Enhancing the GMOD Suite of Genome Annotation and Visualization Tools

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DESCRIPTION (provided by applicant): The Generic Model Organism Database Project is an open-source community effort to bring standardization and interoperability to software tools for genome informatics. The GMOD software suite includes many programs for the analysis, management, visualization and integration of biological data. Amongst the most visible and popular of these tools are the GBrowse genome browser (which makes genome sequence and annotation data accessible over the world-wide web) and its successor JBrowse (which significantly upgrades the GBrowse user interface to make it comparable to newer web applications, such as GMail or Google Maps). Other GMOD tools include Chado (a relational database schema and software layer for managing genome annotations), Apollo (a program with which biocurators can edit annotations), Maker (a workflow automator for generating annotations computationally) and Galaxy (a suite of tools for interactive comparative genomics). During the initial funding period of this proposal, we developed the initial release of JBrowse, enhanced GBrowse to display population diversity data, and established the GMOD Help Desk position to increase penetration of the GMOD tools, especially infrastructural components. In this renewal period, we will continue work on JBrowse, concentrating on scalability to large problems (including display of high-volume short-read sequencing data); extensibility (so as to permit individual GMOD developers to customize their browsers); portability issues (including implementations on mobile devices); and community annotation features (so that scientists can upload, share, review, mark-up and discuss annotations over the web, as well as viewing annotations already in the database). We will also work on developing tools to assist current GBrowse users in migrating to JBrowse, while continuing legacy support for GBrowse. Finally we will continue to support the GMOD Help Desk, with emphasis on transcriptomics and next-generation sequencing data, population genomic and diversity data, workflow and pipeline tools, software interoperability issues, and support of GBrowse and JBrowse.