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, 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.


L.J.K. Durbeck, M. Berzins. “Unstructured Tetrahedral Mesh Quality Analysis Using an Interactive Haptic and Visual Interface,” In Comp. & Vis. Sci., Vol. 5, No. 3, Springer-Verlag, pp. 179--192. 2002.

C.E. Goodyer, M. Berzins. “Eclipse and Ellipse: PSEs for EHL Solutions using IRIS Explorer and SCIRun,” In Proceedings of the International Conference on Computational Science (ICCS) 2002, Amsterdam, The Netherlands, Vol. 2329, Edited by P.M.A. Sloot and C.J.K. Tan and J.J. Dongarra and A.G. Hoekstra, Springer Berlin, pp. 523--532. 2002.

C.E. Goodyer, J. Wood, M. Berzins. “A Parallel Grid Based PSE for EHL Problems,” In Applied Parallel Computing. Advanced Scientific Computing: 6th International Conference, PARA 2002, Proceedings, Espoo, Finland, Vol. 2367, Edited by J. Fagerholm and J. Haatja and J. Jarvinen and M. Lyly and P. Raback and V. Savolainen, Springer Lecture Notes in Computer Science, pp. 521--530. 2002.

P.K. Jimack, R. Mahmood, M.A. Walkley, M. Berzins. “A Multilevel Approach for Obtaining Locally Optimal Finite Element Meshes,” In Adv. Eng. Soft., Vol. 33, pp. 403--415. 2002.

I. Lagzi, A.S. Tomlin, T. Turanyi, L. Haszpra, R. Meszaros, M. Berzins. “Modelling Tropospheric Ozone Formation in Hungary Using an Adaptive Gridding Method,” In Proceedings from the EUROTRAC-2 Symposium 2002, Edited by Garmisch-Partenkirchenand P.M. Midgley and M. Reuters, 2002.

I. Lagzi, A.S. Tomlin, T. Turanyi, L. Haszpra, R. Meszaros, M. Berzins. “Modeling Photochemical Air Pollution in Hungary Using an Adaptive Grid Model,” In Air Pollution modeling and Simulation - Proc.2nd International Conference on Air Pollution Modeling and Simulation (APMS'2001), pp. 264--273. april, 2002.
ISBN: 3540425152, 9783540425151