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Home > News and Events
News and Events:
SCI VisTrails Team Wins Best Paper at Vis 2007
The paper "Querying and Creating Visualizations by Analogy", by Carlos E. Scheidegger, Huy T. Vo, David Koop, Juliana Freire, and Cláudio Silva was selected as the "Best Paper" at IEEE Visualization 2007. In this paper, the authors introduce a new framework that allows users who are not necessarily programmers to query and refine pipelines (or workflows) by analogy. They describe a query-by-example interface which allows users to construct as complex, structure-based queries (e.g., find workflows that resample a data set before extracting an isurface) by example, using the same interface used to build pipelines. They also introduce analogy as a first-class operation to create and refine pipelines. The analogy operation allows casual users to modify pipelines without having to directly edit their definitions. These features have been implemented in their open-source workflow and provenance management system called VisTrails, which can be downloaded from the SCI Website. For more information see:
Feature Story: Announcing VisTrails 1.0!
C. Scheidegger, H. Vo, D. Koop, J. Freire, C.T. Silva. "Querying and Creating Visualizations by Analogy," In IEEE Transactions on Visualization and Computer Graphics 2007, pp. 1560--1567. 2007.
Versions Available: [ PDF ]
Steve Parker Selected Member of DARPA Computer Science Study Group
Dr. Steve Parker has been selected by the Pentagon's Defense Advanced Research Projects Agency (DARPA) to be a member of the 2008 DARPA Computer Science Study Group. The program supports university researchers with research grants for up to three years, while informing them of the Department of Defense's information technology needs and priorities. Dr. Parker will receive $100,000 the first year, and potentially as much as $750,000 during the second and third years. Congratulations Steve!!
CIBC Collaborator Mario Capecchi Wins Nobel Prize!
The NIH Center for Integrative Biomedical Computing (CIBC) and the Scientific Computing and Imaging (SCI) Institute would like to join the international scientific community in extending our heartiest congratulations to our University of Utah colleague Dr. Mario Capecchi as one of the three recipients of the 2007 Nobel Prize in Physiology or Medicine.
This award recognizes the ground-breaking work of Dr. Capecchi and his scientific contemporaries, Dr. Oliver Smithies of Cardiff University in the UK and Dr. Martin Evans of the University of North Carolina at Chapel Hill, in the development of genetic targeting of embryonic stem cells in mice. This novel technique selectively alters individual genes in the mouse DNA. Through studies employing genetic targeting, medical researchers now can better elucidate the roles that particular genes play in the animal development. The application of this method has revolutionized the study of mammalian biology and contributed to the development of new animal models for numerous human diseases in addition to cancers occurring in mice.
Recently, CIBC researchers have joined forces with Dr. Capecchi and his team to develop new methods for phenotyping genetically modified mice through the use of advanced image analysis and visualization techniques. Researchers from the Capecchi lab and the CIBC recently collaborated on a study that resulted in a new process known as microCT-based virtual histology. This technique employs state-of-the-art imaging and visualization techniques to characterize animal development and to observe the effects of the targeted genes more precisely and efficiently. The new methods emerging from this collaboration have the promise of accelerating the pace of understanding within mammalian genetics.
Dr. Capecchi is the first faculty member in the history of the University of Utah to receive the Nobel Prize. He will be honored with this year's others Laureates - including former U.S. Vice President Al Gore and English author Doris Lessing - in a ceremony in Stockholm on December 10.
For additional details on the CIBC-Capecchi collaboration, see:
For more details on this year's Nobel Prize in Physiology or Medicine, see:
SCI and MRL Release FEBio 1.0 Software Suite!
The Scientific Computing and Imaging Institute and the Musculoskeletal Research Laboratories are proud to announce the 1.0 release of the software FEBio, "Finite Elements for Biomechanics". FEBio is a nonlinear finite element software package that is specifically designed to address problems in computational biomechanics. Some of the features of note include capabilities for contact, rigid bodies and kinematic joints, nonlinear anisotropic constitutive models, simulation of active contraction, poroelasticity, element formulations for nearly-incompressible materials and parallel solution of the linear system of equations. After extensive testing in our lab and with our collaborators, we are happy to offer this free software to the research community.
FEBio is currently available for WindowsXP, MacOS/X, Suse Linux (64 bit Opteron/Athlon64) and SGI Altix (64 bit Itanium2). We would be happy to port FEBio to other Unix/Linux platforms. The FEBio distribution includes the User's Manual, Theory Manual and several test problems to verify proper operation.
We are also pleased to announce the 1.0 releases of PreView and PostView – FE preprocessing and postprocessing software packages that support the use of FEBio, as well as other FE solvers. These packages are available at the same web page.
We have big plans for FEBio. Our goal is for FEBio to be the first and best choice for finite element analysis in solid biomechanics. Upcoming new features will include hyperelastic shell elements, enhanced strain tetrahedral elements, a framework for representing mixtures with any number of charged or uncharged solutes, and dedicated forums for user support and discussion. We would be happy to add new constitutive models to FEBio to support your needs. Because of the modular nature of the C++ code, this is an easy task. Finally, if you are interested in helping with the development of FEBio, please contact me about our Developer's Program.
