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,
in press.
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. 2010. In press. 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). 2010. To appear. (BibTeX)
2009
P.-T. Bremer, G.H. Weber, J. Tierny, V. Pascucci, M.S. Day and J.B. Bell.
"Exploring large scale turbulent combustion,"
In: Proceedings of the 5th IEEE International Conference on e-Science,
Oxford, UK, December 2009.
(BibTeX) PDF and LBNL publication number forthcoming.
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.
(BibTeX) PDF and LBNL publication number 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, LBNL-2734E, (accepted for publication) (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)
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)
E. Wes Bethel, Hank Childs, Ajith Mascarenhas, Valerio Pascucci, and
Prabhat. Scientific
Data Managment Challenges in High Performance Visual Data Analysis. In
Arie Shoshani
and Doron Rotem, editors, Scientific Data Management: Challenges,
Existing Technology,
and Deployment. Chapman & Hall/CRC Press, 2008. (LBNL-1449E) (to
appear). (bibtex)
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.
PhyloVista-Bioinformatics-LBNL-54135.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." (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."
Submitted to PGV 2004.Bowman-PGV-LBNL-56977.pdf.
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-SCaleSVolII-VisualizationChapter.pdf
(LBNL/PUB-886 Vol II).
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.
wace03.pdf (LBNL-52940).
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.
IEEE03VisPanelProposal.pdf,
(LBNL-53368 Abs.).
(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.
Weber-PVG2003-LBNL-52469.pdf.
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)
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.
http://www-library.lbl.gov/docs/LBNL/515/63/PDF/LBNL-51563.pdf
(LBNL-51563)
J. Shalf and W. Bethel, "Cactus and Visapult: A Case Study of
Ultra-High Performance Distributed Visualization Using Connectionless
Protocols", Submitted to SC02.
2002/LBNL-50237-CactusVisapult.pdf.
(LBNL 50237)(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", Submitted to IEEE
Visualization 2002.
LBNL-49954-AMRVolumeRendering.pdf. (LBNL 49954)
W. Bethel, S.J. Bastacky and K. Schwartz, "Interactive Stereo
Electron Microscopy Enhanced with Virtual Reality," in Stereoscopic
Displays
and 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.
2002/LBNL-48336-StereoEM.pdf(LBNL 48336). (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)
W. Bethel and S. J. Bastacky, "Measurement of Perceived
Objects."
In IEEE Visualization 99, Late Breaking Hot Topics. LBNL-43446.
(bibtex)(PDF).
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 501–403, 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
W. Bethel, "Modular Virtual Reality Visualization Tools," In
Proceedings
of AVS '95, February 1995. (PDF)(PS)
LBNL-36693.
More information.
J. Horsman and W. Bethel, "Methods of Constructing a 3D
Geological
Model from Scatter Data," In Proceedings of AVS 95, February 1995.
1995/Horsman-AVS95.ps (no LBNL
publication number). More information.
W. Bethel, "Chemical Flooding in a Virtual Environment - A
Survivor's Guide to VR Development," In Proceedings of AVS 94,
May 1994. 1994/LBNL-35262-VRDev.psMore information.
W. Bethel, J. Jacobsen and P. Holland, "Site Remediation in a
Virtual Environment," in Visual Data Exploration and Analysis,
Robert J. Moorhead II, Deborah E. Silver, Samuel P. Uselton, Editors,
Proc. SPIE 2178, pp 78-87, (1994). (PDF)(PS)(bibtex) LBNL-34865.
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.
