Publish and Share Notebooks

How to share or publish notebooks in the GenePattern Notebook environment

Contents

Publishing Notebooks


  • To publicly share a notebook, click the checkbox next to that notebook and then click the "Publish" button on the toolbar above.

  • This will open a dialog with a short form, prompting you to enter the author's name, the quality and a brief description. Fill out this information and then click the "Publish" button on the dialog.

  • Your notebook should now be available to the public and should appear on the "Notebook Library" tab in the "Prerelease" section.

  • The published version of the notebook is a checkpoint of the notebook at the time it was published. Any changes you make to the notebook in the future are not copied over to the published version unless you explicitly choose to update the notebook in the public library.

Updating or Removing a Public Notebook

  • You can update or remove a notebook that you have made public by first clicking the checkbox next to the notebook and then clicking the "Publish" button.
  • In the dialog that comes up you will have the option to edit any of the notebook's metadata, such as author name, description, etc.
  • To update or remove the notebook, click the "Update" or "Unpublish" buttons, respectively.

Sharing Notebooks


GenePattern Notebook provides the ability to share notebooks with others. This allows for easy collaboration between notebook users.

Sharing a Notebook

  • Log in to the GenePattern Notebook Workspace.
  • Click the checkbox next to that notebook you wish to share and then click the "Share" button on the toolbar above.
  • This will open a dialog with a short form, prompting you to enter the username or email of each user with which you wish to share the notebook. Enter this information and click the "Add" button. Do this for each user you wish to share with and then click "Share."
  • A sharing invitation will be sent to these users. Once they accept, they will be able to view and edit the notebook.

Accepting the Invitation

  • Log in to the GenePattern Notebook Workspace.
  • To view your sharing invites, click the "Notebook Library" tab and then click "Shared With Me" on the left. This will display a list of invitations.
  • Click an invite in the list and a dialog box will open, prompting you to accept or decline the invitation. Click the corresponding button.
  • If you accept the invitation, you will be prompted to either run the notebook or close the dialog.

Accessing the Shared Notebook

  • Log in to the GenePattern Notebook Workspace.
  • To view your shared notebooks, click the "Notebook Library" tab and then click "Shared With Me" or "Shared by Me" on the left. This will display a list of notebooks that you are either sharing or which are currently being shared with you.
  • Click the notebook in the list. This will open a dialog with some information about the notebook and your available options.
  • Click the "Run Notebook" button.

Project Sharing and Publishing - Coming in June 2021!

The instructions below are for our upcoming project publishing and sharing functionality.

Contents

Publishing Projects


  • To publicly share a project, click the project's gear menu and then select "Publish" in the list.

  • This will open a dialog with a short form, prompting you to enter the author's name, the quality and a brief description. Fill out this information and then click the "Publish" button on the dialog.

  • Your project is now be available to the public and will appear on the "Public Library" section below.

  • The published version of the project is a checkpoint at the time it was published. Any changes you make to the project in the future are not copied over to the published version unless you explicitly choose to update the project in the public library.

Updating or Removing a Public Project

  • You can update or remove a project that you have made public by first clicking on the gear menu for the project and then selecting "Publishing" in the list.
  • In the dialog that comes up you will have the option to edit any of the project's metadata, such as author name, description, etc.
  • To update or remove the project, click the "Update" or "Unpublish" buttons, respectively.

Sharing Projects


GenePattern Notebook provides the ability to share projects with others. This allows for easy collaboration between users.

Sharing a Project

  • Log in to the GenePattern Notebook Workspace.
  • Find the project you wish to share, click the gear menu on the project and then select "Share."
  • This will open a dialog with a short form, prompting you to enter the username or email of each user with which you wish to share the project. Enter this information. Type comma or tab between users. Do this for each user you wish to share with and then click "Share."
  • A sharing invitation will be sent to these users. Once they accept, they will be able to view and edit the project.

Accepting the Invitation

  • Log in to the GenePattern Notebook Workspace.
  • To view your sharing invites, scroll down to the section named "Shared With Me." This will display a list of invitations.
  • Click "Accept Invite" to accept a sharing invitation. Click "Reject Invite" to reject an invitation.
  • If you accept the invitation, you may then click on the project to access it.

Accessing the Shared Notebook

  • Log in to the GenePattern Notebook Workspace.
  • To view your shared projects, scroll down to the section named "Shared With Me." This will display a list of projects shared with you.
  • Click a project in the list to access it.