2014 | 2013 | 2012 | 2011 | 2010
2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2000
1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993
1989

2014

  1. D.M. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson, and J. Sethian. Structure recognition from high resolution images of ceramic composites. IEEE International Conference on Big Data, October 2014.

  2. K. Odziomek, D.M. Ushizima, M. Haranczyk, and T. Puzyn. Toward quantitative structure activity relationship (qsar) models for nanoparticles. American Chemical Society National Meeting - Scientific Excellence Award, August 2014.

  3. D.M. Ushizima, A.G.C. Bianchi, and C. Carneiro. Segmentation of subcellular compartments combining superpixel representation with voronoi diagrams. IEEE International Symposium on Biomedical Imaging (ISBI) - 1st place in Code Competition, April 2014.(PDF)

  4. Weber, G. H., Johansen, H., Graves, D. T., and Ligocki, T. J., Simulating Urban Environments for Energy Analysis, in: Proceedings Visualization in Environmental Sciences 2014 (EnvirVis 2014), 2014. (BibTeX) (PDF)

  5. Beketayev, K., Yeliussizov, D., Morozov, D., Weber, G. H., and Hamann, B., Measuring the distance between merge trees, in: Bremer, P. T., Hotz, I., Pascucci, V., and Peikert, R., eds., Topological Methods in Data Analysis and Visualization III: Theory, Algorithms, and Applications, Mathematics and Visualization, pp. 151–166, Springer-Verlag, 2014. (BibTeX) (PDF)

  6. Oliver Rübel, Cameron G.R. Geddes, Min Chen, Estelle Cormier-Michel and E. Wes Bethel, "Feature-based Analysis of Plasma-based Particle Acceleration Data," IEEE Transactions on Visualization and Computer Graphics, 20(2):196–210, February 2014. (BibTeX) (PDF)

  7. Hank Childs, Scott Biersdorff, David Poliakoff, David Camp and Allen D. Malony, "Particle Advection Performance Over Varied Architectures and Workloads," IEEE International Conference on High Performance Computing (HiPC 2014). (PDF coming soon)

  8. Alexy Agranovsky, David Camp, Christoph Garth, E. Wes Bethel, Kenneth I Joy, and Hank Childs "Improved Post Hoc Flow Analysis Via Lagrangian Representations," In Proceedings IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV) 2013. (PDF coming soon)


2013

  1. Oliver Rübel, Annette Greiner, Shreyas Cholia, Katherine Louie, E. Wes Bethel, Trent R. Northen, and Benjamin P. Bowen, "OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging," Analytical Chemistry 2013 85 (21), pp 10354-10361.LBNL-6477E. (BibTeX) (PDF) 

  2. E. Wes Bethel and Mark Howison. Performance Optimzation and Auto-tuning. In E. Wes Bethel, Hank Childs, and Charles Hansen, editors, High Performance Visualization—Enabling Extreme Scale Scientfic Insight, Chapman & Hall, CRC Computational Science, pages 307–329. CRC Press/Francis-Taylor Group, Boca Raton, FL, USA, November 2012. http://www.crcpress.com/product/isbn/9781439875728. LBNL-6466E. (bibtex)

  3. Oliver Rübel, E. Wes Bethel, Prabhat, and Kesheng Wu. Query-Driven Visualization and Analysis. In E. Wes Bethel, Hank Childs, and Charles Hansen, editors, High Performance Visualization—Enabling Extreme Scale Scientfic Insight, Chapman & Hall, CRC Computational Science, pages 117–144. CRC Press/Francis-Taylor Group, Boca Raton, FL, USA, November 2012. http://www.crcpress.com/product/isbn/9781439875728. LBNL-6323E. (bibtex)

  4. Charles Hansen, E. Wes Bethel, Thiago Ize, and Carson Brownlee. Rendering. In E. Wes Bethel, Hank Childs, and Charles Hansen, editors, High Performance Visualization—Enabling Extreme Scale Scientfic Insight, Chapman & Hall, CRC Computational Science, pages 49–60. CRC Press/Francis-Taylor Group, Boca Raton, FL, USA, November 2012. http://www.crcpress.com/product/isbn/9781439875728. LBNL-6324E. (bibtex)

  5. E. Wes Bethel and Mark Miller. Remote and Distributed Visualization Architectures. In E. Wes Bethel, Hank Childs, and Charles Hansen, editors, High Performance Visualization—Enabling Extreme Scale Scientfic Insight, Chapman & Hall, CRC Computational Science, pages 25–48. CRC Press/Francis-Taylor Group, Boca Raton, FL, USA, November 2012. http://www.crcpress.com/product/isbn/9781439875728. LBNL-6325E. (bibtex)

  6. E. Wes Bethel, David Camp, Hank Childs, Christoph Garth, Mark Howison, Kenneth I. Joy, and David Pugmire. Hybrid Parallelism. In E. Wes Bethel, Hank Childs, and Charles Hansen, editors, High Performance Visualization—Enabling Extreme Scale Scientfic Insight, Chapman & Hall, CRC Computational Science, pages 261–290. CRC Press/Francis-Taylor Group, Boca Raton, FL, USA, November 2012. http://www.crcpress.com/product/isbn/9781439875728. LBNL-6326E. (bibtex)

  7. Hank Childs, Kwan-Liu Ma, Hongfeng Yu, Brad Whitlock, Jeremy Meredith, Jean Favre, Scott Klasky, Norbert Podhorszki, Karsten Schwan, Matthew Wolf, Manish Parashar, and Fan Zhang. In Situ Processing. In E. Wes Bethel, Hank Childs, and Charles Hansen, editors, High Performance Visualization—Enabling Extreme Scale Scientfic Insight, Chapman & Hall, CRC Computational Science, pages 171–198. CRC Press/Francis-Taylor Group, Boca Raton, FL, USA, November 2012. http://www.crcpress.com/product/isbn/9781439875728. LBNL-6322E. (bibtex)

  8. Hank Childs, David Pugmire, Sean Ahern, Brad Whitlock, Mark Howison, Prabhat, Gunther Weber, and E. Wes Bethel. Visualization at Extreme Scale Concurrency. In E. Wes Bethel, Hank Childs, and Charles Hansen, editors, High Performance Visualization—Enabling Extreme Scale Scientfic Insight, Chapman & Hall, CRC Computational Science, pages 291–306. CRC Press/Francis-Taylor Group, Boca Raton, FL, USA, November 2012. http://www.crcpress.com/product/isbn/9781439875728. LBNL-6321E. (bibtex)

  9. Hank Childs, Eric Brugger, Brad Whitlock, Jeremy Meredith, Sean Ahern, David Pugmire, Kathleen Biagas, Mark Miller, Gunther H. Weber, Hari Krishnan, Thomas Fogal, Allen Sanderson, Christoph Garth, E. Wes Bethel, David Camp, Oliver Rübel, Marc Durant, Jean Favre, Paul Navratil. VisIt: An End-User Tool for Visualzing and Analyzing Very Large Data. In E. Wes Bethel, Hank Childs, and Charles Hansen, editors, High Performance Visualization—Enabling Extreme Scale Scientfic Insight, Chapman & Hall, CRC Computational Science, pages 357–372. CRC Press/Francis-Taylor Group, Boca Raton, FL, USA, November 2012. http://www.crcpress.com/product/isbn/9781439875728. LBNL-6320E. (bibtex)

  10. Kesheng Wu, E. Wes Bethel, Ming Gu, David Leinweber, and Oliver Rübel. A Big Data Approach to Analyzing Market Volatility. Technical report, Social Science Research Network (SSRN), June 2013. Available at SSRN: http://ssrn.com/abstract=2274991, LBNL publication number pending.

  11. Dean Williams, Charles Doutriaux, John Patchett, Sean Williams, Galen Shipman, Ross Miller, Chad Steed, Harinarayan Krishnan, Claudio Silva, Aashish Chaudhary, Peer-Timo Bremer, David Pugmire, E. Wes Bethel, Hank Childs, Prabhat, Berk Geveci, Andrew Bauer, Alexander Pletzer, Jorge Poco, Tommy Ellqvist, Emanuele Santos, Gerald Potter, Brian Smith, Thomas Maxwell, David Kindig, and David Koop. Ultrascale Visualization of Climate Data. IEEE Computer, 46(9):68–76, September 2013. LBNL-6278E. (PDF - LBNL report version) (PDF - IEEE Explore print version) (bibtex)

  12. Hank Childs, Berk Geveci, William J. Schroeder, Jeremy S. Meredith, Kenneth Moreland, Christopher Sewell, Torsten Kuhlen, and E.Wes Bethel. Research Challenges for Visualization Software. IEEE Computer, 46(5):34–42, May 2013. LBNL-6239E. (PDF) (bibtex)

  13. Dmitriy Morozov and Gunther H. Weber. Distributed Merge Trees. In: Proceedings of the 18th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP'13), pp. 93-102, New York, NY, USA, 2013. LBNL-6137E. (BibTeX)

  14. E. Wes Bethel, Prabhat, Suren Byna, Oliver Rübel, K. John Wu, and Michael Wehner. Why High Performance Visual Data Analytics is both Relevant and Difficult. Proceedings of Visualization and Data Analysis 2013, IS&T/SPIE Electronic Imaging 2013, San Francisco CA, USA. LBNL-6063E. (bibtex) (PDF)

  15. David Camp, Hari Krishnan, David Pugmire, Christoph Garth, Ian Johnson, E. Wes Bethel, Kenneth I. Joy, and Hank Childs. "GPU Acceleration of Particle Advection Workloads in a Parallel, Distributed Memory Setting". Proceedings of Eurographics Symposium on Parallel Graphics and Visualization (EGPGV), May 2013, Girona, Spain. LBNL-6146E. (bibtex) (PDF)

  16. Patrick Oesterling, Christian Heine, Gunther H. Weber, and Gerik Scheuermann. Visualizing nD Point Clouds as Topological Landscape Profiles to Guide Local Data Analysis. In: IEEE Transactions on Visualization and Computer Graphics, 19(3): 514-526, 2013. doi: 10.1109/TVCG.2012.120. LBNL-5694E. (BibTeX)

  17. David Camp, Wes Bethel and Hank Childs. "Transitioning Data Flow-Based Visualization Software to Multi-Core Hybrid Parallelism". Proceedings of Data-Flow Execution Models for Extreme Scale Computing (DFM 2013) conference. LBNL-6363E. (bibtex) (PDF)

  18. Cornelius Muller, David Camp, Bernd Hentschel, and Christoph Garth. "Distributed Parallel Particle Advection using Work Requesting". In Proceedings IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV) 2013. LBNL-6467E. (bibtex) (PDF)

2012

  1. Kenes Beketayev, Gunther H. Weber, Dmitriy Morozov, Aidos Abzhanov and Bernd Hamann. Geometry-Preserving Topological Landscapes. In: Proceedings of the Workshop at SIGGRAPH Asia 2012, pp. 155--160, 2012. LBNL-6082E. (BibTeX)

  2. Dogan Demir, Kenes Beketayev, Gunther H. Weber, Peer-Timo Bremer, Valerio Pascucci and Bernd Hamann. Topology Exploration with Hierarchical Landscapes. In: Proceedings of the Workshop at SIGGRAPH Asia 2012, pp. 147--154, 2012. LBNL-6083E. (BibTeX)

  3. Babak Behzad, Joey Huchette, Huong Luu, Ruth Aydt, Suren Byna, Mohamad Chaarawi, Quincey Koziol, Prabhat, Yushu Yao, "Auto-tuning of Parallel I/O parameters for HDF5 Applications", SuperComputing 2012. Poster. (BibTeX)

  4. Joerg Meyer, E. Wes Bethel, Jennifer L. Horsman, Susan S. Hubbard, Harinarayan Krishnan, Alexandru Romosan, Elizabeth H. Keating, Laura Monroe, Richard Strelitz, Phil Moore, Glenn Taylor, Ben Torkian, Timothy C. Johnson, and Ian Gorton. Visual Data Analysis as an Integral Part of Environmental Management. IEEE Transactions on Visualization and Computer Graphics, 18(12):2088–2094, December 2012. LBNL-6599E. (BibTeX) (PDF)

