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  • Data management  (2)
  • Gulf of Maine  (2)
  • Modeling  (2)
  • Back-barrier bays  (1)
  • 1
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Geophysical Research: Oceans 122 (2017): 2760–2780, doi:10.1002/2016JC012318.
    Description: A system of barrier islands and back-barrier bays occurs along southern Long Island, New York, and in many coastal areas worldwide. Characterizing the bay physical response to water level fluctuations is needed to understand flooding during extreme events and evaluate their relation to geomorphological changes. Offshore sea level is one of the main drivers of water level fluctuations in semienclosed back-barrier bays. We analyzed observed water levels (October 2007 to November 2015) and developed analytical models to better understand bay water level along southern Long Island. An increase (∼0.02 m change in 0.17 m amplitude) in the dominant M2 tidal amplitude (containing the largest fraction of the variability) was observed in Great South Bay during mid-2014. The observed changes in both tidal amplitude and bay water level transfer from offshore were related to the dredging of nearby inlets and possibly the changing size of a breach across Fire Island caused by Hurricane Sandy (after December 2012). The bay response was independent of the magnitude of the fluctuations (e.g., storms) at a specific frequency. An analytical model that incorporates bay and inlet dimensions reproduced the observed transfer function in Great South Bay and surrounding areas. The model predicts the transfer function in Moriches and Shinnecock bays where long-term observations were not available. The model is a simplified tool to investigate changes in bay water level and enables the evaluation of future conditions and alternative geomorphological settings.
    Description: New York State Department of Environmental Conservation Grant Number: (NYS-DEC); U.S. Geological Survey (USGS)
    Keywords: Water level ; Back-barrier bays ; Tidal variations ; Storm effects ; Dredging ; Long Island
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 118 (2013): 6319–6328, doi:10.1002/2013JC008939.
    Description: Strong and strategic collaborations among experts from academia, federal operational centers, and industry have been forged to create a U.S. IOOS Coastal and Ocean Modeling Testbed (COMT). The COMT mission is to accelerate the transition of scientific and technical advances from the coastal and ocean modeling research community to improved operational ocean products and services. This is achieved via the evaluation of existing technology or the development of new technology depending on the status of technology within the research community. The initial phase of the COMT has addressed three coastal and ocean prediction challenges of great societal importance: estuarine hypoxia, shelf hypoxia, and coastal inundation. A fourth effort concentrated on providing and refining the cyberinfrastructure and cyber tools to support the modeling work and to advance interoperability and community access to the COMT archive. This paper presents an overview of the initiation of the COMT, the findings of each team and a discussion of the role of the COMT in research to operations and its interface with the coastal and ocean modeling community in general. Detailed technical results are presented in the accompanying series of 16 technical papers in this special issue.
    Description: This project was supported by NOAA via the IOOS Office, award NA10NOS0120063 and NA11NOS0120141, and used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant OCI- 1053575.
    Keywords: Modeling ; Hypoxia ; Inundation ; Waves
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
    Publication Date: 2022-10-27
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Vance, T. C., Wengren, M., Burger, E., Hernandez, D., Kearns, T., Medina-Lopez, E., Merati, N., O'Brien, K., O'Neil, J., Potemrag, J. T., Signell, R. P., & Wilcox, K. From the oceans to the cloud: Opportunities and challenges for data, models, computation and workflows. Frontiers in Marine Science, 6(211), (2019), doi:10.3389/fmars.2019.00211.
    Description: Advances in ocean observations and models mean increasing flows of data. Integrating observations between disciplines over spatial scales from regional to global presents challenges. Running ocean models and managing the results is computationally demanding. The rise of cloud computing presents an opportunity to rethink traditional approaches. This includes developing shared data processing workflows utilizing common, adaptable software to handle data ingest and storage, and an associated framework to manage and execute downstream modeling. Working in the cloud presents challenges: migration of legacy technologies and processes, cloud-to-cloud interoperability, and the translation of legislative and bureaucratic requirements for “on-premises” systems to the cloud. To respond to the scientific and societal needs of a fit-for-purpose ocean observing system, and to maximize the benefits of more integrated observing, research on utilizing cloud infrastructures for sharing data and models is underway. Cloud platforms and the services/APIs they provide offer new ways for scientists to observe and predict the ocean’s state. High-performance mass storage of observational data, coupled with on-demand computing to run model simulations in close proximity to the data, tools to manage workflows, and a framework to share and collaborate, enables a more flexible and adaptable observation and prediction computing architecture. Model outputs are stored in the cloud and researchers either download subsets for their interest/area or feed them into their own simulations without leaving the cloud. Expanded storage and computing capabilities make it easier to create, analyze, and distribute products derived from long-term datasets. In this paper, we provide an introduction to cloud computing, describe current uses of the cloud for management and analysis of observational data and model results, and describe workflows for running models and streaming observational data. We discuss topics that must be considered when moving to the cloud: costs, security, and organizational limitations on cloud use. Future uses of the cloud via computational sandboxes and the practicalities and considerations of using the cloud to archive data are explored. We also consider the ways in which the human elements of ocean observations are changing – the rise of a generation of researchers whose observations are likely to be made remotely rather than hands on – and how their expectations and needs drive research towards the cloud. In conclusion, visions of a future where cloud computing is ubiquitous are discussed.
