Hello Jacopo!
unfortunately, there are not great news with the paper.
The proof-reading phase has been complete.
As I mentioned in a previous mail, there is a proposal to ask PLoS Computational Biology to evaluate publishing this manuscript together with another presenting Biostar, a website for bioinformaticians.
We sent an inquiry to Philip Bourne about this idea, but we did not receive any answer. The last contact I have is from past Friday 13, so I was planning to send another mail tomorrow or the day after (I consider that two weeks is the most prudent interval of time for these matters).
I am afraid this phase can take a while to be solved. If the Biostar manuscript is not ready soon, I will proceed without it. I will keep you informed as soon as there are news.
Cheers,
Giovanni