Publications
Banas, N. S., E. J. Lessard, R. M. Kudela, P. MacCready, T. D. Peterson, B. M. Hickey and E. Frame (2009). "Planktonic growth and grazing in the Columbia River plume region: A biophysical model study." J. Geophys. Res. 114(10): 1029.
Dietrich, C., J. Comba, L. Nedel, C. Scheidegger, J. Schreiner and C. Silva (2009). "Improving Mesh Quality of Marching Cubes Using Edge Transformations." IEEE Transactions on Visualization and Computer Graphics 15(1): 150-159.
Dietrich, C. A., C. E. Scheidegger, J. L. D. Comba, L. P. Nedel and C. T. Silva (2009). "Marching Cubes without Skinny Triangles." Computing in Science and Engineering 11(2): 82-87.
Dietrich, C. A., C. E. Scheidegger, J. M. Schreiner, J. L. D. Comba, L. P. Nedel and C. T. Silva (2009). "Edge Transformations for Improving Mesh Quality of Marching Cubes." IEEE Transactions on Visualization and Computer Graphics 15(1): 150-159.
Frolov, S; Baptista, A; Zhang, Y; Seaton, C (2009). "Estimation of Ecologically Significant Circulation Features of the Columbia River Estuary and Plume Using a Reduced-Dimension Kalman Filter." Continental Shelf Research 29(2) 456-466
Frolov, S., Z. Lu, R. van der Merwe, T.K. Leen, and A.M. Baptista, (2009). Fast Data Assimilation Using a Nonlinear Kalman Filter and a Model Surrogate: an Application to the Columbia River Estuary, Dynamics of Atmospheres and Oceans, 2008.10.004.
Garcia-Mendoza, E., D. Rivas, A. Olivos-Ortiz, A. Almazan-Becerril, C. Castaneda-Vega and J. L. Pena-Manjarrez (2009). "A toxic Pseudo-nitzschia bloom in Todos Santos Bay, northwestern Baja California, Mexico." Harmful Algae 8(3): 493-503.
Ghindilis, A. L., M. W. Smith, K. R. Schwarzkopf, C. Zhan, D. R. Evans, A. M. Baptista and H. M. Simon (2009). "Sensor array: Impedimetric label-free sensing of DNA hybridization in real time for rapid, PCR-based detection of microorganisms." Electroanalysis 21(13): 1459-1468.
Howe, B; Green-Fishback, H; Maier, D (2009). "Scientific Mashups: Runtime-Configurable Data Product Ensembles." Scientific and Statistical Database Management Conference 2009: 19-36.
Kudela, R. M. and T. D. Peterson (2009). "Influence of a buoyant river plume on phytoplankton nutrient dynamics: What controls standing stocks and productivity?" J. Geophys. Res. 114.
Liu, Y., P. MacCready, B. M. Hickey, E. P. Dever, P. M. Kosro and N. S. Banas (2009). "Evaluation of a coastal ocean circulation model for the Columbia River plume in summer 2004." J. Geophys. Res. 114.
Plant, J. N., K. S. Johnson, J. A. Needoba and L. J. Coletti (2009). "NH4-Digiscan: An in situ and laboratory ammonium analyzer for estuarine, coastal, and shelf waters." Limnology and Oceanography: Methods 7(FEB): 144-156.
Rodrigues, M., A. Oliveira, M. Costa, A. B. Fortunado and Y. Zhang (2009). "Sensitivity analysis of an ecological model applied to the Ria de Aveiro." Journal of Coastal Research (Special Issue 56).
Rodrigues, M., A. Oliveira, H. Queiroga, A. B. Fortunado and Y. Zhang (2009). "Three-Dimensional Modeling of the Lower Trophic Levels in the Ria de Aveiro (Portugal)." Ecological Modeling 220(9-10): 1274.
Wang, H., C. E. Scheidegger and C. T. Silva (2009). "Bandwidth Selection and Reconstruction Quality in Point-Based Surfaces." IEEE Transactions on Visualization and Computer Graphics 15(4): 572-582.
2008
Baptista, A; Howe, B; Freire, J; Maier, D; Silva, C (2008). "Scientific Exploration in the Era of Ocean Observatories." IEEE Computing in Science & Engineering 10(3): 53-58.
Bernardon, F; Ha, L; Callahan, S; Comba, J; Silva, C (2008). "Interactive Transfer Function Specification for Direct Volume Rendering of Disparate Volumes." Computing in Science and Engineering.
Freire, J; Koop, D; Santos, E; Silva, C (2008). "Provenance for Computational Tasks: A Survey." Computing in Science and Engineering 10(3): 11-21.
Frolov, S; Baptista, A; Wilkin, M. (2008). "Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory." Continental Shelf Research 28(19): 2644-2658.
Jannasch, H W; Coletti, L J; Johnson, K S; Fitzwater, S E; Needoba, J A; Plant, J N (2008). "Robust mooring systems for continuously monitoring of complex biogeochemical cycles in estuaries: Design, construction and internal results from Elkhorn Slough, CA." Limnology and Oceanography: Methods 6: 263-276.
