and technology official development assistance and the driving of the implementation of South Africa’s National Research and Development Strategy as well as the management of South Africa’s new DST 10 Year Innovation Plan.
Prior to his appointment at DST, Dr Mjwara was the Group Executive: Research and Development; Strategic Human Capital Development at the Council for Scientific and Industrial Research (CSIR). At the CSIR, he was responsible for assisting the CSIR in strengthening its science and technology base including Human Capital Development. In 2001, Dr Mjwara joined the National Laser Centre (NLC) as its head, where he has been instrumental in growing the centre's activities since its inception and in creating a network of centres in Africa, i.e. African Laser Centre (ALC).
He has also held positions at the then Department of Arts, Culture, Science and Technology; as Director of Technology; at the University of Pretoria as professor of Science and Technology Policy and at the Universities of the Witwatersrand, South Africa and Fort Hare as a physics lecturer. He has been involved in the discipline of Management of Technological Innovation as well as in processes for policy formulation. He has led a team that conducted the South African Technology Foresight Project. He has published and presented numerous papers on physics, technology analysis and fore sighting related topics.
Dr Happy Sithole
Director: Centre for High Performance Computing, RSA
Happy Sithole is the Director for the Centre for High Performance Computing in South Africa. He has a PhD in Physics, which focused on Atomistic and Electronic Simulation of Sulphide Minerals. Happy has worked as a Senior Lecturer and Researcher in the Materials Modelling Centre at the University of Limpopo. He has also worked as a Research Scientist at De Beers Consolidated Mines, and later as a Senior Process Engineer at Pebble Bed-Modular Reactor Company. Happy sits in a number of advisory committees of high performance computing, as a programme committee member of both the International Super-Computing Meeting and the Russian High Performance Computing Committee. He also serves as an inquisitor on the “Hot Seat” session at ISC Meetings, a select panel that interrogates technology vendors on their products.
Dr Liesl Zühlke
Paediatric Cardiology, University of Cape Town and Red Cross Children’s Hospital, RSA
Rheumatic Heart Disease and High Performance Computing – a Collaboration to serve South African Communities
Liesl Zühlke graduated from the University of Cape Town Medical School and then qualified as a Paediatrician at the Red Cross War Memorial Children’s Hospital in Cape Town. She trained as a Paediatric Cardiologist in Cape Town and Dusseldorf, Germany with a research secondment to Nijmegen, Holland. In South Africa, she is one of only 25 qualified paediatric cardiologists and one of the few in Africa. Her specific interests are imaging modalities, grown-up congenital heart disease and preventative cardiology as well as global health. These have led to her particular research interest: Rheumatic Heart Disease and echocardiographic screening in asymptomatic schoolchildren. She feels passionately that Rheumatic Heart Disease, a preventable chronic disease of childhood, can be controlled in developing countries using a multi-pronged approach. A previous recipient of the Discovery Academic Excellence Award, a NIH-Fogarty International Clinical Research and the CIDRI Research Fellowship, she now holds the Hamilton Naki Clinical Research Scholarship. She recently graduated with her Master’s in Public Health (Clinical Research Methods) and is completing her Doctoral Studies. Her planned dissertation is entitled “The case for screening for Rheumatic Heart Disease”. She is the secretary of the Western Cape branch of the South African Heart Association, the President of the Paediatric Cardiac Society of South Africa and a member of the local organizing committee of the 2013 6th World Congress of Paediatric Cardiology and Cardiac Surgery to be held in Cape Town in 2013.
Prof. Harold "Skip" Garner
Medical Informatics and Systems, Virginia Tech, USA
Shadowfax, a Heterogenous Computing Environment for Diverse Life and Medical Science Computations
Harold "Skip" Garner is the Professor and Director of the Medical Informatics and Systems Division, Virginia Bioinformatics Institute, Virginia Tech, HHS Research in Research Integrity grantee and founder of HelioText, LLC which provides text analytics services to the US Government.
