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

1998


 S.G. Parker, P. Shirley, Y. Livnat, C.D. Hansen, P.-P. Sloan. “Interactive Ray Tracing for Isosurface Extraction,” In IEEE Visualization '98, pp. 233--238. October, 1998.


S.G. Parker, P. Shirley, B. Smits. “Single Sample Soft Shadows,” School of Computing Technical Report, No. UUCS-98-019, University of Utah, October, 1998.


S.G. Parker, M. Miller, C.D. Hansen, C.R. Johnson, P.-P. Sloan. “An Integrated Problem Solving Environment: The SCIRun Computational Steering System,” In 31st Hawaii International Conference on System Sciences (HICSS-31), Vol. VII, Edited by H. El-Rewini, pub-IEEE, pp. 147--156. January, 1998.

1997


 C.R. Johnson, D.M. Beazley, Y. Livnat, S.G. Parker, J.A. Schmidt, H.W. Shen, D.M. Weinstein. “Applications of Large-Scale Computing and Scientific Visualization in Medicine,” SCI Institute Technical Report, No. UUSCI-1997-001, University of Utah, 1997.


S.G. Parker, D.M. Weinstein, C.R. Johnson. “The SCIRun Computational Steering Software System,” In Modern Software Tools in Scientific Computing, Edited by E. Arge and A.M. Bruaset and H.P. Langtangen, Birkhauser Press, Boston pp. 1--40. 1997.

ABSTRACT

We present the design, implementation and application of SCIRun, a scientific programming environment that allows the interactive construction, debugging, and steering of large-scale scientific computations. Using this "computational workbench," a scientist can design and modify simulations interactively via a dataflow programming model. SCIRun enables scientists to design and modify model geometry, interactively change simulation parameters and boundary conditions, and interactively visualize geometric models and simulation results. We discuss the ubiquitous roles SCIRun plays as a computational tool (e.g. resource manager, thread scheduler, development environment), and how we have applied an object oriented design (implemented in C++) to the scientific computing process. Finally, we demonstrate the application of SCIRun to large scale problems in computational medicine. 1.1 Introduction 1.1.1 Visual Computing and Interactive Steering In recent years, the scientific computing commu...

Keywords: scirun, problem solving environments, ncrr, scientific visualization, pse pses problem solving envoronment, bioelectric fields


 S.G. Parker, D.M. Beazley, C.R. Johnson. “Computational Steering Software Systems and Strategies,” In IEEE Computational Science and Engineering, Vol. 4, No. 4, pp. 50--59. 1997.

1996


 C.R. Johnson, D.M. Beazley, Y. Livnat, S.G. Parker, J.A. Schmidt, H.W. Shen, D.M. Weinstein. “Applications of Large-Scale Computing and Scientific Visualization in Medicine,” In International Journal on Supercomputer Applications and High Performance Computing, 1996.


S.G. Parker, C.R. Johnson. “SCIRun: Applying Interactive Computer Graphics to Scientific Problems,” In SIGGRAPH (applications/demo), 1996.

1995


 C.R. Johnson, S.G. Parker. “Applications in Computational Medicine using SCIRun: A Computational Steering Programming Environment,” In Supercomputer `95, Edited by H.W. Meuer, Springer-Verlag, pp. 2--19. 1995.


S.G. Parker, C.R. Johnson. “SCIRun: A Scientific Programming Environment for Computational Steering,” In Proceedings of the 1995 ACM/IEEE Conference on Supercomputing, San Diego, California, USA, Supercomputing '95, No. 52, ACM, New York, NY, USA 1995.
ISBN: 0-89791-816-9
DOI: 10.1145/224170.224354

1994


 C.R. Johnson, S.G. Parker. “A Computational Steering Model Applied to Problems in Medicine,” In Supercomputing 94, IEEE Press, pp. 540--549. 1994.


S.G. Parker, D.M. Weinstein, C.R. Johnson. “A Morphing Algorithm for Generating Near Optimal Grids: Applications in Computational Medicine,” School of Computing Technical Report, No. UUCS-94-014, University of Utah, 1994.


S.G. Parker, C.R. Johnson. “Interactive Manipulation of Contour Data Using the Layers Program - User Guide,” School of Computing Technical Report, No. UUCS-94-014, University of Utah, 1994.


D.M. Weinstein, S.G. Parker, C.R. Johnson. “A Physically Based Mesh Generation Algorithm: Applications in Computational Medicine,” In IEEE Engineering in Medicine and Biology Society 16th Annual International Conference, IEEE Press, pp. 718--719. 1994.