Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Large scale visualization on the Powerwall.
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

2000


O. Alter, P.O. Brown, D. Botstein. “Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling,” In Proceedings of the National Academy of Sciences, Vol. 97, No. 18, Proceedings of the National Academy of Sciences, pp. 10101--10106. August, 2000.
DOI: 10.1073/pnas.97.18.10101



Th. Apel, M. Berzins, P.K. Jimack, G. Kunert, A. Plaks, I. Tsukerman, M. Walkley. “Mesh Shape and Anistropic Elements: Theory and Practice,” In The Mathematics of Finite Elements and Applications X, Edited by J.R. Whiteman, Elsevier, pp. 367--376. 2000.



M. Berzins, L. Durbeck, P.K. Jimack, M. Walkley. “Mesh Quality and Moving and Meshes for 2D and 3D Unstructured Mesh Solvers,” In Von Karman Institute for Fluid Mechanics 31st Lecture Series on Computational Fluid Mechanics, Edited by N.P. Weatherill and H. Deconinck, Von Karman Institute, March, 2000.
ISSN: 0377-8312



M. Berzins. “An Introduction to Mesh Quality,” In Lectures notes for 31st Lecture Series on Computational Fluid Mechanics, Rhode st Genessee, Brussels, Belgium, Edited by N.P. Weatherill and H. Deconink, Von Karman Institute for Fluid Mechanics, pp. 21 pages. March, 2000.
ISSN: 0377-8312



M. Berzins. “Solution-Based Mesh Quality Indicators for Triangular and Tetrahedral Meshes,” In International Journal of Computational Geometry and Applications, Vol. 10, No. 3, pp. 333-346. June, 2000.



M. Berzins. “A New Metric for Dynamic Load Balancing,” In Applied Mathematical Modelling, Vol. 25, Note: Special issue on dynamic load balancing, pp. 141--151. 2000.



M. Berzins. “A Data-Bounded Quadratic Interpolant on Triangles and Tetrahedra,” In SIAM Journal on Scientific Computing, Vol. 22, No. 1, pp. 177--197. 2000.



R. Bramley, C.R. Johnson, D. Gannon, J. Reynders, T. Hewett, J. Rice. “Workshop on Scientific Knowledge, Information and Computing, SIDEKIC 98,” In Enabling Technologies for Computational Science, Springer, pp. 19-32. 2000.
DOI: 10.1007/978-1-4615-4541-5_2

ABSTRACT

On 4-5 December 1998 researchers from several universities, national laboratories, software companies, and government funding agencies met at Santa Fe, NM for the 1998 Scientific Integrated Development Environments for Knowledge, Information, and Computing Workshop. The purpose of this meeting was to summarize the state-of-the-art in the area of problem-solving environments (PSEs) for scientific and engineering computation, and to map out directions for future research in the area. This report presents some of the results from the meeting and recommends promising areas for further work. This report begins with a justification of the need for PSEs, which are also commonly called computational workbenches. Next a listing of characteristics that many PSEs share is presented, followed by a small sample listing of current systems. Design goals and future directions, with an emphasis on research issues, are outlined, followed by summary findings and conclusions.



J.D. Brederson, M. Ikits, C.R. Johnson, C.D. Hansen, J.M. Hollerbach. “The Visual Haptic Workbench,” In Proceedings of the Fifth PHANToM Users Group Workshop, pp. 46--49. October, 2000.



J.G. Csernansky, L. Wang, S. Joshi, J.P. Miller, M. Gado, D. Kido, D. McKeel, J.C. Morris, M. Miller. “Early DAT is Distinguished from Aging by High-Dimensional Mapping of the Hippocampus. Dementia of the Alzheimer Type,” In Neurology, Vol. 55, No. 11, pp. 1636--1643. December 12, 2000.



A. Deshmukh, C.C. Douglas, M. Ball, R.E. Ewing, C.R. Johnson, C. Kesselman, C. Lee. “Dynamic Data Driven Application Systems: Creating a dynamic and symbiotic coupling of application/simulations with measurements/experiments,” Note: 28 pages, Edited by W. Powell, R. Sharpley, National Science Foundation, 2000.



B.S. Duerstock, C.L. Bajaj, V. Pascucci, D.R. Schikore, K. Lin, R.B. Borgens. “Advances in Three-Dimensional Reconstruction of the Experimental Spinal Cord Injury,” In Computerized Medical Imaging and Graphics, Vol. 24, No. 6, pp. 389--406. 2000.



