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:

Interactive Source Imaging with BioPSE
D.M. Weinstein, L. Zhukov, C.R. Johnson, S.G. Parker, R. Van Uitert, R.S. MacLeod, C.D. Hansen. In Chicago 2000 World Congress on Medical Physics and Biomedical Engineering, Chicago, IL., Note: Refereed abstract., July, 2000.

Independent Component Analysis for EEG Source Localization in Realistic Head Models
L. Zhukov, D. Weinstein, C.R. Johnson. In IEEE Engineering in Medicine and Biology, Vol. 19, No. 3, pp. 87--96. 2000.

Large-Scale Computational Science Applications Using the SCIRun Problem Solving Environment
C.R. Johnson, S.G. Parker, D. Weinstein. In Proceedings of The International Supercomputer Conference 2000, 2000.

The BioPSE Inverse EEG Modeling Pipeline
D.M. Weinstein, P. Krysl, C.R. Johnson. In ISGG 7th International Conference on Numerical Grid Generation in Computation Field Simulations, The International Society of Grid Generation, Mississippi State University pp. 1091--1100. 2000.

3D adaptive unstructured meshes for air pollution modelling
A. Tomlin, S. Ghorai, G. Hart, M. Berzins. In Environmental Management and Health, Vol. 10, No. 4, pp. 267-275. 1999.
DOI: 10.1108/09566169910276238

A Solution Based H1 Norm Triangular Mesh Quality Indicator
M. Berzins. In Grid Generation and Adaptive Algorithms, Edited by Marshal W. Bern, Joseph E. Flaherty, Mitchell Luskin, Springer, pp. 77-88. 1999.

The issue of mesh quality measures for triangular (and tetrahedral) meshes is considered. A new mesh quality measure is based both on geometrical and solution information and is derived by considering the error in the H 1 norm when linear triangular elements are used to approximate a quadratic function. The new measure is then compared with the recent mesh quality measure based on the L 2 norm. Simple examples are used to show that the choice of norm is critical in deciding what is a good triangulation

The SCIRun Parallel Scientific Computing Problem Solving Environment
C.R. Johnson, S.G. Parker. In Ninth SIAM Conference on Parallel Processing for Scientific Computing, 1999.

A Discontinuous Galerkin Spectral/hp Method on Hybrid Grids
R.M. Kirby, T.C. Warburton, I. Lomtev, G.E. Karniadakis. In Journal of Applied Numerical Mathematics, Vol. 33, pp. 393--405. 1999.

The SCIRun Problem Solving Environment: Implementation within a Distributed Environment
M. Miller, C.D. Hansen, C.R. Johnson. In Ninth SIAM Conference on Parallel Processing for Scientific Computing, Note: extended abstract, 1999.

Independent Component Analysis For EEG Source Localization In Realistic Head Models
L. Zhukov, D.M. Weinstein, C.R. Johnson. In Third International Conference on Inverse Problems in Engineering, 1999.

Interactive Simulation and Visualization
C.R. Johnson, S.G. Parker, C.D. Hansen, G.L. Kindlmann, Y. Livnat. In IEEE Computer, Vol. 32, No. 12, pp. 59--65. Dec, 1999.

A Discontinuous Galerkin ALE Method for Compressible Viscous Flows in Moving Domains
I. Lomtev, R.M. Kirby, G.E. Karniadakis. In Journal of Computational Physics, Vol. 155, pp. 128--159. 1999.

Direct Numerical Simulation of Turbulence with a PC/Linux Cluster: Fact or Fiction?
G.-S. Karamanos, C. Evangelinos, R.C. Boes, R.M. Kirby, G.E. Karniadakis. In Proceedings of SuperComputing 1999, Portland, OR, November, 1999.

Lead Field Basis for FEM Source Localization
School of Computing Technical Report, D.M. Weinstein, L. Zhukov, C.R. Johnson. No. UUCS-99-014, University of Utah, Salt Lake City, UT October, 1999.

An Integrated Problem Solving Environment: The SCIRun Computational Steering System
S.G. Parker, M. Miller, C.D. Hansen, C.R. Johnson, P.-P. Sloan. In 31st Hawaii International Conference on System Sciences (HICSS-31), Vol. VII, Edited by H. El-Rewini, pub-IEEE, pp. 147--156. January, 1998.

An Unstructured Finite Volume Algorithm for Predicting Flow in Rivers and Estuaries
P.A. Sleigh, M. Berzins, P.H. Gaskell, N.G. Wright. In Computers and Fluids, Vol. 27, No. 4, pp. 479--508. 1998.

Simulation Steering with SCIRun in a Distributed Memory Environment
M. Miller, C.D. Hansen, S.G. Parker, C.R. Johnson. In Seventh IEEE International Symposium on High Performance Distributed Computing (HPDC-7), Jul, 1998.

SCIRun: Applications to Atmospheric Diffusion Using Unstructured Meshes
C.R. Johnson, M. Berzins, L. Zhukov, R. Coffey. In Numerical Methods for Fluid Dynamics VI, Edited by M.J. Baines, Oxford University Press, pp. 111--122. 1998.

Simulation Steering with SCIRun in a Distributed Memory Environment
M. Miller, C.D. Hansen, C.R. Johnson. In Lecture Notes in Computer Science, Springer-Verlag, In Applied Parallel Computing, 4th International Workshop, PARA'98, Lecture Notes in Computer Science, Vol. 1541, Edited by B. Kagstrom and J. Dongarra and E. Elmroth and J. Wasniewski, Springer-Verlag, Berlin pp. 366--376. 1998.

Adaptive local regularization methods for the inverse ECG problem
C.R. Johnson, R.S. MacLeod. In Progress in Biophysics and Biochemistry, Vol. 69, No. 2/3, pp. 405. Dec, 1998.