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


 S. Means, A.J. Smith, J. Shepherd, J. Shadid, J. Fowler, R. Wojcikiewicz, T. Mazel, G.D. Smith, B.S. Wilson. “Reaction Diffusion Modeling of Calcium Dynamics with Realistic ER Geometry,” In Biophys. J., Vol. 91, pp. 537--557. March, 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.


P. Miller, P.-T. Bremer, W. Cabot, A. Cook, D. Laney, A. Mascarenhas, V. Pascucci. “Application of Morse Theory to Analysis of Rayleigh-Taylor Topology,” In 10th International Workshop on the Physics of Compressible Turbulent Mixing, 2006.


C.R. Johnson, R. Moorhead, T. Munzner, H. Pfister, P. Rheingans, T. Yoo. “NIH/NSF Visualization Research Challenges Report Summary,” Note: NIH/NSF, pp. 66-73. 2006.


T. Munzner, C.R. Johnson, R. Moorhead, H. Pfister, P. Rheingans, T.S. Yoo. “NIH-NSF Visualization Research Challenges Report Summary,” Note: NIH-NSF, pp. 20--24. March/April, 2006.


S. Nagarajan, O. Portniaguine, D. Hwang, C.R. Johnson, K. Sekihara. “Controlled Support MEG Imaging,” In NeuroImage, Vol. 15;33, No. 3, pp. 878--885. 2006.


V. Natarajan, Y. Wang, P.-T. Bremer, V. Pascucci, B. Hamann. “Segmenting Molecular Surfaces,” In Computer Aided Geometric Design, Special Issue on Applications of Geometric Modeling in the Life Sciences, Vol. 23, No. 6, Note: (To appear), pp. 495--509. 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.


O. Nemitz, M. Rumpf, T. Tasdizen, R.T. Whitaker. “Anisotropic Curvature Motion for Structure Enhancing Smoothing of 3D MR Angiography Data,” In Journal of Mathematical Imaging and Vision, Vol. 27, No. 3, pp. 217--229. April, 2006.


J.T. Oden, J. Fish, C.R. Johnson, A. Laub, D. Srolovitz, T. Belytschko, T.J.R. Hughes, D. Keys, L. Petzold, S. Yip. “NSF Blue Ribbon Panel Report on Simulation Based Engineering Science,” Note: NSF Report, 2006.

ABSTRACT

Purpose: To explore the emerging discipline of Simulation Simulation-Based Engineering Science, its major components, its importance to the nation, the challenges and barriers to its advancement, and to recommend to the NSF and the broader community concerned with science and engineering in the United States, steps that could be taken to advance development in this discipline.


 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.G. Parker. “A Component-Based Architecture for Parallel Multi-physics PDE Simulation,” In Future Generation Computer Systems (FGCS), Vol. 22, No. 1-2, Elsevier, pp. 204--216. 2006.


S.G. Parker, K. Zhang, K. Damevski, C.R. Johnson. “Integrating Component-Based Scientific Computing Software,” In Parallel Processing for Scientific Computing, Edited by M.A. Heroux and P. Raghavan and H.D. Simon, SIAM Press, pp. 271--288. 2006.
ISBN: 0-89871-619-5


S.G. Parker, J. Guilkey, T. Harman. “A Component-based Parallel Infrastructure for the Simulation of Fluid Structure Interaction,” In Engineering with Computers, Vol. 22, No. 3-4, Springer London, pp. 277--292. 2006.


S.G. Parker. “Composition of Components in Multiphysics Applications,” In Proceedings of the 12th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, CA, Note: Presented at the Minisymposium on Parallel Dynamic Data Management Infrastructures for Scientific & Engineering Applications, 2006.


S.G. Parker. “Component-Based Multi-Physics Simulations of Fires and Explosions,” In Proceedings of the 12th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, CA, Note: Presented at the Minisymposium on Parallel Dynamic Data Management Infrastructures for Scientific & Engineering Applications, 2006.


S.G. Parker. “Why do Software Engineering Methods Fail for HPC?,” In Presented at Architectures and Algorithms for Petascale Computing, Schloss Dagstuhl, Germany, Vol. Seminar 06071, February, 2006.


S. Parker, K. Zhang, C. Damevski, C.R. Johnson. “Integrating Component-Based Scientific Computing Software,” In Parallel Processing for Scientific Computing, Edited by M.A. Heroux and P. Raghavan and H.D. Simon, SIAM, pp. 271--288. January, 2006.


V. Pascucci. “Topology Diagrams of Scalar Fields in Scientific Visualisation,” In Topological Data Structures for Surfaces, Note: UCRL-BOOK-200013, Edited by Sanjay Rana and Jo Wood, Wiley-Blackwell, pp. 121--129. May, 2006.
DOI: 10.1002/0470020288.ch8


V. Pegoraro, S.G. Parker. “Physically-Based Realistic Fire Rendering,” In Proceedings of the 2006 Eurographics Workshop on Natural Phenomena, pp. 51--59. 2006.