A. Forsberg, R.M. Kirby, D.H. Laidlaw, G.E. Karniadakis, A. van Dam, J. Elion. “Immersive Virtual Reality for Visualizing Flow Through an Artery,” In Proceedings of IEEE Visualization 2000, Salt Lake City, UT, pp. 457--460. October, 2000.



J.D. de St. Germain, J. McCorquodale, S.G. Parker, C.R. Johnson. “Uintah: A Massively Parallel Problem Solving Environment,” In Ninth IEEE International Symposium on High Performance and Distributed Computing, IEEE, Piscataway, NJ, pp. 33--41. Nov, 2000.



S. Ghorai, A.S. Tomlin, M. Berzins. “Resolution of pollutant concentrations in the boundary layer using a fully 3-D adaptive gridding technique,” In Atmospheric Environment, Vol. 34, No. 18, pp. 2851-2863. 2000.



C.E. Goodyer, R. Fairlie, M. Berzins, L.E. Scales. “An In-depth Investigation of the Multigrid Approach to Steady and Transient EHL Problems,” In Thinning Films and Tribological InterfacesProceedings of the 26th Leeds-Lyon Symposium on Tribology, Tribology Series, Vol. 38, Edited by D. Dowson, M. Priest, C.M. Taylor, P. Ehret, T.H.C. Childs, G. Dalmaz, A.A. Lubrecht, Y. Berthier, L. Flamand and J.-M. Georges, Elsevier, pp. 95--102. 2000.
ISSN: 0167-8922

ABSTRACT

Multigrid methods have proved robust and highly desirable in terms of the iteration speed in solving elastohydrodynamic lubrication (EHL) problems. Lubrecht, Venner and Ehret, amongst others, have shown that multigrid can be successfully used to obtain converged solutions for steady problems. steady problems.

A detailed study reinforces these results but also shows, in some cases, that while multigrid techniques give initial rapid convergence, the residuals - having dropped to a low level - may reach a stalling point, mainly due to the cavitation region. The study will explain this behaviour in terms of the iterative scheme and show how, if this happens, the errors in the fine grid solution can be reduced further. Example results of both steady and transient EHL problems (including a thermal viscoelastic case) are shown with further developments into adaptive meshes considered.



C.E. Goodyera, R. Fairliea, M. Berzinsa, L.E. Scales. “An in-depth investigation of the multigrid approach to steady and transient EHL problems,” In 26th Leeds-Lyon Symposium on Tribology, Vol. 38, Elsevier, pp. 95-102. 2000.

ABSTRACT

Multigrid methods have proved robust and highly desirable in terms of the iteration speed in solving elastohydrodynamic lubrication (EHL) problems. Lubrecht, Venner and Ehret, amongst others, have shown that multigrid can be successfully used to obtain converged solutions for steady problems, steady problems. A detailed study reinforces these results but also shows, in some cases, that while multigrid techniques give initial rapid convergence, the residuals - having dropped to a low level - may reach a stalling point, mainly due to the cavitation region. The study will explain this behaviour in terms of the iterative scheme and show how, if this happens, the errors in the fine grid solution can be reduced further. Example results of both steady and transient EHL problems (including a thermal viscoelastic case) are shown with further developments into adaptive meshes considered. © 2000 Elsevier Science B.V. All rights reserved.



R.E. Hogan, K.E. Mark, L. Wang, S. Joshi, M.I. Miller, R. Bucholz. “Mesial Temporal Sclerosis and Temporal Lobe Epilepsy: MR Imaging Deformation-Based Segmentation of the Hippocampus in Five Patients,” In Radiology, Vol. 216, No. 1, pp. 291--297. July, 2000.



R.E. Hogan, K.E. Mark, I. Choudhuri, L. Wang, S. Joshi, M.I. Miller, R. Bucholz. “Magnetic Resonance Imaging Deformation-Based Segmentation of the Hippocampus in Patients with Mesial Temporal Sclerosis and Temporal Lobe Epilepsy,” In J Digit Imaging, Vol. 13, No. 2 (Suppl. 1), pp. 217--218. May, 2000.



R.E. Hogan, R.D. Bucholz, I. Choudhuri, K.E. Mark, C.S. Butler, S. Joshi. “Shape-analysis of hippocampal surface structure in patients with unilateral mesial temporal sclerosis,” In Journal of Digital Imaging, Vol. 13, No. 2, pp. 39--42. 2000.