  5. S. Byna, J. Chou, O. Rubel, Prabhat, H. Karimabadi, W. S. Daughton, V. Roytershteyn, E. W. Bethel, M. Howison, K.-J. Hsu, K.-W. Lin, A. Shoshani, A. Uselton, and K. Wu. "Parallel Data Storage, Analysis, and Visualization of a Trillion Particles", XLDB 2012. Poster. (BibTeX)

  6. Daniela M. Ushizima, Dmitriy Morozov, Gunther H. Weber, Andrea G.C. Bianchi, James A. Sethian, and E. Wes Bethel. Augmented topological descriptors of pore networks for material science. IEEE Transactions on Visualization and Computer Graphics (Proc. IEEE Vis 2012), 18(12):2041-2050, 2012. LBNL-5964E. (BibTeX) (PDF)

  7. Gunther H. Weber, Hank Childs, and Jeremy S. Meredith. Efficient Parallel Extraction of Crack- free Isosurfaces from Adaptive Mesh Renement (AMR) Data. In Proceedings of IEEE Symposium on Large Data Analysis and Visualization (LDAV), pages 31-38, October 2012. LBNL-5799E. (BibTeX) (PDF)

  8. E. Wes Bethel, Hank Childs, and Charles Hansen, editors. High Performance Visualization—Enabling Extreme-Scale Scientific Insight. Chapman & Hall, CRC Computational Science. CRC Press/Francis–Taylor Group, Boca Raton, FL, USA, November 2012. http://www.crcpress.com/product/isbn/9781439875728 (bibtex)

  9. K.E. Kunkel, T.R. Karl, H. Brooks, J. Kossin, J.H. Lawrimore, D. Arndt, L. Bosart, D. Changnon, S.L. Cutter, N. Doesken, K. Emanuel, P.Y. Groisman, R.W. Katz, T. Knutson, J. O'Brien, C.J. Paciorek, T.C. Peterson, K. Redmon, D. Robinson, J. Trapp, R. Vose, S. Weaver, M. Wehner, K. Wolter, and D. Wuebbles. Monitoring and Understanding Trends in Extreme Storms: State of Knowledge. In Bulletin of the American Meteorological Society, 2012. doi: http://dx.doi.org/10.1175/BAMS-D-11-00262.1.

  10. E. Wes Bethel, Rob Ross, Wei-Ken Liao, Prabhat, Karen Schuchardt, Peer-Timo Bremer, Oliver Rübel, Surendra Byna, Kesheng Wu, Fuyu Li, Michael Wehner, John Patchett, Han- Wei Shen, David Pugmire, and Dean Williams. Recent Advances in Visual Data Exploration and Analysis of Climate Data. In SciDAC 3 Principal Investigator Meeting, Rockville, MD, USA, September 2012. (Poster) (bibtex)

  11. Michael Wehner, Surendra Byna, Prabhat, Thomas Yopes, and John Wu. Atmospheric Rivers in the CMIP3/5 Historical and Projection Simulations. In World Climate Research Programme (WCRP) Workshop on CMIP5 Model Analysis, Honolulu, HI, USA, March 2012. Poster. (bibtex)

  12. E. Wes Bethel, Surendra Byna, Jerry Chou, Estelle Cormier-Michel, Cameron G. R. Geddes, Mark Howison, Fuyu Li, Prabhat, Ji Qiang, Oliver Rübel, Robert D. Ryne, Michael Wehner, and Kesheng Wu. Big Data Analysis and Visualization: What Do LINACS and Tropical Storms Have In Common? In 11th International Computational Accelerator Physics Conference, ICAP 2012, Rostock-Warnemünde, Germany, August 2012. LBNL-5766E. (bibtex) (PDF)

  13. Surendra Byna, Jerry Chou, Oliver Rübel, Prabhat, Homa Karimabadi, William S. Daughton, Vadim Roytershteyn, E. Wes Bethel, Mark Howison, Ke-Jou Hsu, Kuan-Wu Lin, Arie Shoshani, Andrew Uselton, and Kesheng Wu, "Parallel I.O, Analysis, and Visualization of a Trillion Particle Simulation," SuperComputing 2012 (SC12), Salt Lake City, Utah, Nov. 10-16, 2012. LBNL-5832E. (BibTeX)(PDF - coming soon) (This article was also featured in the following news releases: i) Linda Via, "Sifting Through a Trillion Electrons: Berkeley researchers design strategies for extracting interesting data from massive scientific datasets," June 26, 2012. [Online at crd.lbl.gov and nersc.gov] and ii)  Today At Berkeley Lab, "NERSC Users Generate a Quickest-Ever, 32-Terabyte 3D Simulation," June 27,2012. )

  14. Oliver Rübel, Cameron, G. R. Geddes, Min Chen, Estelle Cormier-Michel, and E. Wes Bethel, "Query-driven Analysis of Plasma-based Particel Acceleration Data," Poster Abstracts of IEEE VisWeek 2012, Seattle, WA, Oct 14-19, 2012 (Poster). LBNL-5906E. (PDF) (BibTeX)

  15. E. Wes Bethel, David Camp, Hank Childs, Mark Howison, Hari Krishnan, Burlen Loring, Joerg Meyer, Prabhat, Oliver Ruebel, Daniela Ushizima, Gunther Weber. Towards Exascale: High Performance Visualization and Analytics – Project Status Report. Technical Report LBNL-5767E. Lawrence Berkeley National Laboratory, Berkeley CA, USA, 94720. June, 2012. In DOE Exascale Research Conference, April 16–18, 2012, Portland OR, USA. (bibtex) (PDF)

  16. Gunther H. Weber, Dmitriy Morozov, Kenes Beketayev, John Bell, Peer-Timo Bremer, Marc Day, Bernd Hamann, Christian Heine, Maciej Haranczyk, Mario Hlawitschka, Valerio Pascucci, Patrick Oesterling, and Gerik Scheuermann. Topology-based Visualization and Analysis of High-dimensional Data and Time-varying Data at the Extreme Scale. In DOE Exascale Research Conference, Portland, OR, April 2012. LBNL-5691E-Poster.(BibTeX)

  17. Gunther H. Weber and Peer-Timo Bremer. In-situ Analysis: Challenges and Opportunities. Technical Report LBNL-5692E. Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 94720, April 2012. Position paper for DOE Exascale Research Conference in Portland, OR. (BibTeX) (PDF)

  18. Gunther H. Weber, Kenes Beketayev, Peer-Timo Bremer, Bernd Hamann, Maciej Haranczyk, Mario Hlawitschka, and Valerio Pascucci. Comprehensible Presentation of Topological Information. Technical Report LBNL-5693E. Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 94720, April 2012. Status report for DOE Exascale Research Conference in Portland, OR. (BibTeX) (PDF)

  19. Mehmet Balman, Eric Pouyoul, Yushu Yao, E. Wes Bethel, Burlen Loring, Prabhat, John Shalf, Alex Sim, and Brian L. Tierney. Experiences with 100G Network Applications. In Proceedings of the 5th International Workshop on Data Intensive and Distributed Computing (DIDC 2012). Delft, Netherlands. June 2012. (BibTeX) (LBNL pub number coming soon) (PDF coming soon)

  20. Karen L. Schuchardt, Deborah A. Agarwal, Stefan A. Finsterle, Carl W. Gable, Ian Gorton, Luke J. Gosink, Elizabeth H. Keating, Carina S. Lansing, Joerg Meyer, William A.M. Moeglein, George S.H. Pau, Ellen A. Porter, Sumit Purohit, Mark L. Rockhold, Arie Shoshani, and Chandrika Sivaramakrishnan. Akuna - Integrated Toolsets Supporting Advanced Subsurface Flow and Transport Simulations for Environmental Management, XIX International Conference on Computational Methods in Water Resources (CMWR 2012), University of Illinois at Urbana-Champaign, June 17-22, 2012. (BibTeX) (PDF)

  21. E. Wes Bethel. Exploration of Optimization Options for Increasing Performance of a GPU Implementation of a Three-dimensional Bilateral Filter. Technical Report, LBNL-5406E, Lawrence Berkeley National Laboratory, Berkeley CA, USA, 94720. 2012. (BibTeX) (PDF)

  22. E. Wes Bethel and Mark Howison. Multi-core and Many-core Shared-memory Parallel Raycasting Volume Rendering Optimization and Tuning. International Journal of High Performance Computing Applications, 26(4):399–412, November 2012. LBNL-5362E. (bibtex) (Publisher rules prohibit us distributing a PDF of the article)

  23. Samuel Gerber, Oliver Rübel, Peer-Timo Bremer, Valerio Pascucci and Ross T. Whitaker. Morse-Smale Regression. Journal of Computational and Graphical Statistics (in press) (published online Jan.2012). LBNL-5682E. (BibTeX)(PDF)(article at JCGS)(MSR package for R available at CRAN here).

  24. Allen R. Sanderson, Brad Whitlock, Oliver Rübel, Hank Childs, Gunther H. Weber, Prabhat and Kesheng Wu. A System for Query Based Analysis and Visualization, Third International Eurovis Workshop on Visual Analytics EuroVA 2012, K. Matkovic and G. Santucci (Editors), Vienna, Austria, June, 2012, LBNL-5507E. (PDF)(BibTeX)

  25. E. Wes Bethel, David Leinweber, Oliver Rübel, Kesheng Wu (authors in alphabetical order), Federal Market Information Technology in the Post Flash Crash Era: Roles of Supercomputing, The Journal of Trading, Spring 2012, Vol. 7, No. 2, pp. 9-24, DOI: 10.3905/jot.2012.7.2.009 (this article is an extended version of 2011.2) (BibTeX) (article at JOT)

  26. P. Navratil, D. Fussell, C. Lin, and H. Childs. Dynamic Scheduling for Large-Scale Distributed-Memory Ray Tracing, Proceedings of EuroGraphics Symposium on Parallel Graphics and Visualization (EGPGV), pages 61-70, May 2012, LBNL-5930E. Best paper winner. (BibTeX) (PDF)

  27. K. P. Gaither, H. Childs, K. Schulz, C. Harrison, B. Barth, D. Donzis, and P. Yeung. Using Visualization and Data Analysis to Understand Critical Structures in Massive Time Varying Turbulent Flow Simulations. IEEE Computer Graphics and Applications, 32(4):34-45, 2012. LBNL-5911E. (BibTeX) (PDF)

  28. Jihan Kim, Richard Martin, Oliver Rübel, Maciej; Haranczyk and Berend Smit, "High-throughput Characterization of Porous Materials Using Graphics Processing Units,"  Journal of Chemical Theory and Computation, 2012, 8 (5), pp 1684–1693, DOI: 10.1021/ct200787v, March, 2012, LBNL-5409E (BibTeX)(Mansucipt availabe online at JCTC here)

  29. Prabhat, Oliver Rübel, Surendra Byna, Kesheng Wu, Fuyu Li, Michael Wehner and E. Wes Bethel, "TECA: A Parallel Toolkit for Extreme Climate Analysis," Third Worskhop on Data Mining in Earth System Science (DMESS 2012) at the International Conference on Computational Science (ICCS 2012), Omaha, Nebraska, June, 2012.  LBNL-5352E (BibTeX)(PDF)

  30. Soile V.E. Keränen, Oliver Rübel, David W. Knowles and Mark D. Biggin, "Computational modeling of cis-regulatory modules from 3D expression data in Drosophila blastoderm atlas." Drosophila Genetics 2012, March 7-11, 2012, Chicago, IL, USA. LBNL-6318E-Poster. (Poster) (BibTeX)

  31. O. Rübel, S.V.E. Keränen, M.D. Biggin, D.W. Knowles, G.H. Weber, H. Hagen, B. Hamann, and E.W. Bethel, "Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data," Series: Mathematics and Visualization, Visualization in Medicine and Life Sciences II, Progress and New Challenges, Springer Verlag, Heidelberg, Germany, 2012, pp 267-285. LBNL-4891E. (BibTeX) (PDF)

  32. Mark Howison, E. Wes Bethel, Hank Childs. Hybrid Parallelism for Volume Rendering on Large, Multi- and Many-core Systems. IEEE Transactions on Visualization and Computer Graphics, 18(1):17-29, January 2012. LBNL-4370E. (bibtex) (PDF coming soon) LBNL-4370E.

