New GenePattern Notebook Features
October 2019


The following new features have recently been added to the GenePattern Notebook environment.

General Features

  • UI Builder cells now support file uploads larger than 2GB.
  • A "Rich Text" option is now available from the cell type dropdown menu in the notebook toolbar. Selecting this cell type will add a rich text editor cell.
  • The UI Builder now supports R cells through the use of R magic commands. To learn how to use this new feature, please read the R Support section of the Programmatic User Guide.

Programmatic Features

  • Users can now define and import UI Builder widgets within Python modules. To make use of this feature, either upload a Python file using the Upload button in the upper right-hand corner of the Files tab or create new Python script via the New button in the upper right-hand corner of the Files tab. The Python script can then be loaded and run inside a new or existing notebook using the following syntax
    %run myPyScript.py
    The included UI Builder widget will then also be available for reuse within that notebook via the Notebook tab in the tool manager; which can be accessed from either the Tools button in the notebook toolbar, or the button which is available on the left of the screen when a GenePattern cell is selected.
  • Widget and parameter descriptions, for both the UI Builder and GenePattern widgets, now support HTML formatting.
  • The UI Builder now supports the ability to change what tab a tool appears in, in the tool manager. (The default is either “Notebook” or the name of the module/file the tool was imported from.) To learn how to use the origin override, please see the UI Builder> Other Options section of the Programmatic User Guide.

Administrative & Miscellaneous Features

  • The Notebook workspace has been updated to Jupyter 6.
  • UI Builder widgets with no parameters will now be shown in a condensed display.
  • Support for Python 3.5 has been dropped.
  • The rich text widget has been updated to TinyMCE 5
  • Updated to Plotly 4.0 in the Python 3.7 kernel.
  • Template cells have been moved to tab in the tool manager.
  • Updated GenePattern Notebook and GenePattern Notebook Workspace Docker images have been released. These updates are based on the Jupyter Docker Stacks and include improved support for common Python libraries, streamlined configuration, theming support and improved backend configuration.

For technical details, please see the Release Notes