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Publications

2008

Journal Articles

E. W. Anderson, J. Ahrens, K. Heitmann, S. Habib, and C. Silva. "Provenance in Comparative Analysis: A Study in Cosmology" Computing in Science and Engineering, 10(3):30-37, 2008.

John Anderson, Christoph Garth, Mark A. Duchaineau and Kenneth I. Joy. "Discrete Multi-Material Interface Reconstruction for Volume Fraction Data" Proceedings of the European Visualization Conference, Computer Graphics Forum, Vol. 27, No. 3, 2008, 1015-1022.

Cecilia Aragon, Stephen Bailey, Sarah Poon, Karl Runge, and Rollin Thomas, "Sunfall: A Collaborative Visual Analytics System for Astrophysics" Proceedings of SciDAC. LBNL-657E.

A. Baptista, B. Howe, J. Freire, D. Maier, and C. Silva. "Scientific Exploration in the Era of Ocean Observatories" Computing in Science and Engineering, 10(3):53-58, 2008.

L. Bavoil, S. Callahan, and C. Silva. "Robust Soft Shadow Mapping with Depth Peeling" Journal of Graphics Tools, 13(1):19-30, 2008.

J. Bellmann, F. Michel, E. Deines, M. Hering-Bertram, J. Mohring, H. Hagen. "Sound Tracing: Rendering Listener Specific Acoustic Room Properties" Computer Graphics Forum, Volume 27, Issue 3, pp. 943-950, 2008.

K. Bürger, J. Krüger, R. Westermann. "Direct Volume Editing" IEEE Transactions on Visualization and Computer Graphics, 14(6), Proceedings of IEEE Visualization 2008.

S. P. Callahan, J. H. Callahan, C. E. Scheidegger, and C. Silva. "Direct Volume Rendering: A 3D Plotting Technique for Scientific Data", In Computing in Science and Engineering, 10(1):88-92, 2008.

M. Chen, M. Kirby, C. Hansen, T. Moller. "A Staggered Grid for Multi-resolution Volume Rendering" Computer Graphics Forum Journal. Accepted.

J. Daniels, T. Ochotta, L. Ha, and C. Silva. "Spline-Based Feature Curves from Point-Sampled Geometry" The Visual Computer, 24(6):449-462, 2008.

J. Daniels, C. Silva, J. Shepherd, and E. Cohen. "Quadrilateral Mesh Simplification" In ACM Transactions on Graphics (Proceedings of SIGGRAPH Asia 2008).

C. Dietrich, J. Comba, L. Nedel, C. Scheidegger, and C. Silva. "Edge Groups: A New Approach to Understanding the Mesh Quality of Marching Methods" In IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2008).

C. C. Fowlkes, C. L. Luengo Hendriks, S. V. E. Keränen, G. H. Weber, O. Rübel, M.-Y. Huang, S. Chatoor, A. H. DePace, L. Simirenko, C. Henriquez, A. Beaton, R. Weiszmann, S. Celniker, B. Hamann, D. W. Knowles, M. D. Biggin, M. B. Eisen, J. Malik. "A Quantitative Spatio-temporal Atlas of Gene Expression in the Drosophila Blastoderm" Cell Vol 133, 364-374, 18 April 2008.

J. Freire, D. Koop, E. Santos, and C. Silva. "Provenance for Computational Tasks: A Survey" Computing in Science and Engineering, 10(3):11-21, 2008.

Christoph Garth, Xavier Trichoche and Kenneth I. Joy. "Lagrangian Visualization of Flow-Embedded Surface Structures" In Proceedings of the European Visualization Conference, Computer Graphics Forum, Vol. 27, No. 3, pp. 767-774, 2008.

Christoph Garth, Harinan Krishnan, Xavier Tricoche, Thomas Bobach and Kenneth I. Joy. "Generation of Accurate Integral Surfaces in Time-Dependent Vector Fields" IEEE Transactions on Visualization and Computer Graphics, 14(6), Proceedings of IEEE Visualization 2008.

Luke J. Gosink, John C. Anderson, E. Wes Bethel, Kenneth I. Joy. "Query-Driven Visualization of Time-Varying Adaptive Mesh Refinement Data" LBNL-803E. IEEE Transactions on Visualization and Computer Graphics, 14(6), Proceedings of IEEE Visualization 2008.