  33. Ushizima, D.M., Weber, G., Morozov, D., Bethel, W., Sethian, J.A., "Algorithms for Microstructure Description applied to Microtomography", Carbon Cycle 2.0 Symposium, LBNL, Fev. 10. 2012.

  34. David Camp, Hank Childs, Christoph Garth, Dave Pugmire, Kenneth Joy. "Parallel Stream Surface Computation for Large Data Sets". In Proceedings IEEE Symposium on Large-Scale Data Analysis and Visualization 2012. (LBNL-5776E) (PDF) (BibTeX)

2011

  1. MacCarthy, B., Carr, H., Weber, G.H., Topological Galleries: A High Level User Interface for Topology Controlled Volume Rendering. Technical Report LBNL-5019E Lawrence Berkeley National Laboratory, Berkeley CA, USA, 94720. 2012. (BibTeX) (PDF)

  2. Huang, M.-Y., Mackey, L., Keraenen, S.V.E., Weber, G.H., Jordan, M.I., Knowles, D.W., Biggin, M.D. and Hamann, B. (2011), Visually relating gene expression and in vivo DNA binding data (pdf), in: Wu, F.-X., Zaki, M., Morishita, S., Pan, Y., Wong, S., Christianson, A. and Hu, X., eds., Proceedings of IEEE International Conference on Bioinformatics and Biomedicine 2011 (IEEE BIBM 2011), IEEE Computer Society Press, Los Alamitos, California, pp. 586-589. LBNL-5423E. (BibTeX) (PDF)

  3. E. Wes Bethel, David Leinweber, Oliver Rübel, Kesheng Wu (authors in alphabetical order), Federal Market Information Technology in the Post Flash Crash Era: Roles of Supercomputing, Workshop on High Performance Computational Finance at SuperComputing 2011 (SC11), LBNL-5263E, (PDF), (BibTeX). Extended version available at SSRN id1939522 or here. (This article was also featured in: Herbert Lash, "Post 'flash crash' monitoring emerges at Berkeley," Reuters.com.)(Other articles related to CIFT include: i) Jason Zweig, Could Computers Protect the Market From Computers?, Wall Street Journal.com )

  4. R. Ryne, B. Austin, J. Byrd, J. Corlett, E. Esarey, C. G. R. Geddes, W. Leemans, X. Li, Prabhat, J. Qiang, O. Rübel, J.-L. Vay, M. Venturini, K. Wu, B. Carlsten, D. Higdon and N. Yampolsky, "High Performance Computing in Accelerator Science: Past Successes, Future Challenges," ASCR/BES Workshop on Data and Communications in Basic Energy Sciences: Creating a Pathway for Scientific Discovery, Bethesda, MD, USA, October 24-45, 2011, LBNL-5506E-Poster. (BibTeX)

  5. Michael Philpott, Prabhat and Yoshiyuki Kawazoe, "Magnetism and Bonding in Graphene Nanodots with H modified Interior, Edge and Apex". J. Chem Physics, 135-8, August 2011. (BibTeX)

  6. Richard Martin, Prabhat, David Donofrio and Maciek Haranczyk, "Accelerating Analysis of void spaces in porous materials on multicore and GPU platforms". International Journal of High Performance Computing Applications. February 2011. (BibTeX)

  7. Suren Byna, Prabhat, Michael Wehner and John Wu, "Detecting Atmospheric Rivers in Large Climate Datasets". Supercomputing 2011 Workshop on Petascale Data Analytics: Challenges and Opportunities. (BibTeX)

  8. Tina Zhuo, Prabhat, Chris Paciorek and Cari Kaufman, "Distributed Kriging Analysis for Large Spatial Data". IEEE ICDM Workshop on Knowledge Discovery from Climate Data, Vancuover, December, 2011. (BibTeX)

  9. Prabhat, Suren Byna. Chris Paciorek, Gunther Weber, Kesheng Wu, Thomas Yopes, Michael Wehner, William Collins, George Ostrouchov, Richard Strelitz, E. Wes Bethel, "Pattern Detection and Extreme Value Analysis on Large Climate Data", DOE/BER Climate and Earth System Modeling PI Meeting. Washington DC September 19-22, 2011. Poster. (BibTeX)

  10. Christopher Paciorek, Michael Wehner, and Prabhat, "Computationally-efficient Spatial Analysis of Precipitation Extremes Using Local Likelihood", Statistical and Applied Mathematical Sciences Institute Uncertainty Quantification program, Climate Modeling Opening Workshop, Pleasanton, CA, USA, August 29-31, 2011. Poster. (BibTeX)

  11. Weber, G.H., Bremer, P.-T. and Pascucci, V., Topological Cacti: Visualizing Contour-based Statistics, in: Topological Methods in Data Analysis and Visualization II, pp. 63-76, Springer-Verlag, Heidelberg, Germany, 2011. LBNL-5018E. (BibTeX)

  12. Weber, G.H., Bremer, P.T., Gyulassy A., and Pascucci, V., Topology-based Feature Definition and Analysis, in: Numerical Modeling of Space Plasma Flows: Astronum-2010 (Astronomical Society of the Pacific Conference Series), Vol. 444, pp. 292-297, 2011. LBNL-5020E. (BibTeX)

  13. Deines E., Weber, G.H., Garth, C., Van Straalen, B. Borovikov, S., Martin, D.F., and Joy, K.I., On the computation of integral curves in adaptive mesh refinement vector fields, in: Hagen, H., ed., Scientific Visualization, Schloss Dagstuhl - Leibnitz Center for Informatics, Vol. 2, pp. 73-91 2011. LBNL-4972E (BibTeX) (PDF) (Publisher page)

  14. Ushizima, D.M., Parkinson, D., Nico, P., Ajo-Franklin, J., Macdowell, A., Kocar, B., Bethel E.W, Sethian J.A., "Statistical segmentation and porosity quantification of 3D x-ray microtomography", in XXXIV Applications of Digital Image Processing: Proceeding of SPIE 2011, August 2011, San Diego, CA, USA. LBNL publication number pending.

  15. Uselton, A., Ushizima, D.M., "I/O Workload Analysis with Server-side Data Collection", SuperComputing 2011 (SC11) - poster, Seattle, WA, Nov. 13. 2011. LBNL publication number pending.

  16. Prabhat, Quincey Koziol, Karen Schuchardt, E. Wes Bethel, Jerry Chuo, Mark Howison, Mike McGreevy, Bruce Palmer, Oliver Ruebel and John Wu, "ExaHDF5: An I/O Platform for Exascale Data Models, Analysis and Performance", Scientific Discovery Through Advanced Computing 2011, Invited Paper. (BibTeX)(PDF at confernce page)

  17. Maciej Haranczyk, Richard Martin, Prabhat and James Sethian, "Computational Approaches for the High-Throughput Analysis of Porous materials for Energy related applications". Scientific Discovery through Advanced Computing 2011. Invited Paper. (BibTeX)

  18. Ushizima, D.M., Weber, G.H., Ajo-Franklin, J., Kim, Y., Macdowell, A., Morozov, D., Nico, P., Parkinson, D., Trebotich, D., Wan, J., and Bethel E.W., "Analysis and visualization for multiscale control of geologic CO2", in: Journal of Physics: Conference Series, Proceedings of SciDAC 2011, July 2011, Denver, CO, USA. LBNL 4948E.

  19. Jerry Chou, Kesheng Wu, Oliver Rübel, Mark Howison, Ji Qiang, Prabhat, Brian Austin, E. Wes Bethel, Rob D. Ryne, and Arie Shoshani. Parallel Index and Query for Large Scale Data Analysis. In Proceedings of Supercomputing 2011, Seattle, WA, USA, 2011. LBNL-5317E. (PDF) (BibTeX)

  20. Bremer, P.-T., Weber, G.H., Tierny, J., Pascucci, V., Day, M.S., and Bell, J.B., Interactive Exploration and Analysis of Large Scale Turbulent Combustion Using Topology-based Data Segmentatio in: IEEE Transactions on Visualization and Computer Graphics, doi: 10.1109/TVCG.2010.253, 17(9), pp. 1307-1324, 2011. LBNL-5921E. (PDF) (BibTeX)

  21. Luke J. Gosink, Christoph Garth, John C. Anderson, E. Wes Bethel, and Kenneth I. Joy. An Application of Multivariate Statistical Analysis for Query-Driven Visualization. IEEE Transactions on Visualization and Computer Graphics, 17(3):264–275, 2011. LBNL-3536E. http://doi.ieeecomputersociety.org/10.1109/TVCG.2010.80 (PDF) (bibtex)

  22. Beketayev, K., Weber, G.H., Haranczyk, M., Bremer, P.-T., Hlawitschka, M., and Hamann, B., Topology-based Visualization of Transformation Pathways in Complex Chemical Systems, in: Computer Graphics Forum (Special Issue, Proc. Eurographics / IEEE Symposium on Visualization), 30(3), pp. 663-672, European Assiciation for Computer Graphics, June 2011. LBNL-5242E. (PDF), (BibTeX).

  23. E. Wes Bethel, John van Rosendale, Dale Southard, Kelly Gaither, Hank Childs, Eric Brugger, Sean Ahern. "Visualization at Supercomputing Centers: The Tale of Little Big Iron and the Three Skinny Guys." IEEE Computer Graphics and Applications, 31(1):90–95, Jan/Feb 2011. LBNL-4180E. (PDF) (bibtex)

  24. G.H. Weber, P.-T. Bremer, M.S. Day, J.B. Bell, and V. Pascucci. "Feature tracking using reeb graphs." In: V. Pascucci, X. Tricoche, H. Hagen, and J. Tierny, eds., Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications, pp. 241-253. Springer Verlag, 2011. LBNL-4226E. (PDF) (BibTeX)

  25. David Camp, Hank Childs, Amit Chourasia, Christoph Garth, Kenneth Joy. "Evaluating the Benefits of An Extended Memory Hierarchy for Parallel Streamline Algorithms". In Proceedings IEEE Symposium on Large-Scale Data Analysis and Visualization 2011, pp 57-64. (LBNL-5503E) (PDF) (BibTeX)

  26. H. Childs, S. Ahern, J. Meredith, M. Miller, and K. I. Joy. Comparative Visualization Using Cross-Mesh Field Evaluations and Derived Quantities. In Scientific Visualization: Interactions, Features, Metaphors, volume 2 of Dagstuhl Follow-Ups, pages 59-72. Dagstuhl, Germany, 2011 (LBNL-5943E) (PDF) (BibTeX)

  27. H. Childs, E. Brugger, B. Whitlock, J. Meredith, S. Ahern, K. Bonnell, M. Miller, G. H. Weber, C. Harrison, D. Pugmire, T. Fogal, C. Garth, A. Sanderson, E. W. Bethel, M. Durant, D. Camp, J. M. Favre, O. Ruebel, P. Navratil, M. Wheeler, P. Selby, and F. Vivodtzev. VisIt: An End-User Tool For Visualizing and Analyzing Very Large Data. In Proceedings of SciDAC 2011 (LBNL-5945E) (PDF) (BibTeX)

  28. C. Harrison, H. Childs, and K. P. Gaither. Data-Parallel Mesh Connected Components Labeling and Analysis. In Proceedings of EuroGraphics Symposium on Parallel Graphics and Visualization, pages 131-140, April 2011 (LBNL-5944E) (PDF) (BibTeX)

  29. Jerry Chuo, John Wu, Prabhat, "FastQuery: A Parallel Indexing System for Scientific Data", Workshop on Interfaces and Abstractions for Scientific Data Storage, IEEE Cluster 2011. (BibTeX)

  30. Prabhat, Dmitry Zubarev and W. A. Lester, "Statistical Exploration of Electronic Structure of Molecules from Quantum Monte Carlo Simulations". LBL Technical Report, (BibTeX) LBNL-4564E.

