http://lod.bco-dmo.org/id/dataset/546765
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
2015-02-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Coastal shelf trophic structure and energy flow model from the Northern California Current, Georges Bank, the Gulf of Alaska, and the North Sea (Food Webs and Physical Contexts project)
2019-02-21
publication
2019-02-21
revision
BCO-DMO Linked Data URI
2019-02-21
creation
http://lod.bco-dmo.org/id/dataset/546765
Kenneth H. Brink
Woods Hole Oceanographic Institution
principalInvestigator
James Ruzicka
Oregon State University
principalInvestigator
Andrew Solow
Woods Hole Oceanographic Institution
principalInvestigator
John Steele
Woods Hole Oceanographic Institution
principalInvestigator
Dian J. Gifford
University of Rhode Island
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
documentDigital
Cite this dataset as: Brink, K. H., Ruzicka, J., Solow, A., Steele, J., Gifford, D. J. (2019) Coastal shelf trophic structure and energy flow model from the Northern California Current, Georges Bank, the Gulf of Alaska, and the North Sea (Food Webs and Physical Contexts project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2019-02-21 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/546765 [access date]
Coastal shelf trophic structure and energy flow model Dataset Description: <p>This dataset includes complete model parameter files (Northern California Current, Coastal Gulf of Alaska, Georges Bank, North Sea), code files for constructing end-to-end ecosystem models, code files for conducting structural scenario analyses, code files for conducting time-dynamic simulations, code files for Monte Carlo model generation, and documentation describing the use of the model code suite.</p>
<p>There is a manual with basic instructions on the use of the ECOTRAN code suite version 8/5/2018: “<a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/README_ECOTRAN-Manual_08052018.pdf" target="_blank">README_ECOTRAN-Manual_08052018.pdf</a>”. All model code files are in Excel Visual Basic format or in Matlab (www.mathworks.com) format. A summary of submitted files: "<a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/ECOTRAN_model_subdirectories_v2018-08-05.pdf" target="_blank">ECOTRAN_model_subdirectories_v2018-08-05.pdf</a>” The zipped file "<a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/ECOTRAN_08052018.zip">ECOTRAN_08052018.zip</a>" contains the following sub-directories and files: Sub -directory “/FoodWeb_models/ComparativeShelves_models/” includes mass-balanced food web models for the Northern California Current, Coastal Gulf of Alaska, Georges Bank, and the North Sea. There are two files for each model: 1) an excel Visual Basic .xlsm file used to construct the mass-balanced model, and 2) a .csv version of the model parameter set to be read and processed by ECOTRAN. Sub-directory “/FoodWeb_models/TEST_model/” includes a functional example “TEST” mass-balanced food web model. There are three files for the test model: 1) an excel Visual Basic .xlsm file used to construct the mass-balanced model, 2) a .csv version of the model parameter set to be read and processed by ECOTRAN, and 3) a .mat file containing an example set of 1000 generated Monte Carlo models. Sub-directory “/ECOTRAN_code/” includes the main function used to generate an ECOTRAN model from a provided mass-balanced food web model (ECOTRANuncertainty_05062016.m) and seven required supporting functions (f_AggregateResults_EwE_03122015.m, f_CalcPredationMatrix.m, f_ECOfunction_05142015.m, f_read_EwE_csv_02022016.m, f_read_EwE_csv_04292016.m, f_RedistributeCannibalism.m, f_WebProductivityWLoss.m). Sub-directory “/ECOTRAN_code/StaticScenario_code/” includes the main code to perform static scenario analyses (ECOTRAN_StaticScenarios_TEST_08052018.m) and three required supporting functions (f_CompileScenarioResults_08192013.m, f_ScenarioGenerator_08302013.m, p_PlotScenarioResults_02092018.m). Sub-directory “/ECOTRAN_08052018/ECOTRAN_code/TimeDynamic_code/” includes two main code files to perform time-dynamic model simulations within different physical settings (ECOTRANdynamic_context_08032018.m, ECOTRANdynamic_context_basin_08030218.m) and eight required supporting functions (f_ECOTRANode_DefinedBoundary_08032017.m, f_ECOTRANode_DefinedBoundary_basin_08032017.m, f_ECOTRANode_ReflectiveBoundary_05182017.m, f_ECOTRANode_ReflectiveBoundary_basin_05242017.m, f_FunctionalResponse_MonteCarlo_09122016.m, f_InitialProductionRates_05112016.m, f_MichaelisMenten_05152016.m, f_StaticProductionTimeseries_09042017.m). Sub-directory “/ECOTRAN_code/Footprint_and_Reach_code /” includes the main code to calculate footprint and reach metrics from an ECOTRAN end-to-end model (FootprintReach_TEST_07262018.m) and six required supporting functions (f_DietTrace_03152015.m, f_DietTraceDownward_03152015.m, f_Footprint_07272018.m, f_ProductionTrace_07272018.m, f_Reach_01212018.m, p_WebPlotter_01032017.m). Sub-directory “/ECOTRAN_code/MonteCarlo_method1_code/” includes three functions for generating Monte Carlo models for analysis of error propagation within ECOTRAN (f_E2E_MonteCarlo_08032018.m, f_E2E_pedigree_08032018.m, f_TerminalDetritus_08032018.m). Sub-directory “/ECOTRAN_code/MonteCarlo_method2_code/” includes an archival set of seven functions for generating Monte Carlo models using a prior and NO LONGER SUPPORTED method (EwE_MonteCarlo_01182015.m, f_DietPreference_Readjust_04052014.m, f_E2E_MonteCarlo_08032018.m, f_E2E_pedigree_08032018.m, f_EE_MonteCarlo_04092014.m, f_EwEinterval_MonteCarlo_04092014.m, f_EwEnormal_MonteCarlo_04092014.m). Sub-directory “/ECOTRAN_08052018/ECOTRAN_code/Physics_code” includes functions defining model geometries and for generating time-series of advection, mixing, and sinking rates for four different physical environments (f_ECOTRANphysics_upwelling_08022018.m, calcur_res.mat, f_ECOTRANphysics_downwelling_08022018.m, cgoa_ancyc.mat, f_ECOTRANphysics_bank_08022018.m, gb_ancyc.mat, f_ECOTRANphysics_basin_08022018.m, f_LightIntensity.m). Sub-directory “/ECOTRAN_code/MATLAB_ToolBoxes/” includes miscellaneous supporting function suites. The “JornDiedrichsenToolbox” includes modified boxplot functions currently used by the ECOTRAN code suite but can be substituted with other plotting functions. The “NaNSuite” expands upon the built-in Matlab NaN functions. The sub-directory “/ECOTRAN_08052018/ECOTRAN_code/MATLAB_ToolBoxes/ OtherTools/” includes three other required functions that appear in several of the ECOTRAN functions (f_OrdinalDate.m, round2.m, wprctile.m). Sub-directory “/TimeDynamic_simulations/” is an empty directory that is currently referred to by the time-dynamic simulation code files for storing model results.</p>
<p>Sub-directory CGoA-ECOTRAN_GulfOfAlaska_01292019&nbsp;(separate file download: <a href="https://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/CGoA-ECOTRAN_GulfOfAlaska_01292019.zip">CGoA-ECOTRAN_GulfOfAlaska_01292019.zip</a>) contains an expanded ECOTRAN end-to-end model for the western and central Gulf of Alaska. The main document is CGoA-ECOTRAN_Ruzicka_etal_01292019.docx which describes the model and the sources of the model parameter set. Document CGoA-ECOTRAN_ModelParameters_01292019.xlsx contains the model parameters themselves. Five EXCELVisualBasic files representing food webs for Gulf of Alaska are included for use with the ECOTRAN model code: CGoA_inner-Xa_01112019.xlsm, CGoA_MidEast-Xa_01112019.xlsm, CGoA_MidWest-Xa_01112019.xlsm, CGoA_OuterEast-Xa_01112019.xlsm, CGoA_OuterWest-Xa_01112019.xlsm. The ECOTRAN model code is written for the Matlab platform (<a href="http://www.mathworks.com/">www.mathworks.com</a>) and is available online at the NSF Biological and Chemical Oceanography Data Management Office (<a href="https://www.bco-dmo.org/dataset/546765">https://www.bco-dmo.org/dataset/546765</a>).</p>
<p><strong>Older version:</strong><br />
Version 2018-08-05 replaces version 2015-01-20. Archived version of ECOTRAN 2015 code and model results. See Ruzicka et al (2013):<br />
<a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/DATASET_Brink_etal_1-2015.rtf">DATASET_Brink_etal_1-2015.rtf</a> (submission form for 2015 version)<br />
<a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/StructuralScenarios_Oceanography_Dec2013.zip">StructuralScenarios_Oceanography_Dec2013.zip</a><br />
<a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/ECOTRANmodels_MammalAggregation_1-21-2015.zip">ECOTRANmodels_MammalAggregation_1-21-2015.zip</a><br />
<a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/ECOTRANcode_StructuralAnalysis_1-21-2015.zip">ECOTRANcode_StructuralAnalysis_1-21-2015.zip</a></p> Methods and Sampling:
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1258667 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1258667
onGoing
Kenneth H. Brink
Woods Hole Oceanographic Institution
508-289-2535
Physical Oceanography Department MS #21
Woods Hole
MA
02543
USA
kbrink@whoi.edu
pointOfContact
James Ruzicka
Oregon State University
541-867-0382
Hatfield Marine Science Center
Newport
OR
97365
USA
jim.ruzicka@oregonstate.edu
pointOfContact
Andrew Solow
Woods Hole Oceanographic Institution
508-289-2746
Marine Policy Center Crowell House, MS #41
Woods Hole
MA
02543
USA
asolow@whoi.edu
pointOfContact
John Steele
Woods Hole Oceanographic Institution
pointOfContact
Dian J. Gifford
University of Rhode Island
401-874-6690
Narragansett
RI
02882-1197
USA
dgifford@gso.uri.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
Ruzicka_2015
service
Deployment Activity
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.
Analysis of Continental Shelf Ecosystems: Food Web Structure and Functional Relations
https://osprey.bco-dmo.org/project/544746
Analysis of Continental Shelf Ecosystems: Food Web Structure and Functional Relations
<p>Marine ecosystems are characterized by complex interactions among biological components and within the physical setting. The complexity of these systems makes them difficult to understand or interpret based on either observations or models, both of which suffer from incomplete knowledge of the natural system. Of interest to many scientific questions and to management is the utility of broad, simplifying concepts about how such systems operate and how they change over time. Among these concepts are bottom-up control (the idea that nutrient sources and lower trophic levels govern the ecosystem), top-down control (the idea that organisms at the highest trophic levels govern), and regime shifts (major restructuring of the system due to natural or anthropogenic, or combined, forcing).</p>
<p>A basic tenet of biological oceanography is the coupling between physical processes and population dynamics. The study of these connections has been based on certain simplifications, particularly the emphasis on one, or very few, trophic components. The parallel development of trophic network models (e.g., ECOPATH) represents an effort to study the relationships between a more complete spectrum of trophic groups from an energy transfer and predator-prey perspective. Yet, ecosystem structure, function, and behavior depend on the physical context: mixing, advection, water residence time, and seasonality, especially for shelf ecosystems. These terms define production, recycling, and export rates and set the scope of benthic-pelagic coupling, but they are rarely incorporated into trophic network models. There is clear need to develop portable methods of analysis that can illuminate physical-biological interactions across a wide range of ecosystems and demonstrate their effects on system productivity and resilience at all trophic levels. However, there is a simultaneous risk of such models becoming so complex that untangling the mechanisms and artifacts of model dynamics quickly becomes intractable.</p>
<p>A portable, coupled bio-physical model framework of intermediate trophic and physical resolution is a potential solution that will be developed in this project. The goal is to produce models simple enough to understand, but complex enough to be realistic. Thus, about 5 physical boxes and about 20 ecological compartments are expected to be included. The models will be developed for four contrasting, data-rich continental shelf ecosystems. This project will use the range of food webs and physical forcing characteristic of these four systems to do the following. 1. Assess the merits and disadvantages of studying community dynamics in terms of aggregated functional groups as the appropriate level of trophic resolution. 2. Compare the relative roles of physical processes and trophic network structure in determining system productivity, variability, and resilience across all trophic levels, including both pelagic and benthic food webs. 3. Test the applicability of broad concepts of ecosystem behavior such as bottom-up vs. top-down control of community dynamics, or of sudden regime shifts.</p>
<p>The project will contribute to the education of future scientists through participation in active research. The public will be informed about ocean ecosystem issues through development of a museum exhibit. Model code will be provided to the community for further use and development. Collaboration with NOAA scientists will foster application of project results to practical management issues.</p>
Food Webs and Physical Contexts
largerWorkCitation
project
eng; USA
biota
oceans
2019-02-21
Northern California Current, Georges Bank, Gulf of Alaska, North Sea
0
BCO-DMO catalogue of parameters from Coastal shelf trophic structure and energy flow model from the Northern California Current, Georges Bank, the Gulf of Alaska, and the North Sea (Food Webs and Physical Contexts 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
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
1269
https://datadocs.bco-dmo.org/file/xoxPZJLS1RVYl/ECOTRAN_model_links_Ruzicka_2015.csv
ECOTRAN_model_links_Ruzicka_2015.csv
links to ECOTRAN model code, static scenarios, and documentation
J. Ruzicka (OSU)
version: 2015-01-20
download
https://osprey.bco-dmo.org/dataset/546765/data/download
download
onLine
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
Deployment: Ruzicka_2015
Ruzicka_2015
OSU-HMSC
OSU-HMSC
laboratory
Ruzicka_2015
James Ruzicka
Oregon State University
OSU-HMSC
OSU-HMSC
laboratory