Data Intensive Computing
Select Publications
Journal Articles
2009
Babar MA and I Gorton. 2009. "Software Architecture Review: The State of Practice." Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-64262.
Bohn SJ, DA Payne, GC Nakamura, and DV Love. 2009. "Analytics for Massive Heat Maps." In: Visualization and Data Analysis (VDA) Conference, eds. Katy Borner and Jinah Park 7243:1-10. IS&T - The Society for Imaging Science and Technology and SPIE, San Jose, CA.
Borkowski JJ and GF Piepel. 2009. "Uniform Designs for Highly Constrained Mixture Experiments." Journal of Quality Technology 41(1):35-47.
Brouns RA and PJ Hughes. 2009. "Overview of National Security Relevant LDRD Investments at PNNL." Presented by RA Brouns at Presentation for Visitors to PNNL on March 27, 2009. PNNL-SA-65742.
Brown DML. 2009. "Application Trace Data for Jan 2009." PNNL-SA-64613, Pacific Northwest National Laboratory, Richland, WA.
Bystroff C and BJM Webb-Robertson. 2009. "Pairwise Covariance Adds Little to Secondary Structure Prediction but Improves the Prediction of Non-Canonical Local Structure." BMC Bioinformatics 9:429.
Chase JM, I Gorton, C Sivaramakrishnan, MD Almquist, and AS Wynne. 2009. "Kepler + MeDICi Asynchronous Web Services for Data Intensive Workflow Applications." In: The IEEE 7th International Conference on Web Services (ICWS 2009). PNNL-SA-65047, Pacific Northwest National Laboratory, Richland, WA. [Unpublished]
Chin G Jr, A Marquez, S Choudhury, and K Maschhoff. 2009. "Implementing and Evaluating Multithreaded Triad Census Algorithms on the Cray XMT." In: Proceedings of the 2009 Workshop on Multithreaded Architectures and Applications, IEEE International Symposium on Parallel & Distributed Processing (IPDPS09), IEEE Computer Society Press, Los Alamitos, CA. PNNL-SA-64273.
Chin G Jr, D Chavarria-Miranda, C Scherrer, H Trease, and Z Huang. 2009. Task Fliers for June 4th Client Review. PNNL-SA-66759, Pacific Northwest National Laboratory, Richland, WA. [Unpublished]
Cook KA. 2009. "Knowledge Computing Capabilities." Presented by KA Cook (Invited Speaker) at Knowledge Computing Kickoff Meeting, February 4, Baltimore, MD. PNNL-SA-64482.
Gorton I, JM Chase, AS Wynne, and JP Almquist. 2009. "Services + Components = Data Intensive Scientific Workflow Applications with MeDICi ." In: 12th International Symposium on Component Based Software Engineering (CBSE 2009), Lecture Notes in Computer Science, Springer-Verlag, Berlin, Heidelberg, Germany 5582:227-241.
Gracio DK. 2009. "Computing at Pacific Northwest National Laboratory." Presented by DK Gracio March 30 at Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-65592.
Gracio DK, I Gorton, and LA McCue. 2009. "Data-Intensive Computing Supporting Bioinformatics." Presented by DK Gracio (Invited Speaker) at JGI Visit, May 29, Richland, WA. PNNL-SA-66490.
Kalahar BK. 2009. "Pacific Northwest National Lab." Presented by BK Kalahar (Invited Speaker) at WWU ACM Meeting, May 13, Bellingham, WA. PNNL-SA-66452.
Kouzes RT, GA Anderson, ST Elbert, I Gorton, and DK Gracio. 2009. "The Changing Paradigm of Data Intensive Computing." Computer 42(1):26-34.
Liu Y, I Gorton, and VK Lee. 2009. "The Architecture of an Event Correlation Service for Adaptive Middleware-Based Applications." Journal of Systems and Software 81(12):2134-2145.
Love DV, SJ Bohn, DA Payne, and GC Nakamura. 2009. "Analytics for Massive Heat Maps." Presented by DV Love (Invited Speaker) at Visualization and Data Analysis 2009, January 19, San Jose, CA. PNNL-SA-64191.
Madduri K, DA Bader, D Ediger, K Jiang, and D Chavarria-Miranda. 2009. "A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets." In: IEEE International Parallel & Distributed Processing Symposium (IPDPS09). IEEE Computer Society Press, Los Alamitos, CA.
Minsk BS, JL Barr, and AS Wynne. 2009. "Towards Situational Awareness for Emergency Operations." Presented by JL Barr (Invited Speaker), January 29, for U.S. Department of Homeland Security Visit to Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-64365.
Pike WA, J Gerth, and J Talbot. 2009. "Cyber Analytics for US-CERT: Transitioning Network Flow Visualization from the Laboratory to the Watch Floor." Presented by WA Pike (Invited Speaker) at the 3rd Annual U.S. Department of Homeland Security University Network Summit, March 19, Washington, D.C. PNNL-SA-65377.
Recknagle KP, ST Yokuda, MY Ballinger, and JM Barnett. 2009. "Scaled Tests and Modeling of Effluent Stack Sampling Location Mixing." Health Physics 96(2):164-174.
Rose SJ, DW Engel, NO Cramer, and WE Cowley. 2009. "Automatic Extraction of Keywords from Individual Documents." In Text Mining. Wiley Interscience. [In Press]
Sanfilippo AP, RL Baddeley, N Beagley, RM Riensche, and B Gopalan. 2009. "Enhancing Automatic Biological Pathway Induction with GO-based Gene Similarity." In: International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS). Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-65567 [Unpublished]
Thompson LA. 2009. "Poster Presentation." Presented by LA Thompson (Invited Speaker) at Poster Session for HS SRI Interns, on May 22. PNNL-SA-66592.
Trease HE. 2009. "Video Analytics." Presented by HE Trease (Invited Speaker) at Client Presentation at PNNL, February 24, Richland, WA. PNNL-SA-64929.
