Genome data resources are generated in several ‘omics’ projects (sequences, gene predictions, alignments, annotations, RNAseq data, microarray…). In the context of this explosion of data, an environment facilitating the data analysis (storing, visualizing, editing, exporting…) is essential. The GMOD tools help meet this need.
The GMOD (Generic Model Organism Database) project is a collection of interconnected open source software tools and databases for visualizing, annotating, and managing genetic and genomic data. GMOD is also an active community of developers and users facing common challenges with their biological data.
Using the GMOD tools, the platform ABiMS aims to develop a coherent and integrated environment to assist collaborators in the analysis and annotation of genomic data. The platform uses the following tools: CHADO (a database), JBrowse (a genome browser to visualize and explore data) and Apollo (a collaborative platform for manual annotation based on JBrowse).
The platform ABiMS initiated this environment within the EMBRC-France project: many genome browsers have been developed in the context of the Marine Model Organism Database. ABiMS hosts today about fifteen public and private genomes of marine organisms for visualization with JBrowse and annotation with Apollo. Some publicly available instances are: