U.S. Department of Energy

Pacific Northwest National Laboratory

Publications

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Contents

[edit] Select Publications

Journal Articles

[edit] 2012

al-Saffar S. 2012. "Multi-Relational Knowledge Discovery." PNNL-SA-86402, Pacific Northwest National Laboratory, Richland, WA.

Anderson KK, LW Campbell, AM Casella, CJ Gesh, AC Misner, EL Smith, SJ Tobin, HO Menlove, MT Swinhoe, MA Humphrey, SD Amber, P Blanc, T Burr, W Charlton, J Cheatham, D Chichester, JL conlin, S Croft, M Ehinger, JM Eigenbrodt, LG Evans, A Favalli, ML Fensin, CR Freeman, J Galloway, J Gerhart, J Hendricks, V henzl, D Henzlova, J Hu, A Hunt, WE Koehler, TJ Ulrich, H Trellue, SJ Thompson, J Sterbentz, A Stafford, A Solodov, BA Ludewigt, VV Mozin, MA Schear, NP sandoval, C Romano, JG Richard, E rauch, A Rajasingam, AM lafleur, and MW Shaver. 2012. "Technical Cross-Cutting Issues for the Next Generation Safeguards Initiative's Spent Fuel Nondestructive Assay Project." PNNL-SA-86028, Pacific Northwest National Laboratory, Richland, WA.

Asner DM. 2012. "PNNL Belle Computing Summary Feb 2012." Presented by Dr. David Asner (Invited Speaker) at Belle Computing Workshop KEK, KEK Tsukuba Japan, Japan on February 23, 2012. PNNL-SA-85906.

Bell EB, EJ Marshall, RE Hull, AK Fligg, AP Sanfilippo, DS Daly, and DW Engel. 2012. "Classifying Scientific Performance on a Metric-by-Metric Basis." In Proceedings of the Twenty-Fifth International FLAIRS Conference . Proceedings of the Twenty-Fifth International FLAIRS Conference, Marco Island, FL.

Bell EB, EJ Marshall, RE Hull, AK Fligg, AP Sanfilippo, DS Daly, and DW Engel. 2012. "Classifying Scientific Performance on a Metric-by-Metric Basis." Presented by Bell, Eric B (Invited Speaker) at The 25th International Florida AI Research Society Conference, Marco Island, FL on May 23, 2012. PNWD-SA-9843.

Carper RR, K Kowalski, S Krishnamoorthy, SA West, and C Plata. 2012. "A Path Forward: ARRA-enabled 'Barracuda' computing cluster allows scientists to team up on larger problems." PNNL-SA-86361 Pacific Northwest National Laboratory, Richland, WA.

Chen Y, Z Huang and MA Elizondo. 2012. "Value of Faster Computation for Power Grid Operation." Abstract submitted to 8th PP&PSC (Power Plant and Power Systems Control ) symposium, Toulouse, France. PNNL-SA-85204.

Chen X, GE Hammond, and JM Zachara. 2012. "Reducing the Hydrologic and Geochemical Uncertainty for Modeling Uranium Migration at the Hanford 300 Area by Assimilating Multiscale and Multi-type Data." Abstract submitted to DOE-SBR 7th Annual PI Meeting, Washington, DC. PNNL-SA-86769.

Chen Y, MA Elizondo, and Z Huang. 2012. "Value of Faster Computation for Power Grid Operation." In The 8th PP&PSC (Power Plant and Power System Control) Symposium will be held in Toulouse, France, in the period 2-5 September 2012. . PNNL-SA-87327, Pacific Northwest National Laboratory, Richland, WA.

Chavarría-Miranda D, BA Akyol, Z Huang, and JE Dagle. 2011. "Opening Remarks for 1st International Workshop on High Performance Computing, Networking and Analytics for the Power Grid." Presented by Daniel Chavarría-Miranda (Invited Speaker) at Opening Remarks for 1st International Workshop on High Performance Computing, Networking and Analytics for the Power Grid, Seattle, WA on November 13, 2011. PNNL-SA-84059.

Chen Y, Z Huang, and N Zhou. 2011. ""An Advanced Framework for Improving Situational Awareness in Electric Power Grid Operation"." Presented by Yousu Chen (Invited Speaker) at The 18th IFAC World Congress Milan, Italy, Milan, Italy on August 31, 2011. PNNL-SA-82492.

Church JM, DJ Kerbyson, and TP Straatsma. 2012. "eXtreme Scale Computing." PNNL-SA-86849, Pacific Northwest National Laboratory, Richland, WA.

Ciraci S and J Yin. 2011. "Towards a Scalable and Reliable Real Time In-Network Data Analysis Infrastructure." Presented by Selim Ciraci at Large Scale Data Analysis and Visualization on October 23, 2011. PNNL-SA-82429.

Colella WG. 2012. "Independent Analysis of Real-Time Performance Data from Co-Generative Fuel Cell Systems Installed in Buildings." Presented by Whitney G. Colella (Invited Speaker) at Kasit Energy Workshop, Daejeon, Korea, Republic Of on February 16, 2012. PNNL-SA-85672.

Colella WG and HE Dillon. 2012. "Advances in Distributed, Grid-Connected Energy Generation and Storage." Presented by Whitney Colella (Invited Speaker) at Korea Institute of Energy Research Seminar, Daejeon, Korea on February 17, 2012. PNNL-SA-85767.

Colella WG. 2012. "Next Generation Building Energy Technologies: Independent Testing Of Micro Co-Generative Fuel Cell Systems For Light Commercial Buildings." Presented by Whitney Colella (Invited Speaker) At Brown Bag Presentation, Richland, WA on January 25, 2012. PNNL-SA-85349.

Cree JV. 2012. "Scalable Multi-Parent N-Tiered Clustering in WSNs." Abstract submitted to IPSN 2012 PhD Forum, The 11th ACM/IEEE Conference on Information Processing in Sensor Networks PhD Forum, Beijing, China. PNNL-SA-85929.

Cree JV. 2012. "Scalable Multi-Parent N-Tiered Clustering Hierarchy for Duty-Cycled WSNs." Presented by Johnathan Cree at IPSN 2012 PhD Forum, The 11th ACM/IEEE Conference on Information Processing in Sensor Networks PhD Forum , Beijing, China on April 15, 2012. PNNL-SA-87310.

Cree JV. 2012. "Multi-Parent N-Tier Clustering Hierarchy Management for Duty-Cycled WSNs." Presented by Johnathan Cree at IPSN 2012 PhD Forum, The 11th ACM/IEEE Conference on Information Processing in Sensor Networks PhD Forum, Beijing, China on April 10, 2012. PNNL-SA-86972.

Devanathan R, ML Sushko, EM Murphy, and TD Scheibe. 2012. "Multiscale Analysis Platform for Materials Modeling." Presented by Ram Devanathan at Materials Research Society Spring 2012 Meeting, San Francisco, CA on April 11, 2012. PNNL-SA-87107.

Dillon HE, MA Halverson, CA Antonopoulos, RG Lucas, MC Madison, and OV Livingston. 2012. "Do We Really Know how much it Costs to Construct High Performance Buildings?" In ACEEE summer study. PNNL-SA-86431, Pacific Northwest National Laboratory, Richland, WA.

Dillon HE, and WG Colella. 2012. "EVALUATION OF PERFROMANCE DATA FROM COMBINED HEAT AND POWER FUEL CELL SYSTEMS." PNNL-SA-86987, Pacific Northwest National Laboratory, Richland, WA.

Dixon DA, M Dupuis, BC Garrett, JB Neaton, C Plata, MA Tarr, JF Tomb, and JT Golab. 2012. Harnessing the Department of Energy’s High-Performance Computing Expertise to Strengthen the U.S. Chemical Enterprise. PNNL-20896, Pacific Northwest National Laboratory, Richland, WA.

Ely JH, MW Cooper, DA Haas, JC Hayes, JI McIntyre, and BT Schrom. 2012. "Advanced Spectral Analysis for Radioxenon." Presented by James Ely at NDC & A, Cocoa Beach, FL on January 25, 2012. PNNL-SA-85403.

Evans J, G Sandeep, K Karavanic, A Marquez, and G Varsamopoulos. 2012. "Evaluating Performance, Power, and Cooling in High Performance Computing (HPC) Data Centers." In Handbook of Energy-Aware and Green Computing, ed. I Ahmad and S Ranka. Chapman and Hall/CRC, Boca Raton, FL.

Farber RM. 2011. "Seeking wisdom in the clouds." PNNL-SA-77710, Pacific Northwest National Laboratory, Richland, WA.

Fast JE, E Aguayo Navarrete, DC Rodriguez, MS Taubman, BA VanDevender, GA Warren, CD Wilen, LS Wood, and AT Evans. 2012. "Development of Analog Readout, Digital Signal Processing, and Data Analysis Software for Ultra-High Rate HPGe." Abstract submitted to 2012 Nuclear Science Symposium, Medical Imaging Conference & Workshop on Room- Temperature Semiconductor X-Ray and Gamma-, Anaheim, CA. PNNL-SA-87721.

Fast JE. 2012. "Quad Chart Slides for Ultra-Sensitive Nuclear Measurement Initiative." Presented by Jim Fast (Invited Speaker) at Ultra-Sensitive Nuclear Measurement Initiative 2012 July Review, Richland, WA on July 12, 2012. PNNL-SA-88082.

Ferryman TA and BG Amidan. 2012. "Baseline Analysis of PMU Data Based on Real World Data from January 1, 2011 to September 30, 2011." Presented by Tom Ferryman (Invited Speaker) at NASPI Working Group Meeting, Orlando, FL on March 1, 2012. PNNL-SA-85920.

