We really don’t care what statistical method you used

Update: as pointed out in the comments, the amusing error in this article has been “corrected” (or at least, “edited away”). Thanks for your interest.
Update: I note that this article is now “Highly Accessed” ;)

An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver
BMC Systems Biology 2011, 5(Suppl 3):S4

(insert statistical method here). No, really.

With thanks to Simon J Greenhill and Dave Winter.

Comments at journal websites: just turn them off

A couple of years ago, I noted that some journals were not making the process of commenting on articles especially easy. My latest experience suggests that little has changed.

Can a journal make a difference? Let’s find out.

Academic journals. Frankly, I’m not a big fan of any of them. There are too many. They cost too much. Much of what they publish is inconsequential, read by practically no-one or just downright incorrect. Much of the rest is badly-written and boring. The people who publish them have an over-inflated sense of their own importance. They’re hidden behind paywalls. And governed by ludicrous metrics. The system by which articles are accepted or rejected is arcane and ridiculous. I mean, I could go on…

No, what really troubles me about journals is that they only tell a very small part of the story – the flashy, attention-grabbing part called “results”. We learn from high school onwards that a methods section should be sufficient for anyone to reproduce the results. This is one of the great lies of science. Go read any journal in your field and give it a try. It’s even the case in computation, an area which you might think less prone to the problems in reproducing wet-lab science (“the Milli-Q must have been off”).

We have this wonderful thing called the Web now. The Web doesn’t have a page limit, so you can describe things in as much detail as you wish. Better still, you can just post your methods and data there in full, for all to see, download and reproduce to their hearts content. You’d like some credit for doing that though, right?

So if you do research – any kind of research – that involves computation, your code is open-source, reusable, well-documented and robust (think: tests) and you want to share it with the world, head over to a new journal called BMC Open Research Computation, which is now open for submissions. Your friendly team of enlightened editors awaits.

More information at Science in the Open and Saaien Tist. Full disclosure: I’m on the editorial board of this journal and was invited to write a launch post.

Data #fail

Unique, yet identical to each other. What?

One reason why scientists don’t comment at journals

This week, Nature announced a new online commenting facility and noted that:

Online discussions about our research papers are likely to be considerably more subdued, according to the experience of other publishers who already allow commenting.

They offer several reasons why this might be the case. Here’s one: it helps if you make it easy.

Best wishes to Jonathan Eisen

Just wanted to add my voice to the many congratulating Jonathan Eisen: biologist, blogger, Open Access advocate and all-round top bloke on his appointment to PLoS Biology Academic Editor in Chief. You can read his editorial to learn more about his motivation and plans for the journal.

Jonathan, you realise that you’re now the figurehead for the revolution, don’t you ;)