http://lod.bco-dmo.org/id/dataset/658655
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
2016-09-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Source code, license, example input and visualization files for beta-LTRANS-ADCIRC, a particle tracking model that runs with ADCIRC circulation model prediction.
2016-09-13
publication
2016-09-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-02-25
publication
https://doi.org/10.26008/1912/bco-dmo.658655.1
Elizabeth North
University of Maryland Center for Environmental Science
principalInvestigator
Richard Leuttich
University of North Carolina at Chapel Hill
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: North, E., Leuttich, R. (2021) Source code, license, example input and visualization files for beta-LTRANS-ADCIRC, a particle tracking model that runs with ADCIRC circulation model prediction. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-09-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.658655.1 [access date]
Source code, license, example input and visualization files for beta-LTRANS-ADCIRC, a particle tracking model that runs with ADCIRC circulation model prediction. Dataset Description: <p>From&nbsp;http://northweb.hpl.umces.edu/LTRANS.htm</p>
<p><strong>beta-LTRANS-ADCIRC</strong> is based on the&nbsp;<strong>Larval TRANSport Lagrangian model (<a href="http://northweb.hpl.umces.edu/LTRANS.htm">LTRANS v.2b</a>),</strong> an off-line particle-tracking model that runs with the stored predictions of a 3D hydrodynamic model. In this case, LTRANS v.2b has been substantially modified to be able to run with the finite-element circulation predictions of <a href="http://adcirc.org/">ADCIRC</a>. Although LTRANS was built to simulate oyster larvae, it can easily be adapted to simulate passive particles and other planktonic organisms. LTRANS v.2 is written in Fortran 90 and is designed to track the trajectories of particles in three dimensions. It includes a 4th order Runge-Kutta scheme for particle advection and a random displacement model for vertical turbulent particle motion. Reflective boundary conditions, larval behavior, and settlement routines are also included. A brief description of the beta-LTRANS-ADCIRC particle-tracking model can be found <a href="http://northweb.hpl.umces.edu/LTRANS/LTRANS_description.pdf">here</a>&nbsp;(68 KB .pdf). For more information on LTRANS, please see the LTRANS web page. and the application of LTRANS to oyster larvae transport, see <a href="http://northweb.hpl.umces.edu/research/Oyster_larvae_DNR.htm">a summary web page with animations, </a>the publications<a href="http://northweb.hpl.umces.edu/LTRANS-ADCIRC.htm#Northetal2008"> North et al. (2008, 2011</a>), and the <a href="http://northweb.hpl.umces.edu/LTRANS-ADCIRC.htm#Guide">LTRANS v.2 User's Guide</a>. Please cite <a href="http://northweb.hpl.umces.edu/LTRANS-ADCIRC.htm#Northetal2008">North et al. (2011)</a> when referring to LTRANS v.2b. The updates that were made for LTRANS v.2b are listed here.</p>
<p>Elizabeth North of University of Maryland Center for Environmental Science Horn Point Laboratory implemented beta-LTRANS-ADCIRC. Funding was provided by the National Science Foundation Biological Oceanography Program. Steven Suttles and Jason Spires provided valuable assistance.</p>
<p>beta-LTRANS-ADCIRC Code:&nbsp;beta-LTRANS-ADCIRC Open Source Code.&nbsp;We would appreciate knowing who is using LTRANS. If you would like to share this information with us, please send us your name, contact information, and a brief description of how you plan to use this model to&nbsp;<a href="mailto:enorth@umces.edu">enorth@umces.edu</a>&nbsp;with 'LTRANS-ADCIRC' in the subject line.</p>
<p><strong>Access restrictions:</strong> This software is open-source and licensed as stated by MIT/X License, but utilizes external dependencies and program which have different restrictions. Please see the beta-LTRANS-ADCIRC license file and website for more information.</p>
<p><a href="http://dmoserv3.bco-dmo.org/data_docs/EstuarineMetaDyn/betaLTRANS-ADCIRC_website.pdf" target="_blank">PDF of original beta-LTRANS-ADCIRC webpage</a>:&nbsp;http://dmoserv3.bco-dmo.org/data_docs/EstuarineMetaDyn/betaLTRANS-ADCIRC_website.pdf</p>
<p><strong>Code:</strong></p>
<table border="0">
<tbody>
<tr>
<td>
<div><a href="http://dmoserv3.bco-dmo.org/data_docs/EstuarineMetaDyn/betaLTRANS_ADCIRC_License.txt" target="_blank"><strong>betaLTRANS_ADCIRC_License.txt</strong></a></div>
</td>
