KBase Documentation
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      • Access the Narrative Interface
      • Tour the Narrative Interface
      • Narrative Navigator
      • Create a Narrative
      • Explore Data
      • Add Data to Your Narrative
      • Browse KBase Analysis Tools
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      • FAQ: Assembly and Annotation
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      • FAQ: Comparative Genomics
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      • FAQ: Metagenomics & Community Analysis
    • Transcriptomic Analysis
      • FAQ: RNA-seq Analysis
    • Constructing Metabolic Models
      • Constructing and Analyzing Metabolic Flux Models of Microbial Communities
      • FAQ: Metabolic Modeling
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On this page
  • The Welcome Cell
  • Managing Narratives and accessing resources
  • 1. Top menu
  • 2. KBase logo
  • 3. Narrative title and creator
  • 4. Toggle view-only mode
  • 5. Narrative controls
  • 6. Narrative tabs
  • Adding data and apps
  • 7. Data Panel
  • 8. Data Panel controls
  • 9. Data Object
  • 10. Add Data
  • 11. Apps Panel
  • 12. App Controls
  • Running analyses and adding commentary
  • 13. Markdown Cell
  • 14. Data Cell
  • 15. App Cell
  • 16. Markdown and Code Cell buttons

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  1. Getting Started
  2. Narrative Interface User Guide

Tour the Narrative Interface

PreviousAccess the Narrative InterfaceNextNarrative Navigator

Last updated 1 year ago

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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:

  • 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.

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

2. KBase logo

3. Narrative title and creator

Click in this space to name (or rename) your Narrative.

4. Toggle view-only mode

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

10. Add Data

11. Apps Panel

12. App Controls

Running analyses and adding commentary

13. Markdown Cell

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!

Narrative Interface lets you access other from a Narrative.

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

KBase Services Status goes to .

About opens a page that describes the and connects to the .

Contact KBase lets you with your question, bug report, or feature suggestion.

Support brings you to the .

Links to the KBase home page: .

In , you can look at the Narrative but not run or change it.

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 “” section describes how to get more information about each data object.

This opens the Data browser, described in detail in the “” and “” sections, provides options for working with your own data or data from KBase’s reference collection.

This panel lists KBase analysis functions. Clicking the app name or icon beside it will add an analysis cell to your Narrative (see “” for details).

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 , 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 .

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

Narratives
Data Search
a page that describes the current version of the Narrative Interface
KBase User Interface
KBase GitHub
contact the KBase Help Desk
Narrative User Guide
kbase.us
view-only mode
Add Data to your Narrative
Explore Data
Add Data to your Narrative
Analyze Your Data Using KBase Apps
App Catalog
Browse KBase Analysis Tools
Markdown language