Flann NS, A Ghaffarizadeh, GJ Podgorski, SH Kang, SH Kahan, JE McDermott, and I Shmulevich. 2012. "BioCellion: A High-performance Computing Framework for Multiscale Mod- eling and Simulation of Multicellular Biological Systems." Abstract submitted to The Society for Mathematical Biology Annual Meeting and Conference, KY. PNNL-SA-87801.

Fink GA, KS Berenhaut, and CS Oehmen. 2012. "Directional Bias and Pheromone for Detection and Verification on Networks." In Sixth IEEE International Conference on Self- Adaptive and Self-Organizing Systems. PNNL-SA-87555, Pacific Northwest National Laboratory, Richland, WA.

Fridlind AM, A Ackerman, JP Chaboureau, J Fan, WW Grabowski, A Hill, TR Jones, MM Khaiyer, G Liu, P Minnis, H Morrison, L Nguyen, S Park, JC Petch, JP Pinty, C Schumacher, B Shipway, AC Varble, X Wu, S Xie, and M Zhang. 2012. "A Comparison of TWP-ICE Observational Data with Cloud-Resolving Model Results." Journal of Geophysical Research. D. (Atmospheres) 117:Article No. D05204. doi:10.1029/2011JD016595

Fredrickson. 2012. "Integrating Genomics, Geochemistry and Geospatial Data to Understand the Development and Dynamics of High-temperature Acidic Iron-oxide and Sulfur Microbial Mats." Abstract submitted to ISME14 - International Symposium on Microbial Ecology, Copenhagen, Denmark. PNNL-SA-86872.

Freshley MD, VL Freedman, and I Gorton. 2012. "Advanced Simulation Capability for Environmental Management: Development and Demonstrations." In Waste Management 2012. PNNL-SA-85087, Pacific Northwest National Laboratory, Richland, WA.

Garza JM and SB Yabusaki. 2012. "Bacteria to the Rescue." PNNL-SA-85158, Pacific Northwest National Laboratory, Richland, WA.

Gaustad KL, BD Ermold, TR Shippert, SJ Beus, and KM Fox. 2012. "Integrated Software Development Environment: Data Consolidation Tool and Development Framework." Presented by Krista L. Gaustad at ARM 2012 Science Team Meeting, Arlington, VA on March 15, 2012. PNNL-SA-85128.

Gorton I. 2012. "Data Intensive Computing: A Challenge for the 21st Century." In Data Intensive Computing. PNNL-SA-84979, Pacific Northwest National Laboratory, Richland, WA.

Gorton I and MD Freshley. 2011. "Advanced Simulation Capability for Environmental Management (ASCEM): An Overview and Initial Results." PNNL-SA-78675, Pacific Northwest National Laboratory, Richland, WA.

Grate JW and JG Wiley. 2012. "Microanalytics & Microfluidics Focus Area Modeling Focus Area." Presented by Jay W. Grate (Invited Speaker) at PNNL LDRD Annual Review, Richland, WA on April 17, 2012. PNNL-SA-87142.

Greenwood LR, S Simakov, and R Capote Noy. 2012. "Validation Of The International Dosimetry Library Extension Up To 60 MeV." Abstract submitted to 12th International Conference on Radiation Shielding 17th Topical Meeting of the Radiation Protection and Shielding Divi, Nara, Japan. PNWD-SA-9762.

Gu Y, KN Liou, J Jiang, H Su, and X Liu. 2012. "Dust Aerosol Impact on North Africa Climate: A GCM Investigation of Aerosol-Cloud-Radiation Interactions Using A-Train Satellite Data." Atmospheric Chemistry and Physics 12(4):1667–1679. doi:10.5194/acp-12-1667-2012

Hagler CD, and JE Doel. 2012. "Closing the Cloud Deal." In National Laboratories Information Technology Annual Conference (NLIT). PNNL-SA-86090, Pacific Northwest National Laboratory, Richland, WA.

Hagler CD. 2012. "Using SaaS: Can we really do that?" Presented by Clay Hagler (Invited Speaker) at National Laboratories Information Technology Conference (NLIT), Sun Valley, ID on May 29, 2012. PNNL-SA-86044.

Hathaway JE, TC Pulsipher, RP Hafen, KK Anderson, JJ McCullough, GD Williams, DR Weier, and MR Ledbetter. 2012. "The Transition to LED Lighting: Modeling Lumen Degradation as a Measure of Reliability and Quality." Presented by J Hathaway (Invited Speaker) at Conference on Data Analysis (CODA), Santa Fe, NM on March 2, 2012. PNNL-SA-85838.

Hammond GE, PC Lichtner, and ML Rockhold. 2011. "Stochastic Simulation of Uranium Migration at the Hanford 300 Area." Journal of Contaminant Hydrology 120-121:115-128. doi:10.1016/j.jconhyd.2010.04.005

Hammond GE, PC Lichtner, C Lu, and RT Mills. 2012. "PFLOTRAN: Reactive Flow & Transport Code for Use on Laptops to Leadership-Class Supercomputers." In Groundwater Reactive Transport Models, ed. F Zhang, GT Yeh and JC Parker, pp. 141-159. Bentham Science Publishers, Oak Park, IL.

Hanna LA. 2012. Tethys Fact Sheet for GMREC. PNNL-SA-87282, Pacific Northwest National Laboratory, Richland, WA.

Huang Z and Y Chen. 2012. "High Performance Computing for Advanced Smart Grid Applications." Chapter 3 in Smart Grids: Infrastructure, Technology, and Solutions." PNNL-SA-85675, Pacific Northwest National Laboratory, Richland, WA.

Hubert R and NA Baker. 2012. "Community of Research: Nanotechnology Databases and Ontologies." Presented by Nathan A. Baker (Invited Speaker) at US-EU Communities of Research, Grenoble, France on May 31, 2012. PNWD-SA-9865.

Hughes PJ. 2012. Laboratory Directed Research and Development Annual Report for 2011 . PNNL-21238, Pacific Northwest National Laboratory, Richland, WA

Hund G and AJ Kurzrok. 2012. "Nonproliferation as a Corporate Sustainability Issue." PNNL-SA-86471 Pacific Northwest National Laboratory, Richland, WA.

Inskeep W, J Beam, H Bernstein, R Carlson, Z Jay, R Jennings, M Kozubal, A Dohnalkova, RN Brown, HW Kreuzer, MS Lipton, JJ Moran, MF Romine, D Rusch, S Tringe, and JK

Johnson TJ, YF Su, KH Jarman, BM Kunkel, JC Birnbaum, AG Joly, EG Stephan, RG Tonkyn, and RG Ewing. 2012. "Demonstrated Wavelength Portability of Raman Reference Data for Explosives and Chemical Detection." PNNL-SA-85885, Pacific Northwest National Laboratory, Richland, WA.

Kang SH, SH Kahan, JE McDermott, NS Flann, and I Shmulevich. 2012. " On the Simulation of Multicellular Biological Systems." In Supercomputing 2012. PNNL-SA-88206, Pacific Northwest National Laboratory, Richland, WA.

Keyes D, LC McInnes, C Woodward, GE Hammond, and TD Scheibe. 2012. "Multiphysics Simulations: Challenges and Opportunities." PNNL-21110, Pacific Northwest National Laboratory, Richland, WA.

Khaleel MA. 2012. "Creating new computational capabilities to solve problems using extreme scale simulation and data analytics." Presented by Mohammad Khaleel (Invited Speaker) at IDS STPI Visit, Richland, WA on May 11, 2012. PNNL-SA-88052.

Kleese van DK, AM Walker, and M James. 2012. "Integrating Data Management and Collaborative Sharing with Computational Science Processes." Chapter 21 in Handbook of Research on Computational Science and Engineering: Theory and Practice, vol. 2, ed. J Leng and W Sharrock, pp. 506-538. IGI Global, Hershey, PA.

Landers J. 2012. "Mitigating Insider Threat Workshop." Presented by John Sanders (Invited Speaker) at Mitigating Insider Threat Workshop, Beijing, China on July 27, 2012. PNNL-SA-88159.

Li D, G Lin, J Yin, K Kleese van Dam, JP Carson, EC Liu, KL Hui, Y Shi, Y Liu, EG Stephan, and J Laskin. 2012. "Fast Image Processing Software Suite Development for High Resolution Mass Spectrometry Imaging." Abstract submitted to 60th ASMS Conference on Mass Spectrometry and Allied Topics, Vancouver, BC, Canada. PNNL-SA-85699.

Li D, G Lin, J Yin, K Kleese van Dam, JP Carson, M Thomas, S Ryu, EC Liu, KL Hui, YJ Liu, Y Shi, EG Stephan, and J Laskin. 2012. "Fast Image Processing Software Suite Development for High Resolution Mass Spectrometry Imaging ." Presented by Dongsheng Li at 2012 ASMS conference, Vancouver, BC, Canada on May 23, 2012. PNNL-SA-88218.

Livingston OV, HE Dillon, MA Halverson, MC Madison, and RG Lucas. 2012. "Do We Really Know how Much it Costs to Construct High Performance Buildings?" In 2012 ACEEE Summer Study on Energy Efficiency in Buildings. . PNNL-SA-88090, Pacific Northwest National Laboratory, Richland, WA.

Liu Y, JM Chase, and I Gorton. 2012. "A Service Oriented Architecture for Exploring High Performance Distributed Power Models." In 10th International Conference on Service Oriented Computing. PNNL-SA-88094, Pacific Northwest National Laboratory, Richland, WA.

Lu N. 2012. "A Multi-layer Data-driven Reasoning Tool for Smart Grid Integrated Information Systems." Presented by Ning Lu (Invited Speaker) at Information and Communication Technologies for Smart Grid Applications Workshop, Victoria, BC, Canada on February 8, 2012. PNNL-SA-85447.

