Box plots. Like box plots, only…box plots.

On a rare, brief holiday (here and here, if you’re interested; both highly-recommended), I make the mistake of checking my Twitter feed:

This points me to BoxPlotR. It draws box plots. Using Shiny Server. That’s the “innovation”, presumably.

With “quilt plots” and now this, I’m starting to think that I’ve been doing science wrong all these years. If I’d been told to submit the trivial computational work I do every single day to journals, I could have thousands of publications by now.

I’m still pretty relaxed post-holiday, so let’s just leave it there.

Career advice: switching to computational research

Laboratory work, of the “wet” kind, not working out for you? Or perhaps you just need new challenges. Think you have some aptitude with data analysis, computers, mathematics, statistics? Maybe a switch to computational biology is what you need.

That’s the topic of the Nature Careers feature “Computing: Out of the hood“. With thoughts and advice from (on Twitter) @caseybergman, @sarahmhird, @kcranstn, @PavelTomancak, @ctitusbrown and myself.

I enjoyed talking with Roberta and she did a good job of capturing our thoughts for the article. One of these days, I might even write here about my own journey in more detail.

Oops: taxonomy #fail

My journey from bench scientist to bioinformatician began with archaeal genomes. So I was somewhat startled to read The catalytic mechanism for aerobic formation of methane by bacteria, in which we learn about the “ocean-dwelling bacterium Nitrosopumilus maritimus“.

So was Jonathan Eisen of course and you should go and read why. Every top hit in a Web search for that organism tells us that Nitrosopumilus maritimus is an archaeon.

Looking forward to a rapid correction and apology from Nature.

Title edited from “phylogeny” to “taxonomy” at the insistence of @BioinfoTools ;)

Nature on reproducible research

I imagine that most people, when asked “do you think that independent confirmation of research findings is important?” would answer “yes”. I also imagine, when told that in most cases this is not possible, that those people might be concerned or perhaps incredulous. However, this really is the case, which is why I spend much of my working life in a state of concern and incredulity.

Over the years, many articles have been written on how to improve this state of affairs by adopting best practices, collectively-termed reproducible research. One of the latest is an editorial in Nature. I’ve pulled out a few quotes for discussion.
Read the rest…

Science in the petabyte era

Just a brief note: the title of this post is taken from the cover of today’s Nature. It contains several very good feature articles on the challenges of dealing with peta- (and more) byte size datasets, grouped under the heading “Big data”.

Nature contents Sep 4 2008.
Nature News Big Data special.

By far the best of the articles is The future of biocuration: it offers practical recommendations, as opposed to the “gee whizz, what a lot of data” approach. Not least of which: “curators, researchers, academic institutions and funding agencies should, in the next ten years, increase the visibility and support of scientific curation as a professional career.”
Almost as good are Wikiomics, which tackles the lack of participation issue and Welcome to the petacentre, in which Boing-Boing’s Cory Doctorow explores, amongst other places, the Sanger Institute data centre.

So far as I can tell from the Nature News link, these articles are freely-available.

A brief history of the platypus, in 5 parts

Who isn’t fascinated by the strangest of mammals, the platypus? It has fur and lactates, like a mammal. It has a bill and webbed feet, like a bird. It lays eggs and produces venom, like a reptile. It finds prey using electroreception, like sharks. The platypus is so weird that when first described, many scientists assumed that it was a hoax.

To celebrate the publication of the draft platypus genome, here’s a brief guide to this wondrous creature.
Read the rest…