Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Large scale visualization on the Powerwall.
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.

Scientific Computing

Numerical simulation of real-world phenomena provides fertile ground for building interdisciplinary relationships. The SCI Institute has a long tradition of building these relationships in a win-win fashion – a win for the theoretical and algorithmic development of numerical modeling and simulation techniques and a win for the discipline-specific science of interest. High-order and adaptive methods, uncertainty quantification, complexity analysis, and parallelization are just some of the topics being investigated by SCI faculty. These areas of computing are being applied to a wide variety of engineering applications ranging from fluid mechanics and solid mechanics to bioelectricity.


martin

Martin Berzins

Parallel Computing
GPUs
mike

Mike Kirby

Finite Element Methods
Uncertainty Quantification
GPUs
pascucci

Valerio Pascucci

Scientific Data Management
chris

Chris Johnson

Problem Solving Environments
ross

Ross Whitaker

GPUs
chuck

Chuck Hansen

GPUs
       

Scientific Computing Project Sites:


Publications in Scientific Computing:


The Effects of Inhomogeneities and Anisotropies on Electrocardiographic Fields: A Three-Dimensional Finite Element Study
R.N. Klepfer, C.R. Johnson, R.S. MacLeod. In IEEE Transactions on Biomedical Engineering, Vol. 44, No. 8, pp. 706--719. August, 1997.



SPRINT2D Software for Convection Dominated PDEs
M. Berzins, S.V. Pennington, P.R. Pratt, J.M. Ware. In Modern Software Tools in Scientific Computing, Edited by E. Arge and A.M. Bruaset and H.P. Langtangen, Birkhauser Press, 1997.

SPRINT2D is a set of software tools for solving time-dependent partial differential equations in two space variables. The software uses unstructured triangular meshes and adaptive error control in both space and time. This chapter describes the software and shows how the adaptive techniques may be used to increase the reliability of the solution procedure for a challenging combustion problem. The recent construction of a problem solving environment (PSE) has partially automated the use of SPRINT2D. This PSE consists of tools such as a visual domain specification tool, which helps ease the input of complex geometries, and a visual problem specification tool. After describing these components an evaluation will be made of SPRINT2D and its associated PSE.



Effects of Geometric Uncertainty on the Inverse EEG Problem
D.M. Weinstein, C.R. Johnson. In Computational, Experimental, and Numerical Methods for Solving Ill-Posed Inverse Imaging Problems:Medical and Nonmedical Applications, SPIE '97, Vol. 3171, Edited by R.L. Barbour and M.J. Carvlin and M.A. Fiddy, SPIE, pp. 138--145. 1997.



A new relaxation scheme for solving EHL Problems
E. Nurgat, M. Berzins. In 23rd Leeds-Lyon Symposium on Tribology, Tribology Series, Vol. 32, Edited by D.Dowson et al., Elsevier, pp. 125a-134. 1996.
ISBN: 0444828095

A New Relaxation Scheme (NRS) is presented in this paper to solve Elasto Hydrodynamic Lubrication (EHL) point contact problems. The solutions obtained are compared with those obtained by Ehret [6] who employed the Distributive Relaxation Scheme (DRS) of Venner [2]. Results obtained using the two schemes are in close agreement which is very encouraging although it is too early to draw any conclusions. The new relaxation scheme thus provides an alternative approach to the distributive relaxation scheme.



Applications of Large-Scale Computing and Scientific Visualization in Medicine
C.R. Johnson, D.M. Beazley, Y. Livnat, S.G. Parker, J.A. Schmidt, H.W. Shen, D.M. Weinstein. In International Journal on Supercomputer Applications and High Performance Computing, 1996.



SCIRun: Applying Interactive Computer Graphics to Scientific Problems
S.G. Parker, C.R. Johnson. In SIGGRAPH (applications/demo), 1996.



The effects of inhomogeneities and anisotropies on electrocardiographic fields: A three-dimensional finite element study
R.N. Klepfer, C.R. Johnson, R.S. MacLeod. In IEEE Trans. on Biomedical Engineering, 1996.



Local regularization and adaptive methods for the inverse Laplace problem
C.R. Johnson, R.S. MacLeod. In Biomedical and Life Physics, Edited by D.N. Ghista, Vieweg-Verlag, Braunschweig pp. 224--234. 1996.



MeshView: A tool for exploring 3D unstructured tetrahedral meshes
C.S. Gitlin, C.R. Johnson. In 5th International Meshing Roundtable, pp. 333--345. 1996.



An adaptive CFD solver for time-dependent environmental flow problems
M. Berzins, P. Gaskell, A. Sleigh, A.S. Tomlin, J. Ware. In Proceedings of the Institute of Computational Fluid Dynamics Conference, Edited by K.W. Morton, M.J. Baines, Oxford University Press, pp. 311-317. 1995.



Large Scale Biomedical Modeling and Simulation: From Concepts to Results
SCI Institute Technical Report, C.S. Henriquez, C.R. Johnson, K.A. Henneberg L.J., A.E. Pollard. No. UUSCI-1995-001, University of Utah, 1995.



Software Tools for Modeling, Computation, and Visualization in Medicine
C.R. Johnson, R.S. MacLeod, J.A. Schmidt. In CompMed 94 Proceedings, World Scientific, 1995.



An Interactive Computer Model for Defibrillation Device Design
J.A. Schmidt, C.R. Johnson, R.S. MacLeod. In International Congress on Electrocardiology, ICE, pp. 160--161. 1995.



Applications in Computational Medicine using SCIRun: A Computational Steering Programming Environment
C.R. Johnson, S.G. Parker. In Supercomputer `95, Edited by H.W. Meuer, Springer-Verlag, pp. 2--19. 1995.



Applications of Automatic Mesh Generation and Adaptive Methods in Computational Medicine
J.A. Schmidt, C.R. Johnson, J.C. Eason, R.S. MacLeod. In Modeling, Mesh Generation, and AdaptiveMethodsforPartial Differential Equations, Edited by I. Babuska and J.E. Flaherty and W.D. Henshaw and J.E. Hopcroft and J.E. Oliger and T. Tezduyar, Springer-Verlag, pp. 367--390. 1995.



Direct and Inverse Bioelectric Field Problems
C.R. Johnson. In Computational Science Education Project, Edited by E. Oliver and M. Strayer and V. Meiser and D. Zachmann and R. Giles, DOE, Washington, D.C. 1995.



SCIRun: A Scientific Programming Environment for Computational Steering
S.G. Parker, C.R. Johnson. In Proceedings of the 1995 ACM/IEEE Conference on Supercomputing, San Diego, California, USA, Supercomputing '95, No. 52, ACM, New York, NY, USA 1995.
ISBN: 0-89791-816-9
DOI: 10.1145/224170.224354



Numerical Methods for Bioelectric Field Problems
C.R. Johnson. In The Biomedical Engineering Handbook, Edited by J.D. Bronzino, CRC Press, Boca Ratan pp. 161--188. 1995.



Defibsim: An Interactive Defibrillation Device Design Tool
J.A. Schmidt, C.R. Johnson. In IEEE Engineering in Medicine and Biology Society 17th Annual International Conference, IEEE Press, pp. 305--306. 1995.



Dynamic Load-Balancing For PDE Solvers On Adaptive Unstructured Meshes
C. Walshaw, M. Berzins. In Concurrency, Vol. 7, No. 1, pp. 17--28. 1995.