Usability remains a significant barrier to broader adoption of cutting-edge bioinformatics tools, due to a lack of user-friendly web interfaces. The Generic Model Organism Database (GMOD) provides standards-based software components from which web-facing genome databases can be quickly assembled. JBrowse, the genome browser of GMOD, aims to democratize genome informatics by making genome annotations and sequence analysis tools more accessible to the broader community of biologists, using JavaScript and the dynamic web. JBrowse is now in active use by thousands of websites and tens of thousands of users. In this phase of the project, we plan to build a synteny browser into JBrowse, so that users can rapidly navigate between related genomes, view evolutionarily conserved gene structures and their associated alignments, and visualize genome annotations in their phylogenetic context. This synteny browser will have the same responsiveness and interactivity as JBrowse, with smooth panning, zooming, filtering, sorting, and searching available as drag-and-drop operations from within the web browser. We will also significantly improve JBrowse's performance at scale: many JBrowse instances have hundreds or thousands of tracks, demanding efficiency optimizations, more compact visualization, and user interface enhancements to promote data discoverability. We will develop a graphical interface for customizing JBrowse, configuring its appearance and behavior, and installing plugins, in the style of the Wordpress blog platform. We will build on the newly-developed JBrowse analysis server to make standard read-to-reference alignment tools (BWA and BowTie) available to users from within the browser, and we will make new visualizations available for RNA-Seq, population genomics, epigenomics, and other data types. Finally, we will continue GMOD's outreach/helpdesk efforts with focused workshops, training materials, and documentation to maximize the utility of GMOD/JBrowse to the broader community.
The mission of GMOD and JBrowse is to make genome data accessible using the tools of the dynamic web. Over 50,000 users regularly view genome annotations with JBrowse, but currently JBrowse only shows isolated genomes, not relationships between genomes. We propose to add visualizations of evolutionary synteny to JBrowse, along with several other datatypes; to improve JBrowse's performance on large datasets; and to add features allowing customization and administration of JBrowse over the web.
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