Table of Contents

• Dataset Description
  • Data Processing Description
• Data Files
• Parameters
• Deployments
• Project Information
• Funding

From http://northweb.hpl.umces.edu/LTRANS.htm. CHECK FOR UPDATES. NEWER VERSION MAY BE AVAILABLE.

PDF of original LTRANS_v.2b website [2016-09-14]

LTRANS v.2b Model Description

The Larval TRANSport Lagrangian model (LTRANS v.2b) is an off-line particle-tracking model that runs with the stored predictions of a 3D hydrodynamic model, specifically the Regional Ocean Modeling System (ROMS). 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 LTRANS particle-tracking model can be found here (68 KB .pdf). For more information on LTRANS and the application of LTRANS to oyster larvae transport, see a summary web page with animations, the publications North et al. (2008, 2011), and the LTRANS v.2 User's Guide. Please cite North et al. (2011) when referring to LTRANS v.2b. The updates that were made for LTRANS v.2b are listed here. 

The Lagrangian TRANSport (LTRANS v.2b) model is based upon LTRANS v.1 (formerly the Larval TRANSport Lagrangian model). Ian Mitchell made the bug fixes in LTRANS v.2b. Zachary Schlag completed signigicant updates to the code in LTRANS v.2 with input from Elizabeth North, Chris Sherwood, and Scott Peckham. LTRANS v.1 was built by Elizabeth North and Zachary Schlag of University of Maryland Center for Environmental Science Horn Point Laboratory. Funding was provided by the National Science Foundation Biological and Physical Oceanography Programs**, Maryland Department of Natural Resources, NOAA Chesapeake Bay Studies, NOAA Maryland Sea Grant College Program, and NOAA-funded UMCP Advanced Study Institute for the Environment.

A beta version of LTRANS v2b which uses predictions from the circulation model ADCIRC is available here.

LTRANS Code

LTRANS v.2b Open Source Code. 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 LTRANS to enorth@umces.edu. To refer to LTRANS in a peer-reviewed publication, please cite the publication(s) listed in the Description section above.

External Dependencies and Programs. LTRANS v.2b requires NetCDF libraries and uses the following programs to calculate random numbers (Mersenne Twister) and fit tension splines (TSPACK). Because LTRANS v.2 reads-in ROMS-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 LTRANS v.2b in the Random_module.f90 and Tension_module.f90, respectively, they do not share the same license file as LTRANS v.2b. Please review and respect their permissions (links and instructions provided below).

LTRANS v.2b Example Input Files. These files can be used to test LTRANS v.2b. They include examples of particle location and habitat polygon input files (.csv) and ROMS grid and history files (.nc) that are needed to run LTRANS v.2b. Many thanks to Wen Long for sharing the ROMS .nc files. The LTRANS v.2b code above is configured to run with these input files. Note: please download the tar (LTRANSv2.tgz) history files (clippped_macroms_his_*.nc) files between the hours of 5 pm and 6 am Eastern Standard Time because of their large size.

LTRANS v.2b Utilities. 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 LTRANS 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 toenorth@umces.edu.

LTRANS v.2 User's Guide and v.2b Updates 
Please send comments or suggestions regarding the User's Guide to enorth@umces.edu. They will be posted on the list of known LTRANS v.2 bugs and solutions. Also, here is a document that provides a (not elegant) solution to errors (Particle not in v (or u) element or particle jumped over v (or u) element) that can result from single-grid width channels in the hydrodynamic model domain (link). 

Mitchell, I. 2013. Updates in LTRANS v.2b. University of Maryland Center for Environmental Science, Horn Point Laboratory. Cambridge, MD. 2 pp. (93 KB .pdf)

Schlag, Z. R., and E. W. North. 2012. Lagrangian TRANSport model (LTRANS v.2) User’s Guide. University of Maryland Center for Environmental Science, Horn Point Laboratory. Cambridge, MD. 183 pp. (1.7 MB .pdf)

Discussion Forum
If you would like to report bugs and solutions, please e-mail them to Elizabeth North (enorth@umces.edu) and they will be added to this list. There is also a discussion forum topic in the ROMS/TOMS Ocean Modeling Discussion Forum under ROMS/TOMS Applications > User Applications > LTRANS. Here is the link to the topic. If you have questions about LTRANS, please post them at this site and Elizabeth North or other LTRANS Users will answer them.

