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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #365862

Research Project: GrainGenes: Enabling Data Access and Sustainability for Small Grains Researchers

Location: Crop Improvement and Genetics Research

Title: JBrowse Connect: a server API to connect JBrowse instances and users

item YAO, ERIC - University Of California
item BUELS, ROBERT - University Of California
item STEIN, LINCOLN - Ontario Cancer Institute
item Sen, Taner
item HOLMES, IAN - University Of California

Submitted to: PLoS Computational Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/27/2020
Publication Date: 8/18/2020
Citation: Yao, E., Buels, R., Stein, L., Sen, T.Z., Holmes, I. 2020. JBrowse Connect: a server API to connect JBrowse instances and users. PLoS Computational Biology. 16(8).

Interpretive Summary: The JBrowse Connect framework is an optional extension to JBrowse, a genome browser deployed at several thousand websites with users numbering in tens of thousands. Being implemented entirely in the JavaScript computer language, JBrowse is highly interactive, but has previously been usable primarily as the endpoint of an analysis workflow. The extension we have developed allows users to initiate bioinformatics analyses from within the genome browser, opening up new potential for iterative visualization and analytic exploration of genomics data.

Technical Abstract: 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.