Cytoscape WikiDerby can serve as an embedded relational database in Java applications. This may be a solution for use cases that need real-time access to relatively stable data, such as gene aliases and annotations. Getting Derby to work within a Cytoscape plugin was not trivial, so I wanted to share that experience.
Important Links
Offical [http://db.apache.org/derby/ Apache Derby] site
Useful [http://db.apache.org/derby/quick_start.html Quick Start] site for newbies
[http://db.apache.org/derby/derby_downloads.html#Software+required+to+build+Derby Reference] to OSGi (osgi.jar)
- Relevant discussion threads relating to OSGi
Overview
...more to come