Web Apollo architecture. Web Apollo (components within the central turquoise box) acts as a mediating agent between users (top blue box) and external sources and sinks of data (lower green and peach boxes). Two user interface components operate on the client-side, within the browser environment. The JBrowse component visualizes various DNA features, and the Web Apollo component captures user manipulations. The Data Services module dynamically delivers genomic data and features to the user interface as JBrowse compatible JSON. Most of the primary genomic data is harvested and formatted in advance as part of the initial server setup. In addition, data from other sources may be dynamically provided using the Trellis framework or uploaded by the user from the browser. The Annotation Editing Engine and User Management components also sit on the server side. The first responds to users actions on the client by modifying the underlying data models appropriately, and second manages user accounts and login services. Annotations created by users can be exported as either GFF3 or FASTA file, or directly saved to a Chado database (plug-in adapters may be added to export genomic annotations to additional repositories). The arrows indicate where there are interactions between components, with the arrowhead indicating the direction of data flow.
Lee et al. Genome Biology 2013 14:R93 doi:10.1186/gb-2013-14-8-r93