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Title: Outputs from a Regional Ocean Modeling System (ROMS) two-way nested model of the Mid-Atlantic Bight and Delaware Bay for 2009-2015.
This is an archive of model output from the Regional Ocean Modeling System (ROMS) with two grids and two-way nesting. The parent grid resolution (referred to as Doppio) is 7 km and spans the Atlantic Ocean off the northeast United States from Cape Hatteras to Nova Scotia. The refinement grid (referred to as Snaildel) focuses on Delaware Bay and the adjacent coastal ocean at 1 km resolution. This ROMS configuration uses turbulence kinetic energy flux and significant wave height from Simulating Waves Nearshore (SWAN) as surface boundary conditions for turbulence closure.Ocean state variables computed are sea level, velocity, temperature, and salinity. Also inclued are surface and bottom stresses, as well as vertical diffusivity of tracer and momentum.  The files uploaded here are examples of one time record from each of this dataset. Outputs for the full reanalysis, which comprises 14 Terabytes of data, are made available for download via a THREDDS (Thematic Real-time Environmental Distributed Data Services) web service to facilitate user geospatial or temporal sub-setting. The THREDDS catalog URLs and example filenames available here, for the respective collections, are: - 12 minute snapshots of the Doppio domain 2009-2015: https://tds.marine.rutgers.edu/thredds/roms/snaildel/catalog.html?dataset=snaildel_doppio_history - 12 minute snapshots of the Snaildel domain 2009-2015: https://tds.marine.rutgers.edu/thredds/roms/snaildel/catalog.html?dataset=snaildel_snaildel_history   Garwood, J. C., H. L. Fuchs, G. P. Gerbi, E. J. Hunter, R. J. Chant and J. L. Wilkin (2022). "Estuarine retention of larvae: Contrasting effects of behavioral responses to turbulence and waves." Limnol. Oceanogr. 67: 992-1005. Hunter, E. J., H. L. Fuchs, J. L. Wilkin, G. P. Gerbi, R. J. Chant and J. C. Garwood (2022). "ROMSPath v1.0: Offline Particle Tracking for the Regional Ocean Modeling System (ROMS)." Geosci. Model Dev. 15: 4297-4311.  more » « less
Award ID(s):
2051795 1756591
NSF-PAR ID:
10444842
Author(s) / Creator(s):
; ; ; ; ;
Publisher / Repository:
SEANOE
Date Published:
Subject(s) / Keyword(s):
["coastal ocean","ocean circulation model","nesting","Gulf of Maine","Mid-Atlantic Bight","ROMS","Delaware Bay"]
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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    If you have questions or comments about this publication, please open an issue at https://github.com/ParasiteTracker/tpt-reporting or contact the authors by email.

    Funding:
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    References:
    Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.

