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.

SCI Publications

2007


 C.W. Hamman, R.M. Kirby, M. Berzins. “Parallelization and Scalability of a Spectral Element Channel Flow Solver for Incompressible Navier-Stokes Equations,” In Concurrency and Computation: Practice and Experience, Vol. 14, No. 10, pp. 1403--1422. 2007.


C.R. Hamman, R.M. Kirby, M. Berzins. “Parallel Direct Simulation of Incompressible Navier Stokes Equations,” In Concurrency and Computation, Vol. 19, No. 10, pp. 1403-1427. 2007.


R.M. Kirby, Z. Yosibash, G.E. Karniadakis. “Towards Stable Coupling Methods for High-Order Discretizations of Fluid-Structure Interaction: Algorithms and Observations,” In Journal of Computational Physics, Vol. 223, No. 2, pp. 489--518. 2007.


M.D. Meyer, B. Nelson, R.M. Kirby, R.T. Whitaker. “Particle Systems for Efficient and Accurate Finite Element Visualization,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 5, pp. 1015--1026. 2007.


M.D. Meyer, R.M. Kirby, R.T. Whitaker. “Topology, Accuracy, and Quality of Isosurface Meshes Using Dynamic Particles,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 6, IEEE, pp. 1704--1711. Nov, 2007.


E.P. Newren, A.L. Fogelson, R.D. Guy, R.M. Kirby. “Unconditionally Stable Discretizations of the Immersed Boundary Equations,” In Journal of Computational Physics, Vol. 222, No. 2, pp. 702--719. 2007.


E.P. Newren, A.L. Fogelson, R.D. Guy, R.M. Kirby. “Unconditionally Stable Discretizations of the Immersed Boundary Equations,” In Journal of Computational Physics, Vol. 222, No. 2, pp. 702--719. March, 2007.


T. Ochotta, C.E. Scheidegger, J. Schreiner, Y. Lima, R.M. Kirby, C.T. Silva. “A Unified Projection Operator for Moving Least Squares Surfaces,” SCI Institute Technical Report, No. UUSCI-2007-006, University of Utah, 2007.


R. Palmer, G. Gopalakrishnan, R.M. Kirby. “Semantics Driven Dynamic Partial-Order Reduction of MPI-based Parallel Programs,” In Proceedings of Parallel and Distributed Systems: Testing and Debugging (PADTAD), London, UK, Note: Awarded Best Paper, 2007.


S. Pervez, G. Gopalakrishnan, R.M. Kirby, R. Palmer, R. Thakur, W. Gropp. “Practical Model Checking Method for Verifying Correctness of MPI Programs,” In Recent Advances in Parallel Virtual Machine and Message Passing Interface - Proceedings of EuroPVM-MPI 2007, Paris, France, Vol. 4757/2007, pp. 344--353. 2007.


Y. Yang, X. Chen, G. Gopalakrishnan, R.M. Kirby. “Distributed Dynamic Partial Order Reduction Based Verification of Threaded Software,” In Proceedings of Model Checking Software: 14th International SPIN Workshop, Berlin, Germany, Vol. 4595/2007, pp. 58--75. July, 2007.

2006


 C.W. Hamman, R.M. Kirby, J.C. Klewicki. “On the Lamb Vector Divergence as a Momentum Field Diagnostic Employed in Turbulent Channel Flow,” In Proceedings of the 59th Annual Meeting of the American Physical Society, Division of Fluid Dynamics, Tampa Bay, Fl, November, 2006.


I. Ionescu, J.E. Guilkey, M. Berzins, R.M. Kirby, J.A. Weiss. “Simulation of Soft Tissue Failure Using the Material Point Method,” In Journal of Biomechanical Engineering, Vol. 128, No. 6, pp. 917--924. 2006.


R.M. Kirby, C.R. Johnson, M. Berzins. “Involving Undergraduates in Computational Science and Engineering Research: Successes and Challenges,” In Proceedings of Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Lecture Notes in Computer Science, Vol. 3992, May 28-31, 2006.


R.M. Kirby, S.J. Sherwin. “Stabilisation of Spectral/hp Element Methods Through Spectral Vanishing Viscosity: Application to Fluid Mechanics Modelling,” In Computer Methods in Applied Mechanics and Engineering, Vol. 195, pp. 3128--3144. 2006.


R.M. Kirby, S.J. Sherwin. “Aliasing Errors Due to Quadratic Non-Linearities On Triangular Spectral/hp Element Discretisations,” In Journal of Engineering Mathematics, Vol. 56, No. 3, pp. 273--288. 2006.


R.M. Kirby, Z. Yosibash, G.E. Karniadakis. “Towards Stable Coupling Methods for High-Order Discretizations of Fluid-Structure Interaction: Algorithms and Observations,” In Journal of Computational Physics, Vol. 223, No. 2, pp. 489--518. 2006.


R.M. Kirby, S.J. Sherwin. “Aliasing Errors Due to Quadratic Non-Linearities On Triangular Spectral/hp Element Discretisations,” In Journal of Engineering Mathematics, Vol. 56, pp. 273--288. 2006.


H. Marmanis, C.W. Hamman, R.M. Kirby. “A One-Dimensional Model of the Navier-Stokes,” SCI Institute Technical Report, No. UUSCI-2006-012, University of Utah, 2006.


I. Melatti, R. Palmer, G. Sawaya, Y. Yang, R.M. Kirby, G. Gopalakrishnan. “Parallel and Distributed Model Checking in Eddy,” In Model Checking Software: Proceedings of the 13th International SPIN Workshop (SPIN 2006), Austria, Vol. 3925/2006, pp. 108--125. 2006.