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cosima-recipes

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A cookbook 📒 of recipes (i.e., examples) for analysing ocean and sea ice model output. 👩🏽‍🍳🌊👨🏻‍🍳

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- - sphinx.yml
- - 01-Loading-Slicing-Dicing-Output.ipynb
  - 02-ACCESS-NRI_Intake_Catalog.ipynb
  - 03-Maps_with_Cartopy.ipynb
  - README.rst
- - Animations_with_xmovie.ipynb
  - Apply_function_to_every_gridpoint.ipynb
  - CFxarray_and_Pint.ipynb
  - intake_to_dask_efficiently_chunking.ipynb
  - Make_Your_Own_Intake_Datastore.ipynb
  - movie_sst.gif
  - README.rst
  - Spatial_selection.ipynb
  - Submitting_analysis_jobs_to_gadi.ipynb
- README.rst
- Barotropic_Streamfunction.ipynb
- Compare_SSH_model_obs.ipynb
- Compare_SST_SSS_TemperatureSalinity_to_WOA13.ipynb
- Extract_Variables_at_Ocean_Bottom.ipynb
- Hovmoller_Temperature_Depth.ipynb
- README.rst
- Sea_Ice_Coordinates.ipynb
- True_Zonal_Mean.ipynb
- - Bgrid.png
  - contour_schematic.png
  - topographic_gradient_sketch.png
- Along-slope-velocities.ipynb
- Along_Isobath_Average.ipynb
- Create_contour.ipynb
- Cross-contour_transport.ipynb
- Cross-slope_section.ipynb
- Eddy-Mean_Kinetic_Energy_Decomposition.ipynb
- Geostrophic_Velocities_from_Sea_Level.ipynb
- Heaving_Water_mass_transformation_decomposition.ipynb
- Horizontal_Regridding_Compare_Resolutions.ipynb
- Meridional_heat_transport.ipynb
- Nearest_Neighbour_Distance.ipynb
- Neutral_density.ipynb
- Overturning_Circulation.ipynb
- Particle_tracking_with_Parcels.ipynb
- README.rst
- Relative_Vorticity.ipynb
- Sea_Ice_Area_Concentration_Volume_with_Obs.ipynb
- Sea_Ice_Seasonality_Statistics.ipynb
- Surface_Water_Mass_Transformation.ipynb
- Temperature_Salinity_Diagram.ipynb
- Transformation_from_Depth_to_Potential_Density.ipynb
- README.rst
- regional-mom6-forced-by-access-om2.ipynb
- - gear.svg
- - advanced.rst
  - basics.rst
- advanced-recipes.rst
- conf.py
- contributing.rst
- easy-recipes.rst
- guidelines.rst
- index.rst
- Makefile
- regional-specialties.rst
- requirements.txt
- tutorials.rst
- README.md
- test_notebooks.py
.gitignore
.readthedocs.yml
.zenodo.json
LICENSE
README.md

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<br/> <br/>

<a href="https://cosima-recipes.readthedocs.io/en/latest">
    <img alt="latest docs" src="https://img.shields.io/badge/docs-latest-blue.svg">
</a>

<a href="https://doi.org/10.5281/zenodo.14353852">
    <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14353852.svg" alt="DOI">
</a>

# COSIMA Cookbook

This repository is a Cookbook of Recipes 👩🏽‍🍳 👨🏻‍🍳.
A collection of cooking lessons and recipes for analysing ocean and sea ice model output produced by the [Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA)](http://cosima.org.au/).

We explain: a "cooking tutorial" here is a tutorial that teaches you something generic (e.g. about plotting or loading data); a "recipe" is an example of an analysis of some ocean-sea ice model output or some ocean-related observational datasets.
Both "cooking tutorials" and "recipes" come in self-contained and well-documented Jupyter notebooks.
All the tutorials and the recipes combined form a cookbook 📒!

Most recipes use output from the [ACCESS-OM2 model](https://doi.org/10.5194/gmd-13-401-2020), while some also use results from configurations of the [Modular Ocean Model 6 (MOM6)](https://github.com/mom-ocean/MOM6) and remote sensing observations.

To access the data used in these recipes you need an account with the Australian-based [National Computational Infrastructure (NCI)](https://nci.org.au/).

To **get started**, clone this repository in your local space on one of the NCI HPC machines so you can have access to model output. You should then be able to run these recipes (i.e., example analyses) through an [Australian Research Environment (ARE)](https://are.nci.org.au/) JupyterLab session running python or via any other way you might want to run a Jupyter notebook on an NCI HPC machine. You need to join projects _xp65_, _ik11_, _cj50_, and _ol01_ to run the recipes and access the data analysed.

If you plan to use an ARE session, then remember to include the projects in the _Storage_ line: `gdata/xp65+gdata/ik11+gdata/cj50+gdata/ol01` as well as any of your own project you need access to. In _Module directories_, set `/g/data/xp65/public/modules` and in _Modules_ set `conda/analysis3`. Use a _Compute Size_ of `large` or greater.

