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

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.



B. Nelson, R.M. Kirby. “Ray-Tracing Polymorphic Multi-Domain Spectral/hp Elements for Isosurface Rendering,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 12, No. 1, pp. 114--125. 2006.



R. Palmer, S. Barrus, Y. Yang, G. Gopalakrishnan, R.M. Kirby. “Gauss: A Framework for Verifying Scientific Computing Software,” In Electronic Notes on Theoretical Computer Science (ENTCS), Vol. 144, No. 3, pp. 95--106. February, 2006.



S. Pervez, G. Gopalakrishnan, R.M. Kirby, R. Thakur, W. Gropp. “Formal Verification of Programs that use MPI One-Sided Communications,” In Proceedings of EuroPVM-MPI 2006, Bonn, Germany, September 17-20, 2006.



A.R. Sanderson, R.M. Kirby, C.R. Johnson, L. Yang. “Advanced Reaction-Diffusion Models for Texture Synthesis,” In Journal of Graphics Tools, Vol. 11, No. 3, pp. 47--71. 2006.



S.J. Sherwin, R.M. Kirby, J. Peiro, R.L. Taylor, O.C. Zienkiewicz. “On 2D Elliptic Discontinuous Galerkin Methods,” In International Journal of Numerical Methods in Engineering, Vol. 65, No. 5, pp. 752--784. 2006.


2005


M. Berzins, R.M. Kirby, C.R. Johnson. “Integrating Teaching and Research in HPC: Experiences and Opportunities,” In Proceedings of the International Conference on Computational Science (ICCS) 2005, Atlanta, GA, pp. 36--43. 2005.



S.E. Geneser, S. Choe, R.M. Kirby, R.S. MacLeod. “Influence of Stochastic Organ Conductivity in 2D ECG Forward Modeling: A Stochastic Finite Element Study,” In Proceedings of The Joint Meeting of The 5th International Conference on Bioelectromagnetism and The 5th International Symposium on Noninvasive Functional Source Imaging within the Human Brain and Heart, pp. 5528--5531. 2005.



C.W. Hamman, R.M. Kirby, M. Berzins. “Parallelization and Scalability of a Spectral Element Solver,” SCI Institute Technical Report, No. UUSCI-2005-011, University of Utah, 2005.



I. Ionescu, J. Guilkey, M. Berzins, R.M. Kirby, J.A. Weiss. “Computational Simulation of Penetrating Trauma in Biological Soft Tissues Using the Material Point Method,” In Proceedings, Medicine Meets Virtual Reality, Vol. 13, Edited by James D Westwood et al., IOS Press, pp. 213--218. 2005.
ISBN: 1-58603-498-7



R.M. Kirby, D.F. Keefe, D.H. Laidlaw. “Painting and Visualization,” In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 873--891. 2005.
ISBN: 0-12-387582-X



R.M. Kirby, G.E. Karniadakis. “Selecting the Numerical Flux in Discontinuous Galerkin Methods for Diffusion Problems,” In Journal of Scientific Computing, Vol. 22/23, pp. 385--411. 2005.