Lu N, P Du, FL Greitzer, X Guo, RE Hohimer, and YG Pomiak. 2012. "A Multi-layer, Datadriven Advanced Reasoning Tool for Intelligent Data Mining and Analysis for Smart Grids." In 2012 IEEE PES general meeting . PNNL-SA-85049, Pacific Northwest National Laboratory, Richland, WA.

Lu N, YV Makarov, and MCW Kintner-Meyer. 2012. "Energy Storage Applications for Renewable Integration." Presented by Ning Lu (Invited Speaker) at Utah Governor’s Energy Development Summit, Salt Lake City, UT on February 15, 2012. PNNL-SA-86118.

Lu Q, X Gao, S Krishnamoorthy, G Baumgartner, J Ramanujam, and P Sadayappan. 2012. "Empirical Performance Model-Driven Data Layout Optimization and Library Call Selection for Tensor Contraction Expressions." Journal of Parallel and Distributed Computing 72(3):338-362. doi:10.1016/j.jpdc.2011.09.006

Lu N, P Du, PR Paulson, FL Greitzer, X Guo, and MD Hadley. 2012. "The Development of a Smart Distribution Grid Testbed for Integrated Information Management Systems." Presented by Pengwei Du at The second Conference on Innovative Smart Grid Technologies (ISGT 2011), Anaheim, CA on January 17, 2012. PNNL-SA-76787.

Lu N, P Du, Y Sun, and FL Greitzer. 2012. "Data Mining for Residential Smart Meter Data." PNNL-SA-85048, Pacific Northwest National Laboratory, Richland, WA.

Lumetta GJ. 2012. "Radiochemical Processing Developing Advanced Separations and Online Monitoring Methods to Enable Fuel Recycling." Presented by Gregg Lumetta (Invited Speaker) at LDRD Program Review, Richland, WA on April 18, 2012. PNNL-SA-87045.

McCusker JP, T Lebo, A Graves, D Difranzo, P Pinheiro da Silva, and DL McGuinness. 2012. "HTTP Explained." Abstract submitted to IPAW 2012-4th International Provenance and Annotation Workshop, Santa Barbara, CA. PNNL-SA-86461.

Neer MM. 2012. Pacific Northwest Technology Today. PNNL-SA-85104, Pacific Northwest National Laboratory, Richland, WA.

Pinheiro da Silva P, JP McCusker, T Lebo, A Graves, D Difranzo, and DL McGuinness. 2012. "HTTP Explained." In IPAW 2012-4th International Provenance and Annotation Workshop. PNNL-SA-86703, Pacific Northwest National Laboratory, Richland, WA.

Podboy DL. 2012. "Primo: TotalCare Implementation." Presented by David L. Podboy at ELUNA 2012, Salt Lake City, UT on May 10, 2012. PNNL-SA-87558.

Roberts CK. 2012. "International Material Protection." PNNL-SA-86130, Pacific Northwest National Laboratory, Richland, WA.

Rod KA, DM Wellman, M Flury, EM Pierce, JB Harsh, and Z Wang. 2012. "Dynamics of Uranium Release from the Capillary Fringe of Contaminated Hanford Sediments." PNNL-SA-85274, Pacific Northwest National Laboratory, Richland, WA.

Schrempf. 2012. Signature Discovery Initiative Project Fliers. PNNL-SA-86246, Pacific Northwest National Laboratory, Richland, WA.

Schuchardt KL, DA Agarwal, SA Finsterle, CW Gable, I Gorton, LJ Gosink, E Keating, CS Lansing, J Meyer, WAM Moeglein, G Pau, EA Porter, S Purohit, ML Rockhold, A Shoshani, and C Sivaramakrishnan. 2012. "Akuna – Integrated Toolsets Supporting Advanced Subsurface Flow And Transport Simulations For Environmetal Management." In Computational Methods in Water Resources XIX International Conference . PNNL-SA-86251, Pacific Northwest National Laboratory, Richland, WA.

Secchi S, O Villa, and A Tumeo. 2012. "A Bandwidth-Optimized Multi-Core Architecture for Irregular Applications in CCGrid 2012." The 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing.

Seid LE and SJ Harris. 2012. "A Data Driven Approach to Star Schema Generation." Presented by Larry Seid (Invited Speaker) at National Laboratory Information Technology (NLIT) Summit 2012, Sun Valley, ID on May 31, 2012. PNNL-SA-88046.

Seid LE and SJ Harris. 2012. "A Data-Driven Approach to Star-Schema Generation." Abstract submitted to National Laboratories Information Technology (NLIT) Summit 2012, Sun Valley, ID. PNNL-SA-86080.

Setyawan W. 2011. "Searching for Three-Dimensional Topological Insulators through Topological Quantum Phase Transition." PNNL-SA-84249, Pacific Northwest National Laboratory, Richland, WA.

Skomurski FN, TG Levitskaia, SA Bryan, and AJ Casella. 2012. "Spectroscopic On-Line Monitoring for Real-Time Data Collection and Analysis." PNNL-SA-86088, Pacific Northwest National Laboratory, Richland, WA.

Stevens AJ, Y Sun, MN Devarakonda, H Surenahalli, and G Parker. 2012. "Optimal NH3 Storage in SCR Catalysts." Presented by Maruthi Devarakonda at DOE CLEERS Workshop, Dearborn, MI on April 30, 2012. PNNL-SA-87638.

Swanson KR and KA Glass. 2012. "Chinook Login Process: Macintosh External." PNNL-SA-86885 Pacific Northwest National Laboratory, Richland, WA.

Swanson KR and KA Glass. 2012. "Chinook Environment Familiarization." PNNL-SA-86911 Pacific Northwest National Laboratory, Richland, WA.

Swanson KR and KA Glass. 2012. "Chinook Login Process: Windows External." PNNL-SA-86912 Pacific Northwest National Laboratory, Richland, WA.

Swanson KR and KA Glass. 2012. "Chinook Login Process: Windows Internal." PNNL-SA-86913 Pacific Northwest National Laboratory, Richland, WA.

Swanson KR, and KA Glass. 2012. "Chinook Login Process: Linux Internal." PNNL-SA-86714 Pacific Northwest National Laboratory, Richland, WA.

Swanson KR and KA Glass. 2012. "Chinook Login Process: Linux External." PNNL-SA-86715 Pacific Northwest National Laboratory, Richland, WA.

Swanson KR and KA Glass. 2012. "Chinook Login Process: Macintosh Internal." PNNL-SA-86884 Pacific Northwest National Laboratory, Richland, WA.

Tagestad JD. 2012. "Remote Sensing for Energy and Environment Applications." PNNL-SA-87912, Pacific Northwest National Laboratory, Richland, WA.

Thomas DG, S Gaheen, S Harper, M Fritts, F Klaessig, E Hahn-Dantona, D Paik, S Pan, G Stafford, E Freund, J Klemm, and NA Baker. 2012. "NANO-TAB: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format." PNWD-SA-9668, Battelle— Pacific Northwest Division, Richland, WA.

Van Dam HJJ. 2012. "Parallel Quantum Chemistry at the Cross Roads." Chapter 11 in Handbook of Research on Computational Science and Engineering: Theory and Practice, ed. J Leng and WW Sharrock, pp. 239-266. IGI Global, Hershey, PA.

Wallin EL and TC Johnson. 2012. "The Use of Electrical Resistivity Measurements for Monitoring Subsurface Processes: Quantifying Noise and Uncertainty." Presented by Erin Wallin, Tim Johnson at Society of Exploration Geophysics Hydrogeophysics Workshop, Boise, ID on July 10, 2012. PNNL-SA-87094.

Wang N, WJ Gorrissen, V Srivastava, and C Taylor. 2012. "DOE Commercial Building Asset Rating: An Application of Centralized Modeling Tools." In 2012 ASHRAE Annual Conference . PNNL-SA-85031, Pacific Northwest National Laboratory, Richland, WA.

Wescott RE. 2012. "Closing the Gap to Free Cooling in the Data Center." Abstract submitted to NLIT, Sun Valley, ID. PNNL-SA-86058.

Williams LS, SJ Kreyling, ZN Gastelum, KM Whattam, CD Corley, NO Cramer, and ML Gregory. 2012. "Use of Social Media to Target Information-Driven Arms Control and Nonproliferation Verification." Abstract submitted to INMM Annual Meeting, Please select a state. PNNL-SA-85408.

Wong PC, HW Shen, LYR Leung, SM Hagos, SM Libby, TY Lee, X Tong, and K Lu. 2012. "Information Visualization of Large Scale Scientific Model Data." Abstract submitted to IEEE VisWeek 2012, Seattle, WA. PNNL-SA-86629.

Wong PC, HW Shen, LYR Leung, and D Chavarría-Miranda. 2012. "Extreme-Scale Visual Analtyics for Scientific Discoveries." PNNL-21212, Pacific Northwest National Laboratory, Richland, WA.

Wong PC, HP Foote, PS Mackey, G Chin, Jr, Z Huang, and JJ Thomas. 2012. "A Space- Filling Visualization Technique for Multivariate Small World Graphs." IEEE Transactions on Visualization and Computer Graphics 18(5):797-809 . doi:10.1109/TVCG.2011.99 Barb AW, JR Cort, J Seetharaman, S Lew, HW Lee, T Acton, R Xiao, MA Kennedy, L Tong, G Montelione, and JH Prestegard. 2011. "Structures of Domains I and IV from YbbR are representative of a widely distributed protein family." Protein Science 20(2):396-405. doi:10.1002/pro.571

Wu H, JS Kimball, H Li, M Huang, LYR Leung, and R Edler. 2012. "A New Global River Network Database for Macroscale Hydrologic modeling." PNNL-SA-87400, Pacific Northwest National Laboratory, Richland, WA.

Wuennecke MAC and KM Regimbal. 2012. "PNNL Institutional Computing (PIC)." Presented by Kevin Regimbal, Tim Carlson, Doug Baxter (Invited Speaker) at FY12 LDRD Program Review, Richland, WA on April 16, 2012. PNNL-SA-87380.