  31. Jerry Chuo, John Wu, Prabhat, "Design of FastQuery: how to generalize Indexing and Querying systems for scientific data". LBL Tech Report. Publication number pending. (BibTeX)

  32. Jerry Chuo, John Wu, Prabhat, "FastQuery: a general Index and Query system for scientific data", Scientific and Statistical Database Management Conference 2011, Poster. (BibTeX)

  33. Richard Martin, Maciej Haranczyk, Prabhat and James Sethian, "PDE-based analysis of void space of porous materials on multicore CPUs", Manycore and Accelerator-based High-performance Scientific Computing 2011, UC Berkeley. Poster. (BibTeX)

  34. Richard Martin, Thomas Willems, Chris Rycroft, Prabhat, Michael Kazi and Maciej Haranczyk, "High Throughput structure analysis and descriptor generation for crystalline porous materials". International Conference on Chemical Structures 2011. Poster. (BibTeX)


2010

  1. Min-Yu Huang, Gunther H. Weber, Xiao-Yong Li, Mark D. Biggin, and Bernd Hamann. "Quantitative Visualization of ChIP-chip Data by Using Linked Views." In: Proceedings IEEE International Conference on Bioinformatics and Biomedicine 2010 (IEEE BIBM 2010) Workshops, Workshop on Integrative Data Analysis in Systems Biology (IDASB), pp. 195-200. LBNL-4491E. (BibTeX) (PDF)

  2. Patrick Oesterling, Gerik Scheuermann, Sven Teresniak, Gerhard Heyer, Steffen Koch, Thomas Ertl, Gunther H. Weber. "Two-stage Framework for a Topology-Based Projection and Visualization of Classified Document Collections." In Proceedings IEEE Symposium on Visual Analytics Science and Technology (IEEE VAST), pp. 91-98. Salt Lake City, Utah, USA, October 2010. LBNL-4074E. (BibTeX) (PDF)

  3. Mark Howison, Quincey Koziol, David Knaak, John Mainzer, John Shalf. Tuning HDF5 for Lustre File Systems. In IASDS10 – Workshop on Interfaces and Abstractions for Scientific Data Storage, Heraklion, Crete, Greece. September 2010. LBNL-4803E. (bibtex) (PDF)

  4. Mark Howison, Andreas Adelmann, E. Wes Bethel, Achim Gsell, Benedikt Oswald, Prabhat. H5hut: A High-Performance I/O Library for Particle-based Simulations. In IASDS10 – Workshop on Interfaces and Abstractions for Scientific Data Storage, Heraklion, Crete, Greece. September 2010. LBNL-4021E. (bibtex) (PDF)

  5. Tina Zhuo, Prabhat, Chris Paciorek and Cari Kaufman, "Distributed Likelihoods Computation for Large Spatial Data", SuperComputing 2010, Poster. (BibTeX)

  6. E.A. Carvalho, D.M. Ushizima, F.N.S. Medeiros, C.I.O. Martins, R.C.P. Marques, I.N.S. Oliveira, "SAR imagery segmentation by statistical region growing and hierarchical merging", Digital Signal Processing, Elsevier,Volume 20, Issue 5, Pages 1365-1378, Sept 2010. #20 in Top 25 Hottest Articles in Digital Signal Processing. LBNL-3844E.(bibtex)

  7. D. M. Ushizima, F. N. S. Medeiros, J. Cuadros, C. I. O. Martins, "Vessel Network Detection Using Contour Evolution and Color Components", Proceedings of the 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Buenos Aires, Argentina. Sept 2010. (bibtex). LBNL-5428E.

  8. C. Rycroft, D. M. Ushizima, R. Saye, C. M. Ghajar, J. A. Sethian, "Building a physical cell simulation and comparing with confocal microscopy", Bay Area Physical Sciences - Oncology Center (NCI) Meeting 2010, UCSF Medical Sciences, Sept 2010. (PDF)

  9. M. Howison, E. W. Bethel, and H. Childs. "Hybrid Parallelism for Volume Rendering on Large, Multi-core Systems." In Journal of Physics: Conference Series, Proceedings of SciDAC 2010, July 2010, Chattanooga TN, USA. LBNL-4024E. (PDF) (bibtex)

  10. M. Howison, E. W. Bethel, and H. Childs. "Hybrid Parallelism for Volume Rendering on Large, Multi-core Systems." In Astronum 2010, 5th International Conference on Numerical Modeling of Space Plasma Flows, June 2010, San Diego, CA, USA. LBNL-4024E-Conf. (pdf coming soon) (bibtex)

  11. Oliver Rübel, Sean Ahern, E. Wes Bethel, Mark. D Biggin, Hank Childs, Estelle Cormier-Michel, Angela DePace, Michael B. Eisen, Charless C. Fowlkes, Cameron G. R. Geddes, Hans Hagen, Bernd Hamann, Min-Yu Huang, Soile V. E. Keränen, David W. Knowles, Cris L. Luengo Hendriks, Jitendra Malik, Jeremy Meredith, Peter Messmer, Prabhat, Daniela Ushizima, Gunther H. Weber, and Kesheng Wu. Coupling Visualization and Data Analysis for Knowledge Discovery from Multi-dimensional Scientific Data. In Procedia Computer Science, Proceedings of International Conference on Computational Science, ICCS 2010, May 2010. LBNL-3669E. (PDF) (bibtex) (Online at sciencedirect.com)

  12. M. Howison. Comparing GPU Implementations of Bilateral and Anisotropic Diffusion Filters for 3D Biomedical Datasets. Technical Report LBNL-3425E, Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 94720, 2010. (PDF)

  13. T.Fogal, H. Childs, S. Shankar, J. Kruger, R.D. Bergeron, and P. Hatcher. Large Data Visualization on Distributed Memory Multi-GPU Clusters. High Performance Graphics 2010, Saarbruken, Germany, June 2010. LBNL-4571E. (PDF) (bibtex)

  14. J. Meredith and H. Childs. Visualization and Analysis-Oriented Reconstruction of Material Interfaces. Eurographics/IEEE Symposium on Visualization (EuroVis), Bordeaux, France, June 2010. LBNL-4567E. (PDF) (bibtex)

  15. A.Uselton, K.Antypas, D.M.Ushizima, J.Sukharev, "File System Monitoring as a Window Into User I/O Requirements", CUG-2010, Edinburgh, UK, May 24-27th, 2010.,(PDF)

  16. Daniela Ushizima, Cameron Geddes, Estelle Cormier-Michel, E. Wes Bethel, Janet Jacobsen, Prabhat, Oliver Rbel, Gunther Weber, Bernard Hamann, Peter Messmer, Hans Hagen. "Automated Detection and Analysis of Particle Beams in Laser-plasma Accelerator Simulations", In-Tech, 367-389, 2010. LBNL-3845E. (bibtex)

  17. D. M. Ushizima, F. Medeiros, Retinopathy diagnosis from ocular fundus image analysis, Modeling and Analysis of Biomedical Image, SIAM Conference on Imaging Science (IS10), Chicago, Il, April 12-14th, 2010.

  18. D. M. Ushizima and J. Cuadros, "Ocular fundus for retinopathy characterization", Bay Area Vision Meeting, Feb 5th, Berkeley, CA 2010.

  19. Hank Childs, David Pugmire, Sean Ahern, Brad Whitlock, Mark Howison, Prabhat, Gunther Weber, E. Wes Bethel. "Extreme Scaling of Production Visualization Software on Diverse Architectures." IEEE Computer Graphics and Applications, 30(3):22-31, May/June 2010. LBNL-3403E. (Full article) (Preceding technical report) (bibtex)

  20. Martin Isenburg, Peter Lindstrom, and Hank Childs, "Parallel and Streaming Generation of Ghost Data for Structured Grids." IEEE Computer Graphics and Applications, 30(3):32-44, May/June 2010. (Full article) (bibtex)

  21. Mark Howison, E. Wes Bethel, and Hank Childs. "MPI-hybrid Parallelism for Volume Rendering on Large, Multi-core Systems." In Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization, May 2–3, 2010, Norköping, Sweden. LBNL-3297E. Best Paper Award. (bibtex), (PDF).

  22. E. Wes Bethel. Using wesBench to Study the Rendering Performance of Graphics Processing Units. Technical Report LBNL-3025E, Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 94720, 2010. (PDF) (BibTeX)

  23. P.-T. Bremer, G.H. Weber, V. Pascucci, M.S. Day and John B. Bell, Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames. In: : IEEE Transactions on Visualization and Computer Graphics, 16(2): 248-260, 2010. LBNL-2276E. (PDF), (BibTeX).

  24. 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, Vol 7, No.1, Pages 64-79, Jan/Mar 2010. LBNL-382E. (PDF), (BibTeX)

  25. G. H. Weber, S. Ahern, E.W. Bethel, S. Borovikov, H.R. Childs, E. Deines, C. Garth, H. Hagen, B. Hamann, K.I. Joy, D. Martin, J. Meredith, Prabhat, D. Pugmire, O. Rübel, B. Van Straalen and K. Wu. "Recent Advances in VisIt: AMR Streamlines and Query-Driven Visualization." In: Numerical Modeling of Space Plasma Flows: Astronum-2009 (Astronomical Society of the Pacific Conference Series). LBNL-3185E. Vol. 429, pp. 329-334, 2010. (BibTeX), (PDF).

  26. O. Rübel, "Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-energy Physics," Schriftenreihe Informatik, Band 28, Der Dekan (hrsg), Fachbereich Informatik, Technische Universität Kaiserslautert, December, 2009, ISBN 978-3-941438-35-4, ISSN 1610-2673. LBNL-3155E. (BibTeX), (PDF at KLUEDO)

  27. David Camp, Christoph Garth, Hank Childs, David Pugmire, Kenneth Joy, "Streamline Integration using MPI-Hybrid Parallelism on Large Multi-Core Architecture" IEEE Transactions on Visualization and Computer Graphics, 17(11):1702–1713, November 2011, (LBNL-4563E) (BibTeX) (PDF)

2009

  1. Mark Howison and Carlo Sequin. CAD Tools for Creating Space-filling 3D Escher Tiles. In Computer-Aided Design and Applications, (6):737-748, Reno, NV, USA, 2009. LBNL-2467E. (PDF) (bibtex)

  2. C. Garth, E. Deines, K. Joy, E. W. Bethel, H. Childs, G. Weber, S. Ahern, D. Pugmire, A. Sanderson, C. Johnson. "Twists and Turns: Vector Field Visual Data Analysis for Petascale Computational Science." SciDAC Review, Number 15, Winter 2009. (LBNL-2983E). (PDF at scidacreview.org) (Bibtex)

  3. 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, 2009. (LBNL-1449E). (bibtex)

  4. P.-T. Bremer, G.H. Weber, J. Tierny, V. Pascucci, M.S. Day and J.B. Bell. "A Topological Framework for the Interactive Exploration of Large Scale Turbulent Combustion," In: Proceedings of the 5th IEEE International Conference on e-Science, pp. 247-254, 10.1109/e-Science.2009.42, Oxford, UK, December 2009. (BibTeX) (PDF). LBNL-3183E.

  5. D. Pugmire, H. Childs, C. Garth, S. Ahern, G.H. Weber. "Scalable computation of streamlines on very large datasets". In: Proc. Supercomputing SC09. Portland, OR, USA. November 2009. LBNL-3264E. (BibTeX) PDF forthcoming.

  6. O. Rübel, C.G.R. Geddes, E. Cormier-Michel, K. Wu, Prabhat, G.H. Weber, D.M. Ushizima, P. Messmer, H. Hagen, B. Hamann, and E.W. Bethel,  "Automatic Beam Path Analysis of laser Wakefield Particle Acceleration Data", IOP Computational Science & Discovery, 2 015005 (38pp), Nov, 2009, LBNL-2734E. (see also here). (PDF) (BibTeX)  

  7. "Smashing the Trillion Zone Barrier." Article at Scientific Computing. (Not an LBNL publication)

  8. E. W. Bethel, C. Johnson, S. Ahern, J. Bell, P.-T. Bremer, H. Childs, E. Cormier-Michel, M. Day, E. Deines, T. Fogal, C. Garth, C. G. R. Geddes, H. Hagen, B. Hamann, C. Hansen, J. Jacobsen, K. Joy, J. Krüger, J. Meredith, P. Messmer, G. Ostrouchov, V. Pascucci, K. Potter, Prabhat, D. Pugmire, O. Rübel, A. Sanderson, C. Silva, D. Ushizima, G. Weber, B. Whitlock, K. Wu. "Occam's Razor and Petascale Visual Data Analysis." In Journal of Physics Conference Series, Proceedings of SciDAC 2009. LBNL-2210E. (PDF) (bibtex)

  9. K. Wu, S. Ahern, E. W. Bethel, J. Chen, H. Childs, E. Cormier-Michel, C. Geddes, J. Gu, H. Hagen, B. Hamann, W. Koegler, J. Lauret, J. Meredith, P. Messmer, E. Otoo, V. Perevoztchikov, A. Poskanzer, Prabhat, O. Rübel, A. Shoshani, A. Sim, K. Stockinger, G. Weber, W.-M. Zhang. "FastBit: Interactively Searching Massive Data." In Journal of Physics Conference Series, Proceedings of SciDAC 2009. (LBNL-2164E) (PDF), (bibtex)

  10. N. Shah, N., S. E. Dillard, G.H. Weber, B. Hamann. "Volume visualization of multiple alignment of large genomic DNA." In Mathematical Foundations of Scientific Visualization, Computer Graphics, and Massive Data Exploration, Springer-Verlag, Heidelberg, Germany, pp. 325-342, July, 2009. LBNL-63126. (PDF), (BibTeX).