    GloBI Data Review Report

    Datasets under review:
     - University of Michigan Museum of Zoology Insect Division. Full Database Export 2020-11-20 provided by Erika Tucker and Barry Oconner. accessed via https://github.com/EMTuckerLabUMMZ/ummzi/archive/6731357a377e9c2748fc931faa2ff3dc0ce3ea7a.zip on 2022-06-24T14:02:48.801Z
     - Academy of Natural Sciences Entomology Collection for the Parasite Tracker Project accessed via https://github.com/globalbioticinteractions/ansp-para/archive/5e6592ad09ec89ba7958266ad71ec9d5d21d1a44.zip on 2022-06-24T14:04:22.091Z
     - Bernice Pauahi Bishop Museum, J. Linsley Gressitt Center for Research in Entomology accessed via https://github.com/globalbioticinteractions/bpbm-ent/archive/c085398dddd36f8a1169b9cf57de2a572229341b.zip on 2022-06-24T14:04:37.692Z
     - Texas A&M University, Biodiversity Teaching and Research Collections accessed via https://github.com/globalbioticinteractions/brtc-para/archive/f0a718145b05ed484c4d88947ff712d5f6395446.zip on 2022-06-24T14:06:40.154Z
     - Brigham Young University Arthropod Museum accessed via https://github.com/globalbioticinteractions/byu-byuc/archive/4a609ac6a9a03425e2720b6cdebca6438488f029.zip on 2022-06-24T14:06:51.420Z
     - California Academy of Sciences Entomology accessed via https://github.com/globalbioticinteractions/cas-ent/archive/562aea232ec74ab615f771239451e57b057dc7c0.zip on 2022-06-24T14:07:16.371Z
     - Clemson University Arthropod Collection accessed via https://github.com/globalbioticinteractions/cu-cuac/archive/6cdcbbaa4f7cec8e1eac705be3a999bc5259e00f.zip on 2022-06-24T14:07:40.925Z
     - Denver Museum of Nature and Science (DMNS) Parasite specimens (DMNS:Para) accessed via https://github.com/globalbioticinteractions/dmns-para/archive/a037beb816226eb8196533489ee5f98a6dfda452.zip on 2022-06-24T14:08:00.730Z
     - Field Museum of Natural History IPT accessed via https://github.com/globalbioticinteractions/fmnh/archive/6bfc1b7e46140e93f5561c4e837826204adb3c2f.zip on 2022-06-24T14:18:51.995Z
     - Illinois Natural History Survey Insect Collection accessed via https://github.com/globalbioticinteractions/inhs-insects/archive/38692496f590577074c7cecf8ea37f85d0594ae1.zip on 2022-06-24T14:19:37.563Z
     - UMSP / University of Minnesota / University of Minnesota Insect Collection accessed via https://github.com/globalbioticinteractions/min-umsp/archive/3f1b9d32f947dcb80b9aaab50523e097f0e8776e.zip on 2022-06-24T14:20:27.232Z
     - Milwaukee Public Museum Biological Collections Data Portal accessed via https://github.com/globalbioticinteractions/mpm/archive/9f44e99c49ec5aba3f8592cfced07c38d3223dcd.zip on 2022-06-24T14:20:46.185Z
     - Museum for Southern Biology (MSB) Parasite Collection accessed via https://github.com/globalbioticinteractions/msb-para/archive/178a0b7aa0a8e14b3fe953e770703fe331eadacc.zip on 2022-06-24T15:16:07.223Z
     - The Albert J. Cook Arthropod Research Collection accessed via https://github.com/globalbioticinteractions/msu-msuc/archive/38960906380443bd8108c9e44aeff4590d8d0b50.zip on 2022-06-24T16:09:40.702Z
     - Ohio State University Acarology Laboratory accessed via https://github.com/globalbioticinteractions/osal-ar/archive/876269d66a6a94175dbb6b9a604897f8032b93dd.zip on 2022-06-24T16:10:00.281Z
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     - Texas A&M University Insect Collection accessed via https://github.com/globalbioticinteractions/tamuic-ent/archive/f261a8c192021408da67c39626a4aac56e3bac41.zip on 2022-06-24T16:10:58.496Z
     - University of California Santa Barbara Invertebrate Zoology Collection accessed via https://github.com/globalbioticinteractions/ucsb-izc/archive/825678ad02df93f6d4469f9d8b7cc30151b9aa45.zip on 2022-06-24T16:12:29.854Z
     - University of Hawaii Insect Museum accessed via https://github.com/globalbioticinteractions/uhim/archive/53fa790309e48f25685e41ded78ce6a51bafde76.zip on 2022-06-24T16:12:41.408Z
     - University of New Hampshire Collection of Insects and other Arthropods UNHC-UNHC accessed via https://github.com/globalbioticinteractions/unhc/archive/f72575a72edda8a4e6126de79b4681b25593d434.zip on 2022-06-24T16:12:59.500Z
     - Scott L. Gardner and Gabor R. Racz (2021). University of Nebraska State Museum - Parasitology. Harold W. Manter Laboratory of Parasitology. University of Nebraska State Museum. accessed via https://github.com/globalbioticinteractions/unl-nsm/archive/6bcd8aec22e4309b7f4e8be1afe8191d391e73c6.zip on 2022-06-24T16:13:06.914Z
     - Data were obtained from specimens belonging to the United States National Museum of Natural History (USNM), Smithsonian Institution, Washington DC and digitized by the Walter Reed Biosystematics Unit (WRBU). accessed via https://github.com/globalbioticinteractions/usnmentflea/archive/ce5cb1ed2bbc13ee10062b6f75a158fd465ce9bb.zip on 2022-06-24T16:13:38.013Z
     - US National Museum of Natural History Ixodes Records accessed via https://github.com/globalbioticinteractions/usnm-ixodes/archive/c5fcd5f34ce412002783544afb628a33db7f47a6.zip on 2022-06-24T16:13:45.666Z
     - Price Institute of Parasite Research, School of Biological Sciences, University of Utah accessed via https://github.com/globalbioticinteractions/utah-piper/archive/43da8db550b5776c1e3d17803831c696fe9b8285.zip on 2022-06-24T16:13:54.724Z
     - University of Wisconsin Stevens Point, Stephen J. Taft Parasitological Collection accessed via https://github.com/globalbioticinteractions/uwsp-para/archive/f9d0d52cd671731c7f002325e84187979bca4a5b.zip on 2022-06-24T16:14:04.745Z
     - Giraldo-Calderón, G. I., Emrich, S. J., MacCallum, R. M., Maslen, G., Dialynas, E., Topalis, P., … Lawson, D. (2015). VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic acids research, 43(Database issue), D707–D713. doi:10.1093/nar/gku1117. accessed via https://github.com/globalbioticinteractions/vectorbase/archive/00d6285cd4e9f4edd18cb2778624ab31b34b23b8.zip on 2022-06-24T16:14:11.965Z
     - WIRC / University of Wisconsin Madison WIS-IH / Wisconsin Insect Research Collection accessed via https://github.com/globalbioticinteractions/wis-ih-wirc/archive/34162b86c0ade4b493471543231ae017cc84816e.zip on 2022-06-24T16:14:29.743Z
     - Yale University Peabody Museum Collections Data Portal accessed via https://github.com/globalbioticinteractions/yale-peabody/archive/43be869f17749d71d26fc820c8bd931d6149fe8e.zip on 2022-06-24T16:23:29.289Z

