I've added the PowerPoint document that Dr. Loraine mentioned to Google Drive: research-big-lorainelab > IGB Project Documentation and Plans > Galaxy Integration > IGBF-3960 > Bridge-Page-Storyboard.pptx (link)

I will create a new ticket for expanding this storyboard with the help of a naive user. We will then use the storyboard in combination with the ideas generated from this ticket and work on improving our IGB-Galaxy bridge pages.

Closing this ticket!

During a meeting, Paige Kulzer noted she has created a PowerPoint document with multiple screen captures showing her research. This would be a good starting point for creating a storyboard showing the workflow users follow in the different scenarios.

For our next steps, we think we ought to create more formal storyboards showing the workflow. We think that if we do that, it will be more obvious how to improve the workflow and reduce the number failed interactions we think users are having. Specifically, we observed that around half of the time, users who have successfully started IGB are providing a dbkey that IGB recognizes or are not providing a dbkey at all.

Here is a researcher who has done a lot of work in developing web services for looking up synonyms and other information about genes and genomes: https://www.scripps.edu/faculty/su/

Also, Nowlan Freese notes that Galaxy has a listing of available genome version (db key) names in Galaxy.

For review, please take a look through the issues and suggestions I've outlined here. Let's discuss which improvements we'd like to move forward with and make tickets accordingly before closing this ticket.

Variables I've identified and tested:

• Browser (Chrome vs Safari)
• Data type (BAM vs BED)
• Database (Unassigned vs assigned)
• IGB not open
• IGB open, no genome open
• IGB open, wrong genome open
• IGB open, right genome open, wrong version
  Note: OS also seems like an important variable to test, but I don't currently have access to a Windows machine.

Scenarios where the Galaxy BioViz bridge page could be improved:

1. The BioViz navigation bar and footer are not visible when viewing Galaxy BioViz bridge pages on Safari. There is a link to the Download Page present on the bridge page, but no navigation bar means no Install IGB button as well as no Help menu for people to find resources from.
2. The following message is displayed when trying to visualize a file in a Galaxy History with no Database/Build: "The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again." There's a high possibility for confusion here since the message does not provide any resources or instructions for fixing this issue in Galaxy. Also, what motivates an IGB user to fix this issue when the file opens on a custom genome in IGB regardless? They might believe that something is wrong with their data being displayed in IGB if they don't fix this issue, but to my understanding the Database/Build's value has no effect on how data is displayed in IGB.
3. The "Thank you for using IGB!" Galaxy BioViz bridge page is displayed no matter which genome is currently open in IGB (e.g., no genome open, wrong genome open, right genome open but wrong version). The presence of the Database/Build attribute in Galaxy, as well as my intuition, suggests that IGB would use that attribute to open the proper genome in IGB and then load the file for visualization against that genome. Therefore, I think it could be confusing for an IGB user to see this same bridge page for the various scenarios I listed here.

Suggestions for improvements:

1. Sravani has made a ticket for this first issue - see IGBF-3996.
2. Do we need this bridge page? How does Galaxy's Database/Build attribute affect how data is loaded in IGB? If we do decide to improve this page instead of changing it out altogether, this would be a great opportunity to mention and link to a GTN material ("Changing database/build (dbkey)") or possibly our new GTN tutorial. The tutorial includes instructions for assigning that Database/Build field which is what we're currently suggesting users do without providing any further instructions. Also, I suggest that we use the same terminology Galaxy does on this bridge page (e.g., use "Database/Build" instead of "genome version").
3. I suggest adding a line to the "Thank you for using IGB!" Galaxy BioViz bridge page to the effect of, "Make sure you had the right genome open when clicking Display in IGB in Galaxy as your data will simply appear in IGB as a new (empty) track.