"Guys from NCBI said me that they don't give this documentation anybody. And if you want to use the SRA format then you need to use their API." -- Eeeesh, really?? That's pretty terrible.

Open-source (Apache) translator from RIF-BLD to rules that can be executed in Iris (see previous link).

LGPL'ed datalog reasoner.

"CXF helps you build and develop services using frontend programming APIs, like JAX-WS and JAX-RS."

Need to look into Thrift for some of the protocol design I'm doing here at work. Hmmm.

STOMP client -- apparently, ActiveMQ can be a STOMP server.

Referenced on the Google AppEngine Java tutorial -- apparently open-sourced interface to several different persistence APIs.

"The LIRE (Lucene Image REtrieval) library provides a simple way to retrieve images and photos based on their color and texture characteristics. LIRE creates a Lucene index of image features for content based image retrieval (CBIR)."

Aside from PLoS and i2b2, I'm not sure how many of these have a realistic chance of success. MedSphere seems like a kind of competitor to SCF. Still, might be worth a look.

Java GIS software library.

Open source software released at DEFCON 16.