If you have any specific questions about FEBio that are not answered in the manuals, or encounter any problems with download, installation or use, please feel free to contact us and we will do our best to help you out. Contact information is available on the MRL web site.
We are in debt to our lead code developer, Steve Maas, for his outstanding work on this project over the past year, to Gerard Ateshian of Columbia University for his collaboration on the poroelasticity implementation, and to our web page developer Wendy Johnson for designing and implementing the web pages for download site and the database back-end.
Claudio Silva Receives IBM Faculty Award for Third Year Running
Dr. Claudio Silva has been honored once again with a coveted IBM Faculty Award. This award is designed to promote innovative, collaborative research and honor outstanding faculty working in disciplines of interest to IBM. It includes $30,000 to support ongoing research.
Dr. Silva is being recognized for his continuing success in developing efficient rendering techniques for large-scale scientific visualization. The increase in computational power has enabled the generation of large and complex simulations. Scientists and engineers are now faced with an incredible amount of data to analyze. Despite considerable effort, techniques for the visualization of large datasets, common in scientific simulations, still take too long. In addition, most current techniques suffer from strict data size limitations due to the reliance on having the complete datasets in main memory. In order to address the interactivity and scalability requirements, the Dr. Silva and his team are developing novel out-of-core, streaming, and parallel algorithms for optimizing the visualization of large datasets. The development of scalable rendering algorithms is of key importance to the advancement of visualization, graphics, and computational science.
American Scientist Magazine Interviews Steve Parker and Chris Johnson
SCI Institute Moves to New John E. and Marva M. Warnock Engineering Building
CRA-NIH Computing Research Challenges in Biomedicine Workshop Recommendations
SCI Graduate Student Andrew Kensler Wins Mozy Coding Deathmatch
Andrew Kensler took the $10,000 grand prize in Mozy.com's Coding Deathmatch. The contest consisted of three timed rounds of competition, two preliminary rounds were held online and the final round at Mozy.com's American Fork (Utah) headquarters. Only the top eight contestants were allowed to proceed to the final round. Contestants were asked to write programs in any of nine possible languages to to solve a series of problems. The winning code was graded on it's ability to solve the problem in the least amount of execution time.
The problem for the final round was to write a program that would read through a 2GB file of 20 million records of 100 bytes each. The first 8 bytes represented the key for that record and the remainder was a payload. The program had to write out a file containing just the records that would be in the 0, 1M, 2M, 3M... positions as sorted by the key values. Ties between keys were to be broken by original order in the file. Wall-clock execution time of the correct programs was used to decide the final ranking for the contest. Timings were done on a virtual machine with 1GB of RAM and 4GB of scratch disk space available.
The final round was composed of two stages. Contestants were given 45 minutes to write the program and submit the initial version. After that, the contestants were sent to a break room and called out individually to try their programs on a test machine. They were each informed of their comparative times and given 30 more minutes in the second stage to optimize or correct their programs. Timings after the second stage determined the winners.
"My program (written in C++) was the first to be tried and finished in 42.6s. The second place person's program finished in about 3 and a half minutes. No one else had a working program for the first stage. I chose to pass on the second optimization stage and let my program stand as it was. When they evaluated the programs after this second stage, they also tried the programs on a 1/10th size data set to determine the runners up for those who couldn't get their programs to handle the full size data set. In the end, everything remained as it had after the first stage except that one person had managed to get their program working on the smaller 1/10th scale data set for a time of ~36s. This won them third place."
SCI Chief Software Engineer J. Davison de St. Germain was also among the finalists to compete in the final round. You may recall that last year's competition was declared a tie between the eight finalists. SCI software developers McKay Davis, Michael Callahan and Bryan Worthen, competing separately, were among the eight finalist to split the grand prize. They were not allowed to compete in this year's contest.
"I had a lot of fun with it and the folks from Berkely Data Systems were a nice a bunch. I went into the contest thinking that at worst, I'd wash out in the first round and then have the rest of my Saturday afternoon for other things. At best, I'd end up spending almost all of Saturday and perhaps win some cash. Either way, I had little to lose by trying and potentially a lot to gain. I'd definitely recommend that everyone try it next year."
"My wife and I have some ideas on how we'll spend the money. We plan to each splurge a little bit, donate some, and then bank the majority."
Congratulations Andrew!!!
Chris Johnson on Imaging's Future in Medicine and Science (Podcast available)
SCIRun Meets CCA: SCIJump Released for Testing
SCIJump is a computational environment or framework based on the Common Component Architecture (CCA) standard for high performance component frameworks in the scientific computing domain. The SCIJump framework builds on the SCI Institute's SCIRun Problem Solving Environment and implements a parallel component and distributed computation architecture which can support a diverse set of component- based technologies.
Components connect through ports to form a complex application. In SCIJump, distributed components are supported through Remote Method Invocation on a port. Parallel components are managed transparently over an MxN method invocation and data redistribution subsystem. A meta-component model based on CCA is used to accommodate multiple component models such as CCA, VTK, SCIRun Dataflow.
