Technical Strategies for Massive Model Visualization
Abstract: Since the inception of geometric modeling, users have been able to generate more data than any graphics system could handle. 3D models commonplace in film, games, CAD product design, medical imaging, seismic exploration, and information spaces are most problematic This symposium covers advances in level-of-detail and memory management. These are key techniques that effectively overcome rendering, CPU, memory, and disk constraints and let users work with an entire geometric model rather than smaller chunks.
Enrico Gobbetti, Center for Advanced Studies, Research, and Development in Sardinia (CRS4) (Short Bio)
Dave Kasik, Boeing (Short Bio)
Sung-Eui Yoon, Korea Advanced Institute of Science and Technology (KAIST) (Short Bio)
Bio-Geometry: Challenges, Approaches, and Future Opportunities in Proteomics and Drug Discovery
Abstract: Biology has been an experimental science until the recent prominence of Bioinformatics and Computational Biology. With the discovery of the DNA sequence the protein structure determination is now an emerging challenge. The protein structure is closely coupled to the function. Today, with the given increase in available computing power and no-cost storage, the ability to do computational experiments is emerging as a core competence necessary for rapid discovery in the future. The ability to include various complex physics such as electrostatics and hydrophobic interactions in realistic simulations has increased. The discovery of structure of proteins is the next frontier for a number of convergent areas in science. Hence the combination of geometry and physics becomes very critical to do realistic computational experiments. The panelists will review the drivers of this new proteomics revolution. Recent work in the convergent areas for proteomics and drug discovery will be reviewed: multiple docking, protein interaction via structural mapping, combinatorial assembly, fast molecular matching, geometric alignment, electron cryo-microscopy for structure determination, low resolution structure identification, chemical compound navigation for drug discovery, and large bio-chemistry database efforts. Discussions will conclude with the areas that need attention from the bio-geometry and modeling perspectives as well as the types of interdisciplinary interactions that will add value.
Ruth Nussinov, Department of Human Genetics, School of Medicine, Tel Aviv University (Short Bio)
Tao Ju, Department of Computer Science and Engineering, Washington University in St. Louis (Short Bio)
Talapady Bhat, National Institute of Standards and Technology (Short Bio)
Jack Snoeyink, Department of Computer Science, University of North Carolina at Chapel Hill (Short Bio)
Karthik Ramani, Purdue University (Short Bio)
Enrico Gobbetti is the founder and director of the Visual Computing (ViC) group at the Center for Advanced Studies, Research, and Development in Sardinia (CRS4). At CRS4, Enrico developed and managed a graphics research program supported through industrial and government grants. His research interests span many areas of computer graphics. His most recent contributions include a new breed of coarse-grained adaptive multiresolution techniques for processing and rendering large scale geometric models. Enrico holds an Engineering degree (1989) and a Ph.D. degree (1993) in Computer Science from the Swiss Federal Institute of Technology in Lausanne (EPFL).
Dave Kasik, Boeing Senior Technical Fellow, is responsible for visualization and interactive techniques across the enterprise.. His research interests include innovative combinations of basic 3D graphics and user interface technologies and increasing awareness of the impact of visualization technology inside and outside Boeing. Dave has a BA in Quantitative Studies from the Johns Hopkins University and an MS in Computer Science from the University of Colorado. He is an ACM Distinguished Scientist and a member of IEEE, ACM SIGGRAPH, and ACM SIGCHI. He is a member of the editorial board for IEEE Computer Graphics and Applications.
Sung-Eui Yoon is currently an assistant professor at Korea Advanced Institute of Science and Technology (KAIST). He received the B.S. and M.S. degrees in computer science from Seoul National University in 1999 and 2001 respectively. He received his Ph.D. degree in computer science from the University of North Carolina at Chapel Hill in 2005. He was a postdoctoral scholar at Lawrence Livermore National Laboratory. His research interests include visualization, interactive rendering, geometric problems, and cache-coherent algorithms and layouts.
Dr. Ruth Nussinov is a Professor in the Department of Human Genetics, School of Medicine, Tel Aviv University, Tel Aviv, 69978 Israel, and a Senior Principal Scientist and Principal Investigator at the National Cancer Institute. She has received her B. Sc degree in Microbiology from the University of Washington (Seattle, Washington) and her Ph D in Biochemistry from Rutgers University (NJ). She was a Fellow at the Weizmann Institute, and a visiting scientist at the chemistry department at Berkeley and at the Biochemistry department at Harvard. She joined the Medical School at Tel Aviv in 1985 as an Associate Professor. In 1990 she became a Full Professor. Her association with the NIH started in 1983, first with the NICHHD and since 1985 with the NCI. Currently, she has a large group of graduate students in Tel Aviv, in collaboration with Prof. H. Wolfson, from the School of Computer Science. Additionally, she has a group at the NCI. She is an author of over 260 scientific papers. Dr. Nussinov was the developer of the dynamic programming algorithm for RNA secondary structure prediction, first by maximizing the number of base pairs (SIAM, 35: 68-82, 1978) and later introducing 'energy rules' into the algorithm (Proc Natl Acad Sci U S A. 77: 6903-13, 1980; See also Biological sequence analysis (Durbin, Eddy, Krogh & Mitchison, Cambridge University Press, 1998). Dr. Nussinov was also among the pioneers in DNA sequence analysis, with numerous publications on recurrence of nucleotide patterns already in the early-mid 1980's. Until 1990 her papers addressed RNA and DNA sequence and structure and nucleic acid-protein interactions. In 1990 she switched to proteins. Currently her research focuses on computational studies of protein folding, binding and protein function. She addresses Systems Biology and most recently applications of computational biology concepts and strategies toward nanobiology, in nanostructure design. Her research is inter-disciplinary, with a strong component of computer science.
