Girder 101

Logging in

In order to use Girder you need to log in by following the link in the upper right corner of the main page.

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The main Girder’s page

If you don’t have an account yet, you can register by either creating a local account or using OAuth with Google, GitHub or Bitbucket as provider. After a successful login, you will be able to access your folders, notebooks and account settings using the user menu in the upper right corner.

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A view of the main Girder’s page for an authenticated user

Each authenticated user is provided with a free space that can be accessed via user menu in the upper right corner and is initially populated with two folders:

  • Public - folder and its content is visible to all the other users,
  • Private - folder and its content is visible only to you.
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A view showing the userspace along with a user menu in the upper right corner.

You can modify the default permissions as you see fit using the yellow Access Control button.

Browsing Data

You can access the data stored in Girder by following Collections link on the left sidebar menu and following tree like structure in the main view.

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The default collections view.

Interacting with Data

At any place in the collection tree structure you can start Jupyter Notebook using folder actions menu:

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Folder action menu.

Once you click on a Start Notebook item you will be redirected to a persistent notebook. Inside you will find all the data contained in the folder from which you started the notebook along with the content of your girder’s Private folder.

You can view all your currently running notebooks by following My Notebooks from the user menu.

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My Notebooks list view.

Customizing Data in Notebooks

You can easily compose a custom dataset using the available data. In order to do that navigate to your userspace and create a new folder using User actions menu on right hand side:

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Creating a new folder.

Edit the name and the description of your new folder:

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Creating My research experiment folder.

Navigate to any collection and select folder or items using checkboxes on left hand side. Next, select Pick checked resources in the Checked actions menu:

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Selecting resources for a copy.

Go back to your recently created folder and again use the Checked actions menu to Copy picked resources:

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Copying resources to the current folder.

Selecting Start Notebook from the Folder actions menu:

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Copying resources to the current folder.

will redirect you to a notebook that contains newly copied data:

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Contents of data directory inside the Jupyter notebook.

If you go back to the Girder’s original folder, you’ll notice that Folder actions menu contains new items:

  • Visit Notebook - will redirect your browser back to the running notebook.
  • Stop Notebook - will gracefully shut the notebook down.

Upon stopping the notebook all *.ipynb files will be copied back to your Private folder, possibly overwriting current files.