R. M. Kirby and C. Silva. "The Need for Verifiable Visualization" In IEEE Computer Graphics and Applications, 2008.

A. Knoll, Y. Hijazi, C. Hansen, I. Wald, and H. Hagen. "Interactive Ray Tracing of Arbitrary Implicit Functions" Computer Graphics Forum Journal. Accepted, 2008.

A. Knoll, I. Wald and C. Hansen. "Coherent Multiresolution Isosurface Ray Tracing" The Visual Computer, 2008. To Appear.

D. Koop, C. Scheidegger, S. Callahan, J. Freire, and C. Silva. "VisComplete: Data-driven Suggestions for Visualization Systems" In IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2008).

J. Krueger, K. Potter, R. MacLeod, C.R. Johnson. "Unified Volume Format: A General System For Efficient Handling Of Large Volumetric Datasets," In Proceedings of IADIS Computer Graphics and Visualization 2008 (CGV 2008), pp. (accepted). 2008.

G. Li, C. Hansen, X. Tricoche. "Physically-based Dye Advection for Flow Visualization" Computer Graphics Forum Journal, Volume 27, Number 3, 2008, pp. 727-73.

B. Paul, S. Ahern, E. W. Bethel, E. Brugger, R. Cook, J. Daniel, K. Lewis, J. Owen, and D. Southard. "Chromium Renderserver: Scalable and Open Remote Rendering Infrastructure" IEEE Transactions on Visualization and Computer Graphics, 14(3), May/June 2008. LBNL-63693.

K. Potter, J. Krueger, C.R. Johnson. "Towards the Visualization of Multi-Dimentional Stochastic Distribution Data," In Proceedings of The International Conference on Computer Graphics and Visualization (IADIS) 2008, pp. (accepted). 2008.

O. Rübel, G. H. Weber, M-Y Huang, E. W. Bethel, M. D. Biggin, C. C. Fowlkes, C. Luengo Hendriks, S. V. E. Keränen, M. Eisen, D. Knowles, J. Malik, H. Hagen and B. Hamann, "Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data", IEEE Transactions on Computational Biology and Bioinformatics. 2008. (To appear) LBNL-382E.

C. Scheidegger, J. Schreiner, B. Duffy, H. Carr and C. Silva. "Revisiting Histograms and Isosurface Statistics" IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2008).

C. Scheidegger, D. Koop, E. Santos, H. Vo, S. Callahan, J. Freire, and C. Silva. "Tackling the Provenance Challenge One Layer at a Time", In Concurrency And Computation: Practice And Experience, 20(5):473--483, 2008.

C. Silva and J. Tohline. "Guest Editorial: Special Issue on Computational Provenance" In Computing in Science and Engineering, 10(3):9-10, 2008.

A.R. Sanderson, M.D. Meyer, R.M. Kirby, C.R. Johnson. "A Framework for Exploring Numerical Solutions of Advection-Reaction-Diffusion Equations Using a GPU-Based Approach," In Computing and Visualization in Science, published online, 2008.
ISSN: 1432-9360

G., X. Tricoche, D. Weiskopf, C. Hansen. "Flow Charts: Visualization of Vector Fields on Arbitrary Surfaces" IEEE Transactions on Visualization and Computer Graphics, Volume 14, Number 5, 2008, pp. 1067-1080.

G. H. Weber, O. Rübel, M.-Y. Huang, A. H. DePace, C. C. Fowlkes, S. V. E. Keränen, C. L. Luengo Hendriks, H. Hagen, D. W. Knowles, J. Malik, M. D. Biggin and B. Hamann. "Visual exploration of three-dimensional gene expression using physical views and linked abstract views" To appear in:IEEE Transactions on Computational Biology and Bioinformatics. LBNL-63776.

Conference Proceedings

Cecilia Aragon, Sarah Poon, Gregory Aldering, Rollin Thomas, and Robert Quimby, "Using Visual Analytics to Maintain Situation Awareness in Astrophysics" Proceedings of the IEEE Symposium on Visual Analytics Science and Technology (IEEE VAST 2008). LBNL-658E.

S. P. Callahan, J. Freire, C. E. Scheidegger, C. Silva, and Huy T. Vo. "Towards Provenance-Enabling ParaView", Second International Provenance and Annotation Workshop (IPAW 2008).

T. Ellkvist, D. Koop, E. W. Anderson, J. Freire, and C. Silva. "Using Provenance to Support Real-Time Collaborative Design of Workflows" Second International Provenance and Annotation Workshop (IPAW 2008).

