(Last updated March 2017)
In KBase, you can create shareable, reproducible workflows called Narratives that include data, analysis steps, results, visualizations and commentary. The way you access KBase functionality is via the Narrative Interface. This Quick Start provides an overview of several key features of the Narrative Interface. For more detailed information, please see the Narrative Interface User Guide.
Globus provides the secure platform used to manage user access to KBase. From the initial sign-up page, click “Continue” to access a form where you will provide basic account and profile information as well as agree to KBase usage terms and conditions.
Once you fill in the required information and click “Create ID,” check your email for a message from Globus containing a verification code. Follow the instructions in the message to use the code to confirm your account. Upon confirmation, you will be asked to join the KBase users group. Once you join, you are ready to log into KBase.
The Narrative Interface can be accessed at narrative.kbase.us. After you sign in, you will be taken to your Dashboard (details of which can be found here). From the Dashboard, you can open your existing Narratives, access others that have been shared with you, and create new Narratives.
Click the “+ New Narrative” button in the Dashboard to open a new untitled Narrative. A “Welcome to the Narrative Interface” box offers some suggestions for adding content to your Narrative. You can collapse or delete this box using the “…” menu in its top right corner.
Select the “Narrative Tour” from the Help 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.
To load data to your Narrative, click the “Add Data” button, which can be found under the Analyze tab near the top left of the Narrative. The Data Browser will slide out with tabs that show several data sources.
You can choose a dataset already in KBase by selecting any of the first four tabs. The Example tab, for instance, contains sample data from KBase’s reference data collection that can be used to try out the apps.
The Import tab allows you to upload your own data. KBase currently supports upload of Assemblies (assembled contig sequences), expression matrices, flux balance analysis models, genomes, growth media, phenotype sets, and short reads. Please see the Data Upload/Download Guide for more information.
Note that any data you upload to KBase is private unless you choose to share it.
When you hover over a data object in the Data Browser, an “Add” button will appear to its left. Click this button to add the data to your Narrative.
Notice that the data object now appears in your Data Panel. Once you finish adding data, exit the Data Browser by clicking either the “Close” button at the bottom left of the browser window or the arrow at the top right of the Data Panel.
Don’t forget to periodically save your Narrative by clicking the “Save” button at the top right of the interface.
Once data is added to your Narrative, you can analyze it using one or more of the KBase apps listed in the Apps panel below your data.
KBase’s App Catalog (see screenshot below) provides even more options for browsing apps; designating them as favorites; and filtering them based on analysis type, popularity, and more. Access this catalog by clicking the arrow at the top right of the Apps panel.
To add an app to your Narrative from the App Panel or App Catalog, click on its name or icon. You can get more information about an app by hovering over it in the App Panel until a “…” appears.
Fill in all the required fields in your app. Note that some app fields are “smart” and know which data in your Narrative is valid for that field. These “smart” fields have a pulldown list of all the data objects from your Data Panel that you can choose from as input.
When required fields are specified, the red arrows next to those fields will disappear. Click the green “Run” button near the top left of the app cell to start the analysis.
While the analysis is running, you will see the progress in the Job Status tab of the app box. When it finishes, the results will show up in the Result tab.
Please see the KBase Apps section of the Narrative Interface User Guide for more details on running apps.
All Narratives that you create are private by default. You can make a Narrative public or share it with specific collaborators by clicking the “share” button near the top right.
With these basic steps, you now can begin using the Narrative Interface to create Narratives and analyze data. An extensive set of tutorials is available: