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

2006


C.P. Gribble, S.G. Parker. “Enhancing Interactive Particle Visualization with Advanced Shading Models,” In Proceedings of the ACM Siggraph Third Symposium on Applied Perception in Graphics and Visualization, pp. 111--118. 2006.

ABSTRACT

Particle-based simulation methods are used to model a wide range of complex phenomena and to solve time-dependent problems of various scales. Effective visualization of the resulting state should communicate subtle changes in the three-dimensional structure, spatial organization, and qualitative trends within a simulation as it evolves. We take steps toward understanding and using advanced shading models in the context of interactive particle visualization. Specifically, the impact of ambient occlusion and physically based diffuse interreflection is investigated using a formal user study. We find that these shading models provide additional visual cues that enable viewers to better understand subtle features within particle datasets. We also describe a visualization process that enables interactive navigation and exploration of large particle datasets, rendered with illumination effects from advanced shading models. Informal feedback from application scientists indicates that the results of this process enhance the data analysis tasks necessary for understanding complex particle datasets.

Keywords: mpm material point method, rtrt real-time ray tracing, csafe c-safe, rtcenter



T. Ize, I. Wald, C. Robertson, S.G. Parker. “An Evaluation of Parallel Grid Construction for Ray Tracing Dynamic Scenes,” SCI Institute Technical Report, No. UUSCI-2006-025, University of Utah, 2006.



T. Ize, I. Wald, C. Robertson, S.G. Parker. “An Evaluation of Parallel Grid Construction for Ray Tracing Dynamic Scenes,” In Proceedings of the 2006 IEEE Symposium on Interactive Ray Tracing, Vol. 1, pp. 47--55. 2006.



T. Ize, I. Wald, S.G. Parker. “Asynchronous BVH Construction for Ray Tracing Dynamic Scenes,” Note: UUSCI-2006-034, SCI Institute, 2006.



C.R. Johnson, S.G. Parker. “Problem Solving Environments for DDDAS,” In Proceedings of the Ninth Copper Mountain Conference on Iterative Methods, Copper Mountain, CO, Note: Minisymposium: Actually Doing Dynamic Data-driven Application Simulations, April, 2006.



A. Knoll, I. Wald, S.G. Parker, C.D. Hansen. “Interactive Isosurface Ray Tracing of Large Octree Volumes,” SCI Institute Technical Report, No. UUSCI-2006-026, University of Utah, 2006.



G. Kumfert, D.E. Bernholdt, T.G.W. Epperly, J.A. Kohl, L.C. McInnes, S.G. Parker, J. Ray. “How the Common Component Architecture Advances Computational Science,” In J. Phys.: Conf. Ser., Vol. 46, pp. 479--493. 2006.



L.C. McInnes, B.A. Allan, R. Armstrong, S.J. Benson, D.E. Bernholdt, T.L. Dahlgren, L.F. Diachin, M. Krishnan, J.A. Kohl, J.W. Larson, S. Lefantzi, J. Nieplocha, B. Norris, S.G. Parker, J. Ray, S. Zhou. “Parallel PDE-Based Simulations Using the Common Component Architecture,” In Numerical Solution of Partial Differential Equations on Parallel Computers, Lecture Notes in Computational Science and Engineering, Edited by A.M. Bruaset and P. Bjorstad and A. Tveito, Springer, pp. 327--284. 2006.
ISBN: 3-540-29076-1



S.G. Parker. “A Component-Based Architecture for Parallel Multi-physics PDE Simulation,” In Future Generation Computer Systems (FGCS), Vol. 22, No. 1-2, Elsevier, pp. 204--216. 2006.



S.G. Parker, K. Zhang, K. Damevski, C.R. Johnson. “Integrating Component-Based Scientific Computing Software,” In Parallel Processing for Scientific Computing, Edited by M.A. Heroux and P. Raghavan and H.D. Simon, SIAM Press, pp. 271--288. 2006.
ISBN: 0-89871-619-5



S.G. Parker, J. Guilkey, T. Harman. “A Component-based Parallel Infrastructure for the Simulation of Fluid Structure Interaction,” In Engineering with Computers, Vol. 22, No. 3-4, Springer London, pp. 277--292. 2006.



S.G. Parker. “Composition of Components in Multiphysics Applications,” In Proceedings of the 12th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, CA, Note: Presented at the Minisymposium on Parallel Dynamic Data Management Infrastructures for Scientific & Engineering Applications, 2006.



S.G. Parker. “Component-Based Multi-Physics Simulations of Fires and Explosions,” In Proceedings of the 12th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, CA, Note: Presented at the Minisymposium on Parallel Dynamic Data Management Infrastructures for Scientific & Engineering Applications, 2006.



S.G. Parker. “Why do Software Engineering Methods Fail for HPC?,” In Presented at Architectures and Algorithms for Petascale Computing, Schloss Dagstuhl, Germany, Vol. Seminar 06071, February, 2006.



V. Pegoraro, S.G. Parker. “Physically-Based Realistic Fire Rendering,” In Proceedings of the 2006 Eurographics Workshop on Natural Phenomena, pp. 51--59. 2006.



A.J. Stephens, S. Boulos, J. Bigler, I. Wald, S.G. Parker. “An Application of Scalable Massive Model Interaction using Shared-Memory Systems,” In Proceedings of The 8th Eurographics Symposium on Parallel Graphics and Visualization, pp. 19--26. 2006.



I. Wald, T. Ize, A. Kensler, A. Knoll, S.G. Parker. “Ray Tracing Animated Scenes using Coherent Grid Traversal,” In Proceedings of the ACM SIGGRAPH 2006 Conference, ACM, New York, NY, USA pp. 485--493. 2006.
ISSN: 0730-0301
DOI: 10.1145/1179352.1141913



I. Wald, T. Ize, A. Kensler, A. Knoll, S.G. Parker. “Ray Tracing Animated Scenes using Coherent Grid Traversal,” SCI Institute Technical Report, No. UUSCI-2006-014, University of Utah, 2006.



C. Wyman, S.G. Parker, P. Shirley, C.D. Hansen. “Interactive Display of Isosurfaces with Global Illumination,” In IEEE Transactions on Visualization and Comptuer Graphics, Vol. 12, No. 2, March/April, 2006.


2005


Y. Alexeev, B.A. Allan, R.C. Armstrong, D.E. Bernholdt, T.L. Dahlgren, D. Gannon, C.L. Janssen, J.P. Kenny, M. Krishnan, J.A. Kohl, G. Kumfert, L.C. McInnes, J. Nieplocha, S.G. Parker, C. Rasmussen, T.L. Windus. “Component-Based Software for High-Performance Scientific Computing,” In Journal of Physics: Conference Series, Vol. 16, IOP Publishing, pp. 536--540. January, 2005.
DOI: 10.1088/1742-6596/16/1/073