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:

Formal Verification of Programs that use MPI One-Sided Communications
S. Pervez, G. Gopalakrishnan, R.M. Kirby, R. Thakur, W. Gropp. In Proceedings of EuroPVM-MPI 2006, Bonn, Germany, September 17-20, 2006.

Dynamic Contaminant Identification in Water
C.C. Douglas, J.C. Harris, M. Iskandarani, C.R. Johnson, R.J. Lodder, S.G. Parker, M.J. Cole, R. Ewing, Y. Efendiev, R. Lazarov, G. Qin. In Proceedings of Computational Science - ICCS 2006: 6th International Conference, Part III, Reading, UK, May 28-31, 2006, Lecture Notes in Computer Science series, Vol. 3993, Edited by Vassil N. Alexandrov and Geert Dick van Albada and Peter M.A. Sloot and Jack J. Dongarra, Springer-Verlag Heidelberg, pp. 393--400. 2006.

Computational Methods and Software for Bioelectric Field Problems
C.R. Johnson. In Biomedical Engineering Handbook, 2nd Edition, Vol. 1, Ch. 23, Edited by J.D. Bronzino, CRC Press, Boca Raton, pp. 1--23. 2006.

Ray-Tracing Polymorphic Multi-Domain Spectral/hp Elements for Isosurface Rendering
B. Nelson, R.M. Kirby. In IEEE Transactions on Visualization and Computer Graphics, Vol. 12, No. 1, pp. 114--125. 2006.

Integrating Component-Based Scientific Computing Software
S.G. Parker, K. Zhang, K. Damevski, C.R. Johnson. 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

Computational Science: Ensuring America's Competitiveness
D. Reed, R. Bajcsy, J.M. Griffiths, J. Dongarra, C.R. Johnson. Note: President's Information Technology Advisory Committee (PITAC), June, 2005.

Influence of Stochastic Organ Conductivity in 2D ECG Forward Modeling: A Stochastic Finite Element Study
S.E. Geneser, S. Choe, R.M. Kirby, R.S. MacLeod. In Proceedings of The Joint Meeting of The 5th International Conference on Bioelectromagnetism and The 5th International Symposium on Noninvasive Functional Source Imaging within the Human Brain and Heart, pp. 5528--5531. 2005.

Selecting the Numerical Flux in Discontinuous Galerkin Methods for Diffusion Problems
R.M. Kirby, G.E. Karniadakis. In Journal of Scientific Computing, Vol. 22/23, pp. 385--411. 2005.

Visualization in the SCIRun Problem-Solving Environment
D.M. Weinstein, S.G. Parker, J. Simpson, K. Zimmerman, G.M. Jones. In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 615--632. 2005.
ISBN: 0-12-387582-X

Integrating Teaching and Research in HPC: Experiences and Opportunities
M. Berzins, R.M. Kirby, C.R. Johnson. In Proceedings of the International Conference on Computational Science (ICCS) 2005, Atlanta, GA, pp. 36--43. 2005.

Parallelization and Scalability of a Spectral Element Solver
SCI Institute Technical Report, C.W. Hamman, R.M. Kirby, M. Berzins. No. UUSCI-2005-011, University of Utah, 2005.

Dynamic Response of Various Von-Karman Non-Linear Plate Models and their 3-D Counterparts
Z. Yosibash, R.M. Kirby. In International Journal of Solids and Structures, Vol. 42, pp. 2517--2531. 2005.

Computational Simulation of Penetrating Trauma in Biological Soft Tissues Using the Material Point Method
I. Ionescu, J. Guilkey, M. Berzins, R.M. Kirby, J.A. Weiss. In Proceedings, Medicine Meets Virtual Reality, Vol. 13, Edited by James D Westwood et al., IOS Press, pp. 213--218. 2005.
ISBN: 1-58603-498-7

Gauss: A Framework for Verifying Scientific Computing Software
R. Palmer, S. Barrus, Y. Yang, G. Gopalakrishnan, R.M. Kirby. In Proceeding of the Software Model Checking Workshop, Edinburgh, Scotland, July, 2005.

Advanced Modeling and Visualization of Cardiothoracic Electrical Fields
F. Sachse, M. Cole, R.M. Kirby, X. Tricoche, C.R. Johnson. In Proceedings of 13th Medicine Meets Virtual Reality (MMVR13), 2005.

SCIRun/BioPSE: Integrated Problem Solving Environment for Bioelectric Field Problems and Visualization
R.S. Macleod, D.M. Weinstein, J.D. de St. Germain, D.H. Brooks, C.R. Johnson, S.G. Parker. In Proceedings of the Int. Symp. on Biomed. Imag., Arlington, Va, pp. 640--643. April, 2004.

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.