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)
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)
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)
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)
2012
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)
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)
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)
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)
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)
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)
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.
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)
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)
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)
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. )
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)
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)
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)
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)
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)
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)
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)
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)
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,
November 2012. LBNL-5362E.
(bibtex)
(Publisher rules prohibit us distributing a PDF of the article)
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).
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)
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)
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)
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)
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)
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)
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. (Poster) (BibTeX)(LBNL publication number pending)
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)
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.
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.
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
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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.
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.
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)
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)
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.
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)
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)
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)
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).
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)
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)
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)
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)
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)
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)
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)
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.
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)
Jerry Chuo, John Wu, Prabhat, "FastQuery: a general Index and
Query
system for scientific data", Scientific and Statistical Database
Management Conference 2011, Poster. (BibTeX)
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)
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
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)
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)
Tina Zhuo, Prabhat, Chris Paciorek and Cari Kaufman, "Distributed
Likelihoods Computation for Large Spatial Data", SuperComputing 2010,
Poster. (BibTeX)
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)
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.
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)
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)
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)
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)
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)
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)
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)
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)
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)
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.
D. M. Ushizima and J. Cuadros, "Ocular fundus for retinopathy
characterization", Bay Area
Vision Meeting, Feb 5th, Berkeley, CA 2010.
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)
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)
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).
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)
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).
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)
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).
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)
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
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)
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)
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)
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.
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.
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)
"Smashing the Trillion Zone Barrier." Article at Scientific
Computing. (Not an LBNL publication)
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)
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)
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).
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)
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)
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)
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).
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)
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)
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)
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)
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)
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
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)
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)
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)
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)
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)
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)
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)
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)
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).
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).
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)
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)
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)
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)
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)
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.
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.)
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)
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).
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
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)
E. W. Bethel, J. Chen, I. Yoon. "Interactive,
Internet Delivery of
Visualization
via Structured, Prerendered Imagery." Two-page research highlight.
LBNL-63675. (PDF)(bibtex)
E. W. Bethel, L. Gosink, J. Anderson, K. Joy.
"Variable Interactions in
Query-Driven Visualization." Two-page research highlight. LBNL-63674. (PDF)(bibtex)
E. W. Bethel, O. Ruebel, G. Weber. "Visualization
and Analysis of 3D
Gene Expression Data."
Two-page research highlight. LBNL-63658. (PDF)(bibtex)
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)
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)
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.
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)
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)
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)
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)
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)
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)
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).
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).
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)
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)
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)
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).
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).
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)
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)
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)
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
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)
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)
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)
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).
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)
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)
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)
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).
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
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)
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).
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)
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)
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)
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
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)
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)
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).
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
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)
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)
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)
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).
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)
J. Hules, J. Bashor, L. Yarris, J.
McCullough, P. Preuss, W. Bethel. "NERSC
Annual Report 2004".LBNL-57369
(9MB PDF)
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)
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
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
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)
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
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
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
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
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.
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)
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.
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)
I. Bowman, J. Shalf, K.L. Ma. "Performance
Modeling for Grid-Based Visualization." Submitted to HPDC-13.Bowman-HPDC-LBNL-54576.pdf.
LBNL-54576.
J. Shalf, T. Goodale. "GridRun: A Lightweight Packaging and
Execution Environment for Compact, Multi-architecture Binaries."
Submitted to (where?). GridRun-LBNL-54576.
LBNL-54576.
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)
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.
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.
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
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
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
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
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
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)
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).
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)
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)
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)
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)
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)
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
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
"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.")
"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....."
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)
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)
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)
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)
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.)
G. Allen, E. Siedel, and J. Shalf, "Scientific Computing on the
Grid,"
Byte Magazine, Spring 2002. 2002/LBNL-51039-Byte2002.pdf(LBNL 51039)
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)
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)
W. Bethel, B. Tierney, J. Lee, D. Gunter, S. Lau, "Using
High-Speed
WANs and Network Data Caches to Enable Remote and Distributed
Visualization,"
in Proceedings of SC00, November 2000. (LBNL-45365) (PDF)(bibtex)
W. Bethel, "Visapult - A Prototype Remote and Distributed
Application
and Framework," in Siggraph 2000 Applications and Sketches, July 2000.
2000/LBNL-45215-VisapultSiggraph2000.pdf. We describe an approach
used for implementing a highly efficient and scalable method for direct
volume rendering. Our approach uses a pipelined-parallel decomposition
composed of parallel computers and commodity desktop hardware. With our
approach, desktop interactivity is divorced from the latency inherent
in network-based applications. (Bibtex)
W. Bethel, "Visualization Dot Com," in the Visualization
Viewpoints
Column of IEEE Computer Graphics and Applications, May/June 2000. 2000/LBNL-44871-VisapultCGAMay2000.pdf.
