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:


Incorporating patient breathing variability into a stochastic model of dose deposition for stereotactic body radiation therapy
S.E. Geneser, R.M. Kirby, Brian Wang, B. Salter, S. Joshi. In Information Processing in Medical Imaging, Lecture Notes in Computer Science LNCS, Vol. 5636, pp. 688--700. 2009.
PubMed ID: 19694304



Finite Element Discretization Strategies for the Inverse Electrocardiographic (ECG) Problem
D.F. Wang, R.M. Kirby, C.R. Johnson. In Proceedings of the 11th World Congress on Medical Physics and Biomedical Engineering, Munich, Germany, Vol. 25/2, pp. 729-732. September, 2009.



Finite Element Refinements for Inverse Electrocardiography: Hybrid-Shaped Elements, High-Order Element Truncation and Variational Gradient Operator
D.F. Wang, R.M. Kirby, C.R. Johnson. In Proceeding of Computers in Cardiology 2009, Park City, September, 2009.



A Framework for Exploring Numerical Solutions of Advection Reaction Diffusion Equations using a GPU Based Approach
A.R. Sanderson, M.D. Meyer, R.M. Kirby, C.R. Johnson. In Journal of Computing and Visualization in Science, Vol. 12, pp. 155--170. 2009.
DOI: 10.1007/s00791-008-0086-0



Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples
R.S. MacLeod, J.G. Stinstra, S. Lew, R.T. Whitaker, D.J. Swenson, M.J. Cole, J. Krüger, D.H. Brooks, C.R. Johnson. In Philosophical Transactions of The Royal Society A, Mathematical, Physical & Engineering Sciences, Vol. 367, No. 1896, pp. 2293--2310. 2009.



Hexahedral Mesh Generation for Biomedical Models in SCIRun
J.F. Shepherd, C.R. Johnson. In Engineering with Computers, Vol. 25, No. 1, pp. 97--114. 2009.



Comparison of Consistent Integration Versus Adaptive Quadrature for Taming Aliasing Errors
SCI Technical Report, H. Mirzaee, C. Eskilsson, S.J. Sherwin, R.M. Kirby. No. UUSCI-2009-008, SCI Institute, University of Utah, 2009.



The SCIJump Framework for Parallel and Distributed Scientific Computing
S.G. Parker, K. Damevski, A. Khan, A. Swaminathan, C.R. Johnson. In Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications, Edited by Manish Parashar and Xiaolin Li and Sumir Chandra, Wiley-Blackwell, pp. 149--170. 2009.
DOI: 10.1002/9780470558027.ch9



A Meshing Pipeline for Biomedical Models
M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson. In Engineering with Computers, Vol. 25, No. 1, SpringerLink, pp. 115-130. 2009.
DOI: 10.1007/s00366-008-0106-1



Formal Verification of Practical MPI Programs
A. Vo, S. Vakkalanka, M. Delisi, G. Gopalakrishnan, R.M. Kirby, R. Thakur. In Proceedings of 14th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP), Raleigh, NC, pp. 261--270. February 14-18, 2009.



Particle-based Sampling and Meshing of Surfaces in Multimaterial Volumes
M.D. Meyer, R.T. Whitaker, R.M. Kirby, C. Ledergerber, H. Pfister. In IEEE Transactions on Visualization and Computer Graphics, Vol. 14, No. 6, pp. 1539--1546. 2008.



Hexahedral Mesh Generation Constraints
J.F. Shepherd, C.R. Johnson. In Journal of Engineering with Computers, Vol. 24, No. 3, pp. 195--213. 2008.



Filtering in Legendre Spectral Methods
J.S. Hesthaven, R.M. Kirby. In Mathematics of Computation, Vol. 77, No. 263, pp. 1425--1452. 2008.



An Approach to Formalization and Analysis of Message Passing Libraries
R. Palmer, M. DeLisi, G. Gopalakrishnan, R.M. Kirby. In Proceedings of the 12th International Workshop on Formal Methods for Industrial Critical Systems (FMICS 2007), Berlin, Germany, Vol. 4916/2008, Note: Awarded Best Paper., pp. 164--181. 2008.



Application of Stochastic Finite Element Methods to Study the Sensitivity of ECG Forward Modeling to Organ Conductivity
S.E. Geneser, R.M. Kirby, R.S. MacLeod. In IEEE Transations on Biomedical Engineering, Vol. 55, No. 1, pp. 31--40. January, 2008.



A Comparison of Implicit Solvers for the Immersed Boundary Equations
E.P. Newren, A.L. Fogelson, R.D. Guy, R.M. Kirby. In Computer Methods in Applied Mechanics and Engineering, Vol. 197, No. 25--28, pp. 2290--2304. 2008.
DOI: 10.1016/j.cma.2007.11.030



Investigation of Smoothness-Increasing Accuracy-Conserving Filters for Improving Streamline Integration Through Discontinuous Fields
M. Steffen, S. Curtis, R.M. Kirby, J.K. Ryan. In IEEE Transactions on Visualization and Computer Graphics, Vol. 14, No. 3, pp. 680--692. 2008.



Analysis and Reduction of Quadrature Errors in the Material Point Method (MPM)
M. Steffen, R.M. Kirby, M. Berzins. In International Journal for Numerical Methods in Engineering, Vol. 76, No. 6, pp. 922--948. 2008.
DOI: 10.1002/nme.2360



Volumetric Parameterization and Trivariate B-spline Fitting using Harmonic Functions
T. Martin, E. Cohen, R.M. Kirby. In Proceedings of ACM Solid and Physical Modeling, Stony Brook, NY, Note: Awarded Best Paper, pp. 269-280. 2008.



On the Lamb Vector Divergence in Navier-Stokes Flows
C.W. Hamman, J.C. Klewicki, R.M. Kirby. In Journal of Fluid Mechanics, Vol. 610, pp. 261--284. 2008.