First of all, my FindPeaks Application note has finally been accepted into Bioinformatics, in their Advanced Access Section. It's an open access article, so anyone can read it.
Here's the link.
Second, several big decisions have been made, lately. One of them, concerning FindPeaks, is that the software will be going open source (GPL) pretty soon. I think there's still room for at least one more article out of it, so it's not up there yet... but I have a spot on SourceForge for it.
Third, FindPeaks 4.0 is finally building again. After 27,000+ line changes, it's now running and being tested, and is working about as well as I expected (Minor programming errors introduced, but things are going pretty smoothly.) This includes several new file formats, a touch of threading, and a lot more "clean" java code.
And now, back to work.