Webb-Robertson BJM, MM Matzke, and CS Oehmen. 2009. "Dimension Reduction via Unsupervised Learning Yields Significant Computational Improvements for Support Vector Machine Based Protein Family Classification." In: The Seventh International Conference on Machine Learning and Applications, pp. 457-462. IEEE Computer Society Press, Los Alamitos, CA.
2008
Anderson GA, MS Lipton, LA McCue, and I Gorton. 2008. "PNNL-JGI Interactions in Proteogenomics and Informatics." Presented by MS Lipton (Invited Speaker) at BER Review of JHI User Facility, December 4, Walnut Creek, CA. PNNL-SA-63600.
Babar MA, A Northway, I Gorton, P Heuer, and T Nguyen. 2008. "Introducing Tool Support for Managing Architectural Knowledge: An Experience Report." In: The 15th Annual IEEE International Conference and Workshop on the Engineering of Computer Based Systems (ECBS08), pp. 105-113. IEEE Computer Society Press, Los Alamitos, CA.
Brown DML and GR Smith. 2008. "MPP2 Syslog Data (2006-2008)." PNNL-SA-61371 Pacific Northwest National Laboratory, Richland, WA. Bryson KH. 2008. "Barry Merrill's Presentation to the Battelle-Pacific Northwest Division Board Meeting." Presented by B Merrill (Invited Speaker), November 4, Richland, WA. PNNL-SA-63055.
Bylaska EJ and K Kowalski. 2008. "Data Intensive Algorithms in Modeling Electronic Structure of Molecules." Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-62571.
Bystroff C, and BJM Webb-Robertson. 2008. "I-Sites 2007: Pairwise Covariance Adds Little to Secondary Structure Prediction but Improves the Prediction of Non-Canonical Local Structure." BMC Bioinformatics 9:429-438.
Carlson TS. 2008. "Cray XMT resource management." Presented by TS Carlson at SuperComputing 2008, November 17, Austin, TX. PNNL-SA-63513.
Chand KK, L Diachin, XN Li, C Ollivier-Gooch, ES Seol, MS Shephard, T Tautges, and HE Trease. 2008. "Toward Interoperable Mesh, Geometry and Field Components for PDE Simulation Development." Engineering with Computers 24(2):165-182.
Chavarria-Miranda D, J Nieplocha, and I Gorton. 2008. "Hardware-accelerated Components for Hybrid Computing Systems." In: Proceedings of the 2008 CompFrame/HPC-GECO Workshop on Component Based High Performance, Article No. 7, Association for Computing Machinery Press, NY.
Chavarria-Miranda D, A Marquez, J Nieplocha, KJ Maschhoff, and C Scherrer. 2008. "Early Experience with Out-of-Core Applications on the Cray XMT." In: Proceedings of Workshop on Multithreaded Architectures and Applications (MTAAP08). Institute of Electrical and Electronics Engineers, Inc., Miami, FL. PNNL-SA-58480.
Chavarria-Miranda D, J Nieplocha, C Scherrer, HJ Sofia, A Marquez, and DK Gracio. 2008. "Cray XMT Brings New Energy to High-Performance Computing." SciDAC Review Fall Issue (9):36-41.
Chin G Jr, OA Kuchar, and KE Wolf. 2008. "Exploring the Analytical Processes of Intelligence Analysts." In: Proceedings of the 27th International Conference on Human Factors in Computing Systems (CHI09), pp. 11-20, Association for Computing Machinery Press, NY.
Chin G Jr, GC Nakamura, M Singhal, V Gurumoorthi, and NA Freeman-Cadoret. 2008. "Visual Analysis of Dynamic Data Streams." Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-63420. [Unpublished]
Cowell AJ. 2008. "PNNL Overview and Supporting Materials for Presentation to UK MOD." Presented by AJ Cowell (Invited Speaker) at United Kingdom Ministry of Defense, July 9, Salisbury, United Kingdom. PNNL-SA-61240.
Cowell AJ, ML Gregory, HE Trease, EJ Marshall, and AS Wynne. 2008. "Image & Video Analytics." Presented by AJ Cowell (Invited Speaker) at Internal Presentation to Members of the National Reconnaissance Office, September 9, Richland, WA. PNNL-SA-62369.
Domico KO, KR Klicker, and AR Shah. 2008. Bioinformatics Resource Manager (BRM) User Manual 1.5 . PNWD-3879, Battelle-Pacific Northwest Division, Richland, WA.
Domico KO, KR Klicker, and AR Shah. 2008. Bioinformatics Resource Manager (BRM) User Manual 1.6 . PNWD-3903, Battelle-Pacific Northwest Division, Richland, WA.
Farber RM and HE Trease. 2008. "Massively Parallel Near-Linear Scalability Algorithms with Application to Unstructured Video Analysis." In: TACC TeraGrid08 Conference. June 9-13, Las Vegas, NV. PNNL-SA-59990.
Freedman VL, SB Yabusaki, M Rosing, and AL Ward. 2008. "Improving the Computational Efficiency of a Multicomponent Reactive Transport Simulator." Presented by VL Freedman at Computational Methods in Water Resources, July 7, San Francisco, CA. PNNL-SA-61318.
Gorton I. 2008. MeDICi: Middleware for Data-Intensive Computing. Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-62323. [Unpublished]
Gorton I. 2008. "Software Architecture Challenges for Data Intensive Computing." In: Proceedings of the 7th Working IEEE/IFIP Conference on Software Architecture (WICSA08), February 18-22, Vancouver, British Columbia, Canada, pp. 4-6. IEEE Computer Society Press, Los Alamitos, CA.
Gorton I. 2008. "The MeDICi Integration Framework." PNNL-SA-58880.
