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.

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 Berzins

Parallel Computing

Mike Kirby

Finite Element Methods
Uncertainty Quantification

Valerio Pascucci

Scientific Data Management

Chris Johnson

Problem Solving Environments

Amir Arzani

Scientific machine learning
Data-driven fluid flow modeling

Funded Research Projects:

Publications in Scientific Computing:

Display of Vector Fields Using a Reaction Diffusion Model
A.R. Sanderson, C.R. Johnson, R.M. Kirby. In Proceeding of IEEE Visualization 2004, pp. 115--122. 2004.

Computational Engineering and Science Program at the University of Utah
C. DeTar, A.L. Fogelson, C.R. Johnson, C.A. Sikorski, T. Truong. In Proceedings of the International Conference on Computational Science (ICCS) 2004, Lecture Notes in Computer Science (LNCS) 3039, part 4, Edited by M. Bubak et al, pp. 1202--1209. 2004.

Sinc Solution of Biharmonic Problems
F. Stenger, T. Cook, R.M. Kirby. In Canadian Applied Mathematics Quarterly, Vol. 12, No. 3, pp. 391--413. 2004.

Spectral Element and hp Methods
R.M. Kirby, G.E. Karniadakis. In Encyclopedia of Computational Mechanics, Vol. 3, Ch. 3, Edited by E. Stein and R. de Borst and T.J.R. Hughes, John Wiley and Sons, NY, pp. 61--88. 2004.

Biomedical Computing and Visualization Software Environments
C.R. Johnson, R.S. MacLeod, S.G. Parker, D.M. Weinstein. In Comm. ACM, Vol. 47, No. 11, pp. 64--71. 2004.

Influence of Head Tissue Conductivity in Forward and Inverse Magnetoencephalographic Simulations Using Realistic Head Models
R. Van Uitert, C.R. Johnson, L. Zhukov. In IEEE Trans Biomed. Eng., Vol. 51, No. 12, pp. 2129--2137. 2004.

Collocation Methods for the Solution of Von-Karman Dynamic Non-Linear Plate Systems
Z. Yosibash, R.M. Kirby, D. Gottlieb. In Journal of Computational Physics, Vol. 200, No. 2, pp. 432--461. 2004.

Three-dimensional Propagation in Mathematic Models: Integrative Model of the Mouse Heart
C.S. Henriquez, J.V. Tranquillo, D.M. Weinstein, E.W. Hsu, C.R. Johnson. In Cardiac Electrophysiology: From Cell to Bedside, 4th edition, Ch. 30, Edited by D.P. Zipes and J. Jalife, Saunders, pp. 273--281. 2004.

Solution of Von-Karman Dynamic Non-linear Plate Equations Using a Pseudo-spectral Method
R.M. Kirby, Z. Yosibash. In Comp. Meth. Appl. Mech. & Eng., Vol. 193, No. 6-8, pp. 575-599. 2004.

A Software Framework for Solving Problems of Bioelectricity Applying High-Order Finite Elements
M. Cole, F.B. Sachse, D.M. Weinstein, S.G. Parker, R.M. Kirby. In Proceedings of the IEEE Engineering in Medicine and Biology Society 26th Annual International Conference, Vol. 1, pp. 821--824. 2004.

Solution of von-Karman Dynamic Non-Linear Plate Equations Using a Pseudo-Spectral Method
R.M. Kirby, Z. Yosibash. In Computer Methods in Applied Mechanics and Engineering, Vol. 193, No. 6-8, pp. 575--599. 2004.

De-Aliasing on Non-Uniform Grids: Algorithms and Applications
R.M. Kirby, G.E. Karniadakis. In J. Comp. Phys., Vol. 191, No. 1, pp. 267--282. October, 2003.

Workshop on Dynamic Data-Driven Application Systems
C.C. Douglas, M. Cole, Y. Efendiev, R. Ewing, V. Ginting, C.R. Johnson, G.M. Jones, R. Lazarov, C. Shannon, J. Simpson. In ICCS 2003, Melbourne, Australia, June 2-3, 2003.

Volume Currents in Forward and Inverse Magnetoencephalographic Simulations Using Realistic Head Models
R. Van Uitert, D. Weinstein, C.R. Johnson. In Annals of Biomedical Engineering, Vol. 31, pp. 21--31. 2003.

Minimum Support MEG (Magnetoencephalography) Imaging: Study on Effects of Noise, Discretization, Depth, and Separation of Multiple Sources
D. Hwang, O. Portniaguine, S. Nagarajan, C.R. Johnson, K. Sekihara. In World Congress on Medical Physics and Biomedical Engineering, August, 2003.

Influence of Brain Conductivity on Magnetoencephalographic Simulations in Realistic Head Models
R. Van Uitert, C.R. Johnson. In The 25th Annual International Conference of the IEEE Engineering In Medicine And Biology Society, Vol. 3, pp. 2136--2139. September, 2003.

De-Aliasing on Non-Uniform Grids: Algorithms and Applications
R.M. Kirby, G.E. Karniadakis. In Journal of Computational Physics, Vol. 191, pp. 249--264. 2003.

Cramer-Rao Bounds for Nonparametric Surface Reconstruction from Range Data
T. Tasdizen, R.T. Whitaker. In Proceedings of Fourth International Conference on 3-D Imaging and Modeling, pp. 70--77. October, 2003.

Parallel Scientific Computing in C++ and MPI: A Seamless Approach to Parallel Algorithms and their Implementation
G.E. Karniadakis, R.M. Kirby. Cambridge University Press, pp. 628 pages. June, 2003.
ISBN: 0521520800

BioPSE Case Study: Modeling, Simulation, and Visualization of Three Dimensional Mouse Heart Propagation
D.M. Weinstein, J.V. Tranquillo, C.S. Henriquez, C.R. Johnson. In International Journal of Bioelectromagnetism, Vol. 5, No. 1, pp. 314--315. 2003.