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Sargassum growth model

Repository for the interactive notebook and simulations for the article A Lagrangian framework to simulate Sargassum transport and growth by Elena Gianotten, Meike F. Bos, Darshika Manral, Fabio Nauer, Erik Zettler, Linda A. Amaral-Zettler, and Erik van Sebille

How to install

  1. Install Pixi (choose one option below)

    Option A: macOS or Linux Run this command in your terminal:

    curl -fsSL https://pixi.sh/install.sh | sh

    Option B: Windows Run this command in PowerShell:

    powershell -ExecutionPolicy Bypass -c "irm -useb https://pixi.sh/install.ps1 | iex"

  2. Restart your terminal

  3. Clone this repository

    git clone --depth 1 https://github.com/Parcels-code/Sargassum_growth_model.git

  4. Change into the repository directory

    cd Sargassum_growth_model

  5. Install the required dependencies

    pixi install

  6. Start JupyterLab

    pixi run jupyter lab

  7. The interactive_sargassum_notebook.ipynb opens automatically. Run the cells to see the simulations.

Content of this repository

  • interactive_sargassum_notebook.ipynb: The interactive notebook to run the Sargassum growth simulations and visualize the results.
  • src/: A directory containing the source code for the Sargassum growth model, including the transport and growth kernels in src/sargassum_kernels.py.
  • satellite_simulation.py: The script that runs the simulation described in the manuscript with satellite-based initialisation.
  • basin_simulation.py: The script that runs the simulation described in the manuscript with basin-wide initialisation.
  • Manuscript_Figures/: A directory containing the notebooks used to create the figures for the manuscript.