SCI Publications
1998
M. Miller, C.D. Hansen, S.G. Parker, C.R. Johnson.
“Simulation Steering with SCIRun in a Distributed Memory Environment,” In Seventh IEEE International Symposium on High Performance Distributed Computing (HPDC-7), Jul, 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.
G.F. Potts, D.M. Weinstein, B.F. O'Donnell M.E., C.R. Johnson, R.W. McCarley.
“Bioelectric Modeling of the P300 in Schizophrenia,” In Biological Psychiatry (suppl.), pp. 396. 1998.
R. Stevens, H. Fuchs, A. van Dam, P. Hanrahan, C.R. Johnson, C. McMillan, P. Heermann, S. Louis, T. Defanti, D. Reed, E. Cohen.
“Data and Visualization Corridors: Report on the 1998 DVC Workshop Series,” Note: DOE Report, September, 1998.
The Department of Energy and the National Science Foundation sponsored a series of workshops on data manipulation and visualization of large-scale scientific datasets. Three workshops were held in 1998, bringing together experts in high-performance computing, scientific visualization, emerging computer technologies, physics, chemistry, materials science, and engineering. These workshops were followed by two writing and review sessions, as well as numerous electronic collaborations, to synthesize the results. The results of these efforts are reported here. Across the government, mission agencies are charged with understanding scientific and engineering problems of unprecedented complexity. The DOE Accelerated Strategic Computing Initiative, for example, will soon be faced with the problem of understanding the enormous datasets created by teraops simulations, while NASA already has a severe problem in coping with the flood of data captured by earth observation satellites. Unfortunately, scientific visualization algorithms, and high-performance display hardware and software on which they depend, have not kept pace with the sheer size of emerging datasets, which threaten to overwhelm our ability to conduct research. Our capability to manipulate and explore large datasets is growing only slowly, while human cognitive and visual perception are an absolutely fixed resource. Thus, there is a pressing need for new methods of handling truly massive datasets, of exploring and visualizing them, and of communicating them over geographic distances. This report, written by representatives from academia, industry, national laboratories, and the government, is intended as a first step toward the timely creation of a comprehensive federal program in data manipulation and scientific visualization. There is, at this time, an exciting confluence of ideas on data handling, compression, telepresence, and scientific visualization. The combination of these new ideas, which we refer to as Da ta and Visualization Corridors (DVC), can raise scientific data understanding to new levels and will improve the way science is practiced
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.
C.R. Johnson.
“Computational and Numerical Methods for Bioelectric Field Problems,” In Critical Reviews in BioMedical Engineering, Vol. 25, No. 1, pp. 1--81. 1997.
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 Transactions on Biomedical Engineering, Vol. 44, No. 8, pp. 706--719. August, 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.
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.