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


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.

P.A. Sleigh, M. Berzins, P.H. Gaskell, N.G. Wright. “An Unstructured Finite Volume Algorithm for Predicting Flow in Rivers and Estuaries,” In Computers and Fluids, Vol. 27, No. 4, pp. 479--508. 1998.

N. Touheed, P. Selwood, P.K. Jimack, M. Berzins. “Parallel Dynamic Load-Balancing for the Solution of Transient CFD Problems Using Adaptive Tetrahedral Meshes,” In Parallel Computational Fluid Dynamics - Recent Developments and Advances Using Parallel Computers, Edited by D.R. Emerson and A. Ecer and J. Periaux and N. Satufoka and P. Fox, Elsevier Science, pp. 81--88. 1998.


I. Ahmad, M. Berzins. “An Algorithm for ODEs from Atmospheric Dispersion Problems,” In Applied Numerical Mathematics, Vol. 25, pp. 137--149. 1997.

M. Berzins, S.V. Pennington, P.R. Pratt, J.M. Ware. “SPRINT2D Software for Convection Dominated PDEs,” In Modern Software Tools in Scientific Computing, Edited by E. Arge and A.M. Bruaset and H.P. Langtangen, Birkhauser Press, 1997.


SPRINT2D is a set of software tools for solving time-dependent partial differential equations in two space variables. The software uses unstructured triangular meshes and adaptive error control in both space and time. This chapter describes the software and shows how the adaptive techniques may be used to increase the reliability of the solution procedure for a challenging combustion problem. The recent construction of a problem solving environment (PSE) has partially automated the use of SPRINT2D. This PSE consists of tools such as a visual domain specification tool, which helps ease the input of complex geometries, and a visual problem specification tool. After describing these components an evaluation will be made of SPRINT2D and its associated PSE.

M. Berzins, P.J. Capon, P.K. Jimack. “On Spatial Adaptivity and Interpolation when Using the Method of Lines,” In Applied Numerical Mathematics: Transactions of IMACS, Vol. 26, No. 1--2, pp. 117--133. 1997.

D.J. Creasey, D.E. Heard, M. Pilling, B.J. Whitaker, M. Berzins, R. Fairlie. “Visualisation of a Supersonic Free-Jet Expansion Using Laser-Induced Fluorescence Spectroscopy: Application to the Measurement of Rate Constants at Ultralow Temperatures,” In Applied Physics B: Lasers and Optics, Vol. 65, pp. 375--391. 1997.

P. Selwood, N.A. Verhoeven, J.M. Nash, M. Berzins, N.P. Weatherill, P.M. Dew, K. Morgan. “Parallel Mesh Generation and Adaptivity : Partitioning and Analysis,” In Parallel C.F.D.- Proc. of Parallel CFD 96 Conference, Capri, Italy, Edited by A.Ecer and J.Periaux and N.Satufoka and P.Schiano, Elesvier Science BV, May, 1997.
ISBN: 0-444 823271

P. Selwood, M. Berzins, P.M. Dew. “3D Parallel Mesh Adaptivity: Data Structures and Algorithms,” In Proc. of SIAM Conf. on Parallel Processing for Scientific Computing, Minneapolis, MN, USA, pp. (CD-Rom). March, 1997.
ISBN: 0-89871-395-1

W. Speares, M. Berzins. “A 3D Unstructured Mesh Adaptation Algorithm for Time Dependent Shock Dominated Problems,” In Int. Jour Numerical Methods in Fluids, Vol. 25, pp. 81--104. 1997.

A. Tomlin, M. Berzins, J.M. Ware, J. Smith, M. Pilling. “On the use of adaptive gridding methods for modelling chemical transport from multi-scale sources,” In Atmospheric Env., Vol. 31, No. 18, pp. 2945--2959. 1997.


M. Berzins, T.H.C. Childs, G.R. Ryder. “The Selective Laser Sintering of Polycarbonate,” In CIRP Annals, Vol. 45, No. 1, pp. 187--190. 1996.
ISSN: 0007-8506
DOI: 10.1016/S0007-8506(07)63044-3

M. Berzins, J.M. Ware. “Solving Convection and Convection Reaction Problems Using the M.O.L.,” In Applied Numerical Mathematics, Vol. 20, pp. 83--99. 1996.

E. Nurgat, M. Berzins. “A new relaxation scheme for solving EHL Problems,” In 23rd Leeds-Lyon Symposium on Tribology, Tribology Series, Vol. 32, Edited by D.Dowson et al., Elsevier, pp. 125a-134. 1996.
ISBN: 0444828095


A New Relaxation Scheme (NRS) is presented in this paper to solve Elasto Hydrodynamic Lubrication (EHL) point contact problems. The solutions obtained are compared with those obtained by Ehret [6] who employed the Distributive Relaxation Scheme (DRS) of Venner [2]. Results obtained using the two schemes are in close agreement which is very encouraging although it is too early to draw any conclusions. The new relaxation scheme thus provides an alternative approach to the distributive relaxation scheme.