GMOD: A User's Perspective

GMOD tools make it possible for research groups to set up genomic databases without needing to invest significant time and resources into software development. Our team consists exclusively of personnel with formal training in the life sciences, and acquired skills in bioinformatics programming. GMOD software allows us to efficiently provide bioinformatics support to large research communities. The relatively low programming skill level required to apply tools such as GBrowse also allows students with biology backgrounds to carry out GMOD-tool-based projects in bioinformatics training. We leverage a variety of GMOD tools for our projects, including the Bovine Genome Database (http://BovineGenome.org), Hymenoptera Genome Database (http://HymenopteraGenome.org) and OpossumBase (http://OpossumBase.org). These include genome browsers (GBrowse and JBrowse) and Chado databases. To facilitate data exchange, we use controlled vocabulary terms defined by the Sequence Ontology. We have provided resources for community annotation using Apollo, and are currently transitioning to WebApollo. The configurability of GMOD software has allowed us to accommodate the specific types of genomic datasets available in different research communities. We currently provide access to genomes and transcriptomes of 17 species (insects and mammals), and for some of those, we provide alternate versions of genome assemblies. Users have access to data such as computed and manually-annotated genes, protein homologs, orthologs, non-coding RNA, genetic markers, QTL intervals, transcriptome sequence assemblies and quantitative expression data. We will continue to rely heavily on GMOD software to provide resources that support initiatives made possible by next generation sequencing technologies, such as i5k (5000 insect genomes).