Johnson, K S; Needoba, J A (2008). "Mapping the spatial variability of plankton metabolism using nitrate and oxygen sensors on an autonomous underwater vehicle." Limnology and Oceanography: Methods 53 (5 part 2): 2237-2250.
Kirby, R M; Silva, C (2008). "The Need for Verifiable Visualization." IEEE Computer Graphics and Applications 28(5): 78-83.
Koop, D; Scheidegger, C E; Callahan, S P; Vo, H T; Freire, J; Silva, C (2008). "VisComplete: Automating Suggestions for Visualization Pipeline." IEEE Transactions on Visualization and Computer Graphics 14(6): 1691-1698.
Saraceno, M; Strub, P; Kosro, P (2008). "Estimates of sea surface height and near-surface alongshore coastal currents from combinations of altimeters and tide gauges." J. Geophys. Res. 113(C11): 20.
Scheidegger, C; Koop, D; Santos, E; Vo, H; Callahan, S; Freire, J; Silva, C (2008). "Tackling the Provenance Challenge One Layer at a Time." Concurrency And Computation: Practice And Experience(20(5)): 473-483.
Silva, C; Freire, J (2008). "Software Infrastructure for Exploratory Visualization and Data Analysis: Past, Present, and Future." Journal of Physics: Conference Series 125.
Vagin, M Y; Trashin, S A; Karyakin, A A; Mascini, M (2008). Anal. Chem. 80: 7075.
Zhang, Y; Baptista, A (2008). "Benchmarking a new finite-element tsunami model on unstructured grids." Pure and Applied Geophysics 165: 2229-2248.
Zhang, Y; Baptista, A (2008). "SELFE: A semi-implicit Eulerian Lagrangian Finite-element model for cross-scale ocean circulation." Ocean Modelling 21: 3-4, 71-96.
2007
Bernardon, F; Callahan S.; Comba, J; Silva C (2007). "An Adaptive Framework for Visualizing Unstructured Grids with Time-Varying Scalar Fields." Parallel Computing 33(6): 391-405.
Daniels, J., L. Ha, et al. (2007). Robust Smooth Feature Extraction from Point Clouds. Shape Modeling International 2007.
Davidson, S., S. Cohen-Boulakia, et al. (2007). "Provenance in Scientific Workflow Systems." IEEE Data Engineering Bulletin(32(4)): 44-50.
Dang, T., Sergey Frolov, Nirupama Bulusu, Wu-chi Feng, and Antonio Baptista, “Near Optimal Sensor Selection in The CORIE Observation Network for Data Assimilation Using Genetic Algorithms”, In Proceedings of the International Conference on Distributed Computing in Sensor Systems (DCOSS 2007), Santa Fe, New Mexico, June 2007.
Dang, T., Nirupama Bulusu, Wu-chi Feng, “RIDA: A Robust Information-Driven Compression Architecture for Irregular Wireless Sensor Networks”, In Proceedings of European Conference on Sensor Networks (EWSN 2007), Delft, Netherlands, Jan. 2007.
Howe, B., D. Maier, L. Bright. Smoothing the ROI Curve for Scientific Data Management Applications Third Biennial Conference on Innovative Data Systems Research (CIDR 2007).
Howe, B., N. Hagerty, E. Van Matre, D. Maier, A. M. Baptista, C. Seaton, P. Turner, "The Ocean Appliance: Complete Platform Provisioning for Low-Cost Data Sharing, IEEE/MTS Oceans 2007, Vancouver, BC, October 2007.
Myers, E., A. Zhang, F. Aikman, Y. Zhang, A. Baptista, P. Turner and C. Seaton. Evaluation and Transition of a Columbia River Nowcast/Forecast Circulation Model to NOAA’s National Ocean Service,” extended abstract, Coastal Zone ‘07, Portland, OR, July 2007.
Scheidegger, C. E., H. T. Vo, et al. (2007). "Querying and Creating Visualizations by Analogy." IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2007)(13(6)): 1560-1567.
Silva, C., J. Freire, et al. (2007). "Provenance for Visualization: Reproducibility and Beyond." Computing in Science and Engineering(9(5)): 82-89.
van der Merwe, R., T. K. Leen, et al. (2007). "Fast Neural Network Surrogates for Very High Dimensional Physics-Based Models in Computational Oceanography." Neural Networks(20): 462-478.
Zhang, Y., A. Baptista, K. Wang, C. Goldfinger, R. Witter, G. Priest, C. Peterson, K. Cruikshank. “Hydrodynamic simulations of historic tsunamis from the Cascadia Subduction Zone,” extended abstract, Coastal Zone ’07, Portland, OR, July 2007.
2006
Baptista, A., "CORIE: the first decade of a coastal-margin collaborative observatory," presented at Oceans'06, MTS/ IEEE, Boston, MA, 2006.
Bright, L., D. Maier, B. Howe. Managing the Forecast Factory. Proc. ICDE Workshop on Workflow and Data Flow for Scientific Applications (SciFlow), 2006
Other Dissemination Activities DIVR White Paper 2006 (.pdf)
This activity is a white paper written by Eda Davis-Butts and addresses STEM Diversity. The paper was prepared to inform the conversation and the work of a statewide initiative in Oregon. The paper reflects the research framework of The SMILE Program.
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