Monthly Archives: July 2012

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.

PMRetract: now with rake tasks

Bioinformaticians (and anyone else who programs) love effective automation of mundane tasks. So it may amuse you to learn that I used to update PMRetract, my PubMed retraction notice monitoring application, by manually running the following steps in order:

  1. Run query at PubMed website with term “Retraction of Publication[Publication Type]“
  2. Send results to XML file
  3. Run script to update database with retraction and total publication counts for years 1977 – present
  4. Run script to update database with retraction notices
  5. Run script to update database with retraction timeline
  6. Commit changes to git
  7. Push changes to Github
  8. Dump local database to file
  9. Restore remote database from file
  10. Restart Heroku application

I’ve been meaning to wrap all of that up in a Rakefile for some time. Finally, I have. Along the way, I learned something about using efetch from BioRuby and re-read one of my all-time favourite tutorials, on how to write rake tasks. So now, when I receive an update via RSS, updating should be as simple as:

rake pmretract

In other news: it’s been quiet here, hasn’t it? I recently returned from 4 weeks overseas, packed up my office and moved to a new building. Hope to get back to semi-regular posts before too long.