If you have never used the NCI see these [first steps instructions](https://access-hive.org.au/getting_started/) and [getting started with ARE](https://access-hive.org.au/getting_started/are/).

## Contents

* #### [Cooking Tutorials](https://cosima-recipes.readthedocs.io/en/latest/tutorials.html)

The starting point should be all the **Basic** Tutorials:

* #### [Basics](https://cosima-recipes.readthedocs.io/en/latest/cooking-tutorials/basics.html)

The [Introduction: loading, slicing, dicing model output](https://cosima-recipes.readthedocs.io/en/latest/01-Cooking-Tutorials/01-Basics/01-Loading-Slicing-Dicing-Output.html) should be the starting point.

Recipes load model output to using an [_intake catalogue_](https://cosima-recipes.readthedocs.io/en/latest/01-Cooking-Tutorials/01-Basics/02-ACCESS-NRI_Intake_Catalog.html). The intake package is available on the conda-analysis python environments on `xp65`. The [ACCESS-NRI_Intake_Catalog](https://cosima-recipes.readthedocs.io/en/latest/01-Cooking-Tutorials/01-Basics/02-ACCESS-NRI_Intake_Catalog.html) tutorial outlines the basic philosophy of the Intake catalog to load model output variables.

Also included here are some other tutorials, related to techniques (e.g., [Maps_with_Cartopy.ipynb](https://cosima-recipes.readthedocs.io/en/latest/01-Cooking-Tutorials/01-Basics/03-Maps_with_Cartopy.html)).

After going through the **Basic** Tutorials, feel free to browse some of the **Advanced** ones:

* #### [Advanced](https://cosima-recipes.readthedocs.io/en/latest/cooking-tutorials/advanced.html)

### Recipes

The main part of this cookbook: All the recipes!

These are Jupyter notebooks for either simple or not-so-simple diagnostics and analyses. All recipes are aimed to be self-contained and  well-documented and explained.
If you can find a recipe that suits your purposes, then this is the best place to start.

* #### [Easy Recipes](https://cosima-recipes.readthedocs.io/en/latest/easy-recipes.html)

Easier/simpler recipes; a good place to start after you’ve been through the [Cooking Tutorials](https://cosima-recipes.readthedocs.io/en/latest/tutorials.html)

* #### [Advanced Recipes](https://cosima-recipes.readthedocs.io/en/latest/advanced-recipes.html)

More elaborate/advanced recipes.

* #### [Regional Specialties](https://cosima-recipes.readthedocs.io/en/latest/regional-specialties.html)

Recipes for regional configurations.

## Conditions of use for ACCESS-OM2 output

We request that users of ACCESS-OM2 model [code](https://github.com/access-nri/access-om2) or output consider:
1. citing Kiss et al. (2020) ([http://doi.org/10.5194/gmd-13-401-2020](http://doi.org/10.5194/gmd-13-401-2020))
2. including an acknowledgement such as the following:

*The authors thank the vibrant community of the Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA; [http://www.cosima.org.au](http://www.cosima.org.au)) for making the ACCESS-OM2 suite of models available at [https://github.com/COSIMA/access-om2](https://github.com/access-nri/access-om2).*

3. let us know of any publications which use these models or data so we can add them to [our list](https://scholar.google.com/citations?hl=en&user=inVqu_4AAAAJ).

## Contributing

Have you made a recipe for analysing something that is not already included in this cookbook?
You are more than welcome to share it and include it in the cookbook!
Consider **contributing your recipe back to the repository**.
We are always delighted to expand the cookbook with more recipes.
If the process of contributing to the repository sounds a bit intimidating to you, rest assured that we will guide you and help you with submitting your contribution.

To make a contribution follow the steps laid out in the [beginner's guide on how to contribute](
https://cosima-recipes.readthedocs.io/en/latest/contributing.html) and the [wiki](https://github.com/COSIMA/cosima-recipes/wiki). If they sound intimidating then don't worry!
Just raise [an issue](https://github.com/COSIMA/cosima-recipes/issues) explaining briefly what the contribution you want to make is and we'll help out with the process!

Contributors to the COSIMA Cookbook are added to the [**citable DOI**](https://github.com/COSIMA/cosima-recipes?tab=readme-ov-file#citation) entry associated with the repository.
Hence, users who put together a pull request for a new contribution, should ensure that the pull request also modifies the `.zenodo.json` file to include their affiliation details.

## Citation

If you use a recipe from the Cookbook for your research or teaching, or have based your analysis on one of the recipes, we would be grateful if you could cite:

> Constantinou, N. C. et al. (2026). COSIMA Cookbook: A cookbook of recipes for analysing ocean and sea ice model output. Zenodo. doi:[10.5281/zenodo.14353852](https://doi.org/10.5281/zenodo.14353852) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14353852.svg)](https://doi.org/10.5281/zenodo.14353852)