Tao Ju is an Assistant Professor in the Department of Computer Science and Engineering at the Washington University in St. Louis (USA). He obtained his PhD from the Department of Computer Science at Rice University in 2005, received his post-doctoral training from Baylor College of Medicine in Summer 2005. Dr. Ju conducts research in the areas of computer graphics and bio-medical applications, and in particular focuses on algorithms for geometric modeling, processing and their uses in medical imaging and modeling.
Dr. Bhat is a project leader for Bioinformatics at the Chemical Science Division of NIST. His areas of research interests are X-ray crystallography of small chemical compounds and macromolecules, chemical ontology, the Semantic Web, data validation and annotation, software development, bioinformatics, and AIDS research.
At present, Dr.Bhat is project leader for bioinformatics in the Biochemical Science Division, where he played a key role in the development of both the RCSB Protein Data Bank (http://www.rcsb.org/pdb/) and the HIV structural database (http://bioinfo.nist.gov/SemanticWeb_ccr5/chemblast.do). He is the author of over 80 refereed scientific articles with over 9,500 scientific citations and one of his publications has the highest citations among the publications from NIST since 1973. In 1979, Dr. Bhat was the primary technical architect of the Collaborative Computational Project 4 (CCP4, housed at Cambridge UK) that archives and distributes software for macro-molecular crystallography for many laboratories around the world. Subsequently in 1999, the CCPN project for NMR housed at the European Bioinformatics Institute adopted a technical model proposed by him for establishing a software resource for NMR. Dr. Bhat has won several scientific awards including: two Best Publication Awards from the Science Applications International Corporation; the Science Spectrum Traiblazer Award and Emerald Honors for his work on Bioinformatics; and the prestigious Judson C. French award of the National Institute of Standards and Technology.
Jack Snoeyink is a professor in the Department of Computer Science at the University of North Carolina at Chapel Hill. He received his bachelor's degree with honors from Calvin College in 1985, with a double major in Mathematics and Computer Science, and his Ph.D. in Computer Science from Stanford University in 1990. After a postdoctoral year in Utrecht, the Netherlands, he served for eight years on the faculty of the Computer Science Department at the University of British Columbia, Vancouver, Canada, with sabbatical visits to Johns Hopkins University and to INRIA Sophia-Antipolis in France. He joined UNC-Chapel Hill as a full professor in the 1999-2000 academic year. Jack's research area is computational geometry, which is the design and analysis of computer algorithms for problems best stated in geometric form. These arise in many application areas, including Geographic Information Systems (GIS), molecular modeling, robotics, and computer graphics. Jack has contributed to all of these areas, as well as to investigations in the mathematics of how computers can represent and compute with shape and geometric structure.
Professor, School of Mechanical Engineering, Purdue University
Professor, School of Electrical and Computer Engineering, Purdue University (by Courtesy)
Visiting Professor, Computer Science, Stanford University, 2008
Karthik Ramani is a Professor in the School of Mechanical Engineering at Purdue University. He earned his B.Tech from the Indian Institute of Technology, Madras, in 1985, an MS from The Ohio State University, in 1987, and a Ph.D. from Stanford University in 1991, all in Mechanical Engineering. He has worked as a summer intern in Delco Products, Advanced Composites, and as a summer faculty intern in Dow Plastics, Advanced Materials. He was awarded the Dupont Young Faculty Award, the National Science Foundation (NSF) Research Initiation Award, the NSF CAREER Award, the Ralph Teetor Educational Award from the Society of Automotive Engineers, Outstanding Young Manufacturing Engineer Award from the Society of Manufacturing Engineers, and the Ruth and Joel Spira Award for Outstanding contributions to the Mechanical Engineering Curriculum. In 2002, he was recognized by Purdue University through a University Faculty Scholars Award and won the NSF partnership for innovation award. In 2005 he won the Discovery in Mechanical Engineering Award for his work in shape search. In 2006 he won the innovation of the year award (finalist) from the State of Indiana. In 2007 he won the only Research Excellence Award for the College of Engineering at Purdue University. He also serves as the technology advisor at Imaginestics, that has launched the worlds first on-line shape-based search engine for the engineering industry. His interests are in digital and computational geometry, shape design and analysis, search and conceptual design. He serves in the editorial board of Elsevier Journal of Computer-Aided Design. He is also serving on the advisory committee for the National Science Foundation subcommittee on Industrial Innovation and Partnerships for 2007-10. His current work is supported by the NSF (CISE), National Institute of Health, Imaginestics, Purdue PLM Initiative- IBM/EDS/Boeing, St. Vincents Hospital and the Defense Logistics Agency. He received the most cited paper award from the Journal of Computer-Aided Design for two consecutive years 2007 and 2008. In the context of this mini-symposium, he has been working with Professor Daisuke Kihara and published papers related to fast protein tertiary structure search and characterization of protein surfaces in proteomics and bio-geometry for structure determination under an NIH R01 grant.