LTRANS Publications

North, E. W., E. E. Adams, S. Schlag, C. R. Sherwood, R. He, S. Socolofsky. 2011. Simulating oil droplet dispersal from the Deepwater Horizon spill with a Lagrangian approach. AGU Book Series: Monitoring and Modeling the Deepwater Horizon Oil Spill: A Record Breaking Enterprise (request .pdf).

North, E. W., R. R. Hood, S.-Y. Chao, and L. P. Sanford. 2006. Using a random displacement model to simulate turbulent particle motion in a baroclinic frontal zone: a new implementation scheme and model performance tests. Journal of Marine Systems 60: 365-380 (request .pdf).

North, E. W., Z. Schlag, R. R. Hood, L. Zhong, M. Li, and T. Gross. 2006. Modeling dispersal of Crassostrea ariakensis oyster larvae in Chesapeake Bay. Final Report to Maryland Department of Natural Resources, July 31, 2006. 55 p. (request .pdf)

North, E. W., Z. Schlag, R. R. Hood, M. Li, L. Zhong, T. Gross, and V. S. Kennedy. 2008. Vertical swimming behavior influences the dispersal of simulated oyster larvae in a coupled particle-tracking and hydrodynamic model of Chesapeake Bay. Marine Ecology Progress Series 359: 99-115 (request .pdf).

Schlag, Z. R., and E. W. North. 2012. Lagrangian TRANSport model (LTRANS v.2) User’s Guide. University of Maryland Center for Environmental Science, Horn Point Laboratory. Cambridge, MD. 183 pp. (1.7 MB .pdf)

Schlag, Z., E. W. North, and K. Smith. 2008. Larval TRANSport Lagrangian model (LTRANS) User’s Guide. University of Maryland Center for Environmental Science, Horn Point Laboratory. Cambridge, MD. 146 pp. (739 KB .pdf)

BCO-DMO Processing:
- Files were downloaded from PI's site to BCO-DMO
- File names were slightly changed to include PI's file directory
- Links on dataset page are to locally residing files

Additional information can be found at the TRANSPORT website: http://northweb.hpl.umces.edu/TRANSPORT/home.htm

Project description:
This coupled field-and-modeling research project is designed to address fundamental, cutting-edge questions that will significantly enhance our understanding of physical-biological interactions in planktonic organisms and quantify how pelagic life stages influence population dynamics. Technological advances in field methodology and numerical modeling will be integrated and applied to investigate and compare how circulation patterns, larval transport, sub-population connectivity, and population dynamics of the Eastern oyster, Crassostrea virginica, respond to environmental variability and habitat alteration. This project will provide information that will significantly enhance the restoration and management of oysters.

Physical-biological interactions are an integral part of understanding fish, bivalve, and crustacean early-life history and the processes that affect inter-annual variability in their recruitment to reproducing populations. The combined modeling and field approach builds on existing state-of-the-art models, it applies a new technology that will significantly advance our ability to investigate in-situ bivalve larvae dynamics, and it will generate critical information about the early life of oysters (timing of spawning, larval behavior) that is necessary for enhancing our understanding and prediction of recruitment processes.

This research will also advance our understanding of population dynamics of organisms with a pelagic life stages by making quantitative links between larval transport and a full life-cycle model. In doing so, it will provide improved understanding of the inter-relationships between, and relative importance of, larval transport, the connectivity of different reef systems, and adult growth, mortality, and gamete production, and how these relationships are influenced by changes in physical conditions and habitat.

Although focused on the oyster, Crassostrea virginica, the ecological studies and comparisons will result in a significant enhancement in our understanding of the interactions between physical conditions and a suite of bivalve species. This program will benefit society by providing new insights and understanding that will enhance fisheries management capabilities. The numerical tools developed will have the resolution appropriate for helping to guide oyster restoration programs, locate optimal sanctuaries (i.e., marine protected areas), and inform spatial management of oyster harvest. Although the quantitative tools and information generated will directly support oyster management and restoration activities of state and federal partners in Chesapeake Bay, the findings and tools developed in this project will be applicable to many other systems where bivalves comprise an important component of commercial and recreational fisheries. A PhD graduate student will be trained in field and numerical modeling research in this coupled field-and-modeling program. In addition to gaining a solid foundation in a cutting-edge field, the student will have the opportunity to develop science communication skills and interact with management agency representatives.

