When a user first opens a new genome, I think we should do this:

Show a screen that says mostly the same thing as the attached screen captures - CachingSequence1.png &
CachingSequence2.png.

Users would make the decision about caching the sequence at the beginning of their session.

I think it works better for people to see this message in the beginning - before they've started work. Asking them in the middle of the workflow as we do now seems to interrupt their flow and I think may result in their not proceeding with the download.

The screen shots are from OpenHelix GenomeBrowse, a non-open source browser that has borrowed a lot of ideas from IGB and other popular genome browsers.

Our text I think should say:

"Would you like to download the reference sequence? (heading - bold and large font to maximize readability)

For better, faster genome browsing, we recommend you store a local copy of the reference sequence for the selected genome version.
You can continue to use IGB while downloading.

Would you like to download the sequence? The file size is [fill in size] MB.
[checkbox Don't ask me about this genome again.] Yes No
"
(If user types ENTER, download begins)

If the user answers "yes" to the question, then they would see a downloads status window, similar to the attached file - "DownloadsStatus.png"

For more info about OpenHelix GenomeBrowse, see also http://www.ashg.org/2014meeting/abstracts/fulltext/f140123183.htm