  11. C. G. R. Geddes, E Cormier-Michel, E. H. Esarey, C. B. Schroeder, J.-L. Vay, W. P. Leemans, D. L.. Bruhwiler, J. R. Cary, B. Cowan, M. Durant, P. Hamill, P. Messmer, P. Mullowney, C. Nieter, K. Paul, S. Shasharina, S. Veitzer, G. Weber, O. Rübel, D. Ushizima, Prabhat, E. W.Bethel, K. Wu. "Large Fields for Smaller Facility Sources." SciDAC Review, Number 13, Summer 2009. LBNL-2299E. (PDF at the SciDAC Review website), (bibtex)

  12. Luke Gosink, Kesheng Wu, E. Wes Bethel, John D. Owens, Kenneth I. Joy. "Data Parallel Bin-based Indexing for Answering Queries on Multi-core Architectures." In Proceedings of the 21st International Conference on Scientific and Statistical Database Management (SSDBM), pp 110-129. New Orleans, LA, June 2009. (PDF) (bibtex)

  13. Shoaib Kamil, Cy Chan, Sam Williams, Leonid Oliker, John Shalf, Mark Howison, E. Wes Bethel, Prabhat. "A Generalized Framework for Auto-tuning Stencil Computations." In CUG 2009, May 4-7, 2009, Atlanta GA, USA. Best Paper Award winner. (LBNL-2078E). (PDF) (bibtex)

  14. 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." In IEEE Transactions on Computational Biology and Bioinformatics., 6(2), April-June, pp. 296-309, 2009. LBNL-63776. (PDF), (BibTeX).

  15. S. E. Dillard, V. Natarjan, G. H. Weber, V. Pascucci and B. Hamann. Topology-guided Tessellation of Quadratic Elements. In International Journal of Computational Geometry and Applications (IJCGA), 19(2), April, special issue, pp. 196-211, 2009. LBNL-63771. (PDF), (BibTeX)

  16. M. Hlawitschka, G.H. Weber, A. Anwander, O.T. Carmichael, B. Hamann and G. Scheuermann. Interactive Volume Rendering of Diffusion Tensor Data. In Visualization and Processing of Tensor Fields: Advances and Perspectives. Springer-Verlag, Heidelberg, Germany, pp. 161-176, April, 2009. LBNL-2286E. (PDF), (BibTeX)

  17. E. Wes Bethel. "High Performance, Three-dimensional Bilateral Filtering." Lawrence Berkeley National Laboratory, Tech Report LBNL-1601E, 2009. (bibtex) (PDF, 63MB due to numerous high-res images).

  18. Yunfeng Yang, Daniel P Harris, Feng Luo, Wenlu Xiong, Marchin Joachimiak, Liyou Wu, Paramvir Dehal, Janet Jacobsen, Anthony V Palumbo, Adam P. Arkin, and Jizhong Zhou. "Snapshot of iron response in Shewanella oneidensis by gene network reconstruction." BMC Genomics 2009, 10:131. (BibTex)

  19. Sharon Borglin, Dominique Joyner, Janet Jacobsen, Aindrila Mukhopadhyay, Terry C. Hazen. "Overcoming the anaerobic hurdle in phenotype microarrays: Generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough." J. Microbiological Methods, 76 (2), 159-168. February 2009. (PDF) (BibTex) (LBNL-1822E)

  20. E. Wes Bethel, Oliver Rübel, Prabhat, Kesheng Wu, Gunther H. Weber, Valerio Pascucci, Hank Childs, Ajith Mascarenhas, Jeremy Meredith, and Sean Ahern. "Modern Scientific Visualization is More than Just Pretty Pictures." In: Numerical Modeling of Space Plasma Flows: Astronum-2008 (Astronomical Society of the Pacific Conference Series). (LBNL-1450E) (PDF) (bibtex)

  21. C.I.O.Martins, D.M.Ushizima, F.N.S.Medeiros, F.N.Bezerra, R.C.P.Marques, N.D.A.Mascarenhas, "Iterative Self-dual Reconstruction on Radar Image Recovery", Proc. of IEEE Workshop on Applications of Computer Vision, Snowbird, Utah, 37-42, 2009.LBNL-3846E.

2008

  1. Daniela Ushizima, Oliver Rübel, Prabhat, Gunther Weber, E. Wes Bethel, Cecilia Aragon, Cameron Geddes, Estelle Cormier-Michel, Bernd Hamann, Peter Messmer, Hans Hagen. "Automated Analysis for Detecting Beams in Laser Wakefield Simulations". 2008 Seventh International Conference on Machine Learning and Applications, Proceedings of IEEE ICMLA'08, 2008. LBNL-960E. (PDF) (Bibtex)

  2. Regis C. P. Marques, Fatima N. S. Medeiros, Daniela M. Ushizima. "Target Dectection on SAR Images Using Level Set Methods". IEEE Transactions on Systems, Man and Cybernetics, 2008. (to appear) LBNL-958E. (Bibtex)

  3. C.I.O. Martins, R.M.S. Veras, G.L.B. Ramalho, F.N.S. Medeiros, D. M. Ushizima, "Automatic Microaneurysm Detection and Characterization Through Digital Color Fundus Images". Brazilian Artificial Intelligence Community Conference, Tenth Brazilian Symposium on Neural Networks, Proceedings of IEEE SBRN'2008, 2008. (LBNL number pending)

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

  5. 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. (PDF) (bibtex)

  6. 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. LBNL-952E. (PDF) (BibTeX)

  7. 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. (PDF) (BibTeX)

  8. Sarah Poon, Rollin Thomas, Cecilia Aragon, and Brian Lee, "Context-Linked Virtual Assistants for Distributed Teams: An Astrophysics Case Study." CSCW 2008: ACM Conference on Computer Supported Cooperative Work. Best Paper Award Nominee (one of 12 out of 235 submissions). (PDF). (Link to portal.acm.com for bibtex)

  9. Cecilia Aragon, Stephen Bailey, Sarah Poon, Karl Runge, and Rollin Thomas, "Sunfall: A Collaborative Visual Analytics System for Astrophysics." J. Phys.: Conf. Ser. 125 012091 (Proceedings of SciDAC 2008). LBNL-657E. (2008) (PDF), (BibTeX).

  10. 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. (PDF), (BibTeX).

  11. S. Bailey, C. Aragon, R. Romano, R. C. Thomas, B. A. Weaver and D. Wong, "Object classification at the Nearby Supernova Factory." Astronomische Nachrichten Vol. 329, Issue 3, pp. 292-294 (2008). LBNL-696E. (HTML), (BibTeX)

  12. 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, Summer 2008, pp 24-33. LBNL-472E. (PDF at the SciDAC Review website) (bibtex)

  13. 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", GI Lecture Notes in Informatics, Gesellschaft fuer Informatik (GI), Bonn, Germany, 2008. LBNL-249E. (PDF), (BibTeX)

  14. 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. (BibTeX)

  15. 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, April, 2008. LBNL-220E. (PDF), (BibTeX)

  16. William T.C. Kramer, John M. Shalf, E. Wes Bethel, D. Agarwal, Michael Banda, John Hules, Juan C. Meza, Leonid Oliker, Horst Simon, David Skinner, Francesca Verdier, Howard Walter, Michael Wehner, and Katherine Yelick. "HPC in 2016: A View Point from NERSC." Proceedings of the Cray User Group Conference, 2008. Helsinki, Finland.

  17. L. R. Comolli, A. J. Spakowitz, C. E. Siegerist, P. J. Jardin, S. Grimes, D. L. Anderson, C. Bustamante, K. H. Downing. "Three-dimensional Architecture of the Bacteriophage Phi29 Packaged Genome and Elucidation of its Packaging Process." Virology, 371(2):267, February 2008. (LBNL publication number pending.) (PDF unavailable due to publisher's rules.)

  18. 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. (PDF), (bibtex)

  19. J. Chen, I. Yoon and E. W. Bethel. "Interactive, Internet Delivery of Visualization via Structured, Prerendered Multiresolution Imagery." IEEE Transactions on Visualization and Computer Graphics, Volume 14, Number 2, March/April 2008. LBNL-62252. (PDF), (bibtex).

  20. M.-Y. Huang, O. Rübel, G.H. Weber, C.L. Luengo Hendriks, M.D. Biggin, H. Hagen, B. Hamann. "Segmenting Gene Expression Patterns of Early-stage Drosophila Embryos.", In: L. Linsen, H. Hagen, B. Hamann, eds., Mathematical Methods for Visualization in Medicine and Life Sciences. Springer-Verlag, Heidelberg, Germany, January, 2008. LBNL-62450. (PDF), (BibTeX).

2007

  1. K. Joy, M. Miller, H. Childs, E. W. Bethel, J. CLyne, G. Ostouchov, S. Ahern. "Frameworks for Visualization at the Extreme Scale." In Journal of Physics Conference Series, Volume 78, Proceedings of SciDAC 2007, June 2007. LBNL-63762. (PDF), (bibtex)

  2. E. W. Bethel, J. Chen, I. Yoon. "Interactive, Internet Delivery of Visualization via Structured, Prerendered Imagery." Two-page research highlight. LBNL-63675. (PDF) (bibtex)

  3. E. W. Bethel, L. Gosink, J. Anderson, K. Joy. "Variable Interactions in Query-Driven Visualization." Two-page research highlight. LBNL-63674. (PDF) (bibtex)

  4. E. W. Bethel, O. Ruebel, G. Weber. "Visualization and Analysis of 3D Gene Expression Data." Two-page research highlight. LBNL-63658. (PDF) (bibtex)

  5. 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. (PDF) (bibtex)

  6. 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. LBNL-63701. (PDF) (bibtex)

  7. C. Aragon, S. Bailey, S. Poon, K. Runge, R. Thomas, "Sunfall: A Collaborative Visual Analytics System for Astrophysics," Poster at IEEE VAST 2007. LBNL report number requested. (abstract PDF) (poster PDF) (bibtex) Winner of Best Poster Award.

