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


C.E. Goodyer, M. Berzins. “Adaptive Timestepping for Elastohydrodynamic Lubrication Solvers,” In SIAM Journal on Scientific Computing, Vol. 28, No. 2, SIAM, pp. 626-650. 2006.
DOI: 10.1137/050622092

D. Hart, C.E. Goodyer, M. Berzins, P.K. Jimack, L. Scales. “Adjoint Error Estimation and Spatial Adaptivity for EHL-Like Models,” In IUTAM Symposium on Elastohydrodynamics and Micro-elastohydrodynamics, Springer, pp. 47--58. 2006.
DOI: 10.1007/1-4020-4533-6_3

I. Ionescu, J.E. Guilkey, M. Berzins, R.M. Kirby, J.A. Weiss. “Simulation of Soft Tissue Failure Using the Material Point Method,” In Journal of Biomechanical Engineering, Vol. 128, No. 6, pp. 917--924. 2006.

R.M. Kirby, C.R. Johnson, M. Berzins. “Involving Undergraduates in Computational Science and Engineering Research: Successes and Challenges,” In Proceedings of Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Lecture Notes in Computer Science, Vol. 3992, May 28-31, 2006.

H. Lu, M. Berzins, C.E. Goodyer, P.K. Jimack, M. Walkley. “Adaptive High-order Finite Element Solution of Transient Elastohydrodynamic Lubrication Problems,” In Proc. IMechE Part J: J. Engrg. Tribology, Vol. 220, pp. 215--225. 2006.

H. Lu, M. Berzins, P.K. Jimack. “Application of the Adaptive Discontinuous Galerkin Method to Problems in Elastohydrodynamic Lubrication,” In Innovation in Engineering Computational Technology, Edited by B.H.V. Topping and G. Montero and R. Montenegro, Saxe-Coburg Publications, Stirling, pp. 169--191. 2006.


M. Berzins, R.M. Kirby, C.R. Johnson. “Integrating Teaching and Research in HPC: Experiences and Opportunities,” In Proceedings of the International Conference on Computational Science (ICCS) 2005, Atlanta, GA, pp. 36--43. 2005.

M. Berzins. “Preserving Positivity for Hyperbolic PDEs Using Variable-Order Finite Elements with Bounded Polynomials,” In Applied Numerical Mathematics, Vol. 52, No. 2-3, pp. 197--217. February, 2005.

C.E. Goodyer, M. Berzins. “Parallelisation and Scalability Issues in a Multilevel EHL Solver,” Report, No. 2005.05, School of Computing, University of Leeds, 2005.

C.W. Hamman, R.M. Kirby, M. Berzins. “Parallelization and Scalability of a Spectral Element Solver,” SCI Institute Technical Report, No. UUSCI-2005-011, University of Utah, 2005.

D.E. Hart, C.E. Goodyer, M. Berzins, P.K. Jimack, L.E. Scales. “Adjoint Error Estimation for EHL-Like Models,” In Int. J. Numer. Meth. Fluids, Vol. 47, No. 10-11, pp. 1069--1075. 2005.

I. Ionescu, J. Guilkey, M. Berzins, R.M. Kirby, J.A. Weiss. “Computational Simulation of Penetrating Trauma in Biological Soft Tissues Using the Material Point Method,” In Proceedings, Medicine Meets Virtual Reality, Vol. 13, Edited by James D Westwood et al., IOS Press, pp. 213--218. 2005.
ISBN: 1-58603-498-7

H. Lu, M. Berzins, C.E. Goodyer, P.K. Jimack. “High Order Discontinuous Galerkin Method for EHL Line Contact Problems,” In Communication in Numerical Methods in Engineering, Vol. 21, No. 11, pp. 643--650. 2005.


M. Berzins. “Variable Order Finite Elements and Positivity Preservation for Hyperbolic PDEs,” In Applied Numerical Mathematics, Vol. 48, No. 3-4, pp. 253--439. March, 2004.

C.E. Goodyer, R. Fairlie, D.E. Hart, M. Berzins, L.E. Scales. “Calculation of Friction in Steady-State and Transient EHL Simulations Transient Processes in Tribology,” In Transient Processes in Tribology: Proceeding of the 31st Leeds-Lyon Symposium on Tribology, Edited by A.A. Lubrecht and G. Dalmaz, Elsevier, pp. 579--590. 2004.


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.

R. Fairlie, C.E. Goodyer, M. Berzins, L.E. Scales. “Numerical Modelling of Thermal Effects in Elastohydrodynamic Lubrication Solvers,” In Tribological Research and Design for Engineering Systems, Proceedings of the 29th Leeds-Lyon Symposium on Tribology, Edited by D. Dowson et al., Elsevier, pp. 675--683. 2003.

C.E. Goodyer, M. Berzins, P.K. Jimack, L.E. Scales. “Grid-Based Numerical Optimisation in a Problem Solving Environment,” In Proceedings of Second UK E-Science All-Hands Meeting, Nottingham, UK, Edited by S.J. Cox, pp. 854--861. 2003.
ISBN: 1-904425-11-9

M.E. Hubbard, M. Berzins. “A Positivity Preserving Finite Element Method for Hyperbolic Partial Differential Equations,” In Computational Fluid Dynamics 2002, Edited by S. Armfield and P. Morgan and K. Srinivas, Springer-Verlag, pp. 205--210. 2003.

C.H. Leung, M. Berzins. “A Computational Model for Organism Growth based on Surface Mesh Generation,” In Journal of Computational Physics, Vol. 188, No. 1, pp. 75--99. 2003.