Public Notebook Collection

GenePattern Notebook provides a repository where users can publicly disseminate their notebooks. It includes notebooks developed by the GenePattern team demonstrating a number of genomic and machine learning analyses, as well as notebooks contributed by the user community.

When using the GenePattern Public Notebook Collection, users have the ability to publicly share their notebooks and to run notebooks shared by others.

1. Browsing and Loading Public Notebooks

  • Log in to the GenePattern Notebook Repository
  • To view the available notebooks, click the "Public Notebooks" tab and browse through the list.
  • To obtain a copy and run the shared notebook, click the notebook in the list and then select "Get a Copy" on the confirmation dialog that pops up. This will make a copy of the chosen notebook in your current directory, accessible by clicking on the Files tab.
  • To run the notebook, click the "Click here if you would like to open this notebook" link in the resulting dialog, or go back to the "Files" tab and run the notebook as normal from there.

2. Publicly Sharing 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 "Public Notebooks" tab. 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 repository.

3. 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.