Yang Y, TA Ramelot, JR Cort, H Wang, C Ciccosanti, M Jiang, H Janjua, T Acton, R Xiao, JK Everett, G Montelione, and MA Kennedy. 2012. "Solution NMR structure of Dsy0195 homodimer from Desulfitobacterium hafniense: first structure representative of the YabP domain family of proteins involved in spore coat assembly." PNWD-SA-9740, Battelle—Pacific Northwest Division, Richland, WA.

Yang Y, TA Ramelot, JR Cort, A Yee, CH Arrowsmith, G Montelione, and MA Kennedy. 2012. "Solution NMR Structure of Hypothetical Protein CV_2116 from Chromobacterium violaceum." PNNL-SA-86264, Pacific Northwest National Laboratory, Richland, WA.

[edit] 2011

al-Saffar S, CA Joslyn, and AR Chappell. 2011. "Extant Ontological Scaling and Descriptive Semantics for Semantic Structure Discovery in Large Graph Datasets." In IEEE/WIC/ACM International Conference on Web intelligence. PNNL-SA-78877, Pacific Northwest National Laboratory, Richland, WA.

Aguayo Navarrete E, DJ Reid, JE Fast, and JL Orrell. 2011. Design Considerations for Large Mass Ultra-Low Background Experiments. PNNL-20578, Pacific Northwest National Laboratory, Richland, WA.

Asner, DM. 2011. "Belle Computing at PNNL." Abstract submitted to Phone Conversation, Richland, WA. PNNL-SA-79908.

Barr JL, AMB Peddicord, ER Burtner, and HA Mahy. 2011. "Current Domain Challenges in the Emergency Response Community." In ISCRAM. iscram2011, Lisbon, Portugal.

Bisping LE. 2011. EMP Attachment 2 DOE-SC PNNL Site Data Management Plan. PNNL-20919-2, Pacific Northwest National Laboratory, Richland, WA.

Bridges NN. 2011. "Minority Serving Institution (MSI) Initiative - Bridging the Gap." Presented by Novella Bridges (Invited Speaker) at University of South Florida, Tampa, FL on February 22, 2011. PNNL-SA-77840.

Brigantic RT, CD Corley, G Muller, MJ Lancaster, BW Gerber, TK McKenzie, and BM Kunkel. 2011. "Modeling and Visualization of the Role of Global Transportation in Forecasting Disease Risk." Presented by Robert Brigantic (Invited Speaker) at SuperComputing 2011, Seattle WA, WA on November 14, 2011. PNNL-SA-84098.

Brown CF and HE Matthews. 2011. "Environmental Sciences Laboratory." PNNL-SA-82960, Pacific Northwest National Laboratory, Richland, WA.

Cannon WR, CS Oehmen, and JM Garza. 2011. "Driving Biological Analysis at Extreme Scales." Presented by Bill Cannon, Chris Oehmen at Daniel Hitchcock Poster Session, CSF/BSF Richland Campus, WA on February 10, 2011. PNNL-SA-77721.

Carroll TE, and D Grosu. 2011. "An Incentive-Based Distributed Mechanism for Scheduling Divisible Loads in Tree Networks." PNNL-SA-84721, Pacific Northwest National Laboratory, Richland, WA.

Catalyurek U, F Dobrian, AH Gebremedhin, M Halappanavar, and A Pothen. 2011. "Distributed-memory Parallel Algorithms for Matching and Coloring." In Workshop PCO'11 new trends in Parallel Computing and Optimization, in conjunction with IEEE IPDPS 2011, Anchorage, USA, May 16-20, 2011. PNNL-SA-77038, Pacific Northwest National Laboratory, Richland, WA.

Chassin DP. 2011. "Demand Response and Load Modeling: A call to Action." Presented by Chassin, David P. (Invited Speaker) at WESTNet Workshop, Ryerson University, Canada on February 24, 2011. PNNL-SA-77978.

Chassin DP. 2011. "Demand Response and Load Modeling: A call to Action." Presented by David Chassin (Invited Speaker) at Grid Intergration research and Collaborative Activities meeting, University of Victoria, BC, Canada on June 16, 2011. PNNL-SA-77978.

Chavarría-Miranda D, Z Huang, and Y Chen. 2011. "High-Performance Computing (HPC): Application & Use in the Power Grid." In 2012 IEEE PES General Meeting . PNNL-SA-84431, Pacific Northwest National Laboratory, Richland, WA.

Chavarría-Miranda D, JA Daily, S Krishnamoorthy, MK Krishnan, BJ Palmer, and A Vishnu. 2011. "Global Arrays: Into the Future." Presented by Daniel Chavarría-Miranda (Invited Speaker) at Future Approaches to Data Centric Programming for Exascale, Anchorage, AK on May 20, 2011. PNNL-SA-80117.

Chen X, H Murakami, hahn, GE Hammond, ML Rockhold, JM Zachara, and Y Rubin. 2011. "Three-Dimensional Bayesian Geostatistical Aquifer Characterization at the Hanford 300 Area using Tracer Test Data." PNNL-SA-78432, Pacific Northwest National Laboratory, Richland, WA.

Chen Y, Z Huang, and N Zhou. 2011. "An Advanced Framework for Improving Situational Awareness in Electric Power Grid Operation." In Proceedings of the 18th World Congress of the International Federation of Automatic Control (IFAC), August 28-September 2, 2011, Milan, Italy, vol. 18, pp. 12162-12170. International Federation of Automatic Control (IFAC), Laxenburg, Austria. doi:10.3182/20110828-6-IT-1002.03381

Chervitz SA, EW Deutsch, D Field, HE Parkinson, J Quackenbush, P Rocca-Serra, SA Sansone, CJJ Stoeckert, CF Taylor, RC Taylor, and CA Ball. 2011. "Data Standards for Omics Data: the Basis of Data Sharing and Reuse." Chapter 2 in Bioinformatics for Omics Data: Methods and Protocols , vol. 719, ed. B Mayer, pp. 31-69. Humana Press, New York, NY.

Ciraci S, and J Yin. 2011. "Towards a Scalable and Reliable Real Time In-Network Data Analysis Infrastructure. "In IEEE Symposium on Large Scale Data Analysis and Visualization (LDAV 2011), October 23-24, 2011, Providence, Rhode Island, ed. D Rogers and CT Silva, pp. 135-136. IEEE Computer Society, Los Alamitos, CA. doi:10.1109/LDAV.2011.6092336

Colella WG. 2011. "Initial Deployment and Independent Testing of Microcombined Heat and Power Fuel Cell Systems In Light Commercial Buildings." In European Fuel Cell - Piero Lunghi Conference & Exhibition December 14-16, 2011, Rome, Italy. PNNL-SA-84067, Pacific Northwest National Laboratory, Richland, WA.

Colella WG, HE Dillon, RJ Timme, DA King, and JD Holladay. 2011. "Independent Evaluation of Measured Performance Data from Stationary Combined Heat and Power (CHP) Fuel Cell Systems (FCSs) Installed in Light Commercial Buildings." Presented by Whitney G. Colella, (Invited Speaker) at ES Fuel Cell 2011, Orlando, FL on November 2, 2011. PNNL-SA-83880.

Corley CD, RT Brigantic, CF Noonan, MJ Lancaster, CM Benedum, RA Walters, JR Schweighardt, AW Piatt, PC Ellis, JS Chung, AJ Calapristi, CJ Bruckner-Lea, SD Brown, and AK Fligg. 2011. "BioCat: Operational Biosurveillance Model Evaluations and Catalog." Abstract submitted to Super Computing 2011, Seattle, WA. PNNL-SA-82647.

Cort JR, JN Adkins, C Ansong, RN Brown, ED Merkley, ES Nakayasu, KM Meyer, S Imtiaz, and MC Burnet. 2011. "Structural and Functional Characterization of Pathogen Effector - Host Protein Interactions." Presented by John R. Cort (Invited Speaker) at International Conference on Structural Genomics, Toronto, Canada on May 12, 2011. PNNL-SA-80040.

Critchlow TJ, and K Kleese van Dam. 2011. "Big Data Ecosystems Enable Scientific Discovery." HPC Source (November 2011):35-38.

Critchlow TJ, and G Chin, Jr. 2011. "Supercomputing and Scientific Workflows Gaps and Requirements." In IEEE World Congress on Services, July 4-9, 2011, Washington, DC, pp. 208 - 211. IEEE Computer Society, Los Alamitos, CA.

Daily JA, S Krishnamoorthy, and JM Garza. 2011. "Performance Feedback Using TAU." PNNL-SA-78879, Pacific Northwest National Laboratory, Richland, WA.

Dasgupta A, LJ Gosink, and R Kosara. 2011. "Screen-Space Metrics for Exploratory Analysis Using Temporal Parallel Coordinates." In EuroVis. PNNL-SA-84657, Pacific Northwest National Laboratory, Richland, WA.

Dillon HE, MA Halverson, OV Livingston, CA Antonopoulos and MC Madison. 2011. "Do we really know how much it costs to construct high performance buildings?" Abstract submitted to ACEEE, Asilomar, CA. PNNL-SA-83422.

Edmonds JA. 2011. "The Human Dimensions of the Carbon Cycle: Integrated Assessment Modeling." Presented by James Edmonds (Invited Speaker) at U.S. Carbon Cycle Scientific Steering Group, Arlington, VA on September 14, 2011. PNNL-SA-82775.

Frank AM, ME Monroe, AR Shah, JJ Carver, N Bandeira, RJ Moore, GA Anderson, RD Smith, and PA Pevzner. 2011. "Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra." Nature Methods 8(7):587-591. doi:10.1038/nmeth.1609

Ferryman TA, and BG Amidan. 2011. "Investigation of Phase Angle Differences Using Statistical Analysis of Real World State Estimator Data." In Hawaii International Conference on System Sciences - 45 Themes (HICSS-45). PNNL-SA-82581, Pacific Northwest National Laboratory, Richland, WA.

