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Computational Sciences & Mathematics

Scientific Data Management Publications

2013

Gorton I, J Yin, BA Akyol, S Ciraci, T Critchlow, Y Liu, TD Gibson, S Purohit, P Sharma, and M Vlachopoulou. 2013. "GridOPTICS(TM) A Novel Software Framework for Integrating Power Grid Data Storage, Management and Analysis ." In HICSS-46. Hawaii International Conference on System Sciences, Maui.

Kleese van Dam K, JP Carson, AL Corrigan, DR Einstein, ZC Guillen, BS Heath, AP Kuprat, IT Lanekoff, CS Lansing, J Laskin, D Li, Y Liu, MJ Marshall, EA Miller, G Orr, P Pinheiro da Silva, S Ryu, CJ Szymanski, and M Thomas. 2013. "Velo and REXAN - Integrated Data Management and High Speed Analysis for Experimental Facilities ." In 8th IEEE International Conference on EScience 2012, pp. 1-9. IEEE Press, WDC. doi: 10.1109/eScience.2012.6404463

Kleese van Dam K. 2013. "Boosting Big National Lab Data ." Datanami.

2012

Bell EB, SJ Rose, and S Choudhury. 2012. Text Analysis Capability . PNNL-21871, Pacific Northwest National Laboratory, Richland, WA

Chin G, Jr, A Marquez, S Choudhury, and JT Feo. 2012. "Scalable Triadic Analysis of Large-Scale Graphs: Multi-Core vs. Multi-Processor vs. Multi-Threaded Shared Memory Architectures." In Proceedings of the 2012 IEEE 24th International Symposium on Computer Architecture and High Performance Computing, October 24-26, 2012, New York, NY,, pp. 163-170. IEEE Computer Society, Los Alamitos, CA. doi:DOI 10.1109/SBAC-PAD.2012.39

Critchlow TJ, G Abdulla, J Becla, K Kleese van Dam, S Lang, and DL McGuinness. "Data Management Architectures." Chapter 4, p48-84 In Data Intensive Computing: Architectures, Algorithms, and Applications, Ian Gorton and Deb Gracio, editors. Cambridge University Press, 2012

Del Rio NR, and P Pinheiro da Silva. 2012. "Capturing Knowledge about the Use of Visualization Toolkits." In In Discovery Informatics: The Role of AI Research and Innovating Scientific Processes, vol. FS-12-03, ed. Bridewell, Gil, Hirsh, Kleese, Steinhaeuser, pp. 14-20. AAAI Press, Arlington, VA.

Gorton I, C Sivaramakrishnan, GD Black, SK White, S Purohit, CS Lansing, MC Madison, KL Schuchardt, and Y Liu. 2012. "Velo: A Knowledge Management Framework for Modeling and Simulation." Computing in Science & Engineering 14(2):12-23. doi:10.1109/MCSE.2011.116

Hobbie KA, ES Peterson, M Barton, KM Waters, and KA Anderson. 2012. "Integration of Data Systems and Technology Improves Research and Collaboration for a Superfund Research Center." JALA. Journal of the Association for Laboratory Automation 17(4):275-83.

Johnson TJ, YF Su, KH Jarman, BM Kunkel, JC Birnbaum, AG Joly, EG Stephan, RG Tonkyn, RG Ewing, and GC Dunham. 2012. "Demonstrated Wavelength Portability of Raman Reference Data for Explosives and Chemical Detection." International Journal of Spectroscopy 2012:Article No. 297056. doi:10.1155/2012/297056

Lai C, W Xu, and X Sun. 2012. "Development of an Inverse Algorithm for Resonance Inspection." Journal of Vibration and Acoustics 134(5):Article No.: 051017. doi:10.1115/1.4006649

McCusker JP, T Lebo, A Graves, D Difranzo, P Pinheiro da Silva, and DL McGuinness. 2012. "Functional Requirements for Information Resource Provenance on the Web." In IPAW 2012-4th International Provenance and Annotation Workshop. Springer, Santa Barbara, CA.

Melton RB, and TD Halter. 2012. 2011 Transactive Energy Workshop Proceedings May 18-19, 2011, Redwood City, CA . PNNL-SA-86105, Pacific Northwest National Laboratory, Richland, WA.

Melton RB, and TD Halter. 2012. Grid-Interop 2011 Proceedings: Implementing Interoperability, Advancing Smart Grid Standards, Architecture and Community, December 5-8, 2011, Phoenix, AZ . PNNL-SA-89350, Pacific Northwest National Laboratory, Richland, WA.

Oehmen CS, ES Peterson, and JR Teuton. 2012. "Evolutionary Drift Models for Moving Target Defense." In Cyber Security and Information Intelligence Research Workshop (CSIIRW). Oak Ridge National Laboratory, Oak Ridge, TN.

Peterson ES, LA McCue, AC Rutledge, JL Jensen, J Walker, MA Kobold, SR Webb, SH Payne, C Ansong, JN Adkins, WR Cannon, and BJM Webb-Robertson. 2012. "VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data." BMC Genomics 13(1):Article No. 131. doi:10.1186/1471-2164-13-131

Salayandia L, AQ Gates, and P Pinheiro da Silva. 2012. "An Approach to Evaluate Scientist Support in Abstract Workflows and Provenance Traces." In Discovery Informatics Symposium: The Role of AI Research in Innovating Scientific Processes. AAAI Fall Symposium Series., vol. FS-12-03, ed. Bridewell, Gil, Hirsh, Kleese, Steinhaeuser, pp. 45-50. AAAI Press, Arlington, VA.