    Generated on:
    2022-06-24

    by:
    GloBI's Elton 0.12.4 
    (see https://github.com/globalbioticinteractions/elton).

    Note that all files ending with .tsv are files formatted 
    as UTF8 encoded tab-separated values files.

    https://www.iana.org/assignments/media-types/text/tab-separated-values


    Included in this review archive are:

    README:
      This file.

    review_summary.tsv:
      Summary across all reviewed collections of total number of distinct review comments.

    review_summary_by_collection.tsv:
      Summary by reviewed collection of total number of distinct review comments.

    indexed_interactions_by_collection.tsv: 
      Summary of number of indexed interaction records by institutionCode and collectionCode.

    review_comments.tsv.gz:
      All review comments by collection.

    indexed_interactions_full.tsv.gz:
      All indexed interactions for all reviewed collections.

    indexed_interactions_simple.tsv.gz:
      All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.

    datasets_under_review.tsv:
      Details on the datasets under review.

    elton.jar: 
      Program used to update datasets and generate the review reports and associated indexed interactions.

    datasets.zip:
      Source datasets used by elton.jar in process of executing the generate_report.sh script.

    generate_report.sh:
      Program used to generate the report

    generate_report.log:
      Log file generated as part of running the generate_report.sh script
     

     
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  4. This dataset consists of weekly trajectory information of Gulf Stream Warm Core Rings from 2000-2010. This work builds upon Silver et al. (2022a) ( https://doi.org/10.5281/zenodo.6436380) which contained Warm Core Ring trajectory information from 2011 to 2020. Combining the two datasets a total of 21 years of weekly Warm Core Ring trajectories can be obtained. An example of how to use such a dataset can be found in Silver et al. (2022b).

    The format of the dataset is similar to that of  Silver et al. (2022a), and the following description is adapted from their dataset. This dataset is comprised of individual files containing each ring’s weekly center location and its area for 374 WCRs present between January 1, 2000 and December 31, 2010. Each Warm Core Ring is identified by a unique alphanumeric code 'WEyyyymmddA', where 'WE' represents a Warm Eddy (as identified in the analysis charts); 'yyyymmdd' is the year, month and day of formation; and the last character 'A' represents the sequential sighting of the eddies in a particular year. Continuity of a ring which passes from one year to the next is maintained by the same character in the first sighting.  For example, the first ring in 2002 having a trailing alphabet of 'F' indicates that five rings were carried over from 2001 which were still observed on January 1, 2002. Each ring has its own netCDF (.nc) filename following its alphanumeric code. Each file contains 4 variables, “Lon”- the ring center’s weekly longitude, “Lat”- the ring center’s weekly latitude, “Area” - the rings weekly size in km2, and “Date” in days - representing the days since Jan 01, 0000. 