Ferryman TA, and BG Amidan. 2011. Domain-Independent Situational Awareness and Alerting Report System for Time Varying Multivariate Data. PNNL-20791, Pacific Northwest National Laboratory, Richland, WA.

Freshley MD, VL Freedman, and I Gorton. 2011. "Advanced Simulation Capability for Environmental Management (ASCEM): Development and Demonstrations." Abstract submitted to Waste Management Symposia 2012, Phoenix, AZ. PNNL-SA-83060.

Freshley MD, DM Wellman, and RE Gephart. 2011. "Deep Vadose Zone - Applied Field Research Initiative: Knowledge Gaps for Predictive Modeling and Data Integration." Presented by Mark D Freshley at DOE EM TEG Review, Richland, WA on June 27, 2011. Zhang ZF, MD White, DM Wellman, and MD Freshley. 2011. "Deep Vadose Zone - Applied Field Research Initiative: Predictive Modeling and Data Integration." Presented by Z Fred Zhang at DOE EM TEG Review, Richland, WA on June 28, 2011. PNNL-SA-80894.

Garza JM. 2011. Extreme Scale Computing . PNNL-SA-78881, Pacific Northwest National Laboratory, Richland, WA.

Garza JM. 2011. eXtreme Scale Computing Initiative April 2011 newsletter . PNNL-SA-78901, Pacific Northwest National Laboratory, Richland, WA.

Garza JM. 2011. eXtreme Scale Computing Initiative FY11 Jan Newsletter . PNNL-SA-77179, Pacific Northwest National Laboratory, Richland, WA.

Gibson TD, AV Kulkarni, K Kleese van Dam, and TJ Critchlow. 2011. "The Feasibility of Moving PMU Data in the Future Power Grid." In CIGRE Canada Conference on Power Systems: Promoting Better Interconnected Power Systems, September 6-8, 2011, Hallifax, Nova Scotia, Canada. CIGRE, Halifax, NS, Canada.

Glass KA. 2011. "Instrument to Users: Data Management and EMSL." Presented by Kevin A. Glass (Invited Speaker) at Communication at Critical Interfaces: How Scientists Plan to Collaborate in the Modern Era, Richland, WA on April 7, 2011. PNNL-SA-79042.

Gorton I, Y Liu, J Yin, AV Kulkarni, and AS Wynne. 2011. "Towards Composing Data Aware Systems Biology Workflows on Cloud Platforms: A MeDICi-based Approach." In Proceedings. 2011 IEEE International World Congress on Services (SERVICES 2011), July 4-9, 2011, Washington DC, pp. 184-191. IEEE, Piscataway, NJ. doi:10.1109/SERVICES.2011.22

Gorton I, Y Liu, AV Kulkarni, and AS Wynne. 2011. "Towards Composing Data Aware Systems Biology Workflows on Cloud Platforms." Presented by Jenny Liu (Invited Speaker) at IEEE 2011 Services Congress - Fifth International Workshop on Scientific Workflows (SWF 2011), Washington, DC on July 5, 2011. PNNL-SA-81038.

Gosney A, CS Oehmen, and I Gorton. 2011. "An Adaptive Middleware Framework for Optimal Scheduling On Large Scale Compute Clusters." Presented by Arzu Gosney (Invited Speaker) at 8th International Conference on Information Technology : New Generations, Las Vegas, NV on April 12, 2011. PNNL-SA-82413.

Gosney A, JH Miller, I Gorton, and CS Oehmen. 2011. "An Adaptive Middleware Framework for Optimal Scheduling on Large Scale Compute Clusters." In Eighth International Conference on Information Technology: New Generations (ITNG 2011), April 11-13, 2011, Las Vegas, Nevada, ed. S Latifi, pp. 713-718. IEEE Computer Society, Piscataway, NJ. doi:10.1109/ITNG.2011.126

Gracio DK, JR Johnson, III, I Gorton, and WA Pike. 2011. "Data Intensive Analytics for Information Discovery." Presented by Deborah K. Gracio (Invited Speaker) at NanoInformatics 2011, Arlington, VA on December 8, 2011. PNWD-SA-9697.

Greitzer FL. 2011. "Cognitive Informatics." PNNL-SA-84778, Pacific Northwest National Laboratory, Richland, WA.

Hackler VS and CD Hagler. 2011. "Infrastructure as a Service." Presented by Vahid Hackler (Invited Speaker) at SEDP Poster Presentations, Richland, WA on May 19, 2011.

Hammond GE, X Chen, and PC Lichtner. 2011. "Uncertainty Quantification using High Performance Computing for the October 2009 Uranium Desorption Experiment at the Hanford 300 Area IFRC Site." Abstract submitted to DOE-SBR Annual PI Meeting. PNNL-SA-78503.

Hammond GE, and PC Lichtner. 2011. "Using HPC to Understand Roles of Labile and Nonlabile U(VI) on Hanford 300 Area Plume Longevity." PNNL-SA-84075, Pacific Northwest National Laboratory, Richland, WA.

Hammond GE, PC Lichtner, G Bisht, X Chen, J Kumar, C Lu, RT Mills, B Philip, B Smith, D Svyatskiy, AJ Valocchi, and S Karra. 2011. "PFLOTRAN: next-generation petascale subsurface reactive flow and transport code." Abstract submitted to Computatonal Methods in Water Resources 2012, Please select a state. PNNL-SA-83509.

Hammond GE. 2011. "The role of HPC on subsurface simulation of U(VI) transport at the Hanford 300 Area." Abstract submitted to Computational Methods in Water Resources 2012, Please select a state. PNNL-SA-83510.

Hibbard KA, AC Janetos, LYR Leung, LE Clarke, JA Edmonds, AM Thomson, MCW Kintner- Meyer, RH Moss, and JS Rice. 2011. "Regionally Integrated Earth System Modeling: A New Framework." Presented by Kathy Hibbard (Invited Speaker) at AGU Fall Meeting 2011, San Francisco, CA on December 6, 2011. PNNL-SA-84671.

Huang Z. 2011. "Dynamic Paradign for Future Grid Operation." Presented by Zhenyu Huang (Invited Speaker) at SciDAC 2011 Conference – Scientific Discovery through Advanced Computing, Denver, Denver, CO on July 13, 2011. PNNL-SA-81186.

Imhoff CH. 2011. "Power System Transformation-New Roles for Information Technology and High Performance Computing." Presented by Carl H. Imhoff (Invited Speaker) at 2011 IT Day, Kennewick, WA on May 4, 2011. PNNL-SA-79760.

Li D, J Yin, and G Lin. 2011. "Integrating Multimodal Chemical Imaging Instrumentation by Hughes PJ. 2011. Laboratory Directed Research and Development Annual Report for 2010 . PNNL-20487, Pacific Northwest National Laboratory, Richland, WA.

Li D, J Yin, and G Lin. 2011. "Integrating Multimodal Chemical Imaging Instrumentation by Hughes PJ. 2011. Laboratory Directed Research and Development Annual Report for 2010 . PNNL-20487, Pacific Northwest National Laboratory, Richland, WA.

Lichtner PC, GE Hammond, X Chen, RT Mills, B Philip, D Svyatskiy, G Bisht, K Jitendra, C Lu, B Smith, and AJ Valocchi. 2011. "PFLOTRAN: The Next-Generation Peta-Scale Subsurface Reactive Flow and Transport Code." Presented by Peter Lichtner, Glenn Hammond, Richard Mills, Bobby Philip, Daniil Svyatskiy, Gautam Bisht, et al (Invited Speaker) at 2011 DOE BER SBR PI Meeting on April 27, 2011. PNNL-SA-79386.

Hui PSY, S Chikkagoudar, D Chavarría-Miranda, and MR Johnston. 2011. "Towards Real-time Cluster Computing Over Infiniband." Abstract submitted to ACM/IFIP/Usenix Middleware 2011, Lisbon, Portugal. PNNL-SA-80200.

Hui PSY, S Chikkagoudar, D Chavarría-Miranda, and M Johnston. 2011. "Towards Real-Time Cluster Computing Over Infiniband." In ACM/IFIP/Usenix Middleware 2011. PNNL-SA-80380, Pacific Northwest National Laboratory, Richland, WA.

Hui PSY, S Chikkagoudar, D Chavarría-Miranda, A Vishnu, and MR Johnston. 2011. "Poster: Towards a Real-Time Cluster Computing Infrastructure." Presented by Satish Chikkagoudar (Invited Speaker) at 2011 IEEE Real-Time Systems Symposium (WiP Session), Vienna, Austria on November 29, 2011. PNNL-SA-84260.

Hui PSY, S Chikkagoudar, D Chavarría-Miranda, and M Johnston. 2011. "Towards a Real- Time Cluster Computing Infrastructure." Presented by Satish Chikkagoudar (Invited Speaker) at 32nd IEEE Real-Time Systems Symposium (RTSS), Vienna, Austria on November 30, 2011. PNNL-SA-84161.

Jamison JD, and TL Chamberlain. 2011. "Global Threat Reduction Initiative." Presented by Jeremy Jamison, Travis Chamberlain at Global Threat Reduction Initiative, Sierra Leone and Mali, AL, Afghanistan on December 12, 2011. PNNL-SA-84602.

Kassianov EI, D Chand, and M Wang. 2011. "Assessment of MODIS Aerosol Optical Depth over Oceans using 1-year Data from Maritime Aerosol Network ." Abstract submitted to SPIE Remote Sensing, Prague, Czech Republic. PNWD-SA-9549.

Khaleel MA. 2011. Scientific Grand Challenges: Crosscutting Technologies for Computing at the Exascale - February 2-4, 2010, Washington, D.C. PNNL-20168, Pacific Northwest National Laboratory, Richland, WA.