J. Freire and C. Silva. "Towards Enabling Social Analysis of Scientific Data", CHI Social Data Analysis Workshop, 2008.

L. Lins, D. Koop, E. W. Anderson, S. P. Callahan, E. Santos, C. E. Scheidegger, J. Freire, and C. T. Silva. "Examining Statistics of Workflow Evolution Provenance: A First Study" Statistical and Scientific Database Management (SSDBM) 2008.

K. Potter and J. Krueger and C.R. Johnson. "Towards the Visualization of Multi-Dimensional Stochastic Distribution Data" In Proceedings of the International Conference on Computer Graphics and Visualization, July 2008.

D. Pugmire, H. Childs, S. Ahern. "Parallel Analysis and Visualization on Cray Compute Node Linux" In Proceedings of the Cray Users Group Meeting, May 2008.

O. Rübel, Prabhat, K. Wu, H. Childs, J. Meredith, C.G.R. Geddes, E. Cormier-Michel, S. Ahern, G.H. Weber, P. Messmer, H. Hagen, B. Hamann and E.W. Bethel, "High Performance Multivariate Visual Data Exploration for Extremely Large Data" SC08, Austin TX, November, 2008. LBNL-716E.

E. Santos, L. Lins, J. P. Ahrens, J. Freire, and C. Silva. "A First Study on Clustering Collections of Workflow Graphs" Second International Provenance and Annotation Workshop (IPAW 2008).

C. E. Scheidegger, H. T. Vo, D. Koop, J. Freire, and C. Silva. "Querying and Re-Using Workflows with VisTrails", ACM SIGMOD 2008.

D. M. Ushizima, O. Rübel, Prabhat, G. H. Weber, E. W. Bethel, C. R. Aragon, C. G. Geddes, E. Cormier-Michel, and B. Hamann. "Automated analysis for detecting beams in simulations" In Proceedings of the Seventh International Conference on Machine Learning and Applications, Dec. 2008.

G.H. Weber, V. Beckner, H. Childs, T. Ligocki, M. Miller, B. van Straalen, E.W. Bethel. "Visualization of Scalar Adaptive Mesh Refinement Data" in: Numerical Modeling of Space Plasma Flows: Astronum-2007 (Astronomical Society of the Pacific Conference Series), volume 385, pp. 309-320, 2008. LBNL-220E.

H. Wang, C. E. Scheidegger, and C. Silva. "Optimal Bandwidth Selection for MLS Surfaces", IEEE International Conference on Shape Modeling and Applications (SMI), (Awarded Best Paper), 2008.

Posters

E. Wes Bethel, C.R. Johnson, C. Aragon, Prabhat, O. R¨ubel, G.Weber, V. Pascucci, H. Childs, P.-T. Bremer, A. Mascarenhas, B. Whitlock, S. Ahern, J. Meredith, G. Ostrouchov, K. Joy, B. Hamann, C. Garth, M. Cole, C. Hansen, S. Parker, A. Sanderson, C.T. Silva, and X. Tricoche. "DOE SciDAC Visualization and Analytics Center for Enabling Technologies" In 2008 DOE ASCR CS PI Meeting, Denver, CO, USA, April 2008.

O. Rübel, Prabhat, K. Wu, H. Childs, J. Meredith, C.G.R. Geddes, E. Cormier-Michel, S. Ahern, G.H. Weber, P. Messmer, H. Hagen, B. Hamann and E.W. Bethel, "Application of High-performance Visual Analysis Methods to Laser Wakefield Particle Acceleration Data" Poster at IEEE Visualization 2008, Columbus, Ohio, October 19-24, 2008.

Invited Articles

E. Wes Bethel, Chris Johnson, Charles Hansen, Claudio Silva, Steven Parker, Allen Sanderson, Lee Myers, Martin Cole, Xavier Tricoche, Sean Ahern, George Ostrouchov, Dave Pugmire, Jamison Daniel, Jeremy Meredith, Valerio Pascucci, Hank Childs, Peer-Timo Bremer, Ajith Mascarenhas, Ken Joy, Bernd Hamann, Christoph Garth, Cecilia Aragon, Gunther Weber, and Prabhat. "Seeing the Unseeable" SciDAC Review, Number 8, pp 24-33. LBNL-472E, Summer 2008.