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 Environmental Management." In Computational Methods in Water Resources XIX International Conference .

Thomas M, BS Heath, J Laskin, D Li, AP Kuprat, K Kleese van Dam, and JP Carson. 2012. "Visualization of High Resolution Spatial Mass Spectrometric Data during Acquisition." In 34th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 5545-48. IEEE (Institute of Electrical and Electronics Engineers), Piscataway, NJ.

Tilton SC, T Tal, SM Scroggins, J Franzosa, ES Peterson, R Tanguay, and KM Waters. 2012. "Bioinformatics Resource Manager v2.3: An Integrated Software Environment for Systems Biology with microRNA and Cross-species Analysis Tools." BMC Bioinformatics 13:Article No. 311. doi:10.1186/1471-2105-13-311.

2011

Agarwal K, JM Chase, KL Schuchardt, TD Scheibe, BJ Palmer, and TO Elsethagen. 2011. "Design and Implementation of "Many Parallel Task" Hybrid Subsurface Model." In Many-Task Computing on Grids and Supercomputers. Association for Computing Machinery, New York, NY.

Chin G Jr., C Sivaramakrishnan, T Critchlow, K Schuchardt, and AHH Ngu. 2011. "Scientist-Centered Workflow Abstractions via Generic Actors, Workflow Templates, and Context-Awareness for Groundwater Modeling and Analysis." The 5th IEEE International Workshop on Scientific Workflows (SWF 2011) published within the Proceedings of the 7th IEEE World Conference on Services (Services 2011), July, Washington, D.C.

Chin G Jr., S Choudhury, LJ Kangas, SA McFarlane, and A Marquez. 2011. "Evaluating In-Clique and Topological Parallelism Strategies for Junction Tree-Based Bayesian Inference Algorithm on the Cray XMT." In: Proceedings of the IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW 2011), May 16-20, Anchorage, Alaska, pp. 1710-1719. IEEE, Piscataway, New Jersey.  doi:10.1109/IPDPS.2011.328

Critchlow T and G Chin Jr. 2011. "Supercomputing and Scientific Workflows Gaps and Requirements." A short paper The 5th IEEE International Workshop on Scientific Workflows (SWF 2011) published within the Proceedings of the 7th IEEE World Conference on Services (Services 2011), July, Washington, D.C.

Choudhury S, L Holder, G Chin, Jr, and JT Feo. 2011. "Large-Scale Continuous Subgraph Queries on Streams." In Proceedings of the 1st Annual Workshop on High-Performance Computing Meets Databases (HPCBD 2011), November 12-18, 2011, Seattle, Washington, pp. 29-32. Association for Computing Machinery (ACM), New York. doi:10.1145/2125636.2125647

Critchlow T and KK van Dam. 2011. "Big Data Ecosystems Enable Scientific Discovery." HPC Source, Big Data - Forging Frontier, November 2011, p.35-38

Critchlow T, I Altintas, G Chin Jr., D Crawl, H Iyer, A Khan S Klasky, S Koehler, B Ludaescher, P Mouallem, M Nagappan, N Podhorszki, A Shoshani, C Silva, R Tchoua, and M Vouk. 2011. "Working with Workflows: Highlights from 5 years Building Scientific Workflows." In: Proceedings of the SciDAC 2011 Conference, July, Denver, Colorado (invited).

Gándara A, G Chin Jr., PP Silva, S White, C Sivaramakrishnan, and T Critchlow. 2011. "Knowledge Annotations in Scientific Workflows: An Implementation in Kepler." In: Proceedings of the 23rd Scientific and Statistical Database Management Conference (SSDBM), Springer Lecture Notes in Computer Science 6809, JB Cushing, J French, and S Bowers, Editors, Portland Oregon.

Gibson T, A Kulkarni, K K van Dam, and T Critchlow.2011. "The Feasibility of Moving PMU Data in the Future Power Grid." In: Proceedings of the CIGRÉ Canada Conference on Power Systems, September 6-8, Halifax, Nova Scotia. Paper No. CIGRÉ-125, CIGRÉ Canada, Montreal, Quebec.

Jin H, BJM Webb-Robertson, ES Peterson, R Tan, DJ Bigelow, MB Scholand, JR Hoidal, JG Pounds, and RC Zangar. 2011. "Smoking, COPD and 3-Nitrotyrosine Levels of Plasma Proteins." Environmental Health Perspectives 119(9):1314-1320. Available online. doi:10.1289/ehp.1103745

Koeppel BJ, C Lai, and MA Khaleel. 2011. "Effect of Geometry and Operating Parameters on Simulated SOFC Stack Temperature Uniformity." In: Proceedings of ASME 2011 5th International Conference on Energy Sustainability & 9th Fuel Cell Science, Engineering and Technology Conference, August 7-10, Washington, D.C. Technical Publication No. ESFuelCell2011-54803, Engineering Technical Conference, Washington, D.C.

Lai C, X Sun, C Dasch, G Harmon, and M Jones. 2011. "Quantify Resonance Inspection with Finite Element-Based Modal Analyses." Journal of Vibration and Acoustics 133(3): Art. No. 031004. doi:10.1115/1.4002955.

