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.
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.
- 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 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.
- Contact KBase lets you contact the KBase Help Desk with your question, bug report, or feature suggestion.
- KBase Services Status directs to information on service versions and performance.
- KBase UI Plugins lists user interface plugins and their version info and links to GitHub.
- Developer links to developer tools and the configuration editor.
- Public Search can be used to locate data and filter by data types.
- About directs to information about the KBase User Interface and current version.
Click in this space to name (or rename) your Narrative.
- 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.
- 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.
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.
Use these icons to search, filter, sort, and refresh the data in your panel. The right arrow will open the Data Browser (see #10).
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.
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.
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).
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.
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.
Click to add these types of cells to your Narrative. Stay tuned for more documentation on how to use code cells in the future!