Gorton I and AS Wynne. 2008. "Overview of MeDICi." Presented by AS Wynne to Tim Thomas, December 18, at Battelle Seattle Research Center, Seattle, WA. PNNL-SA-63899.
Gorton I, Y Liu, and N Trivedi. 2008. "An Extensible and Lightweight Architecture for Adaptive Server Applications." Software: Practice & Experience 38(8):853-883.
Gorton I, CS Oehmen, and JE McDermott. 2008. "It Takes Glue to Tango: MeDICi Integration Framework Creates Data-Intensive Computing Pipeline." Scientific Computing 25(7):16-24.
Gorton I, JP Almquist, AS Wynne, and JB Chatterton. 2008. "MeDICi: Middleware for Data-Intensive Computing." PNNL-SA-59442. [Unpublished]
Gorton I, P Greenfield, A Szalay, and R Williams. 2008. "Data Intensive Computing in the 21st Century." Computer 41(4):30-32.
Gorton I, AS Wynne, JP Almquist, and JB Chatterton. 2008. "Model-Driven Application Development for the MeDICi Integration Framework: An Experience Report." In: Conference on Component-Based Software Engineering. PNNL-SA-60659. [Unpublished]
Gorton I, AS Wynne, JP Almquist, and JB Chatterton. 2008. "The MeDICi Integration Framework: A Platform for High Performance Data Streaming Applications." In: The 7th IEEE/IFIP Working Conference on Software Architecture (WICSA 2008), February 18-22, pp. 95-104, Vancouver, Canada. IEEE Computer Society Press, Los Alamitos, CA.
Gracio DK. 2008. "Data-Intensive Computing Pacific Northwest National Laboratory." Presented by DK Gracio (Invited Speaker) at General Meeting, October 30, PNNL, Richland, WA. PNNL-SA-63890.
Gracio DK. 2008. "Increasing Research Productivity Through Data Management ." Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-61308.
Gregory ML and CO Berkman. 2008. "Computing and Engineering to Address Global Challenges in Cyber Security, Data Intensive Computing, and Social Modeling." Presented by ML Gregory at 2008 Japan-America Frontiers of Engineering Symposium, November 17, Kobe, Japan. PNNL-SA-63361.
Gregory ML and AJ Cowell. 2008. "High Throughput Video and Image Analysis." Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-61882. [Unpublished]
Hewitt MS and DJ Hachigian. 2008. "Defense and Special Programs wall display." Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-61334.
Khaleel MA. 2008. "Beyond the Desktop." Presented by MA Khaleel (Invited Speaker) at Tech Alliance, November 14, Seattle, WA. PNNL-SA-63751.
Jones MH and X Sun. 2008. "Towards Quantitative Resonance Inspection: Resonance Mode Identification and Modeling." Presented by Cam Dasch (Invited Speaker) at QNDE 2008, July 21, Chicago, IL. PNNL-SA-62722.
Kounev S, I Gorton, and K Sachs. 2008. Performance Evaluation: Metrics, Models and Benchmarks . SPEC International Performance Evaluation Workshop (SIPEW 2008), Lecture Notes in Computer Science, 5119:323 pp.
Kouzes RT, GA Anderson, ST Elbert, I Gorton, and DK Gracio. 2008. "The Changing Paradigm of Data Intensive Computing." Computer 42(1):26-34.
Liu Y, MA Babar, and I Gorton. 2008. "Middleware Architecture Evaluation for Dependable Self-Managing Systems." In: The 4th International Conference on the Quality of Software-Architectures (QoSA 2008), Models and Architectures, Lecture Notes In Computer Science, Springer-Verlag, Berlin, Heidelberg, Germany 5281:189-204.
Liu Y, M Tan, I Gorton, and A Clayphan. 2008. "An Autonomic Middleware Solution for Coordinating Multiple QoS Controls." In: Proceedings of the 6th International Conference on Service-Oriented Computing (ICSOC08), Lecture Notes In Computer Science, Springer-Verlag, Berlin, Heidelberg, Germany 5364:225-240.
Liu Y, L Zhu, L Bass, I Gorton, and M Staples. 2008. "Non-Functional Property Driven Service Governance: Performance Implications." In: Service-Oriented Computing (ICSOC 2007) Workshops, Lecture Notes in Computer Science, Springer-Verlag, Berlin, Heidelberg, Germany 4907:45-55.
Lombardo NJ. 2008. "Standoff Technology Integration and Demonstration Program (STIDP)." Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-63764.
Marquez A. 2008. "Unconventional Architectures for Data Intensive Computing." Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-61597.
Matzke MM, CS Oehmen, and BJM Webb-Robertson. 2008. "Improving the Computational Task of Support Vector Machine Training by Dimension Reduction for the Problem of Protein Family Classification." In: 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. PNNL-SA-60288. [Unpublished]
McColgin DW, WE Cowley, VL Crow, SJ Rose, and ML Gregory. 2008. "Rapid User Guided Analytics - Spring VAC 08." Presented by DW McColgin (Invited Speaker) at VAC Meeting, May 21, Laurel, MD. PNNL-SA-60568.
McDermott JE. 2008. "Topology and Function in Networks inferred from transcriptomics." Abstract submitted to Pacific Biocomputing Symposium, North of Kona, HI. PNNL-SA-63276.
Monchiero M, G Palermo, C Silvano, and O Villa. 2008. "A Modular Approach to Model Heterogeneous MPSoC at Cycle Level." In: The 11th EUROMICRO Conference on Digital System Design Architectures, Methods and Tools (DSD08), pp. 158-164, IEEE Computer Society Press, Los Alamitos, CA.
Oehmen CS. 2008. "Mathematics of Cybersecurity: Enabling Proactive Capabilities." Abstract submitted to SIAM 2009 Conference on Computational Science and Engineering, Miami, FL. PNNL-SA-62206.