Lansing C, Y Liu, J Yin, A Corrigan, Z Guillen, KK van Dam, and I Gorton. 2011. "Designing the Cloud-Based DOE Systems Biology Knowledgebase." In: Proceedings of the 25th IEEE International Symposium on Parallel & Distributed Processing Workshops and Ph.D. Forum, May 16-20, Shanghai, China. IEEE, Piscataway, New Jersey.

McDermott JE, AL Corrigan, ES Peterson, CS Oehmen, G Niemann, E Cambronne, D Sharp, JN Adkins, R Samudrala, and F Heffron. 2011."Computational Prediction of Type III and IV Secreted Effectors in Gram-negative Bacteria." Infection and Immunity 79(1):23-32. doi:10.1128/IAI.00537-10.

McFarlane SA, KL Gaustad, EJ Mlawer, CN Long, and J Delamere. 2011. "Development of a High Spectral Resolution Surface Albedo Product for the ARM Southern Great Plains Central Facility." Atmospheric Measurement Techniques 4(9):1713-1733.  Available online. doi:10.5194/amt-4-1713-2011

Moreau L, B Clifford, J Freire, J Futrelle, Y Gil, P Groth, N Kwasnikowska, S Miles, P Missier, J Myers, BA Plale, YL Simmhan, EG Stephan, and J Van den Bussche. 2011. "The Open Provenance Model Core Specification (v1.1)." Future Generations Computer Systems 27(6):743-756. doi:10.1016/j.future.2010.07.005.

Ngu AH, A Jamnagarwala, G Chin Jr., C Sivaramakrishnan, and T Critchlow. 2011. "Kepler Scientific Workflow Design and Execution with Contexts." International Journal of Computers and Their Applications (IJCA) Special Issue on Scientific Workflows, Provenance and Their Applications 18(3):133.

Olsen B, J Johnson, and T Critchlow. 2011. "Data Intensive Architecture for Scalable Cyber Analytics." In: Proceedings of the 2011 IEEE International Conference on Technologies for Homeland Security, Waltham, Massachusetts.

Pon RK, AF Cardenas, DJ Buttler, and T Critchlow. 2011. "Measuring the Interestingness of Articles in a Limited User Environment." In: Information Processing & Management, Elsevier, Vol 47, Num 1.

Shoshani A, I Altintas, J Chen, G Chin Jr., A Choudhary, D Crawl, T Critchlow, K Gao, B Grimm, H Iyer, C Kamath, A Khan, S Klasky, S Koehler, S Lang, R Latham, JW Li, W Liao, J Ligon, Q Liu, B Ludaescher, P Mouallem, M Nagappan, N Podhorszki, R Ross, D Rotem, N Samatova, C Silva, A Sim, R Tchoua, R Thakur, M Vouk, K Wu, and W Yu. 2011. "The Scientific Data Management Center: Available Technologies and Highlights." In: Proceedings of the SciDAC 2011 Conference, July, Denver, Colorado (invited).

van Dam KK, M James, and A Walker. 2011. "Integrating Data Management and Collaborative Sharing with Computational Science Processes." In: Research Handbook of Computational Science and Engineering: Theory and Practice. IGI-Global, Chapter 21, pp.506-538. doi:10.4018/978-1-61350-116-0.

van Dam KK, D Li, S Miller, J Cobb, M Green, and C Ruby. 2011. "Challenges in Data Intensive Analysis at Scientific Experimental User Facilities." Chapter 10 in: Handbook of Data Intensive Computing, Springer, New York.

Yang C, HT Lim, SC Hwang, D Kim, C Lai, BJ Koeppel, KP Recknagle, and MA Khaleel. 2011. "Modeling on On-Cell Reforming Reaction of Planar SOFT Stack." In: Proceedings of ASME 2011 5th International Conference on Energy Sustainability & 9th Fuel Cell Science, Engineering and Technology Conference, August 7-10, Washington, D.C. American Society of Mechanical Engineers, New York.

2010

Chin G Jr, S Choudhury, LJ Kangas, SA McFarlane, and A Marquez. 2010."Fault Detection in Distributed Climate Sensor Networks using Dynamic Bayesian Networks." In: Proceedings of the 6th IEEE International Conference on e-Science (e-Science 2010), December 7-10, Brisbane, Australia, pp. 121-128. IEEE Computer Society, Los Alamitos, California. doi:10.1109/eScience.2010.22.

Gaustad KL, CJ Flynn, SJ Beus, and BD Ermold. 2010. "The Development of QC Standards for ARM Data Products." In: Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, June 21-25, Chicago, Illinois, pp. 548-553. Association for Computing Machinery (ACM), New York. doi:10.1145/1851476.1851556.

K. Kleese van Dam, T. Critchlow, J. Johnson, I. Gorton, D. Daly, R. Russell, J. Feo. The Future of Data Intensive Science Experimenting in Data - Across the Scales, Across Technologies, Across the Disciplines. PNNL White Paper, November 2010.

Ludaescher BT, I Altintas, S Bowers, J Cummings, TJ Critchlow, E Deelman, D De Roure, J Freire, C Goble, M Jones, S Klasky, T McPhillips, N Podhorszki, C Silva, I Taylor, and M Vouk. 2010. "Scientific Process Automation and Workflow Management." Chapter 13 in: Scientific Data Management: Challenges, Technology, and Deployment. A Shoshani and D Rotem, Editors, pp. 467-508.  CRC Press, Boca Raton, Florida. 

