Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

SCI Publications

2008


 N. Sadeghi, N.L. Foster, A.Y. Wang, S. Minoshima, A.P. Lieberman, T. Tasdizen. “Automatic Classification of Alzheimer,” In Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2008): From Nano to Macro, pp. 408--411. 2008.
DOI: 10.1109/ISBI.2008.4541019


E. Santos, L. Lins, J.P. Ahrens, J. Freire, C.T. Silva. “A First Study on Clustering Collections of Workflow Graphs,” In Proceedings of the Second International Provenance and Annotation Workshop (IPAW 2008), pp. 160--173. 2008.


C.E. Scheidegger, D. Koop, E. Santos, H.T. Vo, S.P. Callahan, J. Freire, C.T. Silva.. “Tackling the Provenance Challenge One Layer at a Time,” In Concurrency Computat.: Pract. Exper., Vol. 20, No. 5, pp. 473--483. 2008.


C.E. Scheidegger, H.T. Vo, D. Koop, J. Freire, C.T. Silva. “Querying and Re-Using Workflows with VisTrails,” In Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data, pp. 1251--1254. 2008.
DOI: 10.1145/1376616.1376747


J.A. Schmidt. “Uintah Application Development,” SCI Technical Report, No. UUSCI-2008-005, University of Utah, 2008.


M. Schott, V. Pegoraro, C.D. Hansen, K. Boulanger, J. Stratton, K. Bouatouch. “A Directional Occlusion Shading Model for Interactive Direct Volume Rendering,” SCI Technical Report, No. UUSCI-2008-009, University of Utah Scientific Computing and Imaging Institute, 2008.


C.E. Scheidegger, J. Schreiner, B. Duffy, H. Carr, C.T. Silva. “Revisiting Histograms and Isosurface Statistics,” In IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2008), Vol. 14, No. 6, pp. 1659--1666. 2008.
DOI: 10.1109/TVCG.2008.160


S. Sharma, S. Vakkalanka, G. Gopalakrishnan, R.M. Kirby, R. Thakur, W. Gropp. “A Formal Approach to Detect Functionally Irrelevant Barriers in MPI Programs,” In Proceedings of EuroPVM-MPI 2008, Dublin, Ireland, Vol. 5205, pp. 265--273. September, 2008.
DOI: 10.1007/978-3-540-87475-1_36

ABSTRACT

We examine the unsolved problem of automatically and efficiently detecting functionally irrelevant barriers in MPI programs. A functionally irrelevant barrier is a set of MPI_Barrier calls, one per MPI process, such that their removal does not alter the overall MPI communication structure of the program. Static analysis methods are incapable of solving this problem, as MPI programs can compute many quantities at runtime, including send targets, receive sources, tags, and communicators, and also can have data-dependent control flows. We offer an algorithm called Fib to solve this problem based on dynamic (runtime) analysis. Fib applies to MPI programs that employ 24 widely used two-sided MPI operations. We show that it is sufficient to detect barrier calls whose removal causes a wildcard receive statement placed before or after a barrier to now begin matching a send statement with which it did not match before. Fib determines whether a barrier becomes relevant in any interleaving of the MPI processes of a given MPI program. Since the number of interleavings can grow exponentially with the number of processes, Fib employs a sound method to drastically reduce this number, by computing only the relevant interleavings. We show that many MPI programs do not have data dependent control flows, thus making the results of Fib applicable to all the input data the program can accept.


 J.F. Shepherd, C.R. Johnson. “Hexahedral Mesh Generation Constraints,” In Journal of Engineering with Computers, Vol. 24, No. 3, pp. 195--213. 2008.


A.G. Shvedko, M.D. Warren, S. Shome, J.G. Stinstra, A.V. Zaitsev. “Influence of the Skeletal Muscle Activity on Time and Frequency Domain Properties of the Body Surface ECG During Evolving Ventricular Fibrillation in the Pig,” In Resuscitation, Vol. 78, No. 2, pp. 215--223. May 24, 2008.
DOI: 10.1016/j.resuscitation.2008.03.010


C.T. Silva, J. Tohline. “Guest Editorial: Special Issue on Computational Provenance,” In Computing in Science and Engineering, Vol. 10, No. 3, pp. 9--10. 2008.


C.T. Silva, J. Freire. “Software Infrastructure for Exploratory Visualization and Data Analysis: Past, Present and Future,” In Journal of Physics: Conference Series (SciDAC 2008 Conference), Vol. 125, 2008.


J. Spjut, D. Kopta, S. Kellis, S. Boulos, E. Brunvand. “TRaX: A Multi-Threaded Architecture for Real-Time Ray Tracing,” In Proceedings of the IEEE Symposium on Application Specific Processors, SASP 2008, Note: Awarded Best Paper, pp. (in press). 2008.


M. Steffen, S. Curtis, R.M. Kirby, J.K. Ryan. “Investigation of Smoothness-Increasing Accuracy-Conserving Filters for Improving Streamline Integration Through Discontinuous Fields,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 14, No. 3, pp. 680--692. 2008.


M. Steffen, R.M. Kirby, M. Berzins. “Analysis and Reduction of Quadrature Errors in the Material Point Method (MPM),” In International Journal for Numerical Methods in Engineering, Vol. 76, No. 6, pp. 922--948. 2008.
DOI: 10.1002/nme.2360


M. Steffen, P.C. Wallstedt, J.E. Guilkey, R.M. Kirby, M. Berzins. “Examination and Analysis of Implementation Choices within the Material Point Method (MPM),” In Computer Modeling in Engineering & Sciences, Vol. 31, No. 2, pp. 107--127. 2008.


J.G. Stinstra, M.A. Jolley, J.D. Tate, D.H. Brooks, J.K. Triedman, R.S. MacLeod. “The Role of Volume Conductivities in Simulation of Implantable Defibrillators,” In Computers in Cardiology, Bologna, Italy, 2008.


J.G. Stinstra, M. Jolley, M. Callahan, D.M. Weinstein, M. Cole, D.H. Brooks, J. Triedman, R.S. MacLeod. “Evaluation of Different Meshing Algorithms in the Computation of Defibrillation Thresholds in Children,” In Proceedings of the 29th Annual International Conference of the IEEE EMBS, pp. 1422-1425. 2008.
ISBN: 978-1-4244-0787-3


M. Styner, I. Oguz, T. Heimann, G. Gerig. “Minimum Description Length with Local Geometry,” In Proceedings of the 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2008), pp. 1283--1286. 2008.
DOI: 10.1109/ISBI.2008.4541238


D.R. Sutherland, Q. Ni, R.S. MacLeod, R.L. Lux, B.B. Punske. “Experimental Measures of Ventricular Activation and Synchrony,” In Pacing and Clinical Electrophysiology, Vol. 31, No. 12, pp. 1560--1570. December, 2008.