Can you use neo4j to store weighted graphs? Looking at their api it doesn't seem like there's any way to specify edge weights (or any other metadata about edges).
http://wiki.neo4j.org/content/Getting_Started_Guide#Create_a...
Weights are treated like any other metadata.
Please let me know if you find anything that can handle negative edge weights well while efficiently tracking shortest paths. I've found some papers with efficient implementations for frequently updated edge weights, but haven't found anything implemented or accessible.