saskiad / example-notebooks

DANDI example notebooks

Example notebooks

This repository contains example notebooks associated with datasets, conference tools, or more generally notebooks that illustrate the use of data on DANDI. This repository is cloned into the DANDI JupyterHub environment. Please note that you will need to visit https://dandiarchive.org and sign in once to get access to the JupyterHub.

Submission instructions

To add new notebooks, please send a Pull Request. Submissions should use the following file structure:

example-notebooks/
└── <dandiset id>/
    └── <org or lab name>/
        └── <mnemonic for paper or analysis>/
            ├── environment.yml
            ├── README.md
            ├── <analysis 1>.ipynb
            ├── <analysis 2>.ipynb
            ├── ...
            └── <analysis n>.ipynb

For example, 000055/bruntonlab/peterson21

The README.md file should explain the goal of the submission, provide links to relevant scientific publications, and explain the purpose of each notebook file.

The environment.yml file should define the dependencies of the environment required for the notebooks to be executed. environment.yml files are like requirements.txt files, but are designed to work with conda. To create this file, follow these steps:

1. Create a new environment: conda create -n <env-name> -python <python-version>
2. Switch into that environment: conda activate <env-name>
3. Use conda install <pkg> and pip install <pkg> to install the necessary dependencies until the notebook(s) run through successfully.
4. Confirm that all the notebooks can be run without error.
5. Export the environment: conda env export > environment.yml.

See detailed instructions for creating a environment.yml file.

Feel free to reach out on the DANDI helpdesk with any questions.