Tour the Narrative Interface

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 keep the Welcome cell, collapse it by clicking the "-" button in the top right corner of the cell or delete it by selecting "Delete cell" from the "..." dropdown menu.

The Welcome Cell

When you first create a Narrative, you may notice the Markdown cell that says "Welcome to the Narrative". This is a quick link to this documentation site and shares information on any service status for kbase.us.

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

Managing Narratives and accessing resources

1. Top menu

Menu options (accessed by clicking the three dark grey small horizontal lines on the upper left of the window) while in a Narrative:

• Narrative Interface lets you access other Narratives 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.

• Shutdown and Restart closes and relaunches the Narrative Interface (which can be useful if your content fails to load or the Narrative appears frozen).

The top-level menu (accessed by clicking the three blue small horizontal lines on the upper left of the window) offers additional possibilities:

• Narrative Interface goes to the main Narrative Interface, which allows you to create, edit, run, and share Narratives.

• New Narrative opens a new Narrative in a new window.

• JGI Search goes to the Data Search tab that can also be reached by the Search icon in the side bar.

• Biochem Search goes to the Compound and Reaction search tabs.

• KBase Services Status goes to a page that describes the current version of the Narrative Interface.

• About opens a page that describes the KBase User Interface and connects to the KBase GitHub.

• Contact KBase lets you contact the KBase Help Desk with your question, bug report, or feature suggestion.

• Support brings you to the Narrative User Guide.

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 controls

• Help menu (“?”) — links to documentation as well as to the Narrative Tour.

• Kernel menu (intended for developers; do not use).

• Share button — make your Narrative public or give specific KBase users the ability to view, edit, or share it further.

• Save icon — Be sure to save your work often.

• User icon — sign in/out or access your user profile.

6. 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.

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. Add Data ).

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. Add Data

This opens the Data 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. Markdown Cell

Use Markdown language to add rich text commentary and graphics to your Narrative.

14. Data Cell

These cells share details and describe individual data objects present within the Narrative. There are cell controls at the top right, similar to app and markdown cells.

15. App Cell

There are several types of cells, including those displaying app inputs and outputs, text and commentary, and code cells for writing custom scripts. The cell controls are at the top right of each cell.

16. 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!