GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
Modware is an easy to use Perl library for querying and modifying genomic data in a Chado database. It provides a powerful link between BioPerl and Chado. This Chado API provides an intutitive way to use Chado from Perl.