Oehmen CS and BJM Webb-Robertson. 2008. "Data-Intensive Machine Learning Applications of Support Vector Machines." Presented by CS Oehmen (Invited Speaker) at N/A, January 24, Richland, WA. PNNL-SA-58790.
Oehmen CS and BJM Webb-Robertson. 2008. "Evaluating the Computational Requirements of Using SVM Software to Train Data-Intensive Problems." In: Machine Learning Research Progress, eds. H Peters and M Vogel, Nova Science Publishers, Hauppauge, NY.
Paulish D, I Gorton, J Tyree, and D Soni. 2008. "Editorial." Journal of Systems and Software 81(9):1441-1442.
Pike WA. 2008. "Composable Analytic Interfaces." Presented by WA Pike at Visit by National Reconnasance Office CTO, September 11, Richland, WA. PNNL-SA-62561.
Pike WA and J Gerth. 2008. "National Cyber Leap Year Concept." Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-63901.
Pike WA, C Scherrer, and SJ Zabriskie. 2008. "Putting Security in Context: Visual Correlation of Network Activity with Real-World Information." In: Proceedings of the Workshop on Visualization for Computer Security (VizSEC07), eds. JR Goodall, G Conti, and K-L Ma, pp. 203-220. Springer-Verlag, Berlin, Heidelberg, Germany. doi:10.1007/978-3-540-78243-8_14
Rose SJ. 2008. ARTASAN, A Real-Time Architecture for Streaming Analytics. Presented by SJ Rose (Invited Speaker) at Internal Client Presentation, September 25, Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-62623.
Rose SJ, JP Almquist, and AS Wynne. 2008. "ARTASAN, A Real-Time Architecture for Streaming Analytics." Presented by JP Almquist (Invited Speaker) at an Internal Presentation to Visitor, October 30, Richland, WA. PNNL-SA-63256.
Rose SJ. 2008. "A Real-Time Architecture for Streaming Analytics." Presented by SJ Rose (Invited Speaker) at ab Internal Client Presentation, August 14, Pacific Northwest National Laboratory, Richland, WA. PNNL-SA-61896.
Scarpazza DP, O Villa, and F Petrini. 2008. "Efficient Breadth-First Search on the Cell/BE Processor." IEEE Transactions on Parallel and Distributed Systems 19(10):1381-1395. doi:10.1109/TPDS.2007.70811
Scarpazza DP, O Villa, and F Petrini. 2008. "Exact Multi-Pattern String Matching on the Cell/B.E. Processor." In: ACM International Conference on Computing Frontiers (CF 2008), May 5-7, Ischia, Italy.
Scarpazza DP, O Villa, and F Petrini. 2008. "High-Speed String Searching against Large Dictionaries on the Cell/B.E. Processor." In: The 22nd IEEE International Parallel & Distributed Processing Symposium, (IPDPS08), April, Miami, FL.
Scarpazza DP, O Villa, and F Petrini. 2008. "String Search on Multicore Processors." Dr. Dobb's Journal (April Issue).
Scherrer C, N Beagley, J Nieplocha, D Chavarria-Miranda, A Marquez, and J Feo. 2008. "Multivariate Counting on the Cray XMT." Presented by C Scherrer (Invited Speaker) at Presentation for Prescott Winter et al., January 24, Richland, WA. PNNL-SA-58850.
Schuchardt KL, TD Gibson, EG Stephan, and G Chin. 2008. "Applying Content Management to Automated Provenance Capture." Concurrency and Computation. Practice & Experience 20(5):541-554.
Scott MJ. 2008. "Impact of New Estimates of Water Availability for Agriculture Under Climate Change: Agricultural Impacts in the Yakima Basin of Washington State." Presented by MJ Scott (Invited Speaker) at Managing Water in a Climate Changing World: Implications for Irrigation, Drainage and Flood Control, USCID Water Management, September 18, Portland, OR. PNWD-SA-8323.
Shah AR, CS Oehmen, and BJM Webb-Robertson. 2008. "SVM-Hustle - An Iterative Semi-Supervised Machine Learning Approach for Pairwise Protein Remote Homology Detection." Bioinformatics 24(6):783-790.
Shaw WJ, JC Linehan, NK Szymczak, DJ Heldebrant, CR Yonker, DM Camaioni, RT Baker, and T Autrey. 2008. "In Situ Multinuclear NMR Spectroscopic Studies of the Thermal Decomposition of Ammonia Borane in Solution." Angewandte Chemie International Edition 47(39):7493-7496. doi:10.1002/anie.200802100
Trease HE, F Dan, RM Farber, and ST Elbert. 2008. "Using Transaction Based Parallel Computing to Solve Graph Problems Associated With High-Throughput Video Surveillance Applications." In: TeraGrid'08, pp. 1-6. PNNL-SA-60172.
Trease, HE, R Farber, A Wynne, and L Trease. 2008. "High-Performance Video Content Analysis Using Hybrid, Multi-Core Processors." In: IASTED Signal and Image Processing 2008 Conference, ed. P. Cristea, Paper No.: 623-088, Acta Press, Calgary, Alberta, Canada.
Villa O, D Chavarria-Miranda, and KJ Maschhoff. 2008. "Input-Independent, Scalable and Fast String Matching on the Cray XMT." In: The 23rd IEEE International Symposium on Parallel & Distributed Processing Symposium (IPDPS09). IEEE Computer Society Press, Los Alamitos, CA.
Webb-Robertson BJM. 2008. "Models for a Priori Identification of Proteotypic Mass Spectrometry Peptides and Proteins." [Unpublished]
Webb-Robertson BJ. 2008. "Peptides and Proteins." Presented by BJM Webb-Robertson (Invited Speaker) at the Third Annual BioProcess International Analytical and Quality Summit, June 4, Cambridge, MA. PNNL-SA-60593.
Webb-Robertson BJM, CS Oehmen, and AR Shah. 2008. "A Feature Integration Approach for a Generalized Support Vector Machine Pairwise Homology Algorithm." Computational Biology and Chemistry 23(6):458-461.
