http://lod.bco-dmo.org/id/dataset/823203
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2020-09-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Model input, output and code for individual-based copepod Calanus finmarchicus populations in Wilkinson Basin (WB), Gulf of Maine
2020-09-03
publication
2020-09-03
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-06-01
publication
https://doi.org/10.26008/1912/bco-dmo.823203.1
Rubao Ji
Woods Hole Oceanographic Institution
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Ji, R. (2022) Model input, output and code for individual-based copepod Calanus finmarchicus populations in Wilkinson Basin (WB), Gulf of Maine. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-09-03 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.823203.1 [access date]
Dataset Description: <p>Model input, output and code for individual-based&nbsp;copepod Calanus finmarchicus populations in&nbsp;Wilkinson Basin (WB),&nbsp;Gulf of Maine.&nbsp; Model output files contain results of backward tracking individal-based runs for copepod Calanus finmarchicus populations.<br />
<br />
This model was published in Ji et al., 2017.</p> Methods and Sampling: <p>Backward tracking individual-based runs for Wilkinson Basin (WB) copepod Calanus finmarchicus populations in the Gulf of Maine.</p>
<p>The detailed description of modeling concepts, equations and interpretation can be found in Ji, et al. (2017):</p>
<p>Methodology summary:<br />
An individual-based model (IBM) was utilized to conduct copepod Lagrangian tracking and life stage development experiments. The model simulations were conducted in the so-called “offline” mode, i.e. the hydrodynamic model simulations were conducted prior to the IBM runs to provide flow fields for Lagrangian tracking and temperature for copepod life stage development. Both flow and temperature fields are stored to allow multiple numerical experiments later, precluding the need to re-run the physical model.&nbsp;</p>
<p>* Copepod life history development is modeled based on temperature- and food-dependency.<br />
* Temperature and flow field are interpolated from FVCOM-GOM3 model forcing.<br />
* Food is estimated from MODIS satellite chlorophyll product.<br />
* Two tracking schemes are used: depth-keeping and DVM.</p>
<p>The hydrodynamic model that generated the forcing data is the 3rd generation Gulf of Maine - Finite Volume Community Ocean Model (FVCOM) developed by collaborators at University of Massachusetts.&nbsp; More details can be found at http://fvcom.smast.umassd.edu/necofs/</p>
<p>There are 6 subfolders in the gom_cfin.tar.gz file available in the Supplemental Documents section of this page:</p>
<p>fiscm: Individual-based model (IBM) source code (in Fortran 95)<br />
gom_hourly_example:&nbsp; One example of hourly hydrodynamic model output as forcing data for the FVCOM IBM model runs. The output can be recreated using model code provided.&nbsp; The full output is publicly available from a THREDDS server through the catalog http://ulysse2.whoi.edu:8080/thredds/catalog/data/gom_cfin/catalog.html in the 'gom3_hourly' subfolder.<br />
data_files:&nbsp; Model configuration code and auxiliary data for model runs, including grid information, coastal and bathymetry, and WB polygon location.&nbsp;<br />
depth_keeping: Depth-keeping model runs, including model setup.&nbsp; One example output netCDF file can be found at "depth_keeping/Year2012Gen2/WB_bit_20120930/example_output_file/fiscm_group_001.nc".&nbsp; &nbsp;The output can be recreated using model code provided.&nbsp; The full output is publicly available from a THREDDS server through the catalog http://ulysse2.whoi.edu:8080/thredds/catalog/data/gom_cfin/catalog.html in the 'depth_keeping' subfolder.<br />
Matlab_data: Model data generated after processing the raw model output netcdf file from depth_keeping folder.<br />
Matlab_scripts: Matlab codes for preparing model run files and postprocessing model output.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1459133 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1459133
completed
Rubao Ji
Woods Hole Oceanographic Institution
508 289 2986
266 Woods Hole Rd. MS# 33, Redfield 2-14
Woods Hole
MA
02543
United States
rji@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: Mechanisms supporting persistence of a key plankton species during climate change on the Northwest Atlantic continental shelf
https://osprey.bco-dmo.org/project/546203
Collaborative Research: Mechanisms supporting persistence of a key plankton species during climate change on the Northwest Atlantic continental shelf
<p><em>Description from NSF award abstract:</em><br />
In the Gulf of Maine region, rapid warming of the ocean surface in recent years has raised concern in the research and resource management communities, fishing industry and the general public about effects on the coastal marine ecosystem. This interdisciplinary, collaborative project will improve understanding of the physical and biological processes controlling the abundance of a planktonic animal that is particularly important in the food web of the northeast coastal ocean. About the size of a grain of rice, the marine copepod <em>Calanus finmarchicus</em> is the primary prey for herring and other forage fish, as well as for the endangered northern right whale. This study will examine whether transport of <em>C. finmarchicus</em> into the Gulf of Maine from cold Canadian waters, in combination with growth and reproduction in the relatively cold Maine Coastal Current, is sufficient to supply the region with the numbers needed to attract and nourish the fish, seabirds and mammals that rely on its energy rich life stages, despite recent ocean warming. The research team will develop a computer model that links extensive understanding of the species' life history with ocean currents and temperature. Results from the model will be tested against field collections at two locations. This study will also contribute to the new Integrated Sentinel Monitoring Network, a joint effort planned by federal and state agencies with academic research participation to monitor future ecosystem change on the northeastern coastal shelf. It will train a graduate student and postdoctoral scientist in interdisciplinary research and also provide support for an early-career investigator.</p>
