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


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.


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.

D.H. Laidlaw, R.M. Kirby, C.D. Jackson, J.S. Davidson, T.S. Miller, M. Silva, W.H. Warren, M. Tarr. “Comparing 2D Vector Field Visualization Methods: A User Study,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 11, No. 1, pp. 59--70. 2005.

R. Palmer, S. Barrus, Y. Yang, G. Gopalakrishnan, R.M. Kirby. “Gauss: A Framework for Verifying Scientific Computing Software,” In Proceeding of the Software Model Checking Workshop, Edinburgh, Scotland, July, 2005.

F. Sachse, M. Cole, R.M. Kirby, X. Tricoche, C.R. Johnson. “Advanced Modeling and Visualization of Cardiothoracic Electrical Fields,” In Proceedings of 13th Medicine Meets Virtual Reality (MMVR13), 2005.

Z. Yosibash, R.M. Kirby. “Dynamic Response of Various Von-Karman Non-Linear Plate Models and their 3-D Counterparts,” In International Journal of Solids and Structures, Vol. 42, pp. 2517--2531. 2005.


M. Cole, F.B. Sachse, D.M. Weinstein, S.G. Parker, R.M. Kirby. “A Software Framework for Solving Problems of Bioelectricity Applying High-Order Finite Elements,” In Proceedings of the IEEE Engineering in Medicine and Biology Society 26th Annual International Conference, Vol. 1, pp. 821--824. 2004.

R.M. Kirby, Z. Yosibash. “Solution of Von-Karman Dynamic Non-linear Plate Equations Using a Pseudo-spectral Method,” In Comp. Meth. Appl. Mech. & Eng., Vol. 193, No. 6-8, pp. 575-599. 2004.

R.M. Kirby, G.E. Karniadakis. “Spectral Element and hp Methods,” In Encyclopedia of Computational Mechanics, Vol. 3, Ch. 3, Edited by E. Stein and R. de Borst and T.J.R. Hughes, John Wiley and Sons, NY, pp. 61--88. 2004.

R.M. Kirby, Z. Yosibash. “Solution of von-Karman Dynamic Non-Linear Plate Equations Using a Pseudo-Spectral Method,” In Computer Methods in Applied Mechanics and Engineering, Vol. 193, No. 6-8, pp. 575--599. 2004.

A.R. Sanderson, C.R. Johnson, R.M. Kirby. “Display of Vector Fields Using a Reaction Diffusion Model,” In Proceeding of IEEE Visualization 2004, pp. 115--122. 2004.