Ngu AH, A Jamnagarwala, G Chin Jr, C Sivaramakrishnan, and TJ Critchlow. 2010. "Context-Aware Scientific Workflow Systems using KEPLER." International Journal of Business Process Integration and Management 5(1):18-31.  doi:10.1504/IJBPIM.2010.033172.

Oehmen CS, ES Peterson, and ST Dowson. 2010. "An Organic Model for Detecting Cyber Events." In: Proceedings of the Sixth Annual Workshop on Cyber Security and Information Intelligence Research, Article No. 66. Association for Computing Machinery, New York. doi:10.1145/1852666.1852740.

Shah AR, JN Adkins, DJ Baxter, WR Cannon, D Chavarría-Miranda, S Choudhury, I Gorton, DK Gracio, TD Halter, N Jaitly, JR Johnson, RT Kouzes, MC Macduff, A Marquez, ME Monroe, CS Oehmen, WA Pike, C Scherrer, O Villa, BJM Webb-Robertson, PD Whitney, and N Zuljevic. 2010. "Applications in Data-Intensive Computing." In: Advances in Computers 79:1-70, M Zelkowitz, Editor. Academic Press Inc., San Diego, California. 

Stephan EG, TD Halter, TJ Critchlow, P Pinheiro Da Silva, and L Salayandia. 2010. "Using Domain Requirements to Achieve Science-Oriented Provenance." In: Provenance and Annotation of Data and Processes - Third International Provenance and Annotation Workshop, IPAW 2010: Lecture Notes in Computer Science 6378:301-303, DL McGuinness, JR Michaelis, and L Moreau, Editors. Springer, New York. doi:10.1007/978-3-642-17819-1_40.

Sun X, C Lai, and C Dasch. 2010. "Quantify Resonance Inspection with Finite Element-Based Modal Analyses." In: Proceedings of the ASME International Mechanical Engineering Congress & Exposition, November 12-18, Vancouver, British Columbia, Paper No. IMECE2010-39497.  ASME, New York. 

Xie S, R McCoy, SA Klein, RT Cederwall, WJ Wiscombe, EE Clothiaux, KL Gaustad, JC Golaz, S Hall, M Jensen, KL Johnson, Y Lin, CN Long, JH Mather, RA McCord, SA McFarlane, G Palanisamy, Y Shi, and DD Turner. 2010. "ARM Climate Modeling Best Estimate Data - A New Data Product for Climate Modelers." Bulletin of the American Meteorological Society 91(1):13-20. doi:10.1175/2009BAMS2891.1.

2009

Chin G Jr, A Marquez, S Choudhury, and K Maschhoff. 2009. "Implementing and Evaluating Multithreaded Triad Census Algorithms on the Cray XMT." In: IEEE International Symposium on Parallel & Distributed Processing (IPDPS 2009), May 25-29, Rome, Italy.  IEEE, Piscataway, New Jersey. doi:10.1109/IPDPS.2009.5161109.

Critchlow TJ. 2009. "Scientific Process Automation Improves Data Interaction." Scientific Computing 26(5):6-9. 

Chase JM, I Gorton, C Sivaramakrishnan, JP Almquist, AS Wynne, G Chin, Jr, and TJ Critchlow. 2009. "Kepler + MeDICi - Service-Oriented Scientific Workflow Applications." In: 2009 IEEE Congress on Services - Part I (Services-1 2009), pp. 275-282.  IEEE, Piscataway, New Jersey. 

Chase JM, I Gorton, C Sivaramakrishnan, JP Almquist, AS Wynne, G Chin, Jr, and TJ Critchlow. 2009. "Kepler + MeDICi." In: 2009 IEEE Congress on Services - I, July 6-10, Los Angeles, California, LJ Zhang, Editor, pp. 275 - 282. IEEE Computer Society, Los Alamitos, California. 

Flannery D, B Matthews, T Griffin, J Bicarregui, M Gleaves, L Lerusse, R Downing, A Ashton, S Sufi, G Drinkwater, and K Kleese van Dam. 2009. "ICAT: Integrating Data Infrastructure for Facilities Based Science." Proceedings of the 5th  IEEE International Conference on e-Science (e-science 2009), December 9-11, Oxford, United Kingdom.

Gibson TD, KL Schuchardt, and EG Stephan. 2009. "Application of Named Graphs Towards Custom Provenance Views." In: 1st Workshop on the Theory and Practice of Provenance (TaPP '09), Paper No. 5.  USENIX, Berkeley, California. 

Joslyn CA, EJ Burke, III, and TJ Critchlow. 2009. "View Discovery in OLAP Databases through Statistical Combinatorial Optimization." In: Proceedings of the 21st International Conference on Scientific and Statistical Database Management, Lecture Notes in Computer Science 5566:37-55.  Springer Verlag, New York. 

Lai C, X Sun, and DW Templeton. 2009. "Analyses of Various Damage Mechanisms in Transparent Armor Subject to Projectile Impact." In: Advances in Ceramic Armor V: Proceedings of the 33rd International Conference on Advanced Ceramics and Composites, pp. 205-212, Wiley, New York. 

