Oceandata Notebooks

Welcome to the repository of tutorials for users of the Ocean Biology Distributed Active Archive Center (OB.DAAC).

For Data Users

Head over to our Help Hub to access the website published from this repository.

For Notebook Authors and Reviewers

The Help Hub team supports development of these resources by authoring or updating content as well as reviewing contributions from the public. We welcome contributions in the form of new notebooks or suggestions from anyone, but ask all to observe our CODE_OF_CONDUCT. Please also take a minute to familiarize yourself with the following information about our notebooks, which are formatted as MyST Markdown rather than as Jupyter Notebooks. Note that our CONTRIBUTING guide is primarily of use to team members.

Editing MyST Markdown

Important

• Edit notebooks in JupyterLab so Jupytext can do its magic.
• The entire notebooks folder is ignored by Git, so it's not present on GitHub.

Keeping Jupyter Notebooks (.ipynb) in a code repository is tough for collaboration because Jupyter Notebooks contain large, binary outputs and metadata that frequently change. By means of the Jupytext extension to JupyterLab, MyST Markdown (.md) files can be opened like notebooks without saving content troublesome for collaboration. Going one step further, Jupytext can pair an actual Jupyter Notebook file with a MyST Markdown file. That lets us enjoy the benefits of Jupyter Notebooks (e.g. saved outputs and metadata) while only storing MyST Markdown in the repository.

What does this mean for authors and reviewers? You can use Jupyter Notebooks in the notebooks folder normally, but you must commit the synchronous changes to the paired MyST Markdown files within the docs/notebooks folder. To create the notebooks folder after cloning the repository, or to add a paired Jupyter Notebook when a new MyST Markdown file is pulled, run the following Terminal command. It tells Jupytext to synchronize, creating if necessary, the paired Jupyter Notebook files with the MyST Markdown files tracked by Git.

jupytext --sync $(git ls-files docs/notebooks)

Create a New Notebook

Note

Create new notebooks by copying COPYME.ipynb into a suitable location within the top-level notebooks folder.

When you save your new notebook, watch for a new markdown file to appear in the docs/notebooks folder and add that file to a commit.

How to Cite

If you reference the tutorials in a publication, or report on work performed using the oceandata-jupyterlab container image, please cite as follows:

Carroll, I., Windle, A., Wang, G., Poulin, C., Foley, S., Gray, P., Holmes, E., Caplan, S., Allen, J., Gao, M., Danenhower, M., Chase, A., Aryal, K., Fu, G., Fasnacht, Z., Werdell, J., & Knowles, D. (2025). Tutorials using data produced by NASA's Ocean Biology Distributed Active Archive Center. Zenodo. https://doi.org/10.5281/zenodo.17642133

Acknowledgements

This repository has greatly benefited from works of multiple open-science projects, notably Learn OLCI and the NASA Earthdata Cloud Cookbook.