O. Rübel, G. H. Weber, M-Y Huang, E. W. Bethel, S. V. E. Keränen, C. C. Fowlkes, C. L. Luengo Hendriks, A. H. DePace, L. Simirenko, M. B. Eisen, M. D. Biggin, H. Hagen, J. Malik, D. W. Knowles and B. Hamann, "PointCloudXplore 2: Visual Exploration of 3D Gene Expression", (To appear) LBNL-249E, GI Lecture Notes in Informatics, Gesellschaft fuer Informatik (GI), Bonn, Germany, 2008.

C. Silva and J. Freire. "Software Infrastructure for Exploratory Visualization and Data Analysis: Past, Present and Future" Journal of Physics: Conference Series (SciDAC 2008 Conference), 2008.

Book Chapters

E. Wes Bethel, Hank Childs, Ajith Mascarenhas, Valerio Pascucci, and Prabhat. "Scientific Data Managment Challenges in High Performance Visual Data Analysis" In Arie Shoshani and Doron Rotem, editors, Scientific Data Management: Challenges, Existing Technology, and Deployment. Chapman & Hall/CRC Press, 2008.

Technical Reports

Luke J. Gosink, Kesheng Wu, E. Wes Bethel, John D. Owens, Kenneth I. Joy. "Bin-Hash Indexing: A Parallel Method for Fast Query Processing" Technical Report LBNL-729E, Lawrence Berkeley National Laboratory, Berkeley CA, USA, 94720, 2008.

2007

E. W. Bethel, O. Ruebel, G. Weber. "Visualization and Analysis of 3D Gene Expression Data." Two-page research highlight. LBNL-63658, Dec 2007.

G. Weber, H. Childs, K. Bonnell, J. Meredith, M. Miller, B. Whitlock, E. W. Bethel. "Production-quality Tools for Adaptive Mesh Refinement Visualization." Two-page research highlight. LBNL-63657, Dec 2007.

E. W. Bethel, J. Chen, I. Yoon. "Interactive, Internet Delivery of Visualization via Structured, Prerendered Imagery." Two-page research highlight. LBNL-63675, Dec 2007.

E. W. Bethel, L. Gosink, J. Anderson, K. Joy. "Variable Interactions in Query-Driven Visualization." Two-page research highlight. LBNL-63674, Dec 2007.

E.W. Bethel, C. Johnson, C. Aragon, Prabhat, O. Ruebel, G. Weber, V. Pascucci, H. Childs, P.-T. Bremer, B. Whitlock, S. Ahern, J. Meredith, G. Ostrouchov, K. Joy, B. Hamann, C. Garth, M. Cole, C. Hansen, S. Parker, A. Sanderson, C. Silva, X. Tricoche. "SciDAC Visualization and Analytcs Center for Enabling Technologies -- Strategy for Petascale Visual Data Analysis Success." CTWatch Quarterly, Volume 3, Number 4, November 2007.

C. Garth, F. Gerhardt, X. Tricoche, H. Hagen. "Efficient Computation and Visualization of Coherent Structures in Fluid Flow Applications," In Proceeding of IEEE Visualization 2007, pp. 1464--1471, Oct 2007.

Luke J. Gosink, John C. Anderson, Kenneth I. Joy, E. Wes Bethel. "Variable Interactions in Query Driven Visualization" In Proceeding of IEEE Visualization 2007, pp. 1400-1407, Oct 2007.

Attila Gyulassy, Vijay Natarajan, Bernd Hamann, Mark Duchaineau, Valerio Pascucci, Eduardo Bringa, Andrew Higginbotham. "Topologically Clean Distance Fields" In Proceeding of IEEE Visualization 2007, pp. 1432-1439, Oct 2007.

Attila Gyulassy, Vijay Natarajan, Bernd Hamann, Valerio Pascucci. "Efficient Computation of Morse-Smale Complexes for Three-dimensional Scalar Functions" In Proceeding of IEEE Visualization 2007, pp. 1440-1447, Oct 2007.

Carlos Scheidegger, Huy Vo, David Koop, Juliana Freire, Claudio Silva. "Querying and Creating Visualizations by Analogy," In Proceeding of IEEE Visualization 2007, pp. 1560--1567, Oct 2007.

I. Wald, H. Friedrich, A. Knoll, C.D. Hansen. "Interactive Isosurface Ray Tracing of Time-Varying Tetrahedral Volumes," In Proceeding of IEEE Visualization 2007, 1727--1734, Oct 2007.