Matthews B,  S Sufi, D Flannery, L Lerusse, T Griffin, M Gleaves, and  K Kleese van Dam. 2009. " Using a Core Scientific Metadata Model in Large-Scale Facilities." Proceedings of the 5th International Digital Curation Conference (IDCC 2009), December 2-4,  London, United Kingdom. 1(5):106-118. Available online.

Salje EKH, E Artacho, KF Austen, RP Bruin, M Calleja, HF Chappell,  G-T Chiang, MT Dove, I Frame, AL Goodwin, K Kleese van Dam, A Marmier, SC Parker, JM Pruneda, IT Todorov, K Trachenko, RP Tyer, AM Walker, and TOH White. 3009. "eScience for Molecular-scale Simulations and the eMinerals Project." Philosophical Transactions of The Royal Society A 367(1890):967-985. doi:10.1098/rsta.2008.0195.

Schuchardt KL, JM Chase, JA Daily, TO Elsethagen, BJ Palmer, and TD Scheibe. 2009. "Application of SALSSA Framework to the Validation of Smoothed Particle Hydrodynamics Simulations of Low Reynolds Number Flows." Journal of Physics: Conference Series 180(1): Art. No. 012065. doi:10.1088/1742-6596/180/1/012065.

Stephan EG, TD Halter, TD Gibson, N Beagley, and KL Schuchardt. 2009. "A Multi-Tier Provenance Model for Global Climate Research." In: International Conference on Network-Based Information Systems (NBIS '09), August 19-21, Indianapolis, Indiana, pp. 481-486.  IEEE, Piscataway, New Jersey. doi:10.1109/NBiS.2009.16.

Stephan EG, JS Burke, CA Carlson, DS Gillen, CA Joslyn, BK Olsen, and TJ Critchlow. 2009. "GeoSpatial Data Analysis for DHS Programs." In: 2009 IEEE Conference on Technologies for Homeland Security, (HST 2009), pp. 553-560.  IEEE, Piscataway, New Jersey. 

Sun X, C Lai, T Gorsich, and DW Templeton. 2009. "Optimizing Transparent Armor Design Subject to Projectile Impact Conditions." In: Ceramic Engineering and Science Proceedings: Advances in Ceramic Armor IV - A Collection of Papers Presented at the 32nd International Conference on Advanced Ceramics and Composites 29(6):15-22.  American Ceramic Society, Westerville, Ohio. 

Thomas GS, WK Nickless, DR Thiede, I Gorton, BJ Pitre, JE Christy, EM Faultersack, and JA Mauth. 2009. "T3: Secure, Scalable, Distributed Data Movement and Remote System Control for Enterprise Level Cyber Security." In: Proceedings of the 33rd Annual IEEE International Computer Software and Applications Conference II:468-472.  IEEE Computer Society, Los Alamitos, California.  doi:10.1109/COMPSAC.2009.177.

Walker AM, RP Bruin, MT Dove, TOH White, K Kleese van Dam, and R P Tyer. 2009. "Integrating Computing, Data and Collaboration Grids: The RMCS Tool."
Philosophical Transactions of The Royal Society A 367(1890):1047-1050. doi:10.1098/rsta.2008.0159.

Wynne AS, I Gorton, JM Chase, and EG Stephan. 2009. MeDICi: An Open Platform for Sensor Integration. PNNL-18716, Pacific Northwest National Laboratory, Richland, Washington. 

2008

Curtis DS, ES Peterson, and CS Oehmen. 2008. "A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application." In: 4th Annual International Conference on Web Information Systems and Technologies, J. Cordeiro, J. Filipe, and S. Hammoudi, Editors, pp. 244-251.  Springer, Berlin, Germany. 

Gibson TD, KL Schuchardt, and EG Stephan.  2008.  "Application of Provenance for Automated and Research Driven Workflows."  In" Second International Provenance and Annotation Workshop, June 17-18, Salt Lake City, Utah. Available online.

Joslyn CA, DS Gillen, JS Burke, TJ Critchlow, M Damante, and R Fernandes. 2008. "Hybrid Multidimensional Relational and Link Analytical Knowledge Discovery for Law Enforcement." In: IEEE Conference on Technologies for Homeland Security, pp. 161-166.  IEEE , Piscataway, New Jersey. 

Liu L, J Zhang, W Han, C Pu, J Caverlee, S Park, TJ Critchlow, D Buttler, and MA Coleman. 2008. "Providing Multi-Page Data Extraction Services with XWRAPComposer." In: Web Services Research and Practices, L-J Zhang, Editor.  CyberTech, Hershey, Pennsylvania 

Moreau L, BT Ludaescher, I Altintas, RS Barga, S Bowers, SP Callahan, G Chin, Jr, B Clifford, S Cohen, S Cohen-Boulakia, S Davidson, E Deelman, L digiampietri, IT Foster, J Freire, J Frew, J Futrelle, TD Gibson, Y Gil, C Goble, J Golbeck, P Groth, DA Holland, S Jiang, J Kim, D Koop, A Krenek, T McPhillips, G Mehta, S Miles, D Metzger, S Munroe, JD Myers, BA Plale, Podhorszki, V Ratnakar, S Emanuele , CE scheidegger, KL Schuchardt, MI Seltzer, YL Simmhan, ST Claudio, P Slaughter, EG Stephan, R Stevens, D Turi, HT Vo, MJ Wilde, J Zhao, and Y Zhao. 2008. "Special Issue: The First Provenance Challenge." Concurrency and Computation. Practice & Experience 20(5):409-418.  doi:10.1002/cpe.v20:5.