Khan T, P Ramuhalli, and S Dass. 2011. "Particle Filter Based Multi-Sensor Fusion For Solving Electromagnetic NDE Inverse Problems." PNNL-SA-80758, Pacific Northwest National Laboratory, Richland, WA.

Kingsinger CR, J Apffel, MS Baker, X Bian, CH Borchers, RA Bradshaw, MY Brusniak, DW Chan, EW Deutsch, B Domon, J Gorman, R Grimm, WS Hancock, H Hermjakob, D Horn, C Hunter, P Kolar, HJ Kraus, H Langen, R Linding, RL Moritz, GS Omenn, R Orlando, A Pandey, P Ping, A Rahbar, R Rivers, SL Seymour, RJ Simpson, D Slotta, RD Smith, SE Stein, DL Tabb, D Tagle, JR Yates, and H Rodriguez. 2011. "Recommendations for mass spectrometry data quality metrics for open access data(corollary to the Amsterdam principles)." Proteomics - Clinical Applications 5(11-12):580-589. doi:10.1002/prca.201100097

Kleese van DK, KA Hibbard, I Gorton, Y Liu, and EG Stephan. 2011. "Integrated Regional Earth Systems Model Initiative - iRESM." Presented by Kerstin Kleese vanDam (Invited Speaker) at IBM onsite visit, PNNL - Richland, WA on October 25, 2011. PNNL-SA-83293.

Kleese Van DK and EG Stephan. 2011. "The Transformational Capabilities offered by Ontologies in Climate Science." Abstract submitted to SuperComputing, Seattle, WA. PNNL-SA-84980. Published in CKD '11 Proceedings of the 2011 workshop on Climate knowledge discovery, p. 5. Association for Computing Machinery, New York, NY.

Kleese van DK and EG Stephan. 2011. "The Transformational Capabilities offered by Ontologies in Climate Science." Presented by Kerstin Kleese van Dam (Invited Speaker) at SuperComputing, Seattle, WA on November 13, 2011. PNNL-SA-84981.

Kleese van DK, JP Carson, AL Corrigan, DE Cowley, DR Einstein, I Gorton, AP Kuprat, D Li, G Lin, Y Liu, PR Paulson, EG Stephan, J Yin, J Laskin, MJ Marshall, A Dohnalkova, and C Yang. 2011. "A Multi-Modality Integration Framework for Chemical Imaging." Presented by Kerstin Kleese vanDam (Invited Speaker) at Chemical Imaging Initiative Annual Review, PNNL Richland, WA on July 27, 2011. PNNL-SA-81460.

Kleese van DK. 2011. "Scientific Data Management at PNNL." Presented by Kerstin Kleese vanDam (Invited Speaker) at IBM Watson Research, Tarrytown, NY on July 26, 2011. PNNL-SA-81680.

Kleese van DK and JM Garza. 2011. "Supporting Data Intensive Science at the Exascale." Presented by Kerstin Kleese van Dam at Daniel Hitchcock Poster Session, BSF/CSF Richland Campus, WA on February 10, 2011. PNNL-SA-77723.

Knapp R, K Karavanic, and A Marquez. 2011. "Power- and Cooling- Aware Parallel Performance Diagnosis. "International Conference on Supercomputing, ICS-2011. PNNL-SA-77421, Pacific Northwest National Laboratory, Richland, WA.

Knapp R, K Karavanic, S Krishnamoorthy, and A Marquez. 2011. "Power- and Cooling-Aware Parallel Performance Diagnosis." In Parallel and Distributed Computing and Systems ~PDCS 2011~. PNNL-SA-84331, Pacific Northwest National Laboratory, Richland, WA.

Kowalski K and JM Garza. 2011. "New theoretical models for high-precision excited-state calculations:excited-state CC methods." PNNL-SA-78878, Pacific Northwest National Laboratory, Richland, WA.

Kreuzer HW, BJM Webb-Robertson, and GL Hart. 2011. "Integration of C, N, O, H, And Sr Isotope Ratios for Geographic Sourcing Of Castor Seeds." Abstract submitted to Isoscapes 2011/Purdue University, Lafayette, IN. PNNL-SA-82295.

Krishnamoorthy S, K Agarwal, C Sivaramakrishnan, RD Adolf, JA Daily, and JM Garza. 2011. "Scalable Performance Diagnostics and Feedback for Massively Parallel Computers." PNNL-SA-78880, Pacific Northwest National Laboratory, Richland, WA.

Lansing CS, Y Liu, J Yin, AL Corrigan, ZC Guillen, K Kleese van Dam, and I Gorton. 2011. "Designing the Cloud-based DOE Systems Biology Knowledgebase." In IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW 2011), May 16-20, 2011, Anchorage, AK, pp. 1062 - 1071. IEEE, Piscataway, NJ. doi:10.1109/IPDPS.2011.261

Lettenmaier DP, N Voisin, and MS Wigmosta. 2011. "Evaluation of Streamflow Uncertainties From Errors in Snow Data Assimilation." Presented by Nathalie Voisin at AGU Fall Meeting 2011, San Francisco, CA on December 8, 2011. PNNL-SA-84717.

Lipton MS and JG Wiley. 2011. "Determining Community Functionality and Predicting Ecosystem Resistance and Resiliency in Response to Environmental Change." Presented by Mary S. Lipton (Invited Speaker) at PNNL LDRD Annual Review, Richland, WA on April 17, 2011. PNNL-SA-87132.

Liu Y. 2011. "Simulating Mechanisms for Resource Allocation in Ultra- Large Scale Systems." In CCGrid 2012 — The 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing . PNNL-SA-84427, Pacific Northwest National Laboratory, Richland, WA.

Lu N, P Du, FL Greitzer, X Guo, YG Pomiak, and RE Hohimer. 2011. "A Multi-layer Datadriven Advanced Reasoning Tool for Intelligent Data Mining and Analysis for Smart Grids ." Abstract submitted to PES 2012 general meeting, San Diego, CA. PNNL-SA-84368.

Lu N, P Du, PR Paulson, FL Greitzer, X Guo, and MD Hadley. 2011. "A Predictive Defense System for the Smart Grid." Abstract submitted to 7th Annual Cyber Security and Information Intelligence Research Workshop October 12-14, 2011, Oakridge, TN. PNNL-SA-82930.

Lu N, P Du, PR Paulson, FL Greitzer, X Guo, and MD Hadley. 2011. "The Development of a Smart Distribution Grid Testbed for Integrated Information Management Systems." In IEEE PES Innovative Smart Grid Technologies Conference (ISGT 2011), January 17-19, 2011, Anaheim, California. Institute of Electrical and Electronics Engineers, Piscataway, NJ. doi:10.1109/ISGT.2011.5759156

Lu N, P Du, PR Paulson, FL Greitzer, X Guo, and MD Hadley. 2011. "A Multi-layer, Hierarchical Information Management System for the Smart Grid." In Proceedings of the 2011 IEEE Power and Energy Society General Meeting, July 24-29, 2011, Detroit, Michigan. Institute of Electrical and Electronics Engineers, Piscataway, NJ. doi:10.1109/PES.2011.6039214

Macduff MC, SJ Beus, BD Ermold, and C Sivaraman. 2011. "ARM netcdf structure versioning." Abstract submitted to American Geophysical Union, San Francisco, CA. PNNL-SA-81965.

Mackey PS, and SM Libby. 2011. "Parallel k-means++: High Performance Seed Selection For Data Clustering." PNNL-SA-84303, Pacific Northwest National Laboratory, Richland, WA.

Madison MC, AJ Cowell, AK Fligg, PC Ellis, RE Hull, AW Piatt, RS Butner, HE Dillon, and CD Corley. 2011. "Knowledge Encapsulation Framework (KEF)." Presented by Shannon Osborn (Invited Speaker) at InterLab 2011 on October 30, 2011. PNNL-SA-83730.

Maiden WM, I Dionysiou, DA Frincke, GA Fink, and DE Bakken. 2011. "DualTrust: A Distributed Trust Model for Swarm-Based Autonomic Computing Systems." In Data Privacy Management and Autonomous Spontaneous Security 5th International Workshop, DPM 2010 and 3rd International Workshop, SETOP 2010, September 23, 2010, Athens, Greece. Lecture Notes in Computer Science, vol. 6514, ed. J Garcia-Alfaro; G Navarro-Arribas; A Cavalli and J Leneutre, pp. 188-202.Springer, Heidelberg, Germany. doi:10.1007/978-3-642-19348-4_14

Malviya A, GA Fink, LH Sego, and BE Endicott-Popovsky. 2011. "Situational Awareness as a Measure of Performance in Cyber Security Collaborative Work." In 8th International Conference on Information Technology: New Generations (ITNG 2011), pp. 937-942. IEEE Conference Publications, Las Vegas, NV.

Marquez A. 2011. "The Energy Smart Data Center." PNNL-SA-77665, Pacific Northwest National Laboratory, Richland, WA.

Marquez A. 2011. "Architecture – Advantages and Opportunities JASON 2011 Summer Study Super-C ." Presented by Andres Marquez (Invited Speaker) at JASON Superconductive Supercomputing, La Jolla, CA on June 15, 2011. PNNL-SA-80598.

Mattigod SV and JH Westsik, Jr. 2011. "DuraLith Data Package - Secondary Waste Form Down Selection Task." Presented by Shas V. Mattigod (Invited Speaker) at Secondary Waste Form Down Selection - Review Panel Meeting, Richland, WA on August 15, 2011. PNNL-SA-82167.

McCullough JJ. 2011. "Federal Technology Deployment Pilot: Exterior Solid State Lighting." Presented by Jeff McCullough at GovEnergy 2011, Cincinnati, OH on August 8, 2011. PNNL-SA-82031.

