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SoupX has finally been accepted for publication! This is a thread about what I learnt over the 2+ years since the first preprint and why it took so long. (I may do another thread about the improvements to the method soon)
This was the first project that I was the “senior author” on and it has taken so long to get published in large part due to mistakes I made in this role. Although personal factors (such as six months of paternity leave) contributed as well.
So here are some of the things I wish I’d understood three years ago. Hopefully, they’ll help others repeating my mistakes…
Early on, we took on collaborators on the project. At the time, I was flattered that someone thought enough of my hobby project to want to work on it. In retrospect, I should have asked what they wanted from the collaboration and been much clearer in outlining my own aims.
My personal opinion is that for methods papers the journal is irrelevant. What matters is that the method is reviewed, easy to use, and maintained. Because of this, I was happy to go with the flow and give any journal a “try”. This wasted a lot of time and achieved nothing.
What I should have realised sooner is being indifferent to the journal should be an active, not passive, decision. I should not have gone along with wasting time applying to places where there was a good chance of editorial rejection on “novelty” or “impact” grounds.
Finally, I’ve learnt a lot about when it is worthwhile appealing a journals decision. If an editor has decided that something is not of interest to the journal, don’t waste time trying to convince them otherwise.
On the other hand, if the decision relates to scientific criticisms raised by a reviewer, then you can at least provide evidence and data to support your appeal and it can be worth the effort.