<td><strong>License file</strong>. This license was based on the ROMS license. Please note that this license applies to all sections of beta-LTRANS-ADCIRC except those listed in the 'External Dependencies and Programs' section below.&nbsp;</td>
</tr>
<tr>
<td>
<div><strong><a href="http://dmoserv3.bco-dmo.org/data_docs/EstuarineMetaDyn/betaLTRANS_ADCIRC.zip">betaLTRANS-ADCIRC.zip</a><br />
<a href="http://dmoserv3.bco-dmo.org/data_docs/EstuarineMetaDyn//betaLTRANS_ADCIRC.tgz">betaLTRANS-ADCIRC.tgz&nbsp;</a></strong><br />
&nbsp;</div>
</td>
<td><br />
<strong>Code and Input Files</strong>. This zip or tarball file contains the beta-LTRANS-ADCIRC code, license, example input and visualization files. Section II of the&nbsp;<a href="http://northweb.hpl.umces.edu/LTRANS-ADCIRC.htm#Guide">LTRANS v.2 User's Guide</a>&nbsp;contains instructions for setting up and running LTRANS v.2b in Linux and Windows environments. Before using this model, please read the&nbsp;<strong>External Dependencies and Programs</strong>&nbsp;section below. This version of LTRANS is parameterized to run with the input files from a test case of ADCIRC which was set up for Shinnecock Inlet. These ADCIRC files are provided in this zip/tar file.</td>
</tr>
</tbody>
</table>
<p>&nbsp;</p>
<p><strong>External Dependencies and Programs</strong>.&nbsp;beta-LTRANS-ADCIRC requires&nbsp;NetCDF libraries&nbsp;and uses the following programs to calculate random numbers (Mersenne Twister) and fit tension splines (TSPACK). Because beta-LTRANS-ADCIRC reads-in ADCIRC-generated NetCDF (.nc) files, it requires that the appropriate NetCDF libraries be installed on your computer (see files and links below). Also, please note that although the Mersenne Twister and TSPACK programs are included in the beta-LTRANS-ADCIRC in the Random_module.f90 and Tension_module.f90, respectively, they do not share the same license file as beta-LTRANS-ADCIRC Please review and respect their permissions (links and instructions provided below).</p>
<table border="0">
<tbody>
<tr>
<td>
<div><a href="http://dmoserv3.bco-dmo.org/data_docs/EstuarineMetaDyn/VF-NetCDF.zip"><strong>VF-NetCDF.zip</strong></a></div>
</td>
<td><br />
<strong>Windows Visual Fortran NetCDF libraries</strong>. These NetCDF files that are compatible with Visual Fortran were downloaded from the&nbsp;<a href="http://www.unidata.ucar.edu/software/netcdf/binaries.html">Unidata NetCDF Binaries</a>&nbsp;Website for LTRANS v.1. The NetCDF 90 files were downloaded from&nbsp;<a href="http://www.unidata.ucar.edu/software/netcdf/docs/other-builds.html#windows_ifort_f90">Building the F90 API for Windows for the Intel ifort compiler</a>website. The VF-NetCDF.zip folder contains README.txt that describes where to place the enclosed files. If these files do not work, you may have to download updated versions or build your own by following the instructions at the&nbsp;<a href="http://www.unidata.ucar.edu/software/netcdf/">UCAR Unidata NetCDF website</a>.&nbsp;<br />
&nbsp;</td>
</tr>
<tr>
<td>
<div><a href="http://www.unidata.ucar.edu/software/netcdf/" target="_blank"><strong>NetCDF website</strong></a></div>
</td>
<td><br />
<strong>Linux NetCDF libraries</strong>. Linux users will likely have to build their own Fortran 90 libraries using the source code/binaries that are available on the&nbsp;<a href="http://www.unidata.ucar.edu/software/netcdf/">UCAR Unidata NetCDF website</a>.<br />
&nbsp;</td>
</tr>
<tr>
<td>
<div><a href="http://dmoserv3.bco-dmo.org/data_docs/EstuarineMetaDyn/FORTRAN_mt19937ar.f"><strong>mt19937ar.f</strong></a></div>
</td>
<td><br />
<strong>Mersenne Twister random number generator</strong>. This program was recoded into F90 and included in the Random_module.f90 in LTRANS. See the&nbsp;<a href="http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html">Mersenne Twister Home Page</a>&nbsp;for more information about this open source program. If you plan to use this program in LTRANS, please send an email to: m-mat @ math.sci.hiroshima-u.ac.jp (remove space) to inform the developers as a courtesy.&nbsp;<br />
&nbsp;</td>
</tr>
<tr>
<td>
<div><strong><a href="http://portal.acm.org/citation.cfm?id=151277" target="_blank">TSPACK</a></strong><a href="http://portal.acm.org/citation.cfm?id=151277" target="_blank"><strong> website</strong></a></div>
</td>
<td><br />
<strong>TSPACK</strong>: <strong>tension spline curve-fitting package</strong>. This program (ACM TOMS Algorithm 716) was created by <a href="http://www.cse.unt.edu/~renka/">Robert J. Renka</a> and is used in LTRANS as part of the water column profile interpolation technique. The original TSPACK code can be found at the link to the left and is copyrighted by the <a href="http://www.acm.org/">Association for Computing Machinery (ACM)</a>. With the permission of Dr. Renka and ACM, TSPACK was modified for use in LTRANS by removing unused code and call variables and updating it to Fortran 90. The modified version of TSPACK is included in the LTRANS source code in the Tension Spline Module (tension_module.f90). If you would like to use LTRANS with the modified TSPACK software, please read and respect the&nbsp;<a href="http://www.acm.org/publications/policies/softwarecrnotice">ACM Software Copyright and License Agreement</a>. For noncommercial use, ACM grants "a royalty-free, nonexclusive right to execute, copy, modify and distribute both the binary and source code solely for academic, research and other similar noncommercial uses" subject to the conditions noted in the license agreement. Note that if you plan commercial use of LTRANS with the modified TSPACK software, you must contact ACM at&nbsp;<a href="mailto:permissions@acm.org">permissions@acm.org</a> to arrange an appropriate license. It may require payment of a license fee for commercial use.</td>
</tr>
</tbody>
</table>
<p>&nbsp;</p>
<table border="0">
<tbody>
<tr>
<td>beta-LTRANS-ADCIRC&nbsp;<strong>Utilities</strong>.&nbsp;The following programs were developed to run LTRANS v.2 or visualize LTRANS v.2 model output. Unless specified otherwise within the program code, these open source programs are considered part of LTRANS and fall under the beta-LTRANS-ADCIRC license. Many thanks to LTRANS users who have made these contributions! If you would like to share a LTRANS utility or your modifications/additions to LTRANS source code, please send them to&nbsp;<a href="mailto:enorth@umces.edu">enorth@umces.edu</a>.</td>
</tr>
</tbody>
</table>
<table border="0">
<tbody>
<tr>
<td>
<div><strong><a href="http://dmoserv3.bco-dmo.org/data_docs/EstuarineMetaDyn/LTRANS_v2_visualization_ADCIRC_closeup.BAS">LTRANS-ADCIRC_viz.BAS</a></strong><br />
<br />
<strong><a href="http://dmoserv3.bco-dmo.org/data_docs/EstuarineMetaDyn/betaLTRANS_ADCIRC_End_polygons.bln">End_polygons.bln</a></strong></div>
</td>
<td><br />
<strong>Surfer/Scripter code for visualizing beta-LTRANS-ADCIRC output</strong>&nbsp;developed by E. W. North. The .BAS file is the program and associated .bln files are needed to visualize the location of bottom habitat.&nbsp;<a href="http://northweb.hpl.umces.edu/LTRANS/betaLTRANS_ADCIRC/betaLTRANS-ADCIRC_test.wmv">Here is an example animation (MB) of LTRANS v.2 model output made with Surfer</a>&nbsp;using the code and example input files provided above. Surfer is a Windows program for contouring and 3D surface mapping. Scripter is an object oriented scripting language (Active X Automation) that comes with, and automates, Surfer. Information on Surfer is available&nbsp;<a href="http://www.goldensoftware.com/products/surfer/surfer.shtml">here</a>&nbsp;and a free demo is available&nbsp;<a href="http://www.goldensoftware.com/demo.shtml">here</a>. Please note that the demo version will not allow export so it is likely that you will not be able to use the demo version to create .gif files for animations.&nbsp;<br />
&nbsp;</td>
</tr>
<tr>
<td>
<div><strong>OceanView in R</strong></div>
</td>
<td>
<p>OceanView, created by Dr. Karline Soetaert, is a set of R functions for visualizing 2-D and 3-D oceanographic data and model output. The package is on the official R site:<a href="http://cran.r-project.org/web/packages/OceanView">http://cran.r-project.org/web/packages/OceanView</a>. There is also a short manual with snapshots of the visualization functions, some of which use LTRANS output as examples:<a href="http://cran.r-project.org/web/packages/OceanView/vignettes/OceanView.pdf">http://cran.r-project.org/web/packages/OceanView/vignettes/OceanView.pdf</a>.</p>
</td>
</tr>
<tr>
<td><strong><a href="http://dmoserv3.bco-dmo.org/data_docs/EstuarineMetaDyn/LTRANS-v2_plot_results.M">plot_results.m</a></strong></td>
<td><strong>MATLAB code for visualizing LTRANS v.2b output.&nbsp;</strong>Here is Matlab M-file which was designed by Yong Kim for LTRANS v.1 and adapted for LTRANS v.2b by Elizabeth North. It should work with beta-LTRANS-ADCIRC It makes a 3D plot of the model bathymetry (from .nc input grid file) and particle locations from LTRANS v.2b .csv output files.&nbsp;<a href="http://northweb.hpl.umces.edu/LTRANS/LTRANS-v2/LTRANS-matlab.wmv">Here is an example animation (MB) of LTRANS v.2b model output made with MATLAB</a>.&nbsp;</td>
</tr>
</tbody>
</table>
<p><strong>LTRANS User's Guide and beta-LTRANS-ADCIRC Description (see Related Publicatsion section):</strong><br />
Please send comments or suggestions regarding the User's Guide to <a href="mailto:enorth@umces.edu">enorth@umces.edu</a>. They will be posted on the list of known LTRANS v.2 bugs and solutions&nbsp;(northweb.hpl.umces.edu/LTRANS/LTRANS-v2b/LTRANSv2b%20bugs%20and%20solutions.txt)</p> Methods and Sampling:
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1155497 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1155497
completed
Elizabeth North
University of Maryland Center for Environmental Science
410-221-8497
5745 Lovers Lane
Cambridge
MD
21613
USA
enorth@umces.edu
pointOfContact
Richard Leuttich
University of North Carolina at Chapel Hill
(252) 726-6841, ext. 137
150 Coker Hall 3431 Arendell Street
Morehead City
NC
28557
rick_luettich@unc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
description
file_download
theme
None, User defined
brief description
file_link
featureType
BCO-DMO Standard Parameters
lab_North_EstuarineMetaDyn
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.
Interacting Effects of Local Demography and Larval Connectivity on Estuarine Metapopulation Dynamics
https://www.bco-dmo.org/project/559332
Interacting Effects of Local Demography and Larval Connectivity on Estuarine Metapopulation Dynamics
<p>Description from NSF award abstract:<br />
The PIs will use the eastern oyster (<em>Crassostrea virginica</em>) in Pamlico Sound, North Carolina, as a model system and will attempt to optimize the design of networks of no-take reserves as a strategy for maintaining metapopulations of this commercially harvested species. The project specifically recognizes that network persistence depends on (1) the potential for growth, survival, and reproduction within reserves, and (2) the potential to distribute offspring among reserves. Thus, demographic processes within reserves and settling areas play important roles, along with variability of physical transport. The PIs plan to:<br />
(1) test and refine 3D bio-physical models of connectivity due to oyster larval transport in a shallow, wind-dominated system;<br />
(2) test, refine, and apply technology to detect natal origins of larvae using geochemical tags in larval shell; and<br />
(3) integrate regional connectivity and demographic rates to model metapopulation dynamics.</p>
<p>This study will produce new tools and test and refine others used for studying larval connectivity, a fundamentally important process in the maintenance of natural populations, and thus in biological conservation and resource management. The tools include a hydrodynamic modeling tool coupled with an open-source particle tracking model that will be available on-line with computer code and user guide. The project will use integrated modeling approaches to evaluate the design of reserve networks: results will be directly useful to improving oyster and ecosystem-based management in Pamlico Sound, and the methods will inform approaches to network design in other locations.</p>
EstuarineMetaDyn
largerWorkCitation
project
eng; USA
oceans
2016-09-13
North Carolina Estuaries
0
BCO-DMO catalogue of parameters from Source code, license, example input and visualization files for beta-LTRANS-ADCIRC, a particle tracking model that runs with ADCIRC circulation model prediction.
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
http://lod.bco-dmo.org/id/dataset-parameter/658676.rdf
Name: description
Units: unitless
Description: Brief description of the file available for download
http://lod.bco-dmo.org/id/dataset-parameter/658677.rdf
Name: file_download
Units: unitless
Description: Link to file
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
268269
https://darchive.mblwhoilibrary.org/bitstream/1912/26741/1/VF-NetCDF.zip
download
146996285
https://darchive.mblwhoilibrary.org/bitstream/1912/26741/2/betaLTRANS_ADCIRC.zip
download
1309
https://darchive.mblwhoilibrary.org/bitstream/1912/26741/3/dataset-658655_beta-ltrans-adcirc-software__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.658655.1
download
onLine
dataset
<p><strong>BCO-DMO Processing:</strong><br />
- Files were downloaded from PI's site to BCO-DMO<br />
- File names were slightly changed to include PI's file directory<br />
- Links on dataset page are to locally residing files</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
Deployment: lab_North_EstuarineMetaDyn
lab_North_EstuarineMetaDyn
UMCES_HPL_labs
laboratory
lab_North_EstuarineMetaDyn
Elizabeth North
University of Maryland Center for Environmental Science
UMCES_HPL_labs
laboratory