Set Up a Notebook Repository¶

To provide pre-packaged example notebooks for your dataset, set up and link a GitHub repository from the File Exploration section of your record. When users click Explore the Data, notebooks from that linked repository are included in their environment.

Create the Repository¶

There are two ways to set up your notebook repository. Most users should choose the automated setup (Option A), which creates and links the repository for you. Use the manual setup (Option B) only if you prefer to manage repository creation yourself.

Option A: Automated Repository Creation (Recommended)¶

This is the easiest way to get a correctly configured repository with starter notebooks.

1. Open your dataset record and go to the File Exploration section
2. Click Setup Repository
3. In the modal, select Create a new repository for me (Recommended)
4. If prompted, authorize MSD-LIVE to access your GitHub account:
   • Click Connect with GitHub
   • Open the GitHub authorization URL that appears
   • Enter the provided authorization code
   • Return and click Next
5. Select the repository owner (typically your project organization) and enter a repository name
6. Click Create Repository

MSD-LIVE will create the repository, pre-populate it with starter notebooks, and automatically add the repository URL to your dataset record.

Option B: Manual Repository Creation¶

If you prefer to create and manage the repository yourself:

1. Create a repository from the MSD-LIVE template repository
2. In your dataset record's File Exploration section, paste the GitHub repository URL into the notebook repository field
3. Save your record changes

Manage Your Repository¶

Adding New Notebooks¶

After your data has been uploaded to your MSD-LIVE dataset and the notebook GitHub repository has been linked, you have two options for creating notebooks.

Option A: Upload notebooks directly¶

1. Clone your repository locally
2. Create new notebooks and a README.md file
3. Commit and push to GitHub
4. The changes will be reflected the next time users open Explore the Data

Option B: Use our Notebook Lab environment (Recommended)¶

Use the Notebook Lab environment to create and manage notebooks in MSD-LIVE.

• Your dataset's data is automatically mounted and accessible
• Built-in GitHub integration allows you to create pull requests directly from the Jupyter Notebook environment
• No need to download and re-upload files manually

Our Notebook Lab help page provides step-by-step notebook authoring instructions.

Reviewing Community Contributions¶

Users can contribute notebooks back to your dataset via pull requests. You can:

• Review pull requests from users
• Suggest changes or improvements
• Merge contributions you want to include
• Decline contributions that don't fit your dataset

See Save Notebooks for more details on the pull request workflow.