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:


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.



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.