Ngu AHH, S Bowers, N Haasch, T McPhillips, and TJ Critchlow. 2008. "Flexible Scientific Workflow Modeling Using Frames, Templates, and Dynamic Embedding." In: Proceedings of the 20th International Conference on Scientific and Statistical Database Management, Lecture Notes in Computer Science 5069:566-572.  Springer Verlag, New York. 

Paulson PR, TD Gibson, KL Schuchardt, and EG Stephan. 2008. Provenance Store Evaluation. PNNL-17237, Pacific Northwest National Laboratory, Richland, Washington. 

Peppler RA, CN Long, DL Sisterson, DD Turner, CP Bahrmann, SW Christensen, KJ Doty, RC Eagan, TD Halter, MD Ivey, NN Keck, KE Kehoe, JC Liljegren, MC Macduff, JH Mather, RA McCord, JW Monroe, ST Moore, KL Nitschke, BW Orr, RC Perez, BD Perkins, SJ Richardson, KL Sonntag, JW Voyles, and R Wagner. 2008. "An Overview of ARM Program Climate Research Facility Data Quality Assurance." The Open Atmospheric Science Journal 2(ISSN 1874-2823):192-216.

Peterson ES, EG Stephan, AL Corrigan, RD Lins, TA Soares, RE Scarberry, SJ Rose, LK Williams, C Lai, TJ Critchlow, and TP Straatsma. 2008. "Northwest Trajectory Analysis Capability: A Platform for Enhancing Computational Biophysics Analysis." In: Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008, pp. 558-562.  CSREA Press, Bogart, Georgia. 

Schuchardt KL, TD Gibson, EG Stephan, and G Chin Jr. 2008. "Applying Content Management to Automated Provenance Capture." Concurrency and Computation. Practice & Experience 20(5):541-554. 

Shah AR, M Singhal, TD Gibson, C Sivaramakrishnan, KM Waters, and I Gorton. 2008. "An Extensible, Scalable Architecture for Managing Bioinformatics Data and Analysis." In: IEEE 4th International Conference on e-Science, December 7-12, Indianapolis, Indiana, pp. 190-197.  IEEE Computer Society, Los Alamitos, California.  doi:10.1109/eScience.2008.69.

2007

Choudhury S and V Chandrasekar. 2007. "Wideband Reception and Processing for Dual-Polarization Radars with Dual Transmitters." Journal of Atmospheric and Oceanic Technology 24(1):95-101. 

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.  doi:10.1088/1742-6596/78/1/012089.

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.  doi:10.1088/1742-6596/78/1/012064

Schuchardt KL, BT Didier, TO Elsethagen, L Sun, V Gurumoorthi, JM Chase, J Li, and TL Windus. 2007. " Basis Set Exchange: A Community Database for Computational Sciences." Journal of Chemical Information and Modeling 47(3):1045-1052. doi:10.1021/ci600510j.

Shah AR, 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. doi:10.1093/bioinformatics/btm031.

Turner DD, SA Clough, JC Liljegren, EE Clothiaux, KE Cady-Pereira, and KL Gaustad. 2007. "Retrieving Liquid Water Path and Precipitable Water Vapor from the Atmospheric Radiation Measurement (ARM) Microwave Radiometers." In: IEEE Transactions on Geoscience and Remote Sensing 45(11 PT. 2):3680-3690.  doi:10.1109/TGRS.2007.903703.

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 Organism." Bioinformatics 23(13):1705-1707.  doi:10.1093/bioinformatics/btm132.

2006

Chin G Jr, EG Stephan, DK Gracio, OA Kuchar, PD Whitney, and KL Schuchardt. 2006. "Developing Concept-Based User Interfaces for Scientific Computing." Computer 39(9):26-34. 

Kiebel GR, KJ Auberry, N Jaitly, D Clark, ME Monroe, ES Peterson, N Tolic, GA Anderson, and RD Smith. 2006. "PRISM: A Data Management System for High-Throughput Proteomics." Proteomics 6(6):1783-1790. doi:10.1002/pmic.200500500.

Long CN, TP Ackerman, KL Gaustad, and JN Cole. 2006. "Estimation of Fractional Sky Cover from Broadband Shortwave Radiometer Measurements." Journal of Geophysical Research D-Atmospheres 111(D11):D11204. doi:10.1029/2005JD006475. 

Oehmen CS, LA McCue, JN Adkins, KM Waters, TS Carlson, WR Cannon, BJM Webb-Robertson, DJ Baxter, ES Peterson, M Singhal, A Shah, and KR Klicker.  2006. "High-Throughput Visual Analytics for Biological Sciences: Turning Data into Knowledge."  Journal of Supercomputing. doi:http://doi.acm.org/10.1145/1188455.1188769.

Talbott TD, KL Schuchardt, EG Stephan, and JD Myers.  2006.  "Mapping Physical Formats to Logical Models to Extract Data and Metadata: The Defuddle Parsing Engine."  In: IPAW'06 International Provenance and Annotation Workshop, May 3-5, Chicago, Illinois, Lecture Notes in Computer Science 4145:73-81. L Moreau and I Foster, Editors. Springer-Verlag, Berlin, Germany. 

