Data Access: An IntroductionDrifter Data and Model OutputParticle Tracking Code and Utilities Data Access There are many ways to track particles referenced in this site. Click on a tab above to see options for data, model output, utilities, and code. Example Distributed Drifter Data and Model Output There are many places that one can now access both observed drifter tracks and modeled output. Given the standards implemented in the last few years by the US Integrated Ocean Observing System, for example, one can easily access these datasets stored in THREDDS/OPENDAP and SOS formats at nearly all the regional websites. There are also codes developed in multiple languages such as MATLAB and PYTHON where the user can query the remote datasets (as demonstrated in our GitHub code at https://github.com/Particles-in-the-Coastal-Ocean) from within their own programming environment. So, rather than point-and-clicking through websites to obtained the desired data, the code can access it directly. We list now a few sites to find various drifter data and model output as well as pointers to the code mentioned above. Again, these lists are growing too rapidly to be comprehensive but it provides at least a few sites that are active at the time of this writing. Drifter Data Global Drifter Project Northeast US NOAA Drifter Project ARGO repository at NODC Model Output Integrated Ocean Observing Systems Mid-Atlantic Regional Association of Ocean Observing Systems (MARACOOS) Northeastern Regional Association of Ocean Observing Systems (NERACOOS) NOAA National Ocean Service Example utilities to access remotely served data and model output There are a variety of ways to access remote data from within your code without having to point and click through websites and download files. These utilities provide powerful method to query various web-served databases in order to extract particular portions of the data. netCDF4 - which comes with most distributions pydap - Another python option netCDF Java Toolbox loaddap Particle Tracking Utilities There are a variety of ways to track particles. These utilities provide powerful method to query various web-served databases in order to extract particular portions of the data. Our Community Particle Tracking Code Repository An electronic archive contains particle tracking codes currently in development and in use in several coastal environments. It is therefore both an archive to support current research as well as an archive of computational products that has been used in published research projects. In all cases the code is provided for experimentation with the caveat that there is still work to be done. The code archive resides in a GitHub account (a web-based hosting service for software development that uses the Git revision control system). The GitHub account is: https://github.com/Particles-in-the-Coastal-Ocean. In the repository, we include: Matlab code for particle tracking in a 2D field (drog2ddt.m) Fortran code for 3D particle tracking (drog3ddt.f) Python particle tracking code (track) for web-served 3D fields. Other Particle Tracking Code Repositories Alternatively, there are other implementations of particle tracking algorithms available in the coastal oceanographic community. We provide a list of algorithms that is not meant to be complete. We separate the algorithms into two categories: 1) code run offline using available model results and 2) web-based particle tracking that does not require any execution by the user (point and click). Many of the web-based routines are now being shared and applied in multiple regions of the globe. Example Offline Particle Tracking Packages LTRANS The Larval TRANSport Lagrangian model is an offline particle-tracking model that uses stored predictions of a 3D hydrodynamic model, specifically the Regional Ocean Modeling System (ROMS). Although LTRANS was built to simulate larvae, it has been adapted to simulate passive particles and other planktonic organisms. LTRANS is written in Fortran 90 and is designed to track the trajectories of particles in three dimensions using a 4th order Runge-Kutta scheme for advection and random displacement to account for vertical turbulence. E. North Ariane Ariane is an offline computational tool (Fortran 90/95) to calculate 3D streamlines from the output velocity field of a finite difference circulation model such as OPA-NEMO, ROMS, or Symphonie. B. Blanke Paegan Transport Paegan Transport is a web service build on a Python library that provides a common data model and methods for particle tracking. It was originally developed as a 3D web-based larval fish and invertebrate transport model connected to ROMS circulation fields for the northeast Pacific. It can be used with any