McDermott JE, KD Jarman, RC Taylor, MJ Lancaster, KB Vartanian, SL Stevens, M Stenzel- Poore, and AP Sanfilippo. 2011. "Modeling Dynamic Regulatory Processes in Stroke." PNNL-SA-81643, Pacific Northwest National Laboratory, Richland, WA.

McFarlane SA, LD Riihimaki, KL Gaustad, SJ Beus, and D Chand. 2011. "Development of Improved Datasets and Metrics for Climate Model Evaluation." Abstract submitted to DOE Climate Modeling Meeting, Washington, DC. PNNL-SA-82162.

McKenna TP. 2011. "PNNL Computing Overview for IBM." Presented by Mohammad A. Khaleel (Invited Speaker) at IBM Watson Research, Tarrytown, NY on July 26, 2011. PNNL-SA-81605.

Meza J, S Hubbard, MD Freshley, I Gorton, D Moulton, and ME Denham. 2011. "Advanced Simulation Capability for Environmental Management (ASCEM): Early Site Demonstration." In Waste Management 2011: Global Achievements and Challenges in Waste Management, February 27-March3, 2011, Phoenix, AZ, p. Paper No. 11560. WM Symposium, Tucson, AZ.

Miller DR, and DS Magetteri. 2011. "Performance Testing." Presented by Dan Miller (Invited Speaker) at Philippines National Police Alarm Response Training, Manila, Philippines on February 15, 2011. PNNL-SA-78070.

Miller DR, DS Magetteri, and JB Gilmore. 2011. "Response Assessment Exercise (Table Top)." Presented by Dan miller, Dan Magetteri, Josh Gilmore (Invited Speaker) at Philippines National Police Alarm Response Training, Manila, Philippines on February 15, 2011.

Miller DR, JB Gilmore, and DS Magetteri. 2011. "Site Response Survey." Presented by Dan Miller, Josh Gilmore, Dan Magetteri (Invited Speaker) at Philippines National Police Alarm Response Training, Manila, Philippines on March 14, 2011. PNNL-SA-78072.

Mioduszewski JR, XY Yu, VR Morris, CM Berkowitz, and JE Flaherty. 2011. "In-Situ Monitoring of Trace Gases in a Non-Urban Environment." Atmospheric Pollution Research 2(1):89-98. doi:10.5094/APR.2011.011

Mishra V, N Voisin, MS Wigmosta, and DP Lettenmaier. 2011. "Effects of stream discharge data assimilation on short-term streamflow forecast skill." Presented by Vimal Mishra at AGU Fall Metting 2011, San Francisco, CA on December 8, 2011. PNNL-SA-84682.

Nadeau JS, BW Wright, and RE Synovec. 2011. "Study of the Interdependency of the Data Sampling Ratio with Retention Time Alignment and Principal Component Analysis for Gas Chromatographic Studies." Abstract submitted to Publish in Journal of Chromatography A. PNNL-SA-80651.

Napier BA, JP Rishel, and NE Bixler. 2011. Preliminary Review of Safety Assessment Issues at Savannah River Site, August 2011. PNNL-20734, Pacific Northwest National Laboratory, Richland, WA.

Nordwall DJ, and BT Didier. 2011. "ESNM Program Review ." Presented by Doug Nordwall (Invited Speaker) at ESNM Program Review , Columbus , OH on September 13, 2011. PNNL-SA-82701.

Oehmen CS. 2011. "Data-Intensive Algorithms for Bioinformatics-Inspired Detection." Presented by Chris Oehmen at Signature Discovery Initiative Mid-Year Review Meeting, Richland/PNNL, WA on March 22, 2011. PNNL-SA-80204.

Ovink JD and N Hiranuma. 2011. "Cloud Droplets, Ready for Prime Time." PNNL-SA-84781, Pacific Northwest National Laboratory, Richland, WA.

Ovink JD. 2011. "How Uranium Sticks to Soil." PNNL-SA-78027, Pacific Northwest National Laboratory, Richland, WA.

Palmer BJ, MK Krishnan, A Vishnu, S Krishnamoorthy, and JA Daily. 2011. "New Developments in the Global Arrays Programming Model." Abstract submitted to SC 11, Seattle, WA. PNNL-SA-81866.

Park J, M Hao, PC Wong, and C Chen. 2011. "Introduction in Visualization and Data Analysis." January 18-19, 2010, San Jose, CA: Proceedings of the SPIE, vol. 7530, ed. J Park, MC Hao, PC Wong and C Chen, p. vii. SPIE, Bellingham, WA. doi:10.1117/12.856032

Peterson ES, KA Hobbie, J Walker, M Barton, K Anderson, and KM Waters. 2011. "Solving the data integration problem for a Superfund Research Program Center." Abstract submitted to SOT Annual Meeting & ToxExpo, San Francisco, CA. PNWD-SA-9600.

Polacco BJ, SO Purvine, EM Zink, SP LaVoie, MS Lipton, AO Summers, and SM Miller. 2011. "Discovering Mercury Protein Modifications in Whole Proteomes Using Natural Isotope Distributions Observed in Liquid Chromatography-Tandem Mass Spectrometry." Molecular & Cellular Proteomics. MCP 10(8):Art. No. 10: M110.004853. doi:10.1074/mcp.M110.004853

Quadrel RW. 2011. "Advanced Data Analytics, Overview of PNNL Capabilities." Presented by Rich Quadrel (Invited Speaker) at CRL Dedication, Richland, WA on April 19, 2011. PNNL-SA-79332.

Rai D, M Yui, HT Schaef, and A Kitamura. 2011. "Thermodynamic Model for SnO2(cr) and SnO2(am) Solubility in the Aqueous Na+-H+ -OH- -Cl- -H2O System." Journal of Solution Chemistry 40(7):1155-1172. doi:10.1007/s10953-011-9723-1

Ramey JA, II, DM Young, and LH Sego. 2011. "A Resampling Approach to Proportion Admissibility Evaluation of Clustering Methods for High-Dimensional Microarray Data." In ICDM 2011 Workshop on Biological Data Mining and its Application in Healthcare. PNNL-SA-81966, Pacific Northwest National Laboratory, Richland, WA.

Roche KJ and JM Garza. 2011. "Computing SLDA, Extension to Exascale Computing." Presented by Ken Roche at Daniel Hitchcock Poster Session, BSF/CSF Richland Campus, WA on February 10, 2011. PNNL-SA-77727.

Scheibe TD, GE Hammond, BJ Palmer, and JM Garza. 2011. "Enabling Breakthroughs in Subsurface Science through High Performance Computing." Presented by Tim Scheibe at Daniel Hitchcock Poster Session, BSF/CSF Richland Campus, WA on February 10, 2011. PNNL-SA-77726.

Schuchardt KL, and JM Garza. 2011. "Scalable Tools for Data Management, Analysis, and Visualization for the Global Cloud Resolving Model." Presented by Karen Schuchardt at Daniel Hitchcock, BSF/CSF Richland Campus, WA on February 10, 2011. PNNL-SA-77725.

Shankaran H and JG Teeguarden. 2011. "Physiologically-based pharmacokinetic model for Fentanyl." Presented by Harish Shankaran (Invited Speaker) at The 13th Expert Consultation Panel Meeting for Provisional Advisory Levels, Cincinnati, OH on July 20, 2011.

Shrestha S, C Si Yu, AM White, JB Manzano Franco, A Marquez, K Cameron, JT Feo, and GR Gao. 2011. "MODA: A Framework for Memory Centric Performance Characterization." In 2012 International Symposium on Code Generation and Optimization. PNNL-SA-83285, Pacific Northwest National Laboratory, Richland, WA.

Singh B, JH Yoon, and PJ Rasch. 2011. "End-to-end experience in data transfer at PNNL." Presented by Balwinder Singh at Supercomputing 2011 conference, Seattle, WA on November 17, 2011. PNNL-SA-84154.

Straatsma TP. 2011. "eXtreme Scale Computing Initiative/Global Arrays/ARMCI Programming model overview." Presented by TP Straatsma (Invited Speaker) at CEA in France, France, France on June 6, 2011. PNNL-SA-80440.

Straatsma TP and JM Garza. 2011. "XSCI: eXtreme Scale Computing LDRD Initiative: Driving Science Toward the Exascale." Presented by TP Straatsma at Daniel Hitchcock Poster Session, BSF/CSF Richland Campus, WA on February 10, 2011. PNNL-SA-77724.

Strom DJ, KE Joyce, JA Maclellan, DJ Watson, TP Lynch, CL Antonio, A Birchall, KK Anderson, and P Zharov. 2011. "Making Sense of Negative Counting Results in a Population." Presented by Daniel J. Strom at 56th Annual Meeting of the Health Physics Society, West Palm Beach, FL on June 27, 2011. PNNL-SA-80881.

Strom DJ, KE Joyce, JA Maclellan, DJ Watson, TP Lynch, CL Antonio, A Birchall, KK Anderson, and P Zharov. 2011. "Making the Most of Uncertain Low-Level Measurements." Presented by Daniel J. Strom (Invited Speaker) at Savannah River Chapter of the Health Physics Society 15th Annual Technical Seminar: "Applications of Statistics in Healt, Aiken, SC on April 15, 2011. PNNL-SA-79373.

Strom DJ, KE Joyce, JA Maclellan, DJ Watson, TP Lynch, CL Antonio, A Birchall, KK Anderson, and P Zharov. 2011. "Making Sense of Negative Counting Results in a Population." Abstract submitted to 56th Annual Meeting of the Health Physics Society, West Palm Beach, FL. PNNL-SA-78533.

Thompson CJ, KB Olsen, PD Thorne, PJ Chamberlain, S Jennings, and P Blicker. 2011. 2010 Hydrologic/Water Quality Study of Cow and Pony Creek Drainages, Rosebud County, Montana . PNWD-4261, Battelle—Pacific Northwest Division, Richland, WA.

