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.

Agency
National Institute of Health (NIH)
Type
Research Project (R01)
Project #
2R01HG004483-07
Application #
8698118
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Wellington, Christopher
Project Start
Project End
Budget Start
Budget End
Support Year
7
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of California Berkeley
Department
Biomedical Engineering
Type
Biomed Engr/Col Engr/Engr Sta
DUNS #
City
Berkeley
State
CA
Country
United States
Zip Code
94704
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