Waters KM, M Singhal, BJM Webb-Robertson, EG Stephan, and JM Gephart. 2006. "Breaking the High-Throughput Bottleneck: New Tools Help Biologists Integrate Complex Datasets." Scientific Computing 23(4):22-26. 

2005

Chin G Jr, EG Stephan, DK Gracio, OA Kuchar, PD Whitney, and KL Schuchardt. 2005. "Scientist-Centered Graph-Based Models of Scientific Knowledge." In:  HCI International 2005: 11th International Conference on Human-Computer Interaction, July 22-27, Caesars Palace, Las Vegas, Nevada.  Lawrence Erlbaum and Associates, Mahwah, New Jersey. 

Gdanitz J, GD Black, CS Lansing, BJ Palmer, and EF Schuchart. 2005. " Registering the Amica Electronic Structure Code in the Extensible Computational Chemistry Environment." Journal of Computational Chemistry 26(3):214-225. 

Kassianov EI, CN Long, and JE Christy. 2005. "Cloud-Base-Height Estimation from Paired Ground-Based Hemispherical Observations." Journal of Applied Meteorology 44(8):1221-1233. 

McFarlane SA, CN Long, and DM Flynn. 2005. "Impact of Island-Induced Clouds on Surface Measurements: Analysis of the ARM Nauru Island Effect Study Data." Journal of Applied Meteorology 44(7):1045-1065. 

Myers JD, TC Allison, SJ Bittner, BT Didier, M Frenklach, WH Green, YL Ho, J Hewson, WS Koegler, CS Lansing, D Leahy, M Lee, R McCoy, M Minkoff, S Nijsure, G von Laszewski, D Montoya, L Oluwole, CM Pancerella, R Pinzon, W Pitz, LA Rahn, B Ruscic, KL Schuchardt, EG Stephan, A Wagner, TL Windus, and C Yang. 2005. "A Collaborative Informatics Infrastructure for Multi-scale Science." Cluster Computing 8(4):243-253. 

Schwidder J, TD Talbott, and JD Myers.  2005.  "Bootstrapping to a Semantic Grid." In: Semantic Infrastructure for Grid Computing Applications 2005.  CEUR-WS Workshop Proceedings, Vol.138. Aachen, Germany. Available online.

Singhal M, KR Klicker, G Chin, Jr, LL Trease, EG Stephan, and DK Gracio. 2005. "Bioinformatics Approach for Exploring MS/MS Proteomics Data." In: Proceedings of the 38th Annual Hawaii International Conference on System Science HICSS '05 held on the Big Island, January, RH Sprague, Editor.  IEEE Computer Society Press, Los Alamitos, California.  doi:10.1109/HICSS.2005.119.

Talbott TD, M Peterson, J Schwidder, and JD Myers.  2005.  "Adapting the Electronic Laboratory Notebook for the Semantic Era." In: Proceedings of the 2005 International Symposium on Collaborative Technologies and Systems, IEEE Computer Society, Los Alamitos, California, pp. 136-143. doi:10.1109/ISCST.2005.1553305.

2004

Chin G Jr, and CS Lansing. 2004. "Capturing and Supporting Contexts for Scientific Data Sharing via the Biological Sciences Collaboratory." In: Proceedings of the 2004 ACM Conference on Computer Supported Cooperative Work, pp. 409-418.  Association for Computing Machinery (ACM), New York. 

Chin G Jr, and CS Lansing. 2004. "The Biological Sciences Collaboratory." In: Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS '04, June 21-24, Las Vegas, Nevada, pp. 91-97.  CSREA Press, Bogart, Georgia. 

Chin G Jr, EG Stephan, and DK Gracio. 2004. "Computing through Scientific Abstractions in SysBioPS ." In: Proceedings of the 2004 IEEE International Conference on Systems, Man and Cybernetics 1:70-75.  IEEE, New York. 

Chin G,Jr, EG Stephan, KR Klicker, AL Corrigan, and HJ Sofia. 2004. "Supporting Computational Visual Theories in Biology." In: The 2004 IEEE Symposium on Visual Languages and Human-Centric Computing, pp. 69-71.  IEEE, Piscataway, New Jersey. 

Havre SL, M Singhal, B Gopalan, DA Payne, KR Klicker, GR Kiebel, KJ Auberry, EG Stephan, BJM Webb-Robertson, and DK Gracio. 2004. "Integrating Evolving Tools for Proteomics Research." In: Proceedings of The 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2004:307-313, F Valafar and H Valafar, Editors.  CSREA Press, Las Vegas, Nevada. 

Klicker KR, M Singhal, EG Stephan, LL Trease, and DK Gracio. 2004. "Computational Cell Environment: A Problem Solving Environment for Integrating Diverse Biological Data." In: Proceedings of the 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2002:422-428, F Valafar and H Valafar, Editors.  CSREA Press, Las Vegas, Nevada. 

Myers JD, M Peterson, KP Saripalli, and T Talbott. 2004. "Electronic Notebooks: An Interface Component for Semantic Records Systems." In: Abstracts of Papers of the American Chemical Society, Part 1, 227:U689-U689. Abstract Number 076-CINF, Washington, American Chemical Society.

