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 Berzins

Parallel Computing

Mike Kirby

Finite Element Methods
Uncertainty Quantification

Valerio Pascucci

Scientific Data Management

Chris Johnson

Problem Solving Environments

Ross Whitaker


Chuck Hansen


Scientific Computing Project Sites:

Publications in Scientific Computing:

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.

Computational Steering Software Systems and Strategies
S.G. Parker, D.M. Beazley, C.R. Johnson. In IEEE Computational Science and Engineering, Vol. 4, No. 4, pp. 50--59. 1997.

An Automatic Adaptive Refinement and Derefinement Method for 3D Elliptic Problems
F. Yu, Y. Livnat, C.R. Johnson. In Applied Numerical Mathematics, 1997.

Computational and Numerical Methods for Bioelectric Field Problems
C.R. Johnson. In Critical Reviews in BioMedical Engineering, Vol. 25, No. 1, pp. 1--81. 1997.

The SCIRun Computational Steering Software System
S.G. Parker, D.M. Weinstein, C.R. Johnson. In Modern Software Tools in Scientific Computing, Edited by E. Arge and A.M. Bruaset and H.P. Langtangen, Birkhauser Press, Boston pp. 1--40. 1997.

We present the design, implementation and application of SCIRun, a scientific programming environment that allows the interactive construction, debugging, and steering of large-scale scientific computations. Using this "computational workbench," a scientist can design and modify simulations interactively via a dataflow programming model. SCIRun enables scientists to design and modify model geometry, interactively change simulation parameters and boundary conditions, and interactively visualize geometric models and simulation results. We discuss the ubiquitous roles SCIRun plays as a computational tool (e.g. resource manager, thread scheduler, development environment), and how we have applied an object oriented design (implemented in C++) to the scientific computing process. Finally, we demonstrate the application of SCIRun to large scale problems in computational medicine. 1.1 Introduction 1.1.1 Visual Computing and Interactive Steering In recent years, the scientific computing commu...

Keywords: scirun, problem solving environments, ncrr, scientific visualization, pse pses problem solving envoronment, bioelectric fields

Applications of Large-Scale Computing and Scientific Visualization in Medicine
SCI Institute Technical Report, C.R. Johnson, D.M. Beazley, Y. Livnat, S.G. Parker, J.A. Schmidt, H.W. Shen, D.M. Weinstein. No. UUSCI-1997-001, University of Utah, 1997.