SCIENTIFIC COMPUTING AND IMAGING INSTITUTE
at the University of Utah

An internationally recognized leader in visualization, scientific computing, and image analysis

SCI Publications

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.


D.M. Weinstein, C.R. Johnson. “Effects of Geometric Uncertainty on the Inverse EEG Problem,” In Computational, Experimental, and Numerical Methods for Solving Ill-Posed Inverse Imaging Problems:Medical and Nonmedical Applications, SPIE '97, Vol. 3171, Edited by R.L. Barbour and M.J. Carvlin and M.A. Fiddy, SPIE, pp. 138--145. 1997.


D.M. Weinstein, C.R. Johnson. “Cache-rings for Memory Efficient Isosurface Construction,” School of Computing Technical Report, No. UUCS-97-016, University of Utah, Salt Lake City, UT 1997.


F. Yu, Y. Livnat, C.R. Johnson. “An Automatic Adaptive Refinement and Derefinement Method for 3D Elliptic Problems,” In Applied Numerical Mathematics, 1997.

1996


C.S. Gitlin, C.R. Johnson. “MeshView: A tool for exploring 3D unstructured tetrahedral meshes,” In 5th International Meshing Roundtable, pp. 333--345. 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.


C.R. Johnson, R.S. MacLeod. “Local regularization and adaptive methods for the inverse Laplace problem,” In Biomedical and Life Physics, Edited by D.N. Ghista, Vieweg-Verlag, Braunschweig pp. 224--234. 1996.


R.N. Klepfer, C.R. Johnson, R.S. MacLeod. “The effects of inhomogeneities and anisotropies on electrocardiographic fields: A three-dimensional finite element study,” In IEEE Trans. on Biomedical Engineering, 1996.


Y. Livnat, H.W. Shen, C.R. Johnson. “A Near Optimal Isosurface Extraction Algorithm Using the Span Space,” In IEEE Transactions on Visual Computer Graphics, Vol. 2, No. 1, pp. 73--84. 1996.


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


H.W. Shen, C.R. Johnson, K.L. Ma. “Global and Local Vector Field Visualization Using Enhanced Line Integral Convolution,” In Symposium on Volume Visualization, IEEE Press, pp. 63--70. 1996.


H.W. Shen, C.D. Hansen, Y. Livnat, C.R. Johnson. “Isosurfacing in Span Space with Utmost Efficiency,” In IEEE Visualization `96, IEEE Press, pp. 287--294. 1996.

1995


P. Gharpure, C.R. Johnson. “A Cellular Automaton Model of Electrical Activation in Canine Ventricles: A Validation Study,” SCI Institute Technical Report, No. UUSCI-1995-002, University of Utah, 1995.


C.S. Henriquez, C.R. Johnson, K.A. Henneberg L.J., A.E. Pollard. “Large Scale Biomedical Modeling and Simulation: From Concepts to Results,” SCI Institute Technical Report, No. UUSCI-1995-001, University of Utah, 1995.


C.R. Johnson, R.S. MacLeod, J.A. Schmidt. “Software Tools for Modeling, Computation, and Visualization in Medicine,” In CompMed 94 Proceedings, World Scientific, 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.


C.R. Johnson. “Direct and Inverse Bioelectric Field Problems,” In Computational Science Education Project, Edited by E. Oliver and M. Strayer and V. Meiser and D. Zachmann and R. Giles, DOE, Washington, D.C. 1995.


C.R. Johnson. “Numerical Methods for Bioelectric Field Problems,” In The Biomedical Engineering Handbook, Edited by J.D. Bronzino, CRC Press, Boca Ratan pp. 161--188. 1995.


R.N. Klepfer, C.R. Johnson, R.S. MacLeod. “The Effects of Inhomogeneities and Anisotropies on Electrocardiographic Fields: A Three-Dimensional Finite Element Study,” In IEEE Engineering in Medicine and Biology Society 17th Annual International Conference, IEEE Press, pp. 233--234. 1995.