Tour the Narrative Interface

Take the tour!

To start the tour, select “Narrative Tour” from the “?” menu. This new feature walks you through the user interface, pointing out various useful aspects of it. We recommend taking the tour even if you’ve used KBase before, as it will help familiarize you with the new version.

When you open a new Narrative, a “Welcome” cell will appear at the top, offering quick tips for getting started and links for accessing help. You can collapse this cell using the “v” icon at the top left, or delete it with the trashcan icon.

Before adding data and analysis steps to your Narrative, take some time to explore a few high-level features of the Narrative Interface.

Not yet updated for Release 3.0

The screenshot above is from the previous release–it will be updated soon. The December 2016 release (3.0) looks a bit different, though the overall operation is similar.

Managing Narratives and accessing resources

1. Top menu

  • Search Data allows you to explore some of the many types of public data integrated into KBase’s reference collection and to perform sequence homology searches.
  • Dashboard lets you access your Dashboard from a Narrative.
  • About the Narrative opens a window describing Narrative Interface properties (including version number) and provides a link to notes about the latest KBase release.
  • Bulk Import goes to the new (beta) interface for uploading large data files or multiple data files at once.
  • Shutdown and Restart closes and relaunches the Narrative Interface (which can be useful if your content fails to load or the Narrative appears frozen).

2. KBase logo — Links to the KBase home page, kbase.us.

3. Narrative title and creator — Click in this space to name (or rename) your Narrative.

4. Toggle view-only mode —  In view-only mode, you can look at the Narrative but not run or change it.

5. Narrative tabs

  • Analyze tab consists of the Data Panel (see #8) and the Apps Panel below it (see #11).
  • Narratives tab allows you to create a new Narrative, copy an existing Narrative, and see a list of other Narratives created by or shared with you.

6. Narrative controls

  • Help menu (“?”) links to documentation as well as to the Narrative Tour.
  • Kernel menu (intended for developers; do not use).
  • Share button lets you make your Narrative public or give specific KBase users the ability to view, edit, or share it further.
  • Save — Be sure to save your work often.
  • Person icon lets you sign in/out or access your user profile.

Adding data and apps

7. Data Panel You can add data to your Narrative by searching KBase’s reference collection, importing datasets from external sources, or generating new data from KBase analyses. All data objects from these activities will be listed in this panel, which is empty when you create or open a new Narrative.

8. Data Panel controls — Use these icons to search, filter, sort, and refresh the data in your panel. The right arrow will open the Data Browser (see #10).

9. Data object — Each data object in the panel can be expanded to see more information about the data and several options for downloading, viewing data provenance, and more. The “Add Data to your Narrative” section describes how to get more information about each data object.

10. Access to Data Browser— This browser, described in detail in the “Explore Data” and “Add Data to your Narrative” sections, provides options for working with your own data or data from KBase’s reference collection.

11. Apps Panel — This panel lists KBase analysis functions. Clicking the app name or icon beside it will add an analysis cell to your Narrative (see “Analyze Your Data Using KBase Apps” for details).

12. App controls  Use these icons to search and refresh the list of apps, as well as expose apps that are available but still in beta. The right arrow will open the App Catalog, which provides advanced options for browsing apps; designating them as favorites; and filtering them based on analysis type, popularity, and more. For additional information, see Browse KBase Analysis Tools.

Running analyses and adding commentary

13. Narrative cell — There are several types of cells, including those displaying app inputs and outputs, text and commentary (in markdown format), and code cells for writing custom scripts. The cell controls are at the top right of each cell.

15. Markdown and code cell buttons — Click to add these types of cells to your Narrative. Stay tuned for more documentation on how to use code cells in the future!