SCIJump is currently in the alpha release stage, but interested users are invited to download it, give it a try and let us know what bugs you run into. Your help could play a vital role in making SCIJump a stable and powerful problem solving environment. SCIJump is currently supported on Linux and Mac OSX platforms. Please contact us or consult the project wiki for information on building the framework on other Unix-based operating systems. You may download it from the SCIJump Wiki.
Won-Ki Jeong Awarded NVIDIA Fellowship
SCI graduate student Won-Ki Jeong was selected as one of 10 applicants to be awarded the coveted NVIDIA Fellowship Award for 2007-2008. The NVIDIA Fellowship Program provides funding to Ph.D. students who are conducting research on topics which are expected to lead to major advances in the graphics and digital media industry, and are investigating innovative ways of leveraging the power of graphics hardware. Won-Ki Jeong's graduate adviser is SCI faculty member Dr. Ross T. Whitaker.
For more information about the award, please see the NVIDIA press release "NVIDIA Awards Fellowships to Top Ph.D. Innovators."
map3d 6.5 Now Available!
The Scientific Computing and Imaging Institute and the Center for Integrative Biomedical Computing are proud to announce the release of map3d version 6.5!
This release includes a number of fixes and additions to the display settings for map3d and major new support for displaying time fiducials. The driving application for this was displaying maps of activation, recovery, start of QRS, etc., both as separate isochronal maps and superimposed on the scalar time series data. If you need this, you will love map3d's new capabilities.
More details about the new features are available in the map3d User's Guide under the "New Features" section. Users are encouraged to participate in the map3d community by joining the map3d-users mailing list. This forum is the place to report bugs, let us know how you are using map3d, or share your insight about how we could make it better. We also encourage members of the scientific community who use map3d in a paper, presentation, poster, or your latest T-shirt design, to let us know about it. We receive funding from the NIH to develop and maintain map3d and we can only do that as long as we show impact. Best of all is when references to map3d are included in acknowledgments sections and bibliographies.
R.S. MacLeod and C.R. Johnson. "Map3d: Interactive Scientific Visualization for Bioengineering Data." In IEEE Engineering in Medicine and Biology Society 15th Annual International Conference, pages 30-31, IEEE Press, 1993.
Independent of whether a reference is included, we encourage authors to inform us of their publications that make use of map3d in any form.
Guido Gerig Joins Scientific Computing and Imaging Institute
Guido Gerig joins the University of Utah's Scientific Computing and Imaging (SCI) Institute as a USTAR faculty member. The Scientific Computing and Imaging (SCI) Institute has established itself as an international research leader in the areas of scientific computing, scientific visualization, and image processing.
USTAR is an innovative, aggressive and far-reaching effort to bolster Utah's economy with high-paying jobs and keep the state vibrant in the Knowledge Age. The USTAR Support Coalition and the Salt Lake Chamber sought public and private investment to recruit world-class research teams in carefully targeted disciplines. These teams will develop products and services that can be commercialized in new businesses and industries.
Dr. Gerig joins the SCI Institute from the University of North Carolina at Chapel Hill where he is a Taylor Grandy Professor with joint appointments in the Department of Computer Science and the Department of Psychiatry. He received his Ph.D. in 1987 from the Swiss Federal Institute of Technology, ETH Zurich, Switzerland and has held his position with UNC-Chapel Hill since August 1998. At the University of Utah, Dr. Gerig will have faculty positions within the School of Computing, Department of Psychiatry and SCI Institute.
Guido Gerig began research in the area of medical image analysis in 1985 at ETH Zurich, Switzerland. Since then, he has led a large number of national and international projects with close multidisciplinary collaboration between medicine, engineering, statistics, industry, and computer science. He has spent several research leaves as a Visiting Assistant Professor at the Brigham and Women's Hospital at Harvard Medical School. Dr. Gerig is a member of the editorial board of the Journal Medical Image Analysis published by Elsevier. He is a board member of MICCAI, the international society organizing the annual conference on Medical Image Computing and Computer Assisted Intervention, and has served on the committees of a number of computer vision and image analysis conferences and workshops. As the director of the UNC Neuroimage Analysis Laboratory, he supports a number of clinical neuroimaging projects with methodology for image processing, registration, atlas building, segmentation, shape analysis, and statistical analysis. Clinical driving problems are neurodevelopmental and neurodegenerative diseases and mental disorders such as schizophrenia, autism, fragile- X, chronic depression and Parkinson's disease. Current key research topics are segmentation of MRI/DTI of the early developing brain in healthy and high-risk subjects, longitudinal analysis of multi-shape complexes to describe growth trajectories of brain structures, building of normative population atlases of volumetric images and embedded shapes, and new methodologies for statistical analysis of brain white matter using diffusion tensor imaging (DTI). Tools and methods developed through driving clinical applications are open source (ITK) and made available to public.
SCI Images Used in Math Awareness Month 2007 Poster "Math and the Brain"
The theme for Mathematics Awareness Month (April) 2007 is "Mathematics and the Brain". SCI Institute Director Chris Johnson serves on the Mathematics Awareness Advisory Board. Two images produced at the SCI Institute are featured on this year's poster.