Webb-Robertson BJM, WR Cannon, CS Oehmen, AR Shah, V Gurumoorthi, MS Lipton, and KM Waters. 2008. "A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics." Bioinformatics 24(13):1503-1509. doi:10.1093/bioinformatics/btn218
Whitney PD. 2008. "Analytics and Algorithms for Data Intensive Computing." Presented by PD Whitney (Invited Speaker), June 10, Data Intensive Computing Annual Review. PNNL-SA-61150.
Wynne AS and I Gorton. 2008. "A Flexible, High Performance Service-Oriented Architecture for Detecting Cyber Attacks." Presented by AS Wynne at Hawaii International Conference on System Sciences (HICSS), January 7, Waikoloa Village, HI. PNNL-SA-58719.
Wynne AS, I Gorton, JP Almquist, J Chatterton, and DA Thurman. 2008. "A Flexible, High Performance Service-Oriented Architecture for Detecting Cyber Attacks." In: Proceedings of the 41st Annual Hawaii International Conference on System Sciences, p. 263. IEEE Computer Society Press, Los Alamitos, CA.
Young J, KH Jarman, PD Whitney, HE Trease, GM Holter, and SD Unwin. 2008. "Selected PNNL Research Activities." PNNL-SA-60559. [Unpublished]
2007
Babar MA and I Gorton. 2007. "Architecture Knowledge Management: Challenges, Approaches, and Tools." In: Proceedings of the 29th IEEE International Conference on Software Engineering. (ICSE07) Companion, May 20-26, pp. 170-171, Minneapolis, MN,. Institute of Electrical and Electronics Engineers, Inc., Piscataway, NJ.
Babar MA and I Gorton. 2007. "A Tool for Managing Software Architecture Knowledge." In: The 2nd Workshop on Sharing and Reusing Architectural Knowledge - Architecture, Rationale, and Design Intent (SHARK/ADI07) at 29th Annual Conference on Software Engineering (ISCE07) May 20-26, pp. 11-18, Minneapolis, MN. Institute of Electrical and Electronics Engineers, Inc., Piscataway, NJ.
Bohn SJ, WE Cowley, R Scarberry, DA Payne, GC Nakamura, and DV Love. 2007. "Information Analytics Using High Performance Computing Techniques and Scalable Interactions." Presented by SJ Bohn (Invited Speaker) at Internal Presentation, August 28, Richland, WA. PNNL-SA-56818.
Bui NB, L Zhu, I Gorton, and Y Liu. 2007. "Benchmark Generation Using Domain Specific Modeling." In: Proceedings of the 2007 IEEE Australian Software Engineering Conference (ASWEC07), April 10-13, pp. 169-180, Melbourne, Victoria, Australia IEEE Computer Society Press, Los Alamitos, CA.
Cannon WR, and BM Webb-Robertson. 2007. "Computational Proteomics: High-throughput Analysis for Systems Biology." In: Biocomputing 2007. Proceedings of the Pacific Symposium, January 3-7, Maui, HI, eds. RB Altman, AK Dunker, L Hunter, T Murray, and TE Klein, pp. 403-408. World Scientific Publishing Company, Singapore.
Cannon WR, BJM Webb-Robertson, M Singhal, LA McCue, JE McDermott, RC Taylor, KM Waters, and CS Oehmen. 2007. "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics." In: Computational and Systems Biology: Methods and Applications. PNNL-SA-57999.
Chavarria-Miranda D and A Marquez. 2007. "Assessing the Potential of Hybrid HPC Systems for Scientific Applications." In: Proceedings of the 2007 ACM International Conference on Computing Frontiers. Association for Computing Machinery Press, NY.
Chavarria-Miranda D, BH Clowers, GA Anderson, and ME Belov. 2007. "Simulating Data Processing for an Advanced Ion Mobility Mass Spectrometer." In: Proceedings of the 1st International Workshop on High-Performance Reconfigurable Computing Technology and Applications (HPRCTA07) held in conjunction with SC07, November 10-16, pp. 21-29, Reno, NV. Association for Computing Machinery Press, NY.
Chin G Jr, DK Gracio, and AR Chappell. 2007. "Concept-Based User Interfaces." In: Yearbook of Science & Technology, McGraw-Hill, NY. PNNL-SA-56766.
Chin SH. 2007. "Data-Intensive Computing Paving Way for Advances in Biology." SciDAC Review (Accepted).
Cowell AJ, ML Gregory, EJ Marshall, I Gorton, D McColgin, SJ Rose, and LR McGrath. 2007. "Sensemaking from Social Media." In: International Conference on Weblogs and Social Media. PNNL-SA-5844.
Farber R. 2007. "Will Your Next Supercomputer Come From Costco?" Scientific Computing 24(5):13+.
Farber R. 2007. "Data Management, the Victorian-Era Child of the 21st Century." Scientific Computing 24(4):12+.
Farber R. 2007. "Balancing Computation and Experiment." Innovation: America's Journal of Technology Commercialization 5(24):24+.
Farber R. 2007. "HPC Balance and Common Sense." Scientific Computing 24(3):12+.
Farber R. 2007. "The HPC Brick Wall.." Scientific Computing 24(6):16+.
Farber R. 2007. "The Cure for HPC Neurosis: Multiple, Virtual Personalities!" Scientific Computing 24(7):16+.
Farber R. 2007. "The Future Looks Bright for Teraflop Computing." Scientific Computing 24(10):34.
Farber R. 2007. "Virtualization as a Vehicle for Linear Storage Scaling." Presented by R Farber (Invited Speaker) at HECIWG FSIO Workshop, August 6, Arlington, VA. PNNL-SA-56506.
Gorton I. 2007. "Incorporating MeDICi Analysis Pipelines into the BRM and Gaggle." Presented by I Gorton (Invited Speaker) at The Gaggle Workshop, August 28, Seattle, WA. PNWD-SA-7911.