    The process of creating the WCR tracking dataset follows the same methodology of the previously generated WCR census (Gangopadhyay et al., 2019, 2020). The Jenifer Clark’s Gulf Stream Charts used to create this dataset are 2-3 times a week from 2000-2010. Thus, we used approximately 1560 Charts for the 10 years of analysis. All of these charts were reanalyzed between 75° and 55°W using QGIS 2.18.16 (2016) and geo-referenced on a WGS84 coordinate system (Decker, 1986). 

     

    Silver, A., Gangopadhyay, A, & Gawarkiewicz, G. (2022a). Warm Core Ring Trajectories in the Northwest Atlantic Slope Sea (2011-2020) (1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6436380

    Silver, A., Gangopadhyay, A., Gawarkiewicz, G., Andres, M., Flierl, G., & Clark, J. (2022b). Spatial Variability of Movement, Structure, and Formation of Warm Core Rings in the Northwest Atlantic Slope Sea. Journal of Geophysical Research: Oceans127(8), e2022JC018737. https://doi.org/10.1029/2022JC018737 

    Gangopadhyay, A., G. Gawarkiewicz, N. Etige, M. Monim and J. Clark, 2019. An Observed Regime Shift in the Formation of Warm Core Rings from the Gulf Stream, Nature - Scientific Reports, https://doi.org/10.1038/s41598-019-48661-9. www.nature.com/articles/s41598-019-48661-9.

    Gangopadhyay, A., N. Etige, G. Gawarkiewicz, A. M. Silver, M. Monim and J. Clark, 2020.  A Census of the Warm Core Rings of the Gulf Stream (1980-2017). Journal of Geophysical Research, Oceans, 125, e2019JC016033. https://doi.org/10.1029/2019JC016033.

    QGIS Development Team. QGIS Geographic Information System (2016).

    Decker, B. L. World Geodetic System 1984. World geodetic system 1984 (1986).

     

    Funded by two NSF US grants OCE-1851242, OCE-212328 {"references": ["Silver, A., Gangopadhyay, A, & Gawarkiewicz, G. (2022). Warm Core Ring Trajectories in the Northwest Atlantic Slope Sea (2011-2020) (1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6436380", "Silver, A., Gangopadhyay, A., Gawarkiewicz, G., Andres, M., Flierl, G., & Clark, J. (2022b). Spatial Variability of Movement, Structure, and Formation of Warm Core Rings in the Northwest Atlantic Slope Sea.\u00a0Journal of Geophysical Research: Oceans,\u00a0127(8), e2022JC018737.\u00a0https://doi.org/10.1029/2022JC018737", "Gangopadhyay, A., G. Gawarkiewicz, N. Etige, M. Monim and J. Clark, 2019. An Observed Regime Shift in the Formation of Warm Core Rings from the Gulf Stream, Nature - Scientific Reports, https://doi.org/10.1038/s41598-019-48661-9. www.nature.com/articles/s41598-019-48661-9.", "Gangopadhyay, A., N. Etige, G. Gawarkiewicz, A. M. Silver, M. Monim and J. Clark, 2020. A Census of the Warm Core Rings of the Gulf Stream (1980-2017). Journal of Geophysical Research, Oceans, 125, e2019JC016033. https://doi.org/10.1029/2019JC016033.", "QGIS Development Team. QGIS Geographic Information System (2016).", "Decker, B. L. World Geodetic System 1984. World geodetic system 1984 (1986)."]} 
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  5. This dataset contains three netcdf files that pertain to monthly, seasonal, and annual fields of surface wind stress, wind stress curl, and curl-derived upwelling velocities over the Northwest Atlantic (80-45W, 30-45N) covering a forty year period from 1980 to 2019. Six-hourly surface (10 m) wind speed components from the Japanese 55-year reanalysis (JRA-55; Kobayashi et al., 2015) were processed from 1980 to 2019 over a larger North Atlantic domain of 100W to 10E and 10N to 80N. Wind stress was computed using a modified step-wise formulation, originally based on (Gill, 1982) and a non-linear drag coefficient (Large and Pond, 1981), and later modified for low speeds (Trenberth et al., 1989). See Gifford (2023) for more details.   

