Now that you are familiar with ways to find and explore data in KBase, you can select or upload data to analyze. Locate the Data Panel along the left side of the screen and click the Add Data button, the red “+” button, or the right arrow at the upper right of the panel to access the slideout Data Browser.
Any data that you upload to KBase is kept private unless you explicitly choose to share it. You can share any of your Narratives (including their associated data) with one or more specific users, or make it publicly available to all KBase users. Please see the Sharing page for more information about how to do that. The Terms and Conditions page describes the KBase data policy.
Let’s look closer at the five tabs of the Data Browser:
If you hover your cursor over any data object under the first four tabs, options will appear allowing you to add that object to your Narrative or find out more about it.
In the previous section, we described the process of adding a genome to your Narrative from the public data in KBase. Now let’s check out the different data types available under the Example tab. The icon to the left of each data object represents its data type.
As described in the previous section, the Add button next to these icons lets you add the data object to your Narrative. You can add more more data to your Narrative from the Example tab to try out various KBase apps.
With the click of a button, you can now transfer microbial genome reads and assemblies from the DOE Joint Genome Institute (JGI) to KBase’s Narrative Interface for assembly, annotation, metabolic modeling, and more. The Push to KBase feature lets you select raw or quality-controlled read data from sequencing projects available on JGI’s website and add them to a Narrative of your choice, all in a few simple steps.
Want to work with the data even faster? Use Push to KBase to launch the Assemble and Annotate Microbial Genome app in a new Narrative where the JGI data will be pre-loaded and ready to analyze.
You can find out more about using the new (beta) Bulk Upload interface in the Bulk Upload Guide. The guide that you are currently looking at discusses how to upload data via the Narrative User interface.
Currently, you can import a genome into your Narrative by (1) uploading a GBK file stored locally on your computer or (2) importing a file from GenBank’s FTP site. This example will demonstrate the first option.
Under the Import tab, select Genome from the “Data Type” dropdown and then click Next.
You will be presented with a panel that has tabs called Upload GenBank File and Import from FTP. Make sure you have chosen the first tab and then click the blue Select file button to browse for a GenBank (GBK) file on your computer. Once you have located the file and see “100.0%” to its right, type in a name for your genome object in the Genome Object ID field (being sure not to use any spaces or special characters in the name).
When completed properly, both required fields will have a green check mark next to them.
When the data has finished uploading, you should see the newly added genome in your Data Panel.
When you’re done adding data objects to your Narrative, you’ll want to close the Data Browser slideout panel, since it covers part of your Narrative main panel. You can use the “Close” button at the lower right corner of the Data Browser, but if you have a small screen, you might not be able to see that button. Another way to close the Data Browser is to click the arrow on the top right of your Data Panel (the same one that opens the Data Browser slideout).
KBase is rolling out new upload interfaces, including Bulk Upload (for large datasets), upload apps, and the ability to drag-and-drop data into your Narrative. We welcome your suggestions for future upload functionality, and bug reports on current uploaders.
Once you have added data–your own data or reference data that is already in KBase–to your Narrative, you will be ready for the exciting part: analyzing it! The next two sections describe how to choose and run an app to analyze your data.