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

2004


 D. Xiu, G.E. Karniadakis. “Supersensitivity Due to Uncertain Boundary Conditions,” In International Journal for Numerical Methods in Engineering, Vol. 61, No. 12, pp. 2114--2138. 2004.
DOI: 10.1002/nme.1152

ABSTRACT

We study the viscous Burgers' equation subject to perturbations on the boundary conditions. Two kinds of perturbations are considered: deterministic and random. For deterministic perturbations, we show that small perturbations can result in O(1) changes in the location of the transition layer. For random perturbations, we solve the stochastic Burgers' equation using different approaches. First, we employ the Jacobi-polynomial-chaos, which is a subset of the generalized polynomial chaos for stochastic modeling. Converged numerical results are reported (up to seven significant digits), and we observe similar 'stochastic supersensitivity' for the mean location of the transition layer. Subsequently, we employ up to fourth-order perturbation expansions. We show that even with small random inputs, the resolution of the perturbation method is relatively poor due to the larger stochastic responses in the output. Two types of distributions are considered: uniform distribution and a 'truncated' Gaussian distribution with no tails. Various solution statistics, including the spatial evolution of probability density function at steady state, are studied.

Keywords: generalized polynomial chaos, stochastic Burgers' equation, supersensitivity, random boundary conditions


 D. Xiu, D.M. Tartakovsky. “A Two-scale Non-perturbative Approach to Uncertainty Analysis of Diffusion in Random Composites,” In SIAM Journal on Multiscale Modeling and Simulation, Vol. 2, No. 4, pp. 662--674. 2004.
DOI: 10.1137/03060268X

ABSTRACT

Many physical systems, such as natural porous media, are highly heterogeneous and characterized by parameters that are uncertain due to the lack of sufficient data. This uncertainty (randomness) occurs on a multiplicity of scales. We focus on random composites with the two dominant scales of uncertainty: large-scale uncertainty in the spatial arrangement of materials and small-scale uncertainty in the parameters within each material. We propose an approach that combines random domain decompositions and polynomial chaos expansions to account for the large and small scales of uncertainty, respectively. We present a general framework and use one-dimensional diffusion to demonstrate that our combined approach provides robust, nonperturbative approximations for the statistics of system states.

Keywords: random fields, moment equations, random domain decomposition, polynomial chaos


 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.


Y. Zhang, J.E. Guilkey, J.B. Hoying, J.A. Weiss. “Mechanical Simulation of Multicellular Structures with the Material Point Method,” In Proceedings of The 6th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering, pp. (6 pages). March, 2004.


K. Zhang, K. Damevski, V. Venkatachalapathy, S.G. Parker. “SCIRun2: A CCA Framework for High Performance Computing,” In Proceedings of The 9th International Workshop on High-Level Parallel Programming Models and Supportive Environments, April, 2004.

2003


 M. Alexa, J. Behr, D. Cohen-Or, S. Fleishman, C.T. Silva, D. Levin. “Computing and Rendering Point Set Surfaces,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 9, No. 1, pp. 3--15. 2003.
ISSN: 1077-2626


O. Alter, P.O. Brown, D. Botstein. “Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms,” In Proceedings of the National Academy of Sciences, Vol. 100, No. 6, Proceedings of the National Academy of Sciences, pp. 3351--3356. March, 2003.
DOI: 10.1073/pnas.0530258100


A. Baptista, T. Leen, Y. Zhang, A. Chawla, D. Maier, Wu-chang Feng, Wu-chi Feng, J. Walpole, C.T. Silva, J. Freire. “Environmental Observation and Forecasting Systems: Vision, Challenges and Successes of a Prototype,” In Proceedings of the International Society for Environmental Information Sciences Annual Conference (ISEIS '2003) on Systems Science and Information Technology for Environmental Applications, Regina, Sask, Canada, July, 2003.


M. Benedikt, C.Y. Chan, W. Fan, J. Freire, R. Rastogi. “Capturing Both Types and Constraints in Data Integration,” In Proceedings of the 2003 ACM SIGMOD International Conference on Management of Data, pp. 277--288. 2003.
ISBN: 1-58113-634-X


M. Berzins, A.G. Wilson. “Spatial Interaction Models and Fisher Information Theory A New Calibration Model,” In Environment and Planning, Vol. 35, pp. 2161--2176. 2003.


M. Bertram, X. Tricoche, H. Hagen. “Adaptive Smooth Scattered Data Approximation for Largescale Terrain Visualization,” In Proceedings of the Joint Eurographics-IEEE TCVG Symposium on Visualization: Data Visualization 2003, pp. 177--184. 2003.


P. Bohannon, J. Freire, J. Haritsa, M. Ramanath, P. Roy, J. Simeon. “Bridging the XML-Relational Divide with LegoDB: A Demonstration,” In International Conference on Data Engineering, pp. 759. 2003.
ISSN: 1063-6382


R. Borgo, R. Scopigno, P. Cignoni, V. Pascucci. “A Progressive Subdivision Paradigm (PSP),” In Proceedings of the Conference on Vision, Modeling and Visualization 2003 (VMV-03), Note: UCRL-PROC-208557, Edited by T. Ertl and B. Girod and G. Greiner and H. Niemann and H.-P. Seidel and E. Steinbach and R. Westermann, Aka GmbH, Berlin, Germany pp. 441--450. Nov, 2003.


P.-T. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci. “A Multi-resolution Data Structure for Two-dimensional Morse Functions,” In Proceedings of IEEE Conference on Visualization (VIS-03), Note: UCRL-JC-154014, pp. 139--146. October, 2003.


J. Cates, R.T. Whitaker. “Interactive Medical Image Segmentation Using the Insight Toolkit,” In Proceedings of The Radiological Society of North America Annual Meeting 2003, November, 2003.


D. Cohen-Or, Y.L. Chrysanthou, C.T. Silva, F. Durand. “A Survey of Visibility for Walkthrough Applications,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 9, No. 3, IEEE Computer Society, Los Alamitos, CA, USA pp. 412--431. 2003.
ISSN: 1077-2626


M. Cole, S.G. Parker. “Dynamic Compilation of C++ Template Code,” In Scientific Programming, Vol. 11, IOS Press, pp. 321--327. 2003.


K. Cole-McLaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci. “Loops in Reeb Graphs of 2-Manifolds,” In Proceedings of the 19th ACM Symposium on Computational Geometry, Note: UCRL-JC-151933, pp. 344--350. June, 2003.


K. Cole-McLaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci. “Loops in Reeb Graphs of 2-Manifolds,” In Proceedings of the 19th ACM Symposium on Computational Geometry, Note: UCRL-JC-151933, pp. 344--350. June, 2003.


A. Corlan, R.S. MacLeod, L.D. Ambroggi. “Low Variability of Autocorrelation Maps with Intrathoracic Heart Position,” In Int. J. Bioelectromag., Vol. 5, No. 1, pp. 139--140. 2003.