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.

Public Health Relevance

The Generic Model Organism Database software suite, especially the genome browser programs GBrowse and JBrowse, have had a transformative effect on model organism genomics. We plan numerous enhancements of these tools to meet the challenges of displaying next-generation sequencing data and community annotation of genomes, and to support migration of the many GBrowse users to the more recent JBrowse. Through continued support of the GMOD Help Desk Position, we will increase penetration and utility of the GMOD software suite.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG004483-05
Application #
8328945
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Bonazzi, Vivien
Project Start
2007-09-01
Project End
2014-05-31
Budget Start
2012-06-01
Budget End
2013-05-31
Support Year
5
Fiscal Year
2012
Total Cost
$427,095
Indirect Cost
$80,282
Name
University of California Berkeley
Department
Biomedical Engineering
Type
Schools of Engineering
DUNS #
124726725
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