Gorton I. 2007. "MeDICi: One Year Old." Presented by I Gorton (Invited Speaker) at DICI Review, August 14, Richland, WA. PNNL-SA-57106.
Gorton I. 2007. "Proposal for a Computer Special Issue on Data Intensive Computing." PNNL-SA-54345. [Accepted] to be published Institute of Electrical and Electronics Engineers.
Gorton I, Y Liu, and N Trivedi. 2007. "An Extensible and Lightweight Architecture for Adaptive Server Applications." Software-Practice & Experience 38(8): 853-883.
Gorton I, JC Melland, and SB Neely. 2007. "MeDICi Integration Framework." Presented by D Hachigian at SuperComputing 2007, November 11, Reno, NV. PNNL-SA-57883.
Gorton I, D Chavarria-Miranda, M Krishnan, and J Nieplocha. 2007. "A High-Performance Event Service for HPC Applications." In: The 3rd International Workshop on Software Engineering for High Performance Computing Applications. IEEE Computer Society Press, Washington D.C.
Gracio DK. 2007. "Data-Intensive Computing Paving the Way for Scientific Discovery." Presented by DK Gracio (Invited Speaker) to DOE Client Yukiko Sekine, August 6, Richland, WA.
Gracio DK. 2007. "Data-Intensive Computing Paving the Way for Scientific Discovery." Presented by DK Gracio (Invited Speaker) at 2007 Fall Creek Falls Conference, September 26, Nashville, TN. PNNL-SA-57409.
Gracio DK, I Gorton, and SH Chin. 2007. "Data Intensive Computing Key to Predictive Science." Breakthroughs - Winter Issue. PNNL-SA-53582.
Gregory ML, AJ Cowell, SJ Rose, and L McGrath. 2007. "Synthesizing information Across Multiple Chat Rooms." In International Conference on Web and Social Media. PNWD-SA-8064. [Unpublished]
Hachigian DJ. 2007. "Data-Intensive Computing: Laying the Foundation for Biological Breakthroughs." DOE Pulse.
Huang Z, RT Guttromson, J Nieplocha, and RG Pratt. 2007. "Transforming Power Grid Operations via High-Performance Computing." Scientific Computing 24(5):1-8.
Kot A, V Tipparaju, J Nieplocha, MT Bruggencate, and N Chrisochoides. 2007. "Evaluation of Remote Memory Access Communication on the Cray XT3." In: Workshop on Communication Architecture for Clusters. International Parallel & Distributed Processing Symposium (IPDPS07), March 26-30, pp. 1-7, Institute of Electrical and Electronics Engineers, Inc., Long Beach, CA.
Krishnan M, SJ Bohn, W Cowley, V, Crow, and JJ Nieplocha. 2007. "Scalable Visual Analytics of Massive Textual Datasets." In: Proceedings of International Parallel & Distributed Processing Symposium (IPDPS07), March 26-30, Institute of Electrical and Electronics Engineers, Inc., Long Beach, CA.
Liu Y and I Gorton. 2007. "Implementing Adaptive Performance Management in Server Applications." In: Proceedings of the 2007 International Workshop ion Software Engineering for Adaptive and Self-Managing Systems (SEAMS07) IEEE Computer Society Press, Washington, D.C.
Liu Y, I Gorton, and VK Le. 2007. "A Configurable Event Correlation Architecture for Adaptive J2EE Applications." In: Proceedings of the 2007 IEEE Australian Software Engineering Conference (ASWEC07), April 10-13, pp. 49-58, Melbourne, Australia. IEEE Computer Society Press, Washington, D.C.
Liu Y, L Zhu, and I Gorton. 2007. "Performance Assessment for e-Government Services: An Experience Report." In: The 10th International ACM SIGSOFT Symposium on Component-Based Software Engineering, Lecture Notes in Computer Science, Springer-Verlag, Berlin, Heidelberg, Germany 4608:74-89.
McDermott JE and N Beagley. 2007. DICI Impact to EBI. Presented by J McDermott and N Beagley (Invited Speakers) at DICI FY07 Annual Review, August 16, Richland, WA. PNNL-SA-56619.
McDermott JE and N Beagley. 2007. EBI-DICI Linkages. Presented by J McDermott (Invited Speaker) at EBI FY07 Annual Review, August 16, Richland, WA. PNNL-SA-56630.
Nieplocha J, D Chavarria-Miranda, V Tipparaju, Z Huang, and A Marquez. 2007. "A Parallel WLS State Estimator for Shared Memory Computers." In: Proceedings of the 8th International Power Engineering Conference (IPEC07), pp. 395-400, Institute of Electrical and Electronics Engineers, Inc., Piscataway, NJ.
Nieplocha J, A Marquez, F Petrini, and D Chavarria-Miranda. 2007. "Unconventional Architectures Address Challenges in High-Throughput Sciences." SciDAC Review. (Fall Issue), pp. 46-50.
Nieplocha J, A Marquez, J Feo, D Chavarria-Miranda, G Chin, Jr, C Scherrer, and N Beagley. 2007. "Evaluating the Potential of Multithreaded Platforms for Irregular Scientific Computations." In: Proceedings of the 4th International Conference on Computing Frontiers, May 7-9, pp. 47-58, Ischia, Italy. Association for Computing Machinery Press, NY.
Pike WA. 2007. "Integrating Knowledge Models into the Scientific Analysis Process." Presented by WA Pike (Invited Speaker) at Workshop on Data and Knowledge Modelling, December 10, Edinburgh, United Kingdom. PNNL-SA-58372.
Pike WA and SB Neely. 2007. "Putting Security in Context." Presented by WA Pike at Supercomputing 2007, November 10. [Poster on NUANCE presented in the PNNL booth at SC07]. PNNL-SA-57718.