    Description: This is PMEL contribution 4873.
    Keywords: Ocean observation ; Ocean modeling and prediction ; Cloud ; Data management ; Archiving ; Technology
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 96–111, doi:10.1016/j.dsr2.2013.11.003.
    Description: The life cycle of Alexandrium fundyense in the Gulf of Maine includes a dormant cyst stage that spends the winter predominantly in the bottom sediment. Wave-current bottom stress caused by storms and tides induces resuspension of cyst-containing sediment during winter and spring. Resuspended sediment could be transported by water flow to different locations in the Gulf and the redistribution of sediment containing A. fundyense cysts could alter the spatial and temporal manifestation of its spring bloom. The present study evaluates model near-bottom flow during storms, when sediment resuspension and redistribution are most likely to occur, between October and May when A. fundyense cells are predominantly in cyst form. Simulated water column sediment (mud) concentrations from representative locations of the Gulf are used to initialize particle tracking simulations for the period October 2010–May 2011. Particles are tracked in full three-dimensional model solutions including a sinking velocity characteristic of cyst and aggregated mud settling (0.1 mm s−1). Although most of the material was redeposited near the source areas, small percentages of total resuspended sediment from some locations in the western (~4%) and eastern (2%) Maine shelf and the Bay of Fundy (1%) traveled distances longer than 100 km before resettling. The redistribution changed seasonally and was sensitive to the prescribed sinking rate. Estimates of the amount of cysts redistributed with the sediment were small compared to the inventory of cysts in the upper few centimeters of sediment but could potentially have more relevance immediately after deposition.
    Description: Research support to all authors, except DJM and VAS, was provided by U.S. Geological Survey. DJM gratefully acknowledges financial support of the National Oceanic and Atmospheric Administration (Grant NA06NOS4780245 for the Gulf of Maine Toxicity (GOMTOX) program) and the Woods Hole Center for Oceans and Human Health through National Science Foundation Grant OCE-1314642 and National Institute of Environmental Health Sciences Grant 1P01ES021923-01. VAS was supported by the North East Consortium Grant NA05NMF4721057.
    Keywords: Sediment connectivity ; Near-bottom circulation ; Harmful Algal Bloom cysts ; Gulf of Maine ; Alexandrium fundyense ; Particle tracking
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 79–95, doi:10.1016/j.dsr2.2013.10.011.
    Description: Cysts of Alexandrium fundyense, a dinoflagellate that causes toxic algal blooms in the Gulf of Maine, spend the winter as dormant cells in the upper layer of bottom sediment or the bottom nepheloid layer and germinate in spring to initiate new blooms. Erosion measurements were made on sediment cores collected at seven stations in the Gulf of Maine in the autumn of 2011 to explore if resuspension (by waves and currents) could change the distribution of over-wintering cysts from patterns observed in the previous autumn; or if resuspension could contribute cysts to the water column during spring when cysts are viable. The mass of sediment eroded from the core surface at 0.4 Pa ranged from 0.05 kg m−2 near Grand Manan Island, to 0.35 kg m−2 in northern Wilkinson Basin. The depth of sediment eroded ranged from about 0.05 mm at a station with sandy sediment at 70 m water depth on the western Maine shelf, to about 1.2 mm in clayey–silt sediment at 250 m water depth in northern Wilkinson Basin. The sediment erodibility measurements were used in a sediment-transport model forced with modeled waves and currents for the period October 1, 2010 to May 31, 2011 to predict resuspension and bed erosion. The simulated spatial distribution and variation of bottom shear stress was controlled by the strength of the semi-diurnal tidal currents, which decrease from east to west along the Maine coast, and oscillatory wave-induced currents, which are strongest in shallow water. Simulations showed occasional sediment resuspension along the central and western Maine coast associated with storms, steady resuspension on the eastern Maine shelf and in the Bay of Fundy associated with tidal currents, no resuspension in northern Wilkinson Basin, and very small resuspension in western Jordan Basin. The sediment response in the model depended primarily on the profile of sediment erodibility, strength and time history of bottom stress, consolidation time scale, and the current in the water column. Based on analysis of wave data from offshore buoys from 1996 to 2012, the number of wave events inducing a bottom shear stress large enough to resuspend sediment at 80 m ranged from 0 to 2 in spring (April and May) and 0 to 10 in winter (October through March). Wave-induced resuspension is unlikely in water greater than about 100 m deep. The observations and model results suggest that a millimeter or so of sediment and associated cysts may be mobilized in both winter and spring, and that the frequency of resuspension will vary interannually. Depending on cyst concentration in the sediment and the vertical distribution in the water column, these events could result in a concentration in the water column of at least 104 cysts m−3. In some years, resuspension events could episodically introduce cysts into the water column in spring, where germination is likely to be facilitated at the time of bloom formation. An assessment of the quantitative effects of cyst resuspension on bloom dynamics in any particular year requires more detailed investigation.