This article examines the seemingly well-worn subject of remote
visualization,
and presents an overview of a prototype system used for distributed,
shared
rendering use to do remote visualization of tera-scale scientific data.
(Bibtex)
T. Ligocki, "Implementing a Visualization Tool for Adaptive Mesh
Refinement
Data using VTK," in Proceedings of Visualization Development
Environments 2000. 2000/LBNL-45394-ChomboVisVTK.pdf.
This paper describes the issues surrounding the visualization of
adaptive mesh refinement (AMR) data and then documents the work done
implementing at tool, ChomboVis,
using VTK to visualization data from
an AMR library, Chombo,
being developed by the Applied
Numerical Algorithms
Group (ANAG)
at LBNL/NERSC.
1999
E. Wes Bethel, Carl Bass, Sharon Rose Clay, Brian Hook, Michael
T.
Jones, Henry Sowizral, and Andries van Dam. "Scene graph APIs: wired or
tired?" (Panel). In SIGGRAPH ''99: ACM SIGGRAPH 99 Conference
abstracts and applications, pages 136–138, New York, NY, USA, 1999.
ACM. (bibtex)
E. Wes Bethel and S. J. Bastacky. "Measurement of Perceived
Objects."
In IEEE Visualization 99, Late Breaking Hot Topics, pages 53-56, San
Francisco, CA, USA, October 1999. LBNL-43446. (PDF). (bibtex)
1998
Sam Uselton, Jim Ahrens, E. Wes Bethel, Lloyd Treinish, and
Andrei
State.
"Multi-source Data Analysis Challenges." In Proceedings of IEEE
Visualization
1998 (panel), pages 501–504, 1998. (bibtex)
1997
Berkeley Lab Research Review – Virtual Reality. This article
descibes the Visualization Group's work in combining scientific
visualization with Virtual Reality. More
information.
1996
W. Bethel (LBL), J. Jacobsen (LBL), A. Austin (BP Exploration),
M.
Lederer (BP Exploration), T. Little (Western Atlas Software),
"Implementing Virtual Reality Interfaces for the Geosciences,"
In Proceedings of Virtual Reality in the Geosciences, Halden, Norway,
1996. 1996/LBNL-38618-VRGeo.ps
Overview of work done in integrating VR into a visualization and
computing environment, with a focus on geoscience applications. More images and info about this paper.
A report on work done under the a research project funded by
the ACTI Initiative, June 1996.
More information about the ACTI project.
1995
E. Wes Bethel. "Modular Virtual Reality Visualization Tools" In
Proceedings of the International Advanced Visual Systems User and
Developer Conference (AVS95), pages 245-254, Boston MA, USA, 1995.
LBNL-36693. (PDF)(PS)(bibtex) More information.
Jennifer Horsman and E. Wes Bethel.
"Methods of Constructing a 3D Geological Model from Scatter Data." In
Proceedings of the International Advanced Visual Systems User and
Developer Conference (AVS95), pages 395-404, Boston MA, USA, 1995.
(No LBNL publication number.) (PS)(bibtex)More information.
Janet Jacobsen, E. Wes Bethel, Akhil Datta-Gupta, and Preston
Holland.
"Virtual Reservoir Development a Reality on Prototype System."
Americal Oil and Gas Reporter, 38(12):78-86, 1995. (bibtex)
1994
E. Wes Bethel. "Chemical Flooding in a Virtual Environment – A
Survivor's Guide to VR Development." In Proceedings of the
International Advanced Visual Systems User and Developer Conference
(AVS94), pages 299-309, Boston MA, USA, May 1994. LBNL-35262. (PS)(bibtex)More information.
E. Wes Bethel, Janet Jacobsen and Preston Holland. "Site
Remediation in a Virtual Environment." In Robert J. Moorhead, Deborah
E. Silver, and Samuel P. Uselton, editors, Visual Data Exploration
and Analysis, Proceedings of SPIE 2178, pages 78-87, 1994.
LBNL-34865. (PDF)(PS)(bibtex) More information.
1993
W. Bethel, "Analytic Rendering of Curvilinear
Volume Data," Technical Report LBNL-33808,
Lawrence Berkeley National Laboratory, 1993. (PDF)(bibtex)
W. Bethel, "Visual Cues Case Study," in Visual Cues,
Keller and Keller, IEEE Computer Society Press, 1993. More information.
1989
E. Wes Bethel and Samuel P. Uselton. Shape Distortion in
Computer-Assisted Keyframe Animation.
In Nadia Megnenat-Thalmann and Daniel Thalmann, editors, State-of-the-art
in Computer Animation, pages 215-224,
Geneva, Switzerland, June 1989. Spring-Verlag. (bibtex)
(for a PDF, please contact Wes via email)
