I am a member of the Bioinformatics Research Group in the Artificial Intelligence Center at SRI International. Our group has developed the Pathway Tools software available on several platforms. Pathway Tools can manipulate Pathway/Genome databases. A description of Pathway Tools can be found here.
Most of our software development uses Common Lisp.
The query language was presented at the June 2006 Pathway Tools Workshop at SRI International. Here are the slides: advanced query language slides (PDF) or advanced query language slides (Power Point)
The language has been named BioVelo. It is available with the release of Pathway Tools version 11.0 and online on our web site BioCyc Advanced Database Search (On that page, you can also click the "Switch to the Free Form Advanced Query Page" to enter any BioVelo queries.).
This tool will be able to automatically display large regulatory networks in a comprehensive manner. The user will be able to interactively modify its layout, for example, by selectively eliminate some sub-networks of nodes.
See the Publications External Link.