Ocean Biogeochemistry Cookbook

This Project Pythia Cookbook covers working with various sources of ocean biogeochemistry data, including Community Earth System Model (CESM) output and observational data.

Motivation

You’ll get a brief introduction to some metrics important to ocean biogeochemistry, from physical quantities like temperature to biological quantities like plankton biomass. You’ll learn some of the data science techniques used to work with this information, and see the relationship between modeled and observational estimates.

Authors

Lev Romashkov, Kristen Krumhardt

Contributors

Structure

Intro

Learn how to read in the main CESM dataset that we’ll be working with, and make a few simple maps.

Nutrients

Explore the distribution of several nutrients in the ocean with maps and vertical profiles, and compare to observational data.

Plankton

Explore the distribution of the phytoplankton and zooplankton functional types represented in CESM, and compare to observational data.

Running the Notebooks

You can either run the notebooks using Binder or on your local machine.

Running on Binder

The simplest way to interact with a Jupyter Notebook is through Binder, which enables the execution of a Jupyter Book in the cloud. The details of how this works are not important for now. All you need to know is how to launch a Pythia Cookbooks chapter via Binder. Simply navigate your mouse to the top right corner of the book chapter you are viewing and click on the rocket ship icon, (see figure below), and be sure to select “launch Binder”. After a moment you should be presented with a notebook that you can interact with. I.e. you’ll be able to execute and even change the example programs. You’ll see that the code cells have no output at first, until you execute them by pressing Shift+Enter. Complete details on how to interact with a live Jupyter notebook are described in Getting Started with Jupyter.

Running on Your Own Machine

If you are interested in running this material locally on your computer, you will need to follow this workflow:

Clone the https://github.com/ProjectPythia/ocean-bgc-cookbook repository:
```
 git clone https://github.com/ProjectPythia/cookbook-example.git
```
Move into the ocean-bgc-cookbook directory
```
cd ocean-bgc-cookbook
```

Create and activate your conda environment from the environment.yml file

conda env create -f environment.yml
conda activate ocean-bgc-cookbook-dev

Move into the notebooks directory and start up Jupyterlab
```
cd notebooks/
jupyter lab
```