Data Access Protocol (DAP) accessible circulation dataset formatted using the network Common Data Format for Climate and Forecast (NetCDF CF). Development PartTracker PartTracker is a particle tracking research tool currently being developed in MatlabTM which is designed to be used with both unstructured and structured model grids and has previously been applied to outputs from SELFE (Semi -implicit Eulerian-Lagrangian Finite- Element model) for the purposes of assessing wastewater and larval dispersal. PartTracker applies the time adaptive composite 4th-5th order Runge-Kutta (RK45) numerical scheme to ensure required minimum standards of accuracy are achieved for individual particle paths. The application of the RK45 approach ensures consistency in particle path accuracy across hydrodynamically complex domains and a range of user defined time steps with the time adaptive aspect of the approach reducing computational overheads in hydrodynamically simple flows by allowing for long time steps. (Knight et al, 2009) Ben Knight (Carthron Institute, New Zealand) WebDrogue WebDrogue is a beta-release Java graphical user interface used to obtain drift predictions from user-specified points in the model domain and can be installed under MS-Windows and Linux. The drift trajectories are computed using circulation derived from the tides, the seasonal mean circulation, wind-driven circulation, and a surface-wind drift. (Hannah, et al.2000) Webmaster Two-Way PTM In order to determine the source of particle arriving at one location, particle tracks can be run backwards to determine a probable source, then forward to determine the robustness of the results given a prescribed randomness. This is described in Isobe, et al, 2009, for example, where it is applied to the East China Sea. A.Isobe ICTHYOP ICTHYOP was developed to study how physical factors (e.g., currents, water temperature) and biological factors (e.g., egg buoyancy, larva growth) affect the dynamics of fish eggs and larvae. It gathers physicians and biologists together around a common tool, easily available and user-friendly. Info OILTRANS OILTRANS is an off-line particle model of oil transport and weathering. Formulations for the dominant oil fate processes of spreading, advection, diffusion, evaporation, emulsification and dispersion have been encoded, providing the model with the ability to accurately predict the horizontal movement of surface oil slick, the vertical entrainment of oil into the water column and the mass balance of spilled oil. (Berry et al, 2012) Alan Berry Sediment Transport A community of models for coastal sediment transport is under development. Some notes on this project are provided here where there is a list of existing models. C.Sherwood Connectivity Modeling System The Connectivity Modeling System is a community multiscale modeling system, based on a stochastic Lagrangian framework. It was developed by Claire Paris at the Rosenstiel School of Marine and Atmospheric Science to study complex larval migrations and give probability estimates of population connectivity. In addition, the CMS can also provide Lagrangian descriptions of oceanic phenomena (advection, dispersion, retention) and can be used in a broad range of applications, from the dispersion and fate of pollutants to marine spatial conservation. C.Paris JLAB JLAB is an open source oceanographic data and analysis software for MATLAB users where there is specific packages for floats and drifters. It also contains a nice compilation of the Global Drifter Program data in the form of mat files. Lilly Example Web-Based Particle Tracking Routines SCCOOS Product that tracks the Monterey Bay flows off California. UNK NCSTATE Product that tracks flow in large Northwest Atlantic ROMS/HYCOM grid. Ruoying He ALAVAI Visualization tool for a surface ocean drift forecast. (Otero et al, 2015) Pablo Otero Connie2 Connie2 is an online tool for marine scientists and managers to investigate patterns of marine spatial connectivity. It has been applied in areas such as larval dispersion and recruitment studies, and the development of scenarios and risk assessments for contaminant dispersion. Connie OSCURS Ocean Surface Current Simulator by W. James Ingraham, Jr. of NOAA's Alaska Fisheries Science Center is described as "a research tool that allows oceanographers and fisheries scientists to perform retrospective analyses of daily ocean surface currents anywhere in a 90-km ocean-wide grid from Baja California to China and from 10N to the Bering Strait." Jim Ingraham NEFSC Northeast Fisheries Science Center provides a utility to track particles through local ocean model fields. Some hindcast and some forecast. Includes drifter tracks to test against. Jim Manning