  8. G. H. Weber, P.-T. Bremer and V. Pascucci. "Topological Landscapes: A Terrain Metaphor for Scientific Data." IEEE Transactions on Visualization and Computer Graphics 13(6), November/December 2007, pages 1416–1423, Proceedings of IEEE Visualization 2007. LBNL-63763. (PDF) (BibTeX)

  9. L. Gosink, J. Anderson, W. Bethel, K. Joy. "Variable Interactions in Query-Driven Visualization." IEEE Transactions on Visualization and Computer Graphics 13(6), November/December 2007, pages 1400–1407, Proceedings of IEEE Visualization 2007. (Best Paper Award Nominee; 1 of 5 from over 216 submissions.) LBNL-63254. (PDF) (bibtex)

  10. S. Bailey, C. Aragon, R. Romano, R. C. Thomas, B. A. Weaver and D. Wong. "How to Find More Supernovae with Less Work: Object Classification Techniques for Difference Imaging." Astrophysical Journal 665:1246T (2007). LBNL-62659. (bibtex)

  11. J.S. Jacobsen, D.C. Joyner, S.E. Borglin, T.C. Hazen, A.P. Arkin, E.W. Bethel. "Visualization of Growth Curve Data from Phenotype Microarray Experiments." In 11th International Conference on Information Visualization IV 2007, Zürich, Switzerland, July 4-6, 2007. IEEE Computer Society Press. (LBNL-63251) (BibTex)

  12. Copin, Y.; Buton, C.; Gangler, E.; Smadja, G.; Pecontal, E.; Rigaudier, G.; Antilogus, P.; Bailey, S.; Pain, R.; Pereira, R.; Wu, C.; Aldering, G.; Aragon, C.; Bongard, S.; Childress, M.; Loken, S.; Nugent, P.; Perlmutter, S.; Runge, K.; Thomas, R. C.; Weaver, B. A.; Baltay, C.; Bauer, A.; Rabinowitz, D.; Scalzo, R. "The Nearby Supernova Factory: toward a high-precision spectro-photometry." Proc. of the French Society of Astronomy and Astrophysics, Grenoble, France (July 2007). LBNL report number requested. (HTML) (bibtex)

  13. Buton, C.; Copin, Y.; Gangler, E.; Smadja, G.; Pecontal, E.; Rigaudier, G.; Antilogus, P.; Bailey, S.; Pain, R.; Pereira, R.; Wu, C.; Aldering, G.; Aragon, C.; Bongard, S.; Childress, M.; Loken, S.; Nugent, P.; Perlmutter, S.; Runge, K.; Thomas, R. C.; Weaver, B. A.; Baltay, C.; Bauer, A.; Rabinowitz, D.; Scalzo, R. "The Supernova Integral Field Spectrograph: keys to high-precision spectro-photometry." Proc. of the French Society of Astronomy and Astrophysics, Grenoble, France (July 2007). LBNL report number requested. (HTML) (bibtex)

  14. O. G. Staadt, V. Natarjan, G. H. Weber, D.F. Wiley, B. Hamann. "Interactive Processing and Visualization of Image Data for Biomedical and Life Science Applications." In: BMC Cell Biology, 8 (Suppl 1):S10 (10 July), BioMed Central Ltd., 2007. LBNL-63127. (HTML), (PDF), (BibTeX).

  15. G.H. Weber, V. Beckner, H. Childs, T. Ligocki, M. Miller, B. van Straalen, E.W. Bethel. "Visualization Tools for Adaptive Mesh Refinement Data." In: W. Benger, R. Heinzel, W. Kapferer, W. Schoor, M. Tyagi, S. Venkataraman, G.H. Weber, eds., Proceedings of the 4th High End Visualization Workshop (Tyrol Austria, June 18-22, 2007). ISBN 978-3-86541-216-4, Lehmanns Media, pp. 12-25, 2007. LBNL-62954. (PDF) (BibTeX).

  16. A. Adelmann, A. Gsell, B. Oswald, T. Schietinger, W. Bethel, J.M. Shalf, C. Siegerist, K. Stockinger. "Progress on H5Part: A Portable High Performance Parallel Data Interface for Electromagnetics Simulations", Particle Accelerator Conference, Albuquerque, New Mexico, USA, June 2007, IEEE Computer Society Press. LBNL-63042. (bibtex) (PDF)

  17. G. H. Weber, S. E. Dillard, H. A. Carr, V. Pascucci, B. Hamann. "Topology-controlled volume rendering." In: IEEE Transactions on Visualization and Computer Graphics, 13(2), pp. 330-341, doi: 10.1109/TVCG.2007.47, 2007. (LBNL-63120, California Digital Library Postprint)(BibTeX)

  18. E. W. Bethel, C. 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. Parker, C. Silva, A. Sanderson, X. Tricoche. "SciDAC Visualization and Analytics Center for Enabling Technology." Journal of Physics Conference Series, SciDAC 2007, June 2007, Volume 78, 2007. LBNL-63542. (PDF) (bibtex)

  19. C.L. Luengo Hendriks, C.C. Fowlkes, S.V.E. Keränen, L. Simirenko, G.H. Weber, O. Rübel, M.-Y. Huang, A.H. DePace, C. Henriquez, X.-Y. Li, H.C. Chu, D.W. Kaszuba, A. Beaton, S. Celniker, B. Hamann, M.B. Eisen, J. Malik, D.W. Knowles, M.D. Biggin. "Virtual embryos as tools for 3D gene expression analyses", 48th Annual Drosophila Research Conference, Philadelphia, Pennsylvania, March 7-11, 2007. LBNL-63062. (PDF), (BibTeX).

  20. Gu, S., Anderson, I., Kunin, V., Cipriano, M., Minovitsky, S., Weber, G.H., Amenta, N., Hamann, B. and Dubchak, I., TreeQ-VISTA: An Interactive Tree Visualization Tool with Functional Annotation Query Capabilities, in: Bioinformatics 23(6), doi: 10.1093/bioinformatics/btl643, 2007. LBNL-61863. (PDF), (BibTeX).

  21. F. Reiss, K. Stockinger, K. Wu, A. Shoshani, J. M. Hellerstein. "Enabling Real-Time Querying of Live and Historical Stream Data" In International Conference on Scientific and Statistical Database Management (SSDBM 2007) Banff, Canada, July 2007, IEEE Computer Society Press. LBNL-61080. (PDF) (bibtex)

  22. C. Aragon and S. Poon. "The Impact of Usability on Supernova Discovery." Workshop on Increasing the Impact of Usability Work in Software Development, CHI 2007: ACM Conference on Human Factors in Computing Systems, San Jose, California, April 2007. LBNL-62380. (bibtex)

  23. C. Aragon and D. Aragon. "A Fast Contour Descriptor Algorithm for Supernova Image Classification." In Proceedings of the SPIE/IS&T Conference on Electronic Imaging, Volume 6469-07, Nasser Kehtarnavaz, Matthias F. Carlsohn, eds. January 2007. LBNL-61182.pdf (bibtex)

  24. R. C. Thomas, G. Aldering, P. Antilogus, C. Aragon, S. Bailey, C. Baltay, E. Baron, A. Bauer, C. Buton, S. Bongard, Y. Copin, E. Gangler, S. Gilles, R. Kessler, S. Loken, P. Nugent, R. Pain, J. Parrent, E. Pecontal, R. Pereira, S. Perlmutter, D. Rabinowitz, G. Rigaudier, K. Runge, R. Scalzo, G. Smadja, L. Wang, B. A. Weaver. "Nearby Supernova Factory Observations of SN 2006D: On Sporadic Carbon Signatures in Early Type Ia Supernova Spectra." In Astrophysical Journal Letters 654:L53-L56, January 2007. LBNL-61745.pdf (bibtex)


2006

  1. Bailey, S.; Aldering, G.; Aragon, C.; Bongard, S.; Childress, M.; Loken, S.; Nugent, P.; Perlmutter, S.; Runge, K.; Scalzo, R.; Romano, R.; Thomas, R.; Weaver, B.; Baltay, C.; Bauer, A.; Herrera, D.; Rabinowitz, D.; Pecontal, E.; Rigaudier, G.; Antilogus, P.; Gilles, S.; Pain, R.; Pereira, R.; Buton, C.; Copin, Y. "How to Find More Supernovae with Less Work: Object Classification Techniques for Difference Imaging." Poster at 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #78.09. December 2006. (bibtex)
  2. Weaver, B. A.; Aldering, G.; Aragon, C.; Bailey, S.; Bongard, S.; Childress, M. J.; Loken, S.; Nugent, P.; Perlmutter, S.; Romano, R.; Runge, K.; Scalzo, R.; Thomas, R. C.; Baltay, C.; Bauer, A.; Herrera, D.; Rabinowitz, D.; Pecontal, E.; Rigaudier, G.; Antilogus, P.; Gilles, S.; Pain, R.; Pereira, R.; Buton, C.; Copin, Y. "The Nearby Supernova Factory." Poster at 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #150.16. December 2006. (bibtex)
  3. R. Romano, C. Aragon and C. Ding. "Supernova Recognition Using Support Vector Machines." Proceedings of the 5th International Conference on Machine Learning and Applications (ICMLA'06), Orlando, FL, December 2006. LBNL-61192.pdf. (bibtex) (Best Paper Award!)

  4. Kurt Stockinger, E. Wes Bethel, Scott Campbell, Eli Dart, Kesheng Wu. "Detecting Distributed Scans Using High-Performance Query-Driven Visualization". In Proceedings of SC06 (Supercomputing). November, 2006. LBNL-60053. (bibtex) (PDF)

  5. E. Wes Bethel, Scott Campbell, Eli Dart, Kurt Stockinger and Kesheng Wu. "Accelerating Network Traffic Analysis Using Query-Driven Visualization." In Proceedings of the 2006 IEEE Symposium on Visual Analytics Science and Technology, pp 115-122, Baltimore MD, October 2006. LBNL-59819. (bibtex) (PDF)

  6. Ryne, R.D. ; Qiang, J. ; Bethel, E.W. ; Pogorelov, I. ; Shalf, J. ; Siegerist, C. ; Venturini, M. ; Dragt, A.J. ; Adelmann, A. ; Abell, D. ; Amundson, J. ; Spentzouris, P. ; Neri, F. ; Walstrom, P. ; Mottershead, C.T. ; Samulyak, R. "Recent Progress on the Marylie/Impact Beam Dynamics Code", 2006 International Computational Accelerator Physics Conference, Chamonix, France, October 2 - 6,2006. LBNL-62017. (bibtex) (PDF).

  7. K. Wu, K. Stockinger, A. Shoshani, W. Bethel. "FastBit - Helps Finding the Proverbial Needle in a Haystack." July, 2006. LBNL/PUB-963 (Two-page research highlight). (bibtex) (PDF)

  8. E. Wes Bethel, S. Campbell, E. Dart, J. Shalf, K. Stockinger, K. Wu. High Performance Visualization Using Query-Driven Visualization and Analytics. LBNL-PUB-959 (Two-page research highlight). July, 2006. (bibtex) (PDF)

  9. E. Wes Bethel, L. Gosink, J. Shalf, K. Stockinger, K. Wu. HDF5-FastQuery: An API for Simplifying Access to Data Storage, Retrieval, Indexing and Querying. LBNL-PUB-958 (Two-page research highlight). June, 2006. (bibtex) (PDF)

  10. O. Rübel, G.H. Weber, S.V.E. Keränen, C.C. Fowlkes, C.L. Luengo Hendriks, L. Simirenko, N.Y. Shah, M.B. Eisen, M.D. Biggin, H. Hagen, D. Sudar, J. Malik, D.W. Knowles, and B. Hamann. PointCloudXplore: a visualization tool for 3D gene expression data. In: H. Hagen, A. Kerren and P. Dannenmann, eds., Visualization of Large and Unstructured Data Sets, GI Lecture Notes in Informatics, Vol. S-4, Gesellschaft fuer Informatik (GI), Bonn, Germany, pp. 107-117. June, 2006. LBNL-62336 (PDF), (BibTeX).

  11. D. Abell, A. Adelmann, J. Amundson, A. Dragt, C. Mottershead, F. Neri, I. Pogorelov, J. Qiang, R. Ryne, J. Shalf, C. Siegerist, P. Spentzouris, E. Stern, M. Venturini, P. Walstrom. "Beam Dynamics." Journal of Physics: Conference Series, SciDAC 2006 Conference, Denver CO. June 25-29, 2006. LBNL-61521. (bibtex)

  12. Cryo-EM and single molecule biophysical studies of dsDNA packaging in Bacillus subtilis bacteriophage Phi 29. Luis R. Comolli, Andrew Spakowitz, Cristina E. Siegerist, Shelley Grimes, Paul Jardine, Kenneth H. Downing, Dwight Anderson and Carlos Bustamante. Gordon Research Conference, Three Dimensional Electron Microscopy, June 25-30, 2006, Il Ciocco, Barga, Italy. LBNL-60633

  13. E. Wes Bethel, C. Johnson, C. Hansen, S. Parker, A. Sanderson, C. Silva, X. Trichoche, V. Pascucci, H. Childs, J. Cohen, M. Duchaineau, D. Laney, P. Lindstrom, S. Ahern, J. Meredith, G. Ostouchov, K. Joy, B. Hamann. VACET: Proposed SciDAC2 Visualization and Analytics Center for Enabling Technologies. Journal of Physics: Conference Series, Vol. 46, 2006, pp. 561-569, SciDAC 2006 Conference, Denver CO. June 25-29, 2006. LBNL-60413. (bibtex) (PDF)

  14. E. Wes Bethel, C. Johnson, C. Hansen, S. Parker, A. Sanderson, C. Silva, X. Trichoche, V. Pascucci, H. Childs, J. Cohen, M. Duchaineau, D. Laney, P. Lindstrom, S. Ahern, J. Meredith, G. Ostouchov, K. Joy, B. Hamann. "Meet the Proposed SciDAC2 Visualization and Analytics Center for Enabling Technologies." This poster was presented at the 2006 SciDAC program meeting in Denver, CO. June, 2006. LBNL-60478. (bibtex) (PDF).

