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


A.S. Tomlin, S. Ghorai, G. Hart, M. Berzins. “3-D Adaptive Unstructured Meshes in Air Pollution Modelling,” In Environmental Modeling and Software, Vol. 15, No. 4, pp. 681--692. 2000.

N. Touheed, P. Selwood, P.K. Jimack, M. Berzins. “A Comparison of Some Dynamic Load Balancing Algorithms for a Parallel Adaptive Flow Solver,” In Parallel Computing, Vol. 26, No. 12, pp. 1535--1554. 2000.


M. Berzins, L.J.K. Durbeck. “Unstructured Mesh Methods Applied to Hyperbolic PDEs with Source Terms: Error Estimates and Mesh Quality,” In Godunov Methods: Theory and Applications Conference and Short Course, Oxford. numeritek Ltd.URL, October, 1999.

M. Berzins, J. Nash, P. Selwood. “Parallel Solution of Reacting Flow Problems using Unstructured Tetrahedral Meshes,” In Proceedings of 9th SIAM Parallel Processing for Scientific Computing, Philadelphia, PA, 1999.
ISBN: 0-89871-435-4

M. Berzins. “A Solution Based H1 Norm Triangular Mesh Quality Indicator,” In Grid Generation and Adaptive Algorithms, Edited by Marshal W. Bern, Joseph E. Flaherty, Mitchell Luskin, Springer, pp. 77-88. 1999.


The issue of mesh quality measures for triangular (and tetrahedral) meshes is considered. A new mesh quality measure is based both on geometrical and solution information and is derived by considering the error in the H 1 norm when linear triangular elements are used to approximate a quadratic function. The new measure is then compared with the recent mesh quality measure based on the L 2 norm. Simple examples are used to show that the choice of norm is critical in deciding what is a good triangulation

M. Berzins. “Mesh Quality - Geometry, Error Estimates or Both?,” In Engineering and Computers, Vol. 15, pp. 236--247. 1999.

T.H.C. Childs, M. Berzins, G.R. Ryder, A. Towtoni. “Selective Laser Sintering of an Amorphous Polymer-Simulations and Experiments,” In Proceedings of the Institution of Mechanical Engineers Part B: Journal of Engineering Manufacture, Vol. 213, No. B4, pp. 333--349. 1999.

J. Nash, P. Dew, M. Berzins. “Using SADTs to Support Irregular Computational Problems,” In International Symposium on Parallel Architectures, Algorithms, and Networks, IEEE Computer Society, Los Alamitos, CA, USA pp. 338--344. 1999.
ISSN: 1087-4089
DOI: 10.1109/ISPAN.1999.778961

J. Nash, M. Berzins, P. Selwood. “A Structured SADT Approach to the Support of a Parallel Adaptive 3D CFD Code,” In Euro-Par'99 Parallel Processing, Springer Nature, pp. 651--658. 1999.
DOI: 10.1007/3-540-48311-x_91

E.M. Nurgat, M. Berzins, L.E. Scales. “Solving EHL Problems Using Iterative Multigrid and Homotopy Methods,” In ASME Journal of Tribology, Vol. 121, pp. 28--34. January, 1999.

P. Selwood, M. Berzins. “Portable Parallel Adaptation of Unstructured Tetrahedral Meshes,” In Concurrency, Vol. 11, No. 13, pp. 1--22. 1999.

A. Tomlin, S. Ghorai, G. Hart, M. Berzins. “3D adaptive unstructured meshes for air pollution modelling,” In Environmental Management and Health, Vol. 10, No. 4, pp. 267-275. 1999.
DOI: 10.1108/09566169910276238

M. Walkley, M. Berzins. “A finite element model for the one-dimensional extended Boussinesq equations,” In International Journal for Numerical Methods in Fluids, Vol. 29, pp. 143--157. 1999.


M. Berzins, P.J. Capon, P.K. Jimack. “On Spatial Adaptivity and Interpolation When Using the Method of Lines,” In Applied Numerical Mathematics, Vol. 26, pp. 117--134. 1998.

M. Berzins. “A Solution-Based Triangular and Tetrahedral Mesh Quality Indicator,” In SIAM Journal on Scientific Computing, Vol. 19, pp. 2051--2060. 1998.

M. Berzins, R. Fairlie, S.V. Pennington, J.M. Ware, L.E. Scales. “SPRINT2D: Adaptive Software for PDEs,” In ACM Transactions on Mathematical Software, Vol. 24, No. 4, pp. 475--499. December, 1998.

G. Hart, A. Tomlin, J. Smith, M. Berzins. “Multi-scale Atmospheric Dispersion Modelling by the Use of Adaptive Grid Techniques,” In Environmental Monitoring and Assessment, Vol. 52, pp. 225--228. 1998.

C.R. Johnson, M. Berzins, L. Zhukov, R. Coffey. “SCIRun: Applications to Atmospheric Diffusion Using Unstructured Meshes,” In Numerical Methods for Fluid Dynamics VI, Edited by M.J. Baines, Oxford University Press, pp. 111--122. 1998.

J. Pan, C.G.W. Sheppard, A. Tindall, M. Berzins, S.V. Pennington, J.M. Ware. “End Gas Inhomogeneity, Autoignition and Knock,” SAE meeting technical report, San Fransisco, CA, No. 982616, SAE, 1998.

P.Selwood, M.Berzins, J. Nash, P.M. Dew. “Portable Parallel Adaptation of Unstructured Tetrahedral Meshes,” In Proceedings of Irregular 98 Conference, Lecture Notes in Computer Science (LNCS), Vol. 1457, Edited by A. Ferreira et al., Springer, pp. 56--67. 1998.