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ocean-bgc-cookbook

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

https://github.com/projectpythia/ocean-bgc-cookbook

Science Score: 67.0%

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Repository

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

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 6
  • Open Issues: 3
  • Releases: 1
Created over 2 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

Ocean Biogeochemistry Cookbook

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nightly-build Binder DOI

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 {kbd}Shift+{kbd}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:

  1. Clone the https://github.com/ProjectPythia/ocean-bgc-cookbook repository:

bash git clone https://github.com/ProjectPythia/cookbook-example.git

  1. Move into the ocean-bgc-cookbook directory bash cd ocean-bgc-cookbook
  2. Create and activate your conda environment from the environment.yml file bash conda env create -f environment.yml conda activate ocean-bgc-cookbook-dev
  3. Move into the notebooks directory and start up Jupyterlab bash cd notebooks/ jupyter lab

Owner

  • Name: Project Pythia
  • Login: ProjectPythia
  • Kind: organization
  • Email: projectpythia@ucar.edu
  • Location: United States of America

Community learning resource for Python-based computing in the geosciences

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this cookbook, please cite it as below."
authors:
  # add additional entries for each author -- see https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md
  - family-names: Romashkov
    given-names: Lev
    orcid: https://orcid.org/0009-0006-4640-3800
    website: https://github.com/rmshkv
    affiliation: UCAR/NCAR 
  - family-names: Krumhardt
    given-names: Kristen
    orcid: https://orcid.org/0000-0002-8980-056X
    website: https://github.com/kristenkrumhardt
    affiliation: UCAR/NCAR
  - name: "Ocean Biogeochemistry Cookbook Contributors" # use the 'name' field to acknowledge organizations
    website: "https://github.com/ProjectPythia/ocean-bgc-cookbook/graphs/contributors"

title: "Ocean Biogeochemistry Cookbook"
abstract: "This Project Pythia Cookbook covers working with various sources of ocean biogeochemistry data, including Community Earth System Model (CESM) output and observational data. It provides a brief introduction to some metrics important to ocean biogeochemistry, from physical quantities like temperature to biological quantities like plankton biomass. It also demonstrates some of the data science techniques used to work with this information, and provides an introduction to the relationship between modeled and observational estimates."

GitHub Events

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  • Issues event: 3
  • Watch event: 1
  • Issue comment event: 8
  • Push event: 56
  • Pull request review event: 4
  • Pull request review comment event: 5
  • Pull request event: 7
  • Fork event: 3
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Last Year
  • Issues event: 3
  • Watch event: 1
  • Issue comment event: 8
  • Push event: 56
  • Pull request review event: 4
  • Pull request review comment event: 5
  • Pull request event: 7
  • Fork event: 3
  • Create event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: about 3 hours
  • Total issue authors: 0
  • Total pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.75
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: about 3 hours
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.75
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • erogluorhan (1)
  • rmshkv (1)
Pull Request Authors
  • jukent (4)
  • brian-rose (1)
  • ktyle (1)
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bug (1)
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Dependencies

.github/workflows/nightly-build.yaml actions
.github/workflows/publish-book.yaml actions
.github/workflows/trigger-book-build.yaml actions
.github/workflows/trigger-delete-preview.yaml actions
.github/workflows/trigger-link-check.yaml actions
.github/workflows/trigger-preview.yaml actions
.github/workflows/trigger-replace-links.yaml actions
  • actions/checkout v4 composite
  • jacobtomlinson/gha-find-replace v3 composite
  • stefanzweifel/git-auto-commit-action v5 composite
environment.yml conda
  • cartopy
  • cftime
  • dask
  • dask-jobqueue
  • distributed
  • h5netcdf
  • ipykernel
  • ipywidgets
  • jupyter-book
  • jupyter_server
  • jupyterlab >=3
  • matplotlib
  • metpy
  • nc-time-axis
  • netcdf4
  • numpy
  • pandas
  • pip
  • pop-tools
  • python
  • rioxarray
  • sphinx-pythia-theme
  • xarray
  • zarr