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North Atlantic Bloom

Investigating the role of vertical nitrate flux on phytoplankton bloom.


Project Organization

├── LICENSE
├── README.md          <- The top-level README for developers using this project.
├── data
│   ├── external       <- Data from third party sources.
│   ├── interim        <- Intermediate data that has been transformed.
│   ├── processed      <- The final, canonical data sets for vizualization.
│   └── raw            <- The original, immutable data dump (model outputs).
│
├── docs               <- A default Sphinx project; see sphinx-doc.org for details
│
├── reports            <- Generated analysis as HTML, PDF, LaTeX, etc.
│   └── figures        <- Generated graphics and figures to be used in reporting
│
└── src                <- Source code for use in this project.
    │
    ├── 00-preprocess
    │   │                 
    │   └── 01-preprocess_external.py           <- preprocess external data
    │
    ├── 01-model
    │   │                 
    │   ├── 01-initial_conditions.py            <- initial conditions for the fine-scale submesoscale simulation
    │   ├── 02-submesoscale.jl                  <- fine-scale submesoscale simulation
    │   ├── 03-initial_conditions_coarse.py     <- initial conditions for the coarse-resolution simulations
    │   ├── 04-coarse_averaging.jl              <- coarse-resolution simulation that prescribes restratification (NVF)
    │   ├── 05-coarse_mle.jl                    <- coarse-resolution simulation with MLE parameterization (MLE)
    │   ├── cumulative_vertical_integration.jl  <- function used for initial geostrophic velocities
    │   ├── mle_parameterization.jl             <- function for computing the eddy stream function from Fox-Kemper et al. (2011)
    │   ├── Manifest.toml                       <- manifest file with for the Julia packages
    │   └── Project.toml                        <- project file with for the Julia packages
    │   
    └── 02-analysis
        ├── 01-video.py                         <- code for generating frames for the video
        ├── 02-3D_plots.py                      <- 3D box plots for w and Ro
        ├── 03-Ro_restratification.py           <- comparison for the evolution of Ro and restratification
        ├── 04-biogeochemistry.py               <- comparing new production between simulations
        ├── 05-nitrate_flux.py                  <- comparing nitrate flux between simulations
        └── cmaps.py                            <- extra colormaps

Project based on the cookiecutter data science project template. #cookiecutterdatascience

Citing this code

The paper:

@ARTICLE{simoessousa2022b,
    AUTHOR={Simoes-Sousa, Iury T. and Tandon, Amit and Pereira, Filipe and Lazaneo, Caue Z. and Mahadevan, Amala},   
    TITLE={Mixed layer eddies supply nutrients to enhance the spring phytoplankton bloom},      
    JOURNAL={Frontiers in Marine Science},      
    VOLUME={9},           
    YEAR={2022},        
    URL={https://www.frontiersin.org/articles/10.3389/fmars.2022.825027},   
    DOI={10.3389/fmars.2022.825027},
    URL={https://doi.org/10.3389/fmars.2022.825027},
    ISSN={2296-7745},
}

The software:

@software{simoessousa2022b_software,
  author       = {Iury T. Simoes-Sousa},
  title        = {{github.com/iuryt/NorthAtlanticBloom}},
  month        = apr,
  year         = 2024,
  publisher    = {Zenodo},
  version      = {v1.0.0},
  doi          = {10.5281/zenodo.10980522},
  url          = {https://doi.org/10.5281/zenodo.10980522},
}