Pike WA, C Scherrer, and SJ Zabriskie. 2007. "Putting Security in Context: Visual Correlation of Network Activity with Real-World Information." Presented by WA Pike at Workshop on Visualization for Computer Security, October 29, Sacramento, CA. PNNL-SA-57961.
Quadrel R. 2007. "DICI and Homeland Security Technology Needs." Presented by R Quadrel (Invited Speaker) at DICI Advisory Review Committee, August 15, Richland, WA.. PNNL-SA-56985.
Ray DA. 2007. "Pacific Northwest National Laboratory Overview." Presented by DA Ray (Invited Speaker) at Presentation at Lawrence Livermore National Laboratory, December 14, Livermore,CA. PNNL-SA-58346.
Sanfilippo AP, B Baddeley, C Posse, and PD Whitney. 2007. "A Layered Dempster-Shafer Approach to Scenario Construction and Analysis." In: IEEE International Conference on Intelligence and Security Informatics 2007 (ISI07), May 23-24, pp. 95-102, New Brunswick, NJ. Institute of Electrical and Electronics Engineers, Inc., Piscataway, NJ.
Scarpazza DP, O Villa, and F Petrini. 2007. "Programming the Cell Processor." Dr. Dobb's Journal 32(4):2628-2630.
Scarpazza DP, O Villa, and F Petrini. 2007. "Peak-Performance DFA-based String Matching on the Cell Processor." In: International Parallel & Distributed Processing Symposium (IPDPS07), Workshop on System Tools. Institute of Electrical and Electronics Engineers, Inc., Piscataway, New Jersey.
Scarpazza DP, O Villa, F Petrini, and J Fernandez-Peinador. 2007. "Challenges in Mapping Graph Exploration Algorithms on Advanced Multi-core Processors." In: International Parallel & Distributed Processing Symposium (IPDPS07). Institute of Electrical and Electronics Engineers, Inc., Piscataway, NJ.
Scarpazza DP, P Mullaney, O Villa, F Petrini, V Tipparaju, and J Nieplocha. 2007. "Transparent System-level Migration of PGAs Applications Using Xen on Infiniband." In: 2007 Institute of Electrical and Electronics Engineers, Inc., International Conference on Cluster Computing, pp. 74-83.
Scherrer C, N Beagley, J Nieplocha, A Marquez, J Feo, and D Chavarria-Miranda. 2007. "Probability Convergence in a Multithreaded Counting Application." In Workshop on Multithreaded Architectures and Application, International Parallel & Distributed Processing Symposium (IPDPS07), pp. 1-5. IEEE Online. Institute of Electrical and Electronics Engineers, Inc., Piscataway, NJ.
Schuchardt KL, GD Black, JM Chase, TO Elsethagen, and L Sun. 2007. "Process Integration, Data Management, and Visualization Framework for Subsurface Sciences." Journal of Physics: Conference Series 78:012064, 1-5.
Schuchardt KL, BJ Palmer, J Daily, TO Elsethagen, and AS Koontz. 2007. "IO Strategies and Data Services for Petascale Data Sets from a Global Cloud Resolving Model." Journal of Physics: Conference Series 78: Art. No. 012089.
Shah A, CS Oehmen, JK Harper, and BJM Webb-Robertson. 2007. "Integrating Subcellular Location for Improving Machine Learning Models of Remote Homology Detection in Eukaryotic Organisms." Computational Biology and Chemistry 31(2):138-142.
Shah A, M Singhal, KR Klicker, EG Stephan, HS Wiley, and KM Waters. 2007. "Enabling High-Throughput Data Management Systems Biology: The Bioinformatics Resource Manager." Bioinformatics 23(7):906-909.
Stephan EG, TJ Critchlow, AL Corrigan, ES Peterson, RD Lins Neto, TA Soares, and T Straatsma. 2007. "Effectively Managing Large-Scale Scientific Simulation Data." In: The 24th International Conference on Data Engineering. PNNL-SA-56017. [Unpublished]
Straatsma T. 2007. "Data-Intensive Computing: Laying the Foundation for Biological Breakthroughs." DOE Pulse 237, June 18th Issue.
Thurman DA, JP Almquist, I Gorton, AS Wynne, and J Chatterton. 2007. "SIFT - A Component-Based Integration Architecture for Enterprise Analytics." In: The 6th International IEEE Conference on Commercial-off-the-Shelf (COTS)-Based Software Systems, (ICCBSS07), 26 February 26-March, pp. 82-92, Banff, Alberta, Canada. Institute of Electrical and Electronics Engineers, Inc., Piscataway, NJ.
Waters KM. 2007. "Bioinformatics Resource Manager: Data Management for Systems Biology." Presented by KM Waters (Invited Speaker) at Gaggle Workshop 2007, August 27, Seattle, WA. PNWD-SA-7914.
Webb-Robertson BJM, and LA McCue. 2007. "In Silico Analysis of Peptide Signatures to Discriminate Microorganisms and A Visual Approach to Multiple Whole-Genome Analysis." Presented by LA McCue (Invited Speaker), December 18, at Visitor Presentation, Richland, WA. PNNL-SA-58981.
Webb-Robertson BJM, JE McDermott, N Beagley, KH Jarman, and LA McCue. 2007. "Biosignature Integration for Evaluating Environmental Stressors." Presented by BJM Webb-Robertson, (Invited Speaker) at The Society of Environmental Toxicology and Chemistry (SETAC07) North America 28th Annual Meeting, November 14, Milwaukee, WI. PNNL-SA-58132.
Webb-Robertson BJM, CS Oehmen, and WR Cannon. 2007. "Support Vector Machine Classification of Probability Models and Peptide Features for Improved Peptide Identification from Shotgun Proteomics." In: The 6th International Conference on Machine Learning and Applications (ICMLA07), pp. 500-505. Institute of Electrical and Electronic Engineers, Inc., Los Alamitos, CA.
