The long-term objective of this project is to democratize the collaborative annotation, analysis, and sharing of genomes, much as the "social web" has democratized web publishing and communication. The main vehicle for this will be JBrowse, the most feature-rich JavaScript/HTML5-based genome browser. This renewal, building on the previously-developed event-driven plugin framework for JBrowse (an example of which is the recent WebApollo app for collaborative curation of genome annotations), will generate a range of "analysis plugins" for interfacing with common tools and visualization paradigms from bioinformatics, phylogenetics, and population genetics, as well as back-end workflow managers (e.g. Galaxy, Maker), analysis packages (Bioconductor), and general queuing engines (SGE) and distributed computation systems (Hadoop MapReduce). A parallel deliverable is a new and completely integrated 2D circular-geometry view within JBrowse, which offers a conveniently dense representation of certain genome relationships (genomic synteny, cancer genome rearrangements, and bacterial genomes) with animated transitions to other views. We will continue in our support and outreach efforts, proactively offering upgrades to the ~3000 current installations of the previous official Genome Browser from the GMOD group (GBrowse), and ensuring that the ~400 current JBrowse installations (and many thousands of JBrowse users) remain up to date with the latest visual analysis tools in the JBrowse toolbox.

Public Health Relevance

This project will provide web-based tools for visualizing, navigating, and analyzing genomes and relationships between genomes. It will be directly useful to clinicians, molecular biologists, bioengineers, and others analyzing genome data in order to understand variant genotypes, comparative genomics, tumorigenesis, and other areas of biology that can be related to genes and genomics.

National Institute of Health (NIH)
Research Project (R01)
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Biodata Management and Analysis Study Section (BDMA)
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Wellington, Christopher
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University of California Berkeley
Biomedical Engineering
Biomed Engr/Col Engr/Engr Sta
United States
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Westesson, Oscar; Skinner, Mitchell; Holmes, Ian (2013) Visualizing next-generation sequencing data with JBrowse. Brief Bioinform 14:172-7
De Maio, Nicola; Holmes, Ian; Schlotterer, Christian et al. (2013) Estimating empirical codon hidden Markov models. Mol Biol Evol 30:725-36
Skinner, Mitchell E; Holmes, Ian H (2010) Setting up the JBrowse genome browser. Curr Protoc Bioinformatics Chapter 9:Unit 9.13
Skinner, Mitchell E; Uzilov, Andrew V; Stein, Lincoln D et al. (2009) JBrowse: a next-generation genome browser. Genome Res 19:1630-8