    After the six-hourly zonal and meridional wind stresses were calculated, the zonal change in meridional stress (curlx) and the negative meridional change in zonal stress (curly) were found using NumPy’s gradient function in Python (Harris et al., 2020) over the larger North Atlantic domain (100W-10E, 10-80N). The curl (curlx + curly) over the study domain (80-45W, 10-80N) is then extracted, which maintain a constant order of computational accuracy in the interior and along the boundaries for the smaller domain in a centered-difference gradient calculation. 

    The monthly averages of the 6-hour daily stresses and curls were then computed using the command line suite climate data operators (CDO, Schulzweida, 2022) monmean function. The seasonal (3-month average) and annual averages (12-month average) were calculated in Python using the monthly fields with NumPy (NumPy, Harris et al., 2020). 

    Corresponding upwelling velocities at different time-scales were obtained from the respective curl fields and zonal wind stress by using the Ekman pumping equation of the study by Risien and Chelton (2008; page 2393). Please see Gifford (2023) for more details.   

    The files each contain nine variables that include longitude, latitude, time, zonal wind stress, meridional wind stress, zonal change in meridional wind stress (curlx), the negative meridional change in zonal wind stress (curly), total curl, and upwelling. Units of time begin in 1980 and are months, seasons (JFM etc.), and years to 2019. The longitude variable extends from 80W to 45W and latitude is 30N to 45N with uniform 1.25 degree resolution.  

    Units of stress are in Pascals, units of curl are in Pascals per meter, and upwelling velocity is described by centimeters per day. The spatial grid is a 29 x 13 longitude x latitude array. 

    Filenames: 

    monthly_windstress_wsc_upwelling.nc: 480 time steps from 80W to 45W and 30N to 45N.

    seasonal_windstress_wsc_upwelling.nc: 160 time steps from 80W to 45W and 30N to 45N.

    annual_windstress_wsc_upwelling.nc: 40 time steps from 80W to 45W and 30N to 45N.

    Please contact igifford@earth.miami.edu for any queries. {"references": ["Gifford, I.H., 2023. The Synchronicity of the Gulf Stream Free Jet and the Wind Induced Cyclonic Vorticity Pool. MS Thesis, University of Massachusetts Dartmouth. 75pp.", "Gill, A. E. (1982). Atmosphere-ocean dynamics (Vol. 30). Academic Press.", "Harris, C.R., Millman, K.J., van der Walt, S.J. et al. Array programming with NumPy. Nature 585, 357\u2013362 (2020). DOI: 10.1038/s41586-020-2649-2.", "Japan Meteorological Agency/Japan (2013), JRA-55: Japanese 55-year Reanalysis, Daily 3-Hourly and 6-Hourly Data, https://doi.org/10.5065/D6HH6H41, Research Data Archive at the National Center for Atmospheric Research, Computational and Information Systems Laboratory, Boulder, Colo. (Updated monthly.)", "Kobayashi, S., Ota, Y., Harada, Y., Ebita, A., Moriya, M., Onoda, H., Onogi, K., Kamahori, H., Kobayashi, C., Endo, H. and Miyaoka, K., 2015. The JRA-55 reanalysis: General specifications and basic characteristics.\u202fJournal of the Meteorological Society of Japan. Ser. II,\u202f93(1), pp.5-48.", "Large, W.G. and Pond, S., 1981. Open ocean momentum flux measurements in moderate to strong winds.\u202fJournal of physical oceanography,\u202f11(3), pp.324-336.", "Risien, C.M. and Chelton, D.B., 2008. A global climatology of surface wind and wind stress fields from eight years of QuikSCAT scatterometer data.\u202fJournal of Physical Oceanography,\u202f38(11), pp.2379-2413.", "Schulzweida, Uwe. (2022). CDO User Guide (2.1.0). Zenodo. https://doi.org/10.5281/zenodo.7112925.", "Trenberth, K.E., Large, W.G. and Olson, J.G., 1989. The effective drag coefficient for evaluating wind stress over the oceans.\u202fJournal of Climate,\u202f2(12), pp.1507-1516."]} 
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