Webb-Robertson BJM, ES Peterson, M Singhal, KR Klicker, CS Oehmen, JN Adkins, and SL Havre. 2007. "PQuad - A Visual Analysis Platform for Proteomic Data Exploration of Microbial Organisms." Bioinformatics 23(13):1705-1707.
Wolf KE, PD Whitney, N Beagley, AM White, C Posse, AS Wynne, I Gorton, G Chin, AR Chappell, J Bruce, B Nickless, R Nelson, SJ Zabriskie, C Scherrer, and WA Pike. 2007. "Decision Support & Control Demonstration." Presented by KE Wolf (Invited Speaker) at Data Intensive Computing Initiative Annual Review, August 14, Richland, WA.. PNNL-SA-56644.
Zhu L and I Gorton. 2007. "UML Profiles for Design Decisions and Non-Functional Requirements." In: The 2nd International Workshop on Sharing and Reusing Architectural Knowledge - Architecture, Rationale, and Design Intent (SHARK/ADI'07: ICSE07 Workshops).
Zhu L, M Staples, and I Gorton.2007. An Infrastructure for Indexing and Organizing Best Practices. In: Realizing Evidence-Based Software Engineering (REBSE2) Workshop (ICSE07), Minneapolis, MN.
Zhu L, Y Liu, NB Bui, and I Gorton. 2007. "Revel8or: Model Driven Capacity Planning Tool Suite." In: Proceedings of the 29th International Conference on Software Engineering (ICSE07), pp. 797-800, Minneapolis, MN.
2006
Beecroft J, D Addison, D Hewson, M McLaren, D Roweth, F Petrini, and J Nieplocha. 2006. "QsNetII : Defining High-Performance Network Design." IEEE Micro 25(4):34-47.
Chavarria-Miranda D, J Nieplocha, and V Tipparaju. 2006. "Topology-Aware Tile Mapping for Clusters of SMPs." In: Proceedings of the 2006 ACM International Conference on Computing Frontiers. ACM, Ischia, Italy.
Frachtenberg E, D Feitelson, F Petrini, and J Fernandez. 2006. "Adaptive Parallel Job Scheduling with Flexible CoScheduling." IEEE Transactions on Parallel and Distributed Systems 16(11):1066-1077.
Garcia PE, J Fernandez, F Petrini, and JM Garcia. 2006. "Cluster Computing with QsNetII." In: Euro PVM/MPI 2005, September, Sorrento, Italy.
Garcia PE, J Fernandez, F Petrini, and JM Garcia. 2006. "Assessing MPI Performance on QsNetII." In: Euro PVM/MPI 2005, September, Sorrento, Italy.
Gorton I, Y Liu, and N Trivedi. 2006. "An Extensible, Lightweight Architecture for Adaptive J2EE Applications ." In: Proceedings of the 6th International Workshop on Software Engineering and Middleware (SEM06). Foundations of Software Engineering, pp. 47-54. Association for Computing Machinery Press, NY.
Jiang S, K Davis, F Petrini, X Ding, and X Zhang. 2006. "COCA: A Locality-Aware Cooperative Cache Management Protocol to Improve Network File System Performance." In: Proceedings of the 26th International Conference on Distributed Computing Systems, July, pp.42-42, Lisboa, Portugal.
Krishnan M and J Nieplocha. 2006. "Memory Efficient Parallel Matrix Multiplication Operation for Irregular Problems." In: Proceedings of the 20th IEEE International Parallel & Distributed Processing Symposium (IPDPS06). ACM SIGMICRO Computing Frontiers, Ischia, Italy.
Manke KL. 2006. "Comin' Atcha!" Innovation: America's Journal of Technology Commercialization 4(5):14-16.
Melland JC and CS Oehmen. 2006. "ScalaBLAST Solves Problems in Record Time." PNNL-SA-51821. IEEE Supercomputing November - Video.
Nieplocha J, V Tipparaju, and M Krishnan. 2006. "Optimizing Strided Remote Memory Access Operations on the Quadrics QsNetII Network Interconnect." In: Proceedings of the 8th International Conference on High-Performance Computing in Asia-Pacific Region, 2005, pp. 28-35. Institute of Electrical and Electronics Engineers, Inc., Piscataway, NJ.
Oehmen C and J Nieplocha. 2006. "ScalaBLAST: A Scalable Implementation of BLAST for High-Performance Data-Intensive Bioinformatics Analysis." In: IEEE Transactions on Parallel and Distributed Systems 17(8):740-749.
Petrini F, J Nieplocha, and V Tipparaju. 2006. "SFT: Scalable Fault Tolerance." In: ACM SIGOPS Operating Systems Review 40(2):55-62.
Petrini F, A Moody, J Fernandez, E Frachtenberg, and DK Panda. 2006. "NIC-Based Reduction Algorithms for Large-scale Clusters." International Journal of High Performance Computing and Networking (IJHPCN) 4(3/4):122-136.
Schuchardt K. 2006. "Towards a Provenance Architecture." Presented by K Schuchardt (Invited Speaker) at the Kepler Provenance Working Meeting, January 19, San Diego, CA.
Schuchardt KL, TD Gibson, EG Stephan, and G Chin Jr. 2006. "Applying Content Management to Automated Provenance Store." Concurrency and Computation: Practice & Experience 20(5):541-554.
Wong PC, HP Foote, G Chin, JR, PS Mackey, and KA Perrine. 2006. "Graph Signatures for Visual Analytics." In: IEEE Transactions on Visualization and Computer Graphics 12(6):1399-1413.
Wong PC, SJ Rose, G Chin Jr, D Frincke, RA May II, C Posse, AP Sanfilippo, and JJ Thomas. 2006. "Walking the Path" A New Journey to Explore and Discover through Visual Analytics." Information Visualization 5(4):237-249.