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

2005


 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.

2004


 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.


F. Stenger, T. Cook, R.M. Kirby. “Sinc Solution of Biharmonic Problems,” In Canadian Applied Mathematics Quarterly, Vol. 12, No. 3, pp. 391--413. 2004.


Z. Yosibash, R.M. Kirby, D. Gottlieb. “Collocation Methods for the Solution of Von-Karman Dynamic Non-Linear Plate Systems,” In Journal of Computational Physics, Vol. 200, No. 2, pp. 432--461. 2004.

2003


 R.M. Kirby, G.E. Karniadakis. “De-Aliasing on Non-Uniform Grids: Algorithms and Applications,” In J. Comp. Phys., Vol. 191, No. 1, pp. 267--282. October, 2003.


G.E. Karniadakis, R.M. Kirby. “Parallel Scientific Computing in C++ and MPI: A Seamless Approach to Parallel Algorithms and their Implementation,” Cambridge University Press, pp. 628 pages. June, 2003.
ISBN: 0521520800


R.M. Kirby, G.E. Karniadakis. “De-Aliasing on Non-Uniform Grids: Algorithms and Applications,” In Journal of Computational Physics, Vol. 191, pp. 249--264. 2003.

2002


 R.M. Kirby, G.E. Karniadakis. “Coarse Resolution Turbulence Simulations With Spectral Vanishing Viscosity - Large-Eddy Simulations (SVV-LES),” In J. Fluids Eng., Vol. 124, No. 4, pp. 886-891. 2002.


R.M. Kirby, G.E. Karniadakis. “Coarse Resolution Turbulence Simulations With Spectral Vanishing Viscosity - Large-Eddy Simulations (SVV-LES),” In Journal of Fluids Engineering, Vol. 124, No. 4, pp. 886--891. 2002.

2001


 R.M. Kirby, G.E. Karniadakis, O. Mikulchenko, K. Mayaram. “Integrated Simulation for MEMS: Coupling Flow-Structure-Thermal-Electrical Domains,” In The MEMS Handbook, Edited by M. Gad-el-Hak, Informa UK Limited, 2001.


R.M. Kirby, G.E. Karniadakis. “Under-Resolution and Diagnostics in Spectral Simulations of Complex-Geometry Flows,” In Turbulent Flow Computation, Edited by D. Drikakis and B. Geurts, Springer, pp. 1--42. 2001.


R.M. Kirby, G.E. Karniadakis, O. Mikulchenko, K. Mayaram. “An Integrated Simulator for Coupled Domain Problems in MEMS,” In Journal of Microelectromechanical Systems, Vol. 10, No. 3, pp. 379--399. 2001.