Tomlinson JM, JL Brenguier, and R Shetter. 2011. "Establishment of an Inventory of International Airborne Science Capabilities." Abstract submitted to XXII Congress of the Internaional Society for Photogrammetry and Remote Sensing meeting, Melbourne, Australia. PNNL-SA-83700.

Trease HE. 2011. "Information Physics." PNNL-SA-84779, Pacific Northwest National Laboratory, Richland, WA.

van Dam HJJ, A Vishnu, and WA De Jong. 2011. "Providing fault tolerance in extreme scale parallel applications What can the HPC community learn from the Database community." Presented by Huub van Dam at Workshop on High Performance Computing Meets Databases (HPCDB), Seattle, WA on November 18, 2011. PNNL-SA-84136.

van Dam HJJ, A Vishnu and WA De Jong. 2011. "Designing a Scalable Fault Tolerance Model for High Performance Computational Chemistry: A Case Study with Coupled Cluster Perturbative Triples." Journal of Chemical Theory and Computation 7(1):66-75. doi:10.1021/ct100439u

Villa O. 2011. "Exploring Advanced Architectures for Exascale." Presented by Oreste Villa (Invited Speaker) at Invited talk at the University of Milan and Cagliari, Cagliari, Italy on March 14, 2011. PNNL-SA-76982.

Voisin N, MS Wigmosta, AM Coleman, ER Venteris, R Skaggs, V Mishra, S Shukla, and DP Lettenmaier. 2011. "Water Use Optimization Toolset : hydrologic forecasting." Presented by Nathalie Voisin, Mark Wigmosta, Andre Coleman (Invited Speaker) at National Weather Service - Office of Hydrologic Development seminar, Silver Springs, MD on November 1, 2011. PNNL-SA-84424.

Voisin N, V Mishra, DP Lettenmaier, and MS Wigmosta. 2011. "Near real time data assimilation and uncertainties for hydrological forecasting ." Presented by Nathalie Voisin (Invited Speaker) at HEPEX International workshop on Post-processing and Verification of hydrological ensemble predictions, Delft, Netherlands on June 8, 2011. PNNL-SA-80422.

Voisin N, V Mishra, DP Lettenmaier, and MS Wigmosta. 2011. "Near real time data assimilation and uncertainties for hydrological forecasting ." Presented by Nathalie Voisin (Invited Speaker) at HEPEX International workshop on Post-processing and Verification of hydrological ensemble predictions, Delft, Netherlands on June 8, 2011. PNNL-SA-79337.

Wasem MR and KK van Dam. 2011. "PNNL’s Kleese van Dam Makes Sense of the Data Landscape." PNNL-SA-77363, Pacific Northwest National Laboratory, Richland, WA.

Webb-Robertson BJM and CD Corley. 2011. "Fusion of Experimental and Textual Data for Bioforensic Analyses." Abstract submitted to 2011 Chemical and Biological Defense Science and Technology (CBD S&T) Conference, Las Vegas, NV. PNNL-SA-80855.

Wellman DM, HE Matthews and JC Melland. 2011. Communications Plan for the Deep Vadose Zone-Applied Field Research Initiative. PNNL-20528, Pacific Northwest National Laboratory, Richland, WA.

Wellman DM, TC Johnson, RM Smith, MJ Truex, and HE Matthews. 2011. Deep Vadose Zone-Applied Field Research Initiative Fiscal Year 2011 Annual Report. PNNL-20757, Pacific Northwest National Laboratory, Richland, WA.

Wellman DM, L Zhong, and TS Ledbetter. 2011. "Foam Appears to be a Promising Solution for Vadose Zone Contaminants." PNNL-SA-81088 Pacific Northwest National Laboratory, Richland, WA.

Wescott RE. 2011. "PNNL’s Evolution in Data Centers and Monitoring." Presented by Ralph Wescott (Invited Speaker) at SC11 International Conference for High Performance Computing, Networking, Storage and Analysis, Seattle, WA on November 14, 2011. PNNL-SA-84031.

Wescott RE. 2011. "PNNL's Evolution in Data Centers and Monitoring." Presented by Ralph E. Wescott (Invited Speaker) at Data Center World, Orlando, FL on September 11, 2011. PNNL-SA-82488.

Wigmosta MS, N Voisin, AM Coleman, ER Venteris, R Skaggs, DP Lettenmaier, and V Mishra. 2011. Enhanced Hydrologic Forecast System: Integrated Forecast Model and Advanced Data Assimilation for the Water Use Optimization Toolset. PNNL-20852, Pacific Northwest National Laboratory, Richland, WA.

Wootan DW, RP Omberg, BJ Makenas, JV Nelson, JR, DL Nielsen, and DL Polzin. 2011. "Securing Operating Data from Passive Safety Tests at the Fast Flux Test Facility." In Transactions of the American Nuclear Society Annual Meeting, pp. 894-895. American Nuclear Soceity, La Grange Park, IL.

Wootan DW, RP Omberg, BJ Makenas, JV Nelson, JR, and DL Polzin. 2011. "Securing Operating Data From Passive Safety Tests at the Fast Flux Test Facility." In American Nuclear Society Annual Meeting. American Nuclear Society, La Grange Park, IL.

Wootan DW, RP Omberg, BJ Makenas, DL Nielsen, JV Nelson, JR, and DL Polzin. 2011. "Knowledge Preservation at the Fast Flux Test Facility." In American Nuclear Society 2011 Winter Meeting. American Nuclear Society, La Grange Park, IL.

Wootan DW, RP Omberg, BJ Makenas, DL Nielsen, JV Nelson, JR, and DL Polzin. 2011. "Preserving Physics Knowledge at the Fast Flux Test Facility." In PHYSOR 2012 Advances in Reactor Physics. PNNL-SA-83641, Pacific Northwest National Laboratory, Richland, WA.

Wootan DW, RP Omberg, BJ Makenas, DL Nielsen, JV Nelson, JR, and DL Polzin. 2011. "Knowledge Management at the Fast Flux Test Facility." Presented by David Wootan (Invited Speaker) at Global 2011, Makuhari, Japan on December 11, 2011. PNNL-SA-83605.

Wootan DW, RP Omberg, BJ Makenas, DL Nielsen, JV Nelson, JR, and DL Polzin. 2011. "Knowledge Management at the Fast Flux Test Facility." Presented by David W. Wootan at American Nuclear Society Annual Meeting, Washington DC on November 2, 2011. PNNL-SA-83605. Wootan DW, RP Omberg, BJ Makenas, DL Nielsen, JV Nelson, JR, and DL Polzin. 2011. "Securing Operating Data from Passive Safety Tests at the Fast Flux Test Facility." Presented by Bruce Makenas at American Nuclear Society Annual Meeting, Hollywood, FL on June 27, 2011. PNNL-SA-81012.

Wright KA. 2011. "PNNL’s support to the Department of Energy’s Global Threat Reduction Initiative." PNNL-SA-77666, Pacific Northwest National Laboratory, Richland, WA.

Wuennecke MAC, M Halappanavar, and JT Feo. 2011. Center for Adaptive Supercomputing Software newsletter - April 2011. PNNL-SA-78980, Pacific Northwest National Laboratory, Richland, WA.

Wuennecke MAC and DJ Haglin. 2011. "Novel High Performance Hybrid System for Semantic Factoring of Graph Databases." PNNL-SA-82464, Pacific Northwest National Laboratory, Richland, WA.

Wuennecke MAC, KM Regimbal, and RM Russell. 2011. "PNNL Institutional Computing." PNNL-SA-84093, Pacific Northwest National Laboratory, Richland, WA.

Wynne AS. 2011. "Middleware Case Study: MeDICi." Chapter 10 in Essential Software Architecture, 2nd Edition, ed. I Gorton, pp. 147-164. Springer, New York, NY.

Xie YL. 2011. "BENCHMARKING LOADS AND PROFILES OF PNC BANK." Presented by Yulong Xie (Invited Speaker) at SEDP Poster Presentation, Richland Community Center, WA on May 11, 2011. PNNL-SA-79995.

Yabusaki SB, and JM Garza. 2011. "eSTOMP: Extreme-Scale Computing for Subsurface Science and Engineering." PNNL-SA-79509, Pacific Northwest National Laboratory, Richland, WA.

Zhou N. 2011. "6.3 Missing Data and Outliers (Zhou)." In IEEE Task Force on Modal Identification of Electromechanical Modes . PNNL-SA-79095, Pacific Northwest National Laboratory, Richland, WA.

[edit] 2010

Kurath DE, and BE Wells. 2010. "Hanford Waste Data: Update Summary and Preliminary Comparison of Simulants to Particulate Data." Presented by Beric Wells at Client, Richland WA, Richland, WA on June 2, 2010. PNNL-SA-80594.

O’Neil LR. 2010. "A Scientific Data Management System: Connecting Users and Data." Abstract submitted to Information Management Conference (IMC), Las Vegas, NV. PNNL-SA-75342.

Webb-Robertson BJM, ES Peterson, J Walker, JL Jensen, S Hashemi, JN Adkins, and AC Rutledge. 2010. "Comparative Visual and Statistical Exploration of Multiple Bacterial Omic-based Data Sources through the VESPA Platform. Abstract submitted to Conference: Pep Talk: Protein Data Integration and Interrogation (http://www.chi-peptalk.com/pnf), San Diego, CA. PNNL-SA-73692.

Webb-Robertson BJM, K Ratuiste, and CS Oehmen. 2010. "Physicochemical property distributions for accurate and rapid pairwise protein homology classification." BMC Bioinformatics 11:145-152.

[edit] 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.

[edit] 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]

[edit] 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.

[edit] 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.

Last Update: 13 July 2011 | Pacific Northwest National Laboratory