JBrowse Connect: A server API to connect JBrowse instances and users

We describe JBrowse Connect, an optional expansion to JBrowse that allows live messaging via WebSockets, notifications for new annotation tracks, heavy-duty analyses initiated by the user from within the browser, and other dynamic features. We present JBlast, an example application of JBrowse Connect that allows users to specify and execute BLAST searches, managed by a Galaxy instance, as well as tracking job progress and viewing results, all in the context of the browser.