O. Rübel, G. H. Weber, M-Y Huang, E. W. Bethel, M. D. Biggin, C. C. Fowlkes,
C. Luengo Hendriks, S. V. E. Keränen, M. Eisen, D. Knowles, J. Malik,
H. Hagen and B. Hamann,
"Integrating Data Clustering and Visualization for the Analysis of 3D Gene
Expression Data."
IEEE Transactions on Computational Biology and Bioinformatics. 2008. (To appear)
LBNL report number pending.
(PDF),
(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. (To appear)
LBNL-249E. (PDF),
(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, 2008. LBNL-220E.
(PDF),
(BibTeX)
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)
G. H. Weber, O. Rübel, M.-Y. Huang, A. H. DePace, C. C. Fowlkes,
S. V. E. Keränen, C. L. Luengo Hendriks, H. Hagen, D. W. Knowles,
J. Malik, M. D. Biggin and B. Hamann.
"Visual exploration of three-dimensional gene expression using physical views
and linked abstract views."
To appear in:IEEE Transactions on Computational Biology and Bioinformatics.
LBNL-63776.
(PDF), (BibTeX).
S. E. Dillard, V. Natarjan, G. H. Weber, V. Pascucci and B. Hamann.
Topology-guided Tessellation of Quadratic Elements.
To appear in: International Journal of Computational Geometry and Applications (IJCGA).
LBNL-63771.
(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).
N. Shah, N., S. E. Dillard, G.H. Weber, B. Hamann. "Volume visualization of
multiple alignment of large genomic DNA." To appear in: Mathematical Foundations of
Scientific Visualization, Computer Graphics, and Massive Data Exploration,
Springer-Verlag, Heidelberg, Germany, 2008. LBNL-63126.
(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. 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 accepted to 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.
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)
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)
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. 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
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."
LBNL-PUB-963 (Two-page research highlight).
(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).
(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).
(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.
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.
(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. 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)
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. (PDF coming soon).
(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.
LBNL-60005.
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). LBNL-60053.
(bibtex)(PDF)
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
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)
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."
(LBNL-58170 PDF)
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."
LBNL-59166
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.
Co-EuroVis05-LBNL-55353.pdf.
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.).
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.
Kreylos-ProteinShop-Vis2003.pdf (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)
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
W. Bethel and S. J. Bastacky, "Measurement of Perceived Objects."
In IEEE Visualization 99, Late Breaking Hot Topics.
1999/LBNL-43446-VirtualProtractor.pdf.
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.
