Cytoscape WikiI have been playing around with using [http://db.apache.org/derby/ Derby] to associate databases with cytoscape networks. Derby can serve as an embedded relational database in Java applications. This may be a solution for use cases that need real-time access 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
http://db.apache.org/derby/ - Offical Apache Derby site http://db.apache.org/derby/quick_start.html - Useful Quick Start site for newbies [http://db.apache.org/derby/derby_downloads.html#Software+required+to+build+Derby Related software] - Reference to OSGi (osgi.jar)
- Relevant discussion threads relating to OSGi
Overview
...more to come