  15. A. Fruchter, A. Levan, L. Strolger, P. Vreeswijk, S. Thorsett, D. Bersier, I. Burud, J. Castro Cer�n, A. Castro-Tirado, C. Conselice, T. Dahlen, H. Ferguson, J. Fynbo, P. Garnavich, R. Gibbons, J. Gorosabel, T. Gull, J. Hjorth, S. Holland, C. Kouveliotou, Z. Levay, M. Livio, M. Metzger, P. Nugent, L. Petro, E. Pian, J. Rhoads, A. Riess, K. Sahu, A. Smette, N. Tanvir, R. Wijers, S. Woosley. Long gamma-ray bursts and core-collapse supernovae have different environments. In Nature 441:463-468, May 25, 2006. LBNL-60278. (bibtex)

  16. O. Rübel, G.H. Weber, S.V.E. Keränen, C.C. Fowlkes, C.L. Luengo Hendriks, L. Simirenko, N.Y. Shah, M.B. Eisen, M.D. Biggin, H. Hagen, J.D. Sudar, J. Malik, D.W. Knowles, and B. Hamann. PointCloudXplore: Visual analysis of 3D gene expression data using physical views and parallel coordinates. In: B. Sousa Santos, T. Ertl, and K.I. Joy, eds., Data Visualization 2006 (Proceedings of EuroVis 2006), Eurographics Association, Aire-la-Ville, Switzerland, pp. 203-210. May, 2006. LBNL-60005.(BibTeX)

  17. L. Gosink, J. Shalf, K. Stockinger, K. Wu, W. Bethel. "HDF5-FastQuery: Accelerating Complex Queries on HDF Datasets using Fast Bitmap Indices." In Proceedings of the 18th International Conference on Scientific and Statistical Database Management, July 2006, Vienna Austria. LBNL-59602. (PDF), (bibtex)

  18. Michael J. Fero, Harley McAdams, Luis R. Comolli, Cristina Siegerist, Kenneth Downing. A model for murine layer growth and cell shape during cell division in Caulobacter, Biophysical Society Annual Meeting, Salt Lake City, Utah, February 18-22, 2006. LBNL-60153

  19. M. Sullivan, D. Howell, K. Perrett, P. Nugent, P. Astier, E. Aubourg, D. Balam, S. Basa, R. Carlberg, A. Conley, S. Fabbro, D. Fouchez, J. Guy, I. Hook, H. Lafoux, J. Neill, R. Pain, N. Palanque-Delabrouille, C. Pritchet, N. Regnault, J. Rich, R. Taillet, G. Aldering, S. Baumont, J. Bronder, M. Filiol, R. Knop, S. Perlmutter and C. Tao. Photometric Selection of High-Redshift Type Ia Supernova Candidates. The Astrophysical Journal, 131:960-972, February 2006. LBNL-60286. (bibtex)

  20. Tom Goodale, Shantenu Jha, Hartmut Kaiser, Thilo Kielmann, Pascal Kleijer, Gregor von Laszewski, Craig Lee, Andre Merzky, Hrabri Rajic, John Shalf. "SAGA: A Simple API for Grid Applications -- High-Level Application Programming on the Grid". Accepted for publication in Computational Methods in Science and Technology 2006. LBNL-59066 (PDF coming soon) (Link to abstract, PDF, bibtex, at LSU)

  21. C. Crawford, O. Kreylos, B. Hamann, S. Crivelli. "Visualization of Force Fields in Protein Structure Prediction". In Proceedings of the SPIE/IS&T Conference on Electronic Imaging, Volume 6060, Robert F. Erbacher, Jonathan C. Roberts, Matti T. Gröhn, Katy Börner, eds., January 2006. LBNL-58169. (Bibtex) (PDF).

  22. J. Chen, I. Yoon, E. Wes Bethel. "Interactive, Internet Delivery of Scientific Visualization via Structured, Prerendered Imagery." In Proceedings of the 2006 SPIE/IS&T Conference on Electronic Imaging, Volume 6061, A 1-10, January 2006. LBNL-57528. (bibtex) (PDF)


2005

  1. Scalzo, R. A.; Aldering, G.; Aragon, C.; Bailey, S.; Bongard, S.; Bailey, S.; Kocevski, D.; Loken, S.; Nugent, P.; Perlmutter, S.; Thomas, R. C.; Wang, L.; Weaver, B. A.; Antilogus, P.; Gilles, S.; Pain, R.; Pereira, R.; Blanc, N.; Copin, Y.; Gangler, E.; Sauge, L.; Smadja, G.; Bonnaud, C.; Pecontal, E.; Kessler, R.; Baltay, C.; Rabinowitz, D.; Bauer, A.; "Status of the Candidate Search at the Nearby Supernova Factory." Poster at 2005 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 207, #171.03. December 2005. (bibtex)

  2. T.C. Lu, N. Max, J. Ding, E. W. Bethel, S. Crivelli. "DockingShop: A Tool for Interactive Molecular Docking." Lawrence Berkeley National Laboratory. Technical Report LBNL-58170, 2005. (PDF) (bibtex)

  3. L. Gosink, J. Shalf, K. Stockinger, K. Wu, W. Bethel. "HDF5-FastQuery: Accelerating Complex Queries on HDF Datasets using Fast Bitmap Indices." Part of the 2005 HDF Workshop, San Francisco CA, 30 Nov - 02 Dec 2005. HDF5-FastQuery-LBNL-59602-Abs.pdf (LBNL-59602-Abs) (Slides from presentation at the HDF workshop.) (bibtex)

  4. W. Bethel, S. Campbell, E. Dart, J. Lee, S. A. Smith, K. Stockinger, B. Tierney, K. Wu. "Interactive Analysis of Large Network Data Collections Using Query-Driven Visualization." Technical Report LBNL-59166. (PDF) (bibtex)

  5. H. Simon, W. Kramer, D. Bailey, M. Banda, W. Bethel, J. Craw, W. Fortney, J. Hules, N. Meyer, J. Meza, E. Ng, L. Rippe, W. Saphir, F. Verdier, H. Walter, K. Yelick. "Science-Driven Computing: NERSC's Strategic Plan for 2005-2010." LBNL-57582.pdf (4MB).

  6. K. Stockinger, K. Wu, S. Campbell, S. Lau, M. Fisk, E. Gavrilov, A. Kent, C. Davis, R. Olinger, R. Young, J. Prewitt, P. Weber, T. Caudell, W. Bethel, S. Smith. "Network Traffic Analysis with Query-Driven Visualization - SC05 HPC Analytics Challenge Results". Accepted for publication as part of the SC05 Conference Proceedings. LBNL-68768. (PDF) (bibtex)

  7. K. Stockinger, J. Shalf, K. Wu, W. Bethel. "Query-Driven Visualization of Large Data Sets." In Proceedings of IEEE Visualization 2005, pp. 167-174. Minneapolis, MN., October 23-28, 2005. QueryDrivenVis-LBNL-57511.pdf. (bibtex) (LBNL-57511)

  8. J. Hules, J. Bashor, L. Yarris, J. McCullough, P. Preuss, W. Bethel. "NERSC Annual Report 2004". LBNL-57369 (9MB PDF)

  9. C. Co, A. Friedman, D. Grote, J.L. Vay, W. Bethel, K. Joy. "Interactive Methods for Exploring Particle Simulation Data." Accepted for publication in EuroVis05. LBNL-55353. (PDF) (bibtex)

  10. K. Stockinger, J. Shalf, W. Bethel, K. Wu. "DEX: Increasing the Capability of Scientific Data Analysis Pipelines by Using Efficient Bitmap Indices to Accelerate Scientific Visualization." 2005 Scientific and Statistical Database Management Conference (SSDBM-2005), Santa Barbara, California, June 27-29, 2005. (LBNL-57023) (PDF), (bibtex)

  11. L. Oliker , A. Canning , J.T. Carter , J. Shalf , D.E. Skinner , S. Ethier , R. Biswas, J. Djomehri, R. Van der Wijngaart, "Performance Evaluation of the SX-6 Vector Architecture for Scientific Computations," Concurrency and Computation Journal: Practice and Experience, Vol 17:1, Jan 2005, pp69-93 (LBNL-54904) CCPE05.pdf

  12. H.D. Simon, W.T. Kramer, W. Saphir, J. Shalf, D.H. Bailey, L. Oliker, M. Banda, C. W. McCurdy, J. Hules, A. Canning, M. Day, P. Colella, D. Serafini, M.F. Wehner, P. Nugent, "Science-Driven System Architecture: A New Process for Leadership Class Computing," Journal of the Earth Simulator, vol 2, pp 2-10, March 2005. (LBNL-56545) JES2-Simon.pdf

  13. L. Oliker, A. Canning, J. Carter, J. Shalf, H.D. Simon, S. Ethier, D. Parks, S. Kitawaki, Y. Tsuda and T. Sato, "Performance of Ultra-Scale Applications on Leading Vector and Scalar HPC Platforms," Journal of the Earth Simulator, Volume 3, April 2005. (LBNL-58047)

  14. S.A. Kamil, P.J.R Husbands, L. Oliker, J. Shalf, K.A. Yelick,"Impact of Modern Memory Subsystems on Cache Optimizations for Stencil Computations," Presented at ACM SIGPLAN Memory Systems Performance Conference (ACM-MSP2005), Chicago, June 12, 2005. (LBNL-58050) msp2005.pdf

  15. A. Adelmann, R.D. Ryne, C. Siegerist, J. Shalf,"From Visualization to Data Mining with Large Data Sets," Particle Accelerator Conference (PAC05), Knoxville TN., May 16-20, 2005. (LBNL-57603) FPAT082.pdf

  16. A. Adelmann, R.D. Ryne, J. Shalf, C. Siegerist,"H5Part: A Portable High Performance Parallel Data Interface for Particle Simulations," Particle Accelerator Conference (PAC05), Knoxville TN., May 16-20, 2005. FPAT083.pdf

  17. J. Shalf,S.A. Kamil, L. Oliker, D. Skinner,"Analyzing Ultra-Scale Application Communication Requirements for a Reconfigurable Hybrid Interconnect," Supercomputing 2005, Seattle WA., November 12-18, 2005. (LBNL-58052) sc2005.pdf

  18. S.A. Kamil, J. Shalf, L. Oliker, D. Skinner," Understanding Ultra-Scale Application Communication Requirements," IEEE International Symposium on Workload Characterization (IISWC) Austin Texas, October 6-8, 2005. (LBNL-58059) iiswc05.pdf.



2004

  1. S. Crivelli, O. Kreylos, B. Hamann, N. Max, W. Bethel. "ProteinShop: A Tool for Interactive Protein Manipulation and Steering." Journal of Computer Aided Molecular Design (JCAMD)., Volume 18, Number 4, pp 271-285, April 2004. (PDF), (bibtex)

  2. N. Shah, A. Poliakov, D. Ryaboy, M. Teplitsky, B. Hamann, E. Rubin and I. Dubchak. "Vista Tools for Interactive Visualization and Analysis of Multiple Alignments of DNA Sequences and Whole Genomes". Conference abstract at The Biology of Genomes, May 12-16, 2004, Cold Spring Harbor, NY, USA. Shah-LBNL-55394-Abs.pdf.

  3. N. Shah, G. Weber, S. Dillard, B. Hamann. "Volume Visualization of Multiple Alignment of Genomic DNA." Submitted to 2004 IEEE Symposium on Information Visualization. GenomicVolViz-IEEEVis04-LBNL-55386.pdf.

  4. N. Shah, O. Couronne, L. Pennacchio, M. Brudno, S. Batzoglou, W. Bethel, E. Rubin, B. Hamann, I. Dubchak. "Phylo-VISTA: Interactive Visualization of Multiple DNA Sequence Alignments." In Bioinformatics 20(5), May 2004, pp 636-643. LBNL-54135. (PDF) (bibtex)

  5. N. Shah, O. Couronne, L. Pennacchio, M. Brudno, S. Batzoglou, W. Bethel, E. Rubin, B. Hamann, I. Dubchak. "Phylo-VISTA: Interactive Visualization of Multiple DNA Sequence Alignments." (Brief two-page abstract) PhyloVista-Abstract-LBNL-54136.pdf.

  6. C. Co, A. Friedman, D. Grote, J.L. Vay, W. Bethel, K. Joy. "Interactive Methods for Exploring Particle Simulation Data." Submitted to IEEE Visualization 2004 (Application Paper). Note: a more recent version of the paper was accepted for publication in EuroVis05. Link to the Vis04 submission. LBNL-55353.

  7. I. Bowman, J. Shalf, K.L. Ma, W. Bethel. "Performance Modeling for 3D Visualization in a Heterogeneous Computing Environment." Technical Report LBNL-56977, Lawrence Berkeley National Laboratory, Berkeley CA, USA. 2004. (PDF) (bibtex)

  8. I. Bowman, J. Shalf, K.L. Ma. "Performance Modeling for Grid-Based Visualization." Submitted to HPDC-13. Bowman-HPDC-LBNL-54576.pdf. LBNL-54576.

  9. J. Shalf, T. Goodale. "GridRun: A Lightweight Packaging and Execution Environment for Compact, Multi-architecture Binaries." Submitted to (where?). GridRun-LBNL-54576. LBNL-54576.

  10. W. Bethel, R. Frank, S. Fulcomer, C. Hansen, K. Joy, J. Kohl, D. Middleton. "Visual Data Analysis - Report of the Visualization Breakout Session at the 2003 SCaLeS Workshop - Volume II." Arlington, VA, June 2003. (Volume II of the Visualization Chapter completed 1/12/04.) LBNL-PUB-886 Vol II. (PDF) (bibtex)

  11. J. Shalf, E. Wes Bethel, C. Siegerist. "Personal Display Wall." A two-page report describing our low-cost tiled display device built in-house using commercial, off-the-shelf components. LBNL-PUB-894-PersonalDisplayWall.pdf
    Build your own from plans:
    PDW.pdf

  12. C. Siegerist, J. Shalf, E. Wes Bethel. "Visportal: Increasing Scientific Productivity by Simplifying Access to and Use of Remote Computational Resources." A two-page report describing the Visualization Portal project. LBNL-PUB-893-Visportal.pdf.

  13. C. Siegerist, J. Shalf, E. Wes Bethel. "Interactive Remote and Distributed Visualization of Fusion Simulation Results." A two-page report describing our use of a pipelined-parallel architecture to provide interactive, remote visualization capabilities to the Fusion simulation community who use the NERSC facility. LBNL-PUB-892-RemoteVisFusion.pdf.

  14. G. Griem, L. Oliker, J. Shalf, K. Yelick, "Identifying Performance Bottlenecks on Modern Microarchitectures using an Adaptable Probe," 3rd International Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems (PMEO-PDS), 2004. pmeo_2004.pdf

  15. A. Canning, J. Carter, J. Shalf, and S. Ethier. "Scientific Computations on Modern Parallel Vector Systems," In Proceedings of the IEEE Conference on Supercomputing, Nov. 2004. (LBNL-55279)
    (Nominated: Best Paper Award) SC04.pdf


2003

  1. G. Allen, K. Davis, K. N. Dolkas, N. D. Doulamis, T. Goodale, T. Kielmann, A. Merzky, J. Nabrzyski, J. Pukacki, T. Radke, M. Russell, E. Seidel, J. Shalf, I. Taylor, "Enabling Applications on the Grid - A GridLab Overview," International Journal on High Performance Computing Applications, Volume 17, No. 4, Winter 2003, pp. 449-466. (LBNL-54107). LBNL-54107-gridlab.pdf

  2. L. Oliker, A. Canning, J. Carter, J. Shalf, D. Skinner, S. Ethier, R. Biswas, J. Djomehri, R. Van der Wijngaart,"Evaluation of Cache-based Superscalar and Cacheless Vector Architectures for Scientific Computations", Proceedings of Supercomputing 2003, Phoenix AZ, 2003. SC03_SX6.pdf

  3. J. Shalf, M.J. Bennett, G. Bell. "Transport Requirements for High Performance Network Applications that are NOT FTP" Submitted to the Second International Workshop on Protocols for Fast Long-Distance Networks (PFLDnet 2004), Chicago Il. 2004. PFLDGridAppReqs.pdf

  4. C. Siegerist, P. Shetty, W. Bethel, T.J. Jankun-Kelly, O. Kreylos, K.L. Ma, J. Shalf. "VisPortal: Deploying grid-enabled visualization tools through a web-portal interface." Wide Area Collaborative Environments Workshop, Seattle, WA., June 2003. LBNL-52940. (PDF) (bibtex)

  5. W. Bethel, R. Frank, S. Fulcomer, C. Hansen, K. Joy, J. Kohl, D. Middleton. "Visual Data Analysis - Report of the Visualization Breakout Session at the 2003 SCaLeS Workshop." Arlington, VA, June 2003. SCaLeS-VisBreakoutTreatise-Final-LBNL.pdf (LBNL/PUB-886).

  6. W. Bethel, G. Abram, J. Shalf, R. Frank, J. Ahrens, S. Parker, N. Samatova, M. Miller. "Interoperability of Visualization Software and Data Models is Not an Achievable Goal." A Panel at 2003 IEEE Visualization. LBNL-53368 Abs. (PDF) (bibtex)

  7. G. Weber, M. Ohler, O. Kreylos, J. Shalf, W. Bethel, B. Hamann, G. Scheuermann, Parallel Cell Projection Rendering of Adaptive Mesh Refinement Data. In Proceedings of IEEE Symposium on Parallel and Large-Data Visualization and Graphics 2003, October 20-21, 2003, Seattle, Washington, USA, pp. 51-60. LBNL-52469. (PDF) (bibtex)

  8. O. Kreylos, N. Max, B. Hamann, S. Crivelli, W. Bethel. "Interactive Protein Manipulation." In Proceedings of IEEE Visualization 2003, October 19-24, 2003, Seattle, Washington, USA, pp 581-588. LBNL-52414. (PDF) (bibtex)   (Winner of the Best Application Paper Award)

  9. Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, Wes Bethel, Edward M. Rubin, Bernd Hamann and Inna Dubchak, Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments. LBNL Technical Report LBNL-52539. For more information about Multi-sequence alignment, please visit the PhyloVista web site. (PDF) (bibtex)

  10. W. Bethel and J. Shalf, "Consuming Network Bandwidth with Visapult." In _The Visualization Handbook_, C. Hansen and C. Johnson (eds.), Elsevier, 2005 (submitted and accepted in 2003, finally in print in 2005). 2003/LBNL-52171-VisapultChapter.pdf . This book chapter describes our experiences winning the SC Bandwidth Challenge three years in a row, including detailed technical information about how we are able to consume extremely large amounts of network bandwidth. (Bibtex)

  11. Jiann-Liang Chen (UCD/LBNL-Visualization), Zhaojun Bai (UCD), Terry J. Ligocki (LBNL-ANAG), "Segmentation of Piecewise Linear Vector Fields," Submitted to review for inclusion in an upcoming book entitled "Geometric Modeling for Scientific Visualization" published by Springer-Verlag. (LBNL-52025) 2003/LBNL-52025-Chen-SV.pdf

  12. Jiann-Liang Chen (UCD/LBNL-Visualization), Zhaojun Bai (UCD), Bernd Hamann (UCD/LBNL-Visualization), Terry J. Ligocki (LBNL-ANAG), "A Normalized-Cut Algorithm for Hierarchical Vector Field Data Segmentation," Accepted to 2003 SPIE/IS&T Visual Data Exploration and Analysis Conference (the formal bibliographic citation will be forthcoming), San Jose, CA, January 2003. (LBNL-52024) 2003/LBNL-52024-Chen-VDA.pdf

2002

  1. "Tutorial: Using HDF5 for Scientific Data Analysis," John Shalf, LBL. PowerPoint Presentation / PDF File (no LBNL number)

  2. "Lawrence Berkeley National Lab Leads International Team to Win High-Performance Computing Bandwidth Challenge", Jon Bashor, LBL. http://www.lbl.gov/cs/Archive/othernews112502.html (No LBNL number - this is an internal "news story.")

  3. "Berkeley Lab-led International Team Wins Bandwidth Challenge at SC02," in Supercomputing Online at http://www.supercomputingonline.com/article.php?sid=2914. (No LBNL number - this is an external publication/press release.) "The team won top honors for the Highest Performing Application, moving data at a peak speed of 16.8 gigabits, or 16.8 billion bits of data, per second, which was more than five times higher than the team's record-setting win at the SC2001 conference....."


  4. J. Shalf and W. Bethel, "How the Grid Will Affect the Architecture of Future Visualization Systems," IEEE Computer Graphics and Applications, Volume 23, Number 2, March/April 2003, pp 6-9. LBNL-51723. (PDF) (Bibtex) Also, check out the final camera ready version created by IEEE. You can also grab the camera ready copy directly from IEEE.

  5. B. Hamann, E. W. Bethel, H. Simon, J. Meza, NERSC "Visualization Greenbook" : Future Visualization Needs of the DOE Computational Science Community Hosted at NERSC. The International Journal of High Performance Computing Applications, Volume 17, Number 2, Summer 2003, pp 97-124. LBNL-51699. (PDF), (bibtex)

  6. J. Shalf and E. W. Bethel, "Cactus and Visapult: An Ultra-High Performance Grid-Distributed Visualization Architecture Using Connectionless Protocols." IEEE Computer Graphics and Applications, Volume 23, Number 2, March/April 2003, pp. 51-59. (PDF) You can also grab the camera-ready PDF created by the nice folks at IEEE. (Bibtex)

  7. T.J. Jankun-Kelly, O. Kreylos, J. Shalf, Kwan-Liu Ma, B. Hamann, K. Joy, E.W. Bethel, "Deploying Web-based Visual Exploration Tools on the Grid." IEEE Computer Graphics and Applications, Volume 23, Number 2, March/April 2003, pp. 40-49. LBNL-51553. (PDF) (bibtex)

  8. J. Shalf and W. Bethel, "Cactus and Visapult: A Case Study of Ultra-High Performance Distributed Visualization Using Connectionless Protocols". Technical Report LBNL-50237, Lawrence Berkeley National Laboratory, Berkeley CA, USA, 94720. (PDF) (Bibtex)

  9. Steve Fisher (ed), "Berkeley Lab Proves 10-Gigabit Ethernet Data Transfer is a Reality," in Supercomputing Online at http://www.supercomputingonline.com/article.php?sid=2252. (No LBNL number - this is an external publication.)

  10. G. Allen, E. Siedel, and J. Shalf, "Scientific Computing on the Grid," Byte Magazine, Spring 2002. 2002/LBNL-51039-Byte2002.pdf (LBNL 51039)

  11. O. Kreylos, G. Weber, W. Bethel, J. Shalf, B. Hamann, K. Joy, "Remote Interactive Direct Volume Rendering of AMR Data." Technical Report LBNL-49954, Lawrence Berkeley National Laboratory, Berkeley CA, USA, 97420. (PDF) (bibtex)

  12. W. Bethel, S.J. Bastacky and K. Schwartz, "Interactive Stereo Electron Microscopy Enhanced with Virtual Reality." In Stereoscopic Displaysand Virtual Reality Systems IX, Andrew J. Woods, John O. Merritt, Stephen A. Benton, Mark T. Bolas, Editors, Proceedings of SPIE Vol. 4660, pp 391-400, 2002. LBNL-48336. (PDF) (bibtex)


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