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Definitely neo4j. If you're on a mac, it's just 'brew install neo4j' and boom you have the free community edition.

Depending on what OP was after, neo4j is hardly a single file, in-process database.

Well, that is not strictly true. You can use neo4j embedded within Java: http://neo4j.com/docs/stable/tutorials-java-embedded.html

You are correct. I was responding more to this:

> easy to install, relatively easy to use, with good reliability, for experimentation