<p>The project will take a process modeling approach that takes into account regional and mesoscale interaction between life history and bathymetry and circulation to improve understanding of planktonic species distribution shifts. It will combine two decades of research on <em>Calanus finmarchicus</em> life history, including diapause, with a high resolution regional circulation model into an innovative application of a three dimensional, physical-biological model. The modeling approach represents an advancement of climate forecasts of species ranges by coupling a Lagrangian perspective with local processes to better resolve complex range boundaries. It will use Lagrangian parameters such as finite-scale or finite-time Lyapunov exponents, translating particle trajectories into scalar fields that represent the structure of the advective regime. The model will be informed by and tested with measurements of vital rates and demographic data collected on a research vessel at two time series stations. It will be used in backward-in-time and forward-in-time modes to test hypotheses about sources and destinations of <em>C. finmarchicus</em> in the Gulf of Maine, effects of match/mismatch in phenologies, and exploration effects of climate forced scenarios on advective pathways.</p>
Calanus Persistence GoM
largerWorkCitation
project
eng; USA
oceans
-69.86333
-69.86333
42.86167
42.86167
2012-01-01
2012-12-31
Gulf of Maine/Northwest Atlantic Ocean
0
BCO-DMO catalogue of parameters from Model input, output and code for individual-based copepod Calanus finmarchicus populations in Wilkinson Basin (WB), Gulf of Maine
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
91839226439
https://darchive.mblwhoilibrary.org/bitstream/1912/28955/1/gom_cfin.tar.gz
download
https://doi.org/10.26008/1912/bco-dmo.823203.1
download
onLine
dataset
<p>Backward tracking individual-based runs for Wilkinson Basin (WB) copepod Calanus finmarchicus populations in the Gulf of Maine.</p>
<p>The detailed description of modeling concepts, equations and interpretation can be found in Ji, et al. (2017):</p>
<p>Methodology summary:<br />
An individual-based model (IBM) was utilized to conduct copepod Lagrangian tracking and life stage development experiments. The model simulations were conducted in the so-called “offline” mode, i.e. the hydrodynamic model simulations were conducted prior to the IBM runs to provide flow fields for Lagrangian tracking and temperature for copepod life stage development. Both flow and temperature fields are stored to allow multiple numerical experiments later, precluding the need to re-run the physical model.&nbsp;</p>
<p>* Copepod life history development is modeled based on temperature- and food-dependency.<br />
* Temperature and flow field are interpolated from FVCOM-GOM3 model forcing.<br />
* Food is estimated from MODIS satellite chlorophyll product.<br />
* Two tracking schemes are used: depth-keeping and DVM.</p>
<p>The hydrodynamic model that generated the forcing data is the 3rd generation Gulf of Maine - Finite Volume Community Ocean Model (FVCOM) developed by collaborators at University of Massachusetts.&nbsp; More details can be found at http://fvcom.smast.umassd.edu/necofs/</p>
<p>There are 6 subfolders in the gom_cfin.tar.gz file available in the Supplemental Documents section of this page:</p>
<p>fiscm: Individual-based model (IBM) source code (in Fortran 95)<br />
gom_hourly_example:&nbsp; One example of hourly hydrodynamic model output as forcing data for the FVCOM IBM model runs. The output can be recreated using model code provided.&nbsp; The full output is publicly available from a THREDDS server through the catalog http://ulysse2.whoi.edu:8080/thredds/catalog/data/gom_cfin/catalog.html in the 'gom3_hourly' subfolder.<br />
data_files:&nbsp; Model configuration code and auxiliary data for model runs, including grid information, coastal and bathymetry, and WB polygon location.&nbsp;<br />
depth_keeping: Depth-keeping model runs, including model setup.&nbsp; One example output netCDF file can be found at "depth_keeping/Year2012Gen2/WB_bit_20120930/example_output_file/fiscm_group_001.nc".&nbsp; &nbsp;The output can be recreated using model code provided.&nbsp; The full output is publicly available from a THREDDS server through the catalog http://ulysse2.whoi.edu:8080/thredds/catalog/data/gom_cfin/catalog.html in the 'depth_keeping' subfolder.<br />
Matlab_data: Model data generated after processing the raw model output netcdf file from depth_keeping folder.<br />
Matlab_scripts: Matlab codes for preparing model run files and postprocessing model output.</p>
Specified by the Principal Investigator(s)
<p>Matlab coding developed for post-processing model output.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact