Figure 11.

Software architecture. This schematic demonstrates the conceptual structure of the TFe software. Written mainly in the Perl programming language, the software is essentially a collection of Perl 'scripts' that runs on an Apache web server, in a UNIX-compatible environment. The software relies on MySQL for data storage, and a number of third party modules. Over 40 'front line' scripts (shown as the red rectangle) generate individual pages such as the home page and article page. These front line scripts are backed by a cluster of three TFe Perl modules (shown as the green circles): (1) the 'database updater', which is summoned pro re nata whenever the TFe database needs to be maintained or updated with new content from external sources such as NCBI; (2) the 'main module', which contains shared subroutines such as those that generate page headers; and (3) the 'database handler', which forms the gateway between all components of the TFe software and the TFe database. The database (shown as the yellow cylinder) is stored on a separate database server and communicates with the rest of the TFe software via fiber optic. It contains cached copies of third party resources so that the TFe software does not have to constantly retrieve data from the 'cloud'. This optimizes performance. The web API (shown as the purple rectangle) is directly connected to the ultra small and efficient database handler module. In bypassing activation of the large main module and database updater, the web API is able to run faster than the web-based interface. GO, Gene Ontology; MGI, Mouse Genome Informatics.

Yusuf et al. Genome Biology 2012 13:R24   doi:10.1186/gb-2012-13-3-r24
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