Prof. Thomas Franz
Biomechanical Sciences, University of Cape Town, RSA
HPC for Simulation and Modelling of Cardiac Infarcation for the Development of Novel and Effective Treatment
Dr Thomas Franz received MSc and PhD degrees in Mechanical Engineering from the Universities of Hannover and Bremen, Germany, in 1992 and 1998. With post-doctoral fellowships from the South African National Research Foundation and the Claude Harris Leon Foundation, he extended his research at the Centre for Research in Computational and Applied Mechanics at the University of Cape Town, South Africa, between 1998 and 2001. In 2002, he joined the Chris Barnard Division of Cardiothoracic Surgery at the University of Cape Town. He has been heading the Biomechanical Sciences Group which focuses on computational and applied biomechanics in the development of regenerative therapies for cardiovascular diseases, the most severe class of chronic diseases. At present, Dr Franz supervises and co-supervises 21 students (2 post-doc, 7 PhD, 4 MSc, 8 BSc). Dr Franz was recently awarded the ad hominem promotion to Associate Professor from the Faculty of Health Sciences of the University of Cape Town.
Prof. Athol Kemball
University of Illinois & National Centre for Supercomputing Applications (NCSA), USA
Data-intensive Observational Astronomy
Athol Kemball is Associate Professor of Astronomy at the University of Illinois at Urbana-Champaign (UIUC) and faculty affiliate in the Center for Extreme-Scale Computing (CESC) at the National Center for Supercomputing Applications (NCSA). His research interests include computation and data-intensive radio astronomy and the science these techniques enable. He has held research and management positions at the national observatories prior to his current appointment at UIUC.
Dr Rudolph Pinaar
Technical Director and Staff Scientist, Fetal-Neonatal Neuroimaging & Developmental Science Center (FNNDSC), Children’s Hospital Boston (CHB), USA
Practical High Performance Computing in Neuroscience Research: A Case Study from Boston Children's Hospital
Rudolph Pinaar received his Bachelors and Masters Degrees in Electronic Engineering at the University of Pretoria, South Africa before completing a Doctoral Degree in Applied Biomedical Engineering at the Cleveland Clinic Foundation / Cleveland State University. As Technical Director of the FNNDSC, he is responsible for the neoro-radiological computational infrastructure, which includes the first high performance computer cluster established at the CHB. He is interested in understanding the normal development of the brain as expressed in its folding and complex internal connectivity architecture. Rudolph also works actively to try to bridge the gap between the research and clinical worlds by helping design and deploy web-based research imaging tools.
His research interests include:
• Cortical surface reconstructions from structural MRI
• Curvature and shape analysis
• Connectivity and relationships with physical shape of brain
• High performance scientific computing tool development and deployment
Dr Jonathan Sievers
Joseph Henry Laboratories of Physics, Princeton University, USA
High Performance Computing and Astronomy
Jon Sievers has worked in a variety of fields in cosmology, with a main emphasis on using HPC to study the cosmic microwave background and galaxy clusters. Much of the data he has used has come from some of the highest permanent telescopes in the world, located in the Chilean Andes at altitudes of over 5,000 metres. Dr Sievers did his graduate work at Caltech and did a postdoc at the Canadian Institute for Theoretical Astrophysics before moving to Princeton University.
Prof. Marius Potgieter
Centre for Space Research, University of the North West, RSA
Impact of High Performance Computing on Computational Space and Astrophysics in South Africa
Prof. Marius Potgieter is a member of the Centre of Excellence in Space Research at the North-West University in Potchefstroom. He is a Professor of Physics, specializing in computational aspects and modelling of Space Physics, Heliospheric Physics and Cosmic Rays. He spent time as a postdoctoral fellow at NASA’s Goddard Space Flight Center in Greenbelt, Maryland, and as a visiting professor in France, Germany, Italy, Switzerland and the USA. He was a guest scientist on the Ulysses Mission, funded by ESA & NASA and has close collaborations with teams on the VOYAGER and PAMELA space missions. He has published numerous research papers internationally and gave numerous invited talks on his research at international conferences. He served on the organizing committees of many international conferences and workshops, e.g. COSPAR, and as secretary of IUPAP’s Cosmic Ray Commission and as member of the steering committees of the International Heliophysical Year (IHY) and the International Space Weather Initiative (ISWI). He is presently the chairperson of the SA National COSPAR committee and represents South Africa on the COSPAR Council. He was the principal investigator of the flagship research project on Computational Space Physics and Astrophysics, supported through the CHPC from 2007-2009.
Prof. Michael Gee
Faculty of Mechanical Engineering & Munich School of Engineering Technische Universität München, GER
Mechanics and High Performance Computing including Cardiac Mechanics
Michael Gee holds a PhD in Civil Engineering from Universität Stuttgart (2004), his work experience includes the following:
4/2011–today - Associate Professor Mechanics & High Performance Computing Faculty of Mechanical Engineering & Munich School of Engineering (MSE) Technische Universität München.
9/2006–4/2011 - Senior Scientist, permanent position), Institute for Computational Mechanics, Faculty of Mechanical Engineering, Technische Universität München.
Dr George Vacek
Global Head: Life Sciences, Convey Computer Cooperation, USA
Better Computing for Better Bioinformatics
George Vacek joined the Convey Computer Corporation as the global head of Life Sciences in 2009. Prior to joining Convey, he held responsibility for the success of Scientific Research solutions in Hewlett Packard's High-Performance Computing Division for three and a half years. Throughout his career, he has held business and technical roles in the computational life sciences, yielding more than 30 peer-reviewed research publications and contributions to several widely used programs, including Schrödinger's Jaguar. He earned his Ph.D. in Chemistry from the University of Georgia in 1995. He also holds an M.B.A. from Portland State University and Bachelor's degrees in Physics and Mathematics from the University of Wisconsin
Chief Scientist, Co-Founder, and Director: Convey Computer Corporation
Big Data Ops vs. HPC Flops, Applications and Architectures
Wallach is a founder of Convey Computer Corporation and is an adviser to venture capital firms CenterPoint Ventures, Sevin-Rosen and InterWest Partners. Previously, he served as vice president of technology for Chiaro Networks Ltd., and as co-founder, chief technology officer and senior vice president of development of Convex Computer Corporation. After Hewlett-Packard Co. bought Convex, Wallach became chief technology officer of HP's Enterprise Systems Group. Wallach served as a consultant to the U.S. Department of Energy's Advanced Simulation and Computing Program at Los Alamos National Laboratory from 1998 to 2007. He was also a visiting professor at Rice University in 1998 and 1999, and was manager of advanced development for Data General Corporation. His efforts on the MV/8000 are chronicled in Tracy Kidder's Pulitzer Prize winning book, "The Soul of a New Machine." Wallach, who has 37 patents, is a member of the National Academy of Engineering, an IEEE Fellow, and was a founding member of the Presidential Information Technology Advisory Committee. He is the 2008 recipient of IEEE's prestigious Seymour Cray Award. He is currently a member of a national research council study on Cyber Security.
Prof. David Sept
Associate Professor, Department of Biomedical Engineering, Center for Computational Medicine and Bioinformatics
Quantifying the Pharmacokinetic Behavior of Nanoparticle Therapeutics
Prof. Sept’s research is in the areas of protein biophysics, small molecule and protein design, nanoparticle pharmacokinetics, and systems biology. He is Director of the Computational Protein Biophysics Lab and has more than 75 peer-reviewed publications from work funded through National Science Foundation, National Institutes of Health, National Cancer Institute and the Department of Defense.
Dr Hakizumwami Birali Runesha
Director of Research Computing: University of Chicago
Exploiting Parallelism and Scalability on HPC systems for the design of medical devices and GWAS applications
Birali holds a Ph.D. in Civil Engineering from Old Dominion University and has more than 20 years of experience in High Performance Computing (HPC) and scientific software development. Prior to joining the University of Chicago, he served for 13 years as Director of Scientific Computing and Applications at the University of Minnesota Supercomputing Institute. Before joining Minnesota, he was a Research Associate at the Hong Kong University of Science and Technology developing and implementing parallel computing algorithms for engineering applications, a research associate for the Multidisciplinary Parallel-Vector Computer Center at Old Dominion University and an assistant professor at the University of Kinshasa.
Dr. Runesha’s research interests are in parallel computing, sparse numerical libraries, finite element analysis and design optimization in engineering. With the advent of big data, he has been leading many initiatives for domain specific data management implementations and investigating running HPC applications in the cloud. He has written multiple parallel codes including solvers for civil, mechanical and aerospace engineering large-scale finite element applications. He has served as principal investigator on a number of research grants and is the author of a number of journal articles, proceedings and conference papers. He has given many invited talks, seminars, courses and workshops on various HPC related topics.