Gunther H. Weber, Peer-Timo Bremer,Valerio Pascucci. "Topological Landscapes: A Terrain Metaphor for Scientific Data," In Proceeding of IEEE Visualization 2007, pp. 1416-1423, Oct 2007.

A. Wiebel, X. Tricoche, D. Schneider, Heike Jänicke, Gerik Scheuermann "Generalized Streak Lines: Analysis and Visualization of Boundary Induced Vortices," In Proceeding of IEEE Visualization 2007, pp. 1735-1742, Oct 2007.

Sung-Eui Yoon and Peter Lindstrom. "Random-Accessible Compressed Triangle Meshes," In Proceeding of IEEE Visualization 2007, pp. 1536--1543, Oct 2007.

"Topological Analysis Provides Deeper Insight into Hydrodynamic Instabilities" ASCR Computing News Roundup, September 2007.

V. Pascucci, G. Scorzelli, P.-T. Bremer, and A. Mascarenhas. "Robust On-line Computation of Reeb Graphs: Simplicity and Speed" In Proceeding of SIGGRAPH 2007 (ACM Transation on graphics), pp. 58-1 to 58-9, Aug 2007.

Sean Ahern. "Petascale visual data analysis in a production computing environment" In Journal of Physics, Conference Series, volume 78, Proceedings of SciDAC 2007, June 2007.

E.W. Bethel, C.R. Johnson, K. Joy, S. Ahern, V. Pascucci, H. Childs, J. Cohen, M. Duchaineau, B. Hamann, C. Hansen, D. Laney, P. Lindstrom, J. Meredith, G. Ostrouchov, S.G. Parker, C.T. Silva, A. Sanderson, X. Tricoche. "SciDAC Visualization and Analytics Center for Enabling Technology," In Journal of Physics, Conference Series, volume 78, Proceedings of SciDAC 2007, June 2007.

P.-T. Bremer, E.M. Bringa, M.A. Duchaineau, A.G. Gyulassy, D. Laney, A. Mascarenhas and V. Pascucci. "Topological Feature Extraction and Tracking" In Journal of Physics, Conference Series, volume 78, Proceedings of SciDAC 2007, June 2007.

Hank Childs. "Architectural challenges and solutions for petascale postprocessing" In Journal of Physics, Conference Series, volume 78, Proceedings of SciDAC 2007, June 2007.

C. Jones, K.-L. Ma, A. Sanderson, L. Myers. "Visual Interrogation of Gyrokinetic Particle Simulations," In Journal of Physics, Conference Series, volume 78, Proceedings of SciDAC 2007, June 2007.

Kenneth I. Joy, Mark Miller, Hank Childs, E. Wes Bethel, John Clyne, George Ostrouchov, Sean Ahern. "Frameworks for Visualization at the Extreme Scale" In Journal of Physics, Conference Series, volume 78, Proceedings of SciDAC 2007, June 2007.

Gunther H. Weber, Vincent E. Beckner, Hank Childs, Terry J. Ligocki, Mark C. Miller, Brian Van Straalen and E. Wes Bethel. "Visualization Tools for Adaptive Mesh Refinement Data" In Proceedings of the 4th High-End Visualization Workshop, Tyrol, Austria, June, 2007.

2006

E. Wes Bethel (LBNL), Chris Johnson (Utah), Ken Joy (UC Davis), Sean Ahern (ORNL), Valerio Pascucci (LLNL), Jonathan Cohen (LLNL), Mark Duchaineau (LLNL), Bernd Hamann (UC Davis), Charles Hansen (Utah), Dan Laney (LLNL), Peter Lindstrom (LLNL), Jeremy Meredith (ORNL), George Ostrouchov (ORNL), Steven Parker (Utah), Claudio Silva (Utah), Xavier Tricoche (Utah), Allen Sanderson (Utah), Hank Childs (LLNL). Poster presentation: "VACET: Meet the SciDAC Visualization and Analytics Center for Enabling Technologies" Presented at SciDAC 2006, Denver Co., June, 2006.

Kurt Stockinger, E. Wes Bethel, Scott Campbell, Eli Dart, Kesheng Wu. "Detecting Distributed Scans Using High-Performance Query-Driven Visualization" In Proceedings of Supercomputing 2006 (accepted) 2006.