Dataset: Gulf of Maine Calanus finmarchicus model

Name: Model input, output and code for individual-based copepod Calanus finmarchicus populations in Wilkinson Basin (WB), Gulf of Maine
Published: 2020-09-03
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.823203.1

Spatial Extent: N:42.86167 E:-69.86333 S:42.86167 W:-69.86333

Temporal Extent: 2012-01-01 - 2012-12-31

Project:

Collaborative Research: Mechanisms supporting persistence of a key plankton species during climate change on the Northwest Atlantic continental shelf (Calanus Persistence GoM)

Principal Investigator:

Rubao Ji (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2020-09-03

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Model input, output and code for individual-based copepod Calanus finmarchicus populations in Wilkinson Basin (WB), Gulf of Maine

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2020-09-03	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.823203.1	2022-06-01

Description

Model input, output and code for individual-based copepod Calanus finmarchicus populations in Wilkinson Basin (WB), Gulf of Maine. Model output files contain results of backward tracking individal-based runs for copepod Calanus finmarchicus populations.

This model was published in Ji et al., 2017.

Methods & Sampling

Backward tracking individual-based runs for Wilkinson Basin (WB) copepod Calanus finmarchicus populations in the Gulf of Maine.

The detailed description of modeling concepts, equations and interpretation can be found in Ji, et al. (2017):

Methodology summary:
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.

* Copepod life history development is modeled based on temperature- and food-dependency.
* Temperature and flow field are interpolated from FVCOM-GOM3 model forcing.
* Food is estimated from MODIS satellite chlorophyll product.
* Two tracking schemes are used: depth-keeping and DVM.

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. More details can be found at http://fvcom.smast.umassd.edu/necofs/

There are 6 subfolders in the gom_cfin.tar.gz file available in the Supplemental Documents section of this page:

fiscm: Individual-based model (IBM) source code (in Fortran 95)
gom_hourly_example: 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. 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.
data_files: Model configuration code and auxiliary data for model runs, including grid information, coastal and bathymetry, and WB polygon location.
depth_keeping: Depth-keeping model runs, including model setup. One example output netCDF file can be found at "depth_keeping/Year2012Gen2/WB_bit_20120930/example_output_file/fiscm_group_001.nc". The output can be recreated using model code provided. 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.
Matlab_data: Model data generated after processing the raw model output netcdf file from depth_keeping folder.
Matlab_scripts: Matlab codes for preparing model run files and postprocessing model output.

Data Processing Description

Matlab coding developed for post-processing model output.

Data Files

File

Gulf of Maine Calanus finmarchicus model
filename: gom_cfin.tar.gz

(GZIP (.gz), 85.53 GB)
MD5:b062cb4d17a1f137c5059effe0771187

This folder (gom_cfin) contains backward tracking individual-based runs for Wilkinson Basin (WB) copepod Calanus finmarchicus populations in the Gulf of Maine.

The detailed description of modeling concepts, equations and interpretation can be found at:

Ji, R., Z. Feng, B. T. Jones, C. Thompson, C. Chen, N. R. Record, and J. A. Runge. 2017. Coastal amplification of supply and transport (CAST): a new hypothesis about the persistence of Calanus finmarchicus in the Gulf of Maine. ICES Journal of Marine Science, https://doi.org/10.1093/icesjms/fsw253.

There are 6 subfolders:

fiscm: Individual-based model (IBM) source code (in Fortran 95)

gom_hourly_example:  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.  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.

data_files:  Model configuration code and auxiliary data for model runs, including grid information, coastal and bathymetry, and WB polygon location.

depth_keeping: Depth-keeping model runs, including model setup.  One example output netCDF file can be found at "depth_keeping/Year2012Gen2/WB_bit_20120930/example_output_file/fiscm_group_001.nc".   The output can be recreated using model code provided.  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.

Matlab_data: Model data generated after processing the raw model output netcdf file from depth_keeping folder.

Matlab_scripts: Matlab codes for preparing model run files and postprocessing model output.