Publications Produced as a Result of this Research:

Gallego, A., E.W. North and E.D. Houde. 2012. Understanding and quantifying mortality in pelagic, early life stages of marine organisms — Old challenges and new perspectives. Journal of Marine Systems 93: 1-3.

Goodwin, J. D., and E.W. North. In prep. Identifying factors that influence the swimming behavior of Crassostrea virginica larvae in Choptank River and calculating their mortality.

Goodwin, J. D., E. W. North, and C. M. Thompson. 2014. Evaluating and improving a semi-automated image analysis technique for identifying bivalve larvae. Limnology and Oceanography: Methods 12: 548-562. DOI: 10.4319/lom.2014.12.548

Goodwin, J. D., E. W. North, and V. S. Kennedy. 2016. Identification of eastern oyster Crassostrea virginica larvae using polarized light microscopy in a mesohaline region of Chesapeake Bay. Journal of Shellfish Research 35(1): 157-168.

Goodwin, J. D., E. W. North, C. M. Thompson, I. Mitchell and H.M McFadden. In press.  Improving a semi-automated classification technique for bivalve larvae: automated image acquisition and measures of quality control. Limnology and Oceanography: Methods.

North, E. W., D. M. King, J. Xu, R. R. Hood, R. I. E. Newell, K. T. Paynter, M. L. Kellogg, M. K. Liddel, and D. F. Boesch. 2010. Linking optimization and ecological models in a decision support tool for oyster restoration and management. Ecological Applications 20(3): 851–866.

Spires, J. E., E. W. North, and W. Long. In prep. The influence of salinity-induced mortality on larval transport between eastern oyster (Crassostrea virginica) reefs in an oligohaline estuary: model simulations and implications for restoration. Estuaries and Coasts.

Thompson, C. M., E. W. North, V. S. Kennedy, and S. N. White. 2015. Classifying bivalve larvae using shell pigments identified by Raman spectra. Analytical and Bioanalytical Chemistry 407:3591-3604, DOI 10.1007/s00216-015-8575-8

Thompson, C.M., E.W. North, S.N. White, and S.M. Gallager. 2014. An analysis of bivalve larval shell pigments using micro-Raman spectroscopy. Journal of Raman Spectroscopy 45(5):349-358

Dissertations and Theses:

Goodwin, J. D. 2015. Integrating automated imaging and a novel identification technique to estimate mortality and factors that determine the vertical distribution of Crassostrea virginica larvae. Ph.D. Dissertation. University of Maryland College Park and the University of Maryland Center for Environmental Science.

Spires, J. E. The exchange of eastern oyster (Crassostrea virginica) larvae between subpopulations in the Chotpank and Little Choptank Rivers: model simulations, the influence of salinity, and implications for restoration. Master of Science Thesis, University of Maryland College Park and Center for Environmental Science, 79 pp.

Books and One-Time Proceedings:

Anthony, Z. 2014. Optimal microscope and camera settings for counting and identifying copepods (Acartia tonsa) using a newly developed semi-automated image analysis technology. Undergraduate Research Report. 14 pp.

Hinson, K. I., E.W. North, and C.M. Thompson. 2011. New technologies to support shellfish restoration. Research Experience for Undergraduates (REU) final report.

Mitchell, I. 2013. Updates in LTRANS v.2b. University of Maryland Center for Environmental Science, Horn Point Laboratory. Cambridge, MD. 2 pp.

North, E. W. 2010. Q&A: Elizabeth North. 10/01/2009-09/30/2010, ICES Insight, September 2010, vol. 47, p. 43-44.

Schlag, Z. R., and E. W. North. 2012. Lagrangian TRANSport model (LTRANS v.2) User’s Guide. University of Maryland Center for Environmental Science, Horn Point Laboratory. Cambridge, MD. 183 pp.