    Description: Research support to Donald M. Anderson and Bruce A. Keafer provided through the Woods Hole Center for Oceans and Human Health; National Science Foundation Grants OCE-0430724 and OCE-0911031; and National Institute of Environmental Health Sciences Grant 1-P50-ES012742-01; the ECOHAB Grant program through NOAA Grants NA06NOS4780245 and A09NOS4780193; the MERHAB Grant program through NOAA Grant NA11NOS4780025; and the PCMHAB Grant program through NOAA Grant NA11NOS4780023. Research support to all other authors was provided by U.S. Geological Survey.
    Keywords: Sediment transport ; Bottom stress ; Sediment resuspension ; Harmful algal blooms ; Gulf of Maine ; Alexandrium fundyense ; HAB
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Marine Science and Engineering 4 (2016): 68, doi:10.3390/jmse4040068.
    Description: Digital catalogs of ocean data have been available for decades, but advances in standardized services and software for catalog searches and data access now make it possible to create catalog-driven workflows that automate—end-to-end—data search, analysis, and visualization of data from multiple distributed sources. Further, these workflows may be shared, reused, and adapted with ease. Here we describe a workflow developed within the US Integrated Ocean Observing System (IOOS) which automates the skill assessment of water temperature forecasts from multiple ocean forecast models, allowing improved forecast products to be delivered for an open water swim event. A series of Jupyter Notebooks are used to capture and document the end-to-end workflow using a collection of Python tools that facilitate working with standardized catalog and data services. The workflow first searches a catalog of metadata using the Open Geospatial Consortium (OGC) Catalog Service for the Web (CSW), then accesses data service endpoints found in the metadata records using the OGC Sensor Observation Service (SOS) for in situ sensor data and OPeNDAP services for remotely-sensed and model data. Skill metrics are computed and time series comparisons of forecast model and observed data are displayed interactively, leveraging the capabilities of modern web browsers. The resulting workflow not only solves a challenging specific problem, but highlights the benefits of dynamic, reusable workflows in general. These workflows adapt as new data enter the data system, facilitate reproducible science, provide templates from which new scientific workflows can be developed, and encourage data providers to use standardized services. As applied to the ocean swim event, the workflow exposed problems with two of the ocean forecast products which led to improved regional forecasts once errors were corrected. While the example is specific, the approach is general, and we hope to see increased use of dynamic notebooks across geoscience domains.
    Keywords: Numerical modeling ; Reproducibility ; Catalog services ; Data services ; Web services ; Metadata ; Ocean forecasting ; Ocean modeling ; Data management ; Data system ; Interoperability ; OPeNDAP ; THREDDS ; CSW ; Jupyter Notebooks
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here by permission of Taylor & Francis for personal use, not for redistribution. The definitive version was published in Journal of Operational Oceanography 10 (2017): 115-126, doi:10.1080/1755876X.2017.1322026.
    Description: This paper outlines strategies that would advance coastal ocean modeling, analysis and prediction as a complement to the observing and data management activities of the coastal components of the U.S. Integrated Ocean Observing System (IOOS®) and the Global Ocean Observing System (GOOS). The views presented are the consensus of a group of U.S. based researchers with a cross-section of coastal oceanography and ocean modeling expertise and community representation drawn from Regional and U.S. Federal partners in IOOS. Priorities for research and development are suggested that would enhance the value of IOOS observations through model-based synthesis, deliver better model-based information products, and assist the design, evaluation and operation of the observing system itself. The proposed priorities are: model coupling, data assimilation, nearshore processes, cyberinfrastructure and model skill assessment, modeling for observing system design, evaluation and operation, ensemble prediction, and fast predictors. Approaches are suggested to accomplish substantial progress in a 3-8 year timeframe. In addition, the group proposes steps to promote collaboration between research and operations groups in Regional Associations, U.S. Federal Agencies, and the international ocean research community in general that would foster coordination on scientific and technical issues, and strengthen federal-academic partnerships benefiting IOOS stakeholders and end users.
    Description: 2018-05-20
    Keywords: Coastal ocean ; Modeling ; Forecasting ; Real-time ; Operational ; Data assimilation ; Cyberinfrastructure ; Skill assessment ; Model coupling ; Observing system design ; GOOS
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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