Myers JD, TC Allison, S Bittner, BT Didier, M Frenklach, WH Green, YL Ho, J Hewson, WS Koegler, CS Lansing, D Leahy, M Lee, R McCoy, M Minkoff, S Nijsure, G von Laszewski, DW Montoya, CM Pancerella, R Pinzon, W Pitz, L Rahn, B Ruscic, KL Schuchardt, EG Stephan, AF Wagner, TL Windus, and C Yang. 2004. "A Collaborative Informatics Infrastructure for Multi-scale Science." In: Proceedings of the Second International Workshop on Challenges of Large Applications in Distributed Environments. CLADE 2004, Honolulu Hawaii, pp. 24-33.  IEEE, Piscataway, New Jersey. 

Singhal M, EG Stephan, KR Klicker, LL Trease, G Chin, Jr, DK Gracio, and DA Payne. 2004. "Enabling Systems Biology: A Scientific Problem-Solving Environment." In: International Conference on Computational Science, June 6-9, 2004, Krakow, Poland, pp. 540-547.  Springer-Verlag, Berlin, Germany. 

Stephan EG, G Chin Jr, AL Corrigan, KR Klicker, and HJ Sofia. 2004. "Synchronized Biological Knowledge and Data Management: A Hybrid Approach." In: Proceedings of the 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences. . F  Valafar and H Valafar, Editors, pp. 105-110.  CSREA Press, Las Vegas, Nevada. 

2003

Ackerman TP, DM Flynn, and RT Marchand. 2003. "Quantifying the Magnitude of Anomalous Solar Absorption." Journal of Geophysical Research D-Atmospheres 108(D9):4273. doi:10.1029/2002JD002674.

Myers JD, CM Pancerella, CS Lansing, KL Schuchardt, and BT Didier. 2003. "Multi-scale Science: Supporting Emerging Practice with Semantically Derived Provenance." In: Proceedings of the Workshop on Semantic Web Technologies for Searching and Retrieving Scientific Data , N Ashish and C Goble, Editors.  Sun SITE Central Europe (CEUR), Aachen, Germany. 

Pancerella CM, J Hewson, WS Koegler, D Leahy, M Lee, L Rahn, C Yang, JD Myers, BT Didier, R McCoy, KL Schuchardt, EG Stephan, TL Windus, K Amin, S Bittner, CS Lansing, M Minkoff, S Nijsure, G von Laszewski, R Pinzon, B Ruscic, AF Wagner, B Wang, W Pitz, YL Ho, DW Montoya, L Xu, TC Allison, WH Green, and M Frenklach. 2003. "Metadata in the Collaboratory for Multi-Scale Chemical Science." In: DC-2003: Proceedings of the 2003 International Conference on Dublin Core and Metadata Applications: Supporting Communities of Discourse and Practice - Metadata Research & Applications, Article No. 13.  Dublin Core Metadata Initiative (DCMI), Dublin, Ohio. 

2002

Barnard JC and DM Flynn. 2002. "A Comparison Between Modeled and Measured Clear-Sky Radiative Shortwave Fluxes in Arctic Environments, with Special Emphasis on Diffuse Radiation." Journal of Geophysical Research D-Atmospheres 107(D19):4383. doi:10.1029/2001JD001442.

Long CN, TP Ackerman, and JE Christy. 2002. "Variability Across the ARM SGP Area by Temporal and Spatial Scale." In: Atmospheric Radiation Measurements and Applications in Climate, Proceedings- SPIE The International Society of Optical Engineering 4815:51-57. JA Shaw, Editor.  SPIE - The International Society for Optical Engineering, Bellingham, Washington. 

Schuchardt KL, JD Myers, and EG Stephan. 2002. "A Web-Based Data Architecture for Problem-Solving Environments: Application of Distributed Authoring and Versioning to the Extensible Computational Chemistry Environment." Cluster Computing 5(3):287-296. 

2001

Myers JD, ES Mendoza, and BL Hoopes. 2001. "A Collaborative Electronic Laboratory Notebook." In: Proceedings of the IASTED International Conference, Internet and Multimedia Systems and Applications, August 13-16, Honolulu, Hawaii. MH Hamza, Editor, pp. 334-338.  IASTED/Acta Press, Anaheim, California. 

Saffer JD, CL Albright, AJ Calapristi, G Chen, VL Crow, SD Decker, KM Groch, SL Havre, JM Malard, TJ Martin, NE Miller, PJ Monroe, LT Nowell, DA Payne, JF Reyes Spindola, RE Scarberry, HJ Sofia, LC Stillwell, GS Thomas, SJ Thurston, LK Williams, and SJ Zabriskie. 2001. "Visualization and Integrated Data Mining of Disparate Information." In: Chemical Data Analysis in the Large: The Challenge of the Automation Age, Proceedings of the Beilstein-Institut International Workshop, May 22-26, 2000 Bozen, Italy , MG Hicks, Editor.  Beilstein-Institut, Frankfurt am Main, Germany.

Schuchardt KL, JD Myers, and EG Stephan. 2001. "Open Data Management Solutions for Problem Solving Environments: Application of Distributed Authoring and Versioning to the Extensible Computational Chemistry Environment." In: Proceedings of the 10th IEEE International Symposium on High Performance Distributed Computing, IEEE Computer Society, pp. 228-238.  IEEE Computer Society Press, Piscataway, New Jersey.

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