Monthly Archives: August 2011

Popular topics at the BioStar Q&A site

Which topics are the most popular at the BioStar bioinformatics Q&A site?

One source of data is the tags used for questions. Tags are somewhat arbitrary of course, but fortunately BioStar has quite an active community, so “bad” tags are usually edited to improve them. Hint: if your question is “How to find SNPs”, then tagging it with “how, to, find, snps” won’t win you any admirers.

OK: we’re going to grab the tags then use a bunch of R packages (XML, wordcloud and ggplot2) to take a quick look.

Read the rest…

Monitoring PubMed retractions: updates

chart

PubMed cumulative retractions 1977-present

There’s been a recent flurry of interest in retractions. See for example: Scientific Retractions: A Growth Industry?; summarised also by GenomeWeb in Take That Back; articles in the WSJ and the Pharmalot blog; and academic articles in the Journal of Medical Ethics and Infection & Immunity.

Several of these sources cite data from my humble web application, PMRetract. So now seems like a good time to mention that:

  • The application is still going strong and is updated regularly
  • I’ve added a few enhancements to the UI; you can follow development at GitHub
  • I’ve also added a long-overdue about page with some extra information, including the fact that I wrote it :)

Now I just need to fix up my Git repositories. Currently there’s one which pushes to GitHub and a second, with a copy of the Sinatra code for pushing to Heroku, which isn’t too smart.

BioRuby development: feedback on using Git

Everyone likes constructive feedback. I received a couple of great comments on my previous post, which warrant a brief discussion.

@vlandham points out that when the main BioRuby repository updates, you’ll want to update your local repository. Using git, you do that by adding a remote which points to the original repository, from which you can fetch updates and merge with your local version:

git remote add upstream https://github.com/bioruby/bioruby.git
# fetch/merge only when main repo updates
git fetch upstream
git merge upstream master

This is described at the GitHub help page Fork A Repo.

Michael points to an article titled A successful Git branching model. It suggests that when developing new features you create a feature branch (also called topic branch). This can help with the management of new features and creates a more complete commit history if/when the new feature is merged back into your development repository. The article also suggests a main branch for development named develop, rather than the default master.

I haven’t quite got my head around all the ins-and-outs of the article yet, but it’s well worth a read.

A beginner’s guide to BioRuby development

I’m the “biologist-turned-programmer” type of bioinformatician which makes me a hacker, not a developer. Most of the day-to-day coding that I do goes something like this:

Colleague: Hey Neil, can you write me a script to read data from file X, do Y to it and output a table in file Z?
Me: Sure… (clickety-click, hackety-hack…) …there you go.
Colleague: Great! Thanks.

I’m a big fan of the Bio* projects and have used them for many years, beginning with Bioperl and more recently, BioRuby. And I’ve always wanted to contribute some code to them, but have never got around to doing so. This week, two thoughts popped into my head:

  • How hard can it be?
  • There isn’t much introductory documentation for would-be Bio* developers

The answer to the first question is: given some programming experience, not very hard at all. This blog post is my attempt to address the second thought, by writing a step-by-step guide to developing a simple class for the BioRuby library. When I say “beginner’s guide”, I’m referring to myself as much as anyone else.
Read the rest…

ISMB coverage on Twitter? It’s possible there was…

Peter writes:

I wonder if part of the drop off is live bloggers moving to platforms like Twitter? I can tell you it seemed like there were almost as many tweets for one SIG (#bosc2011) as for the whole of #ISMB / #ECCB2011, and I personally didn’t post anything to FriendFeed but posted lots on Twitter.

Well, there’s a problem with using Twitter for analysis of conference coverage. Let’s try searching for ISMB-related tweets using the twitteR package:

library(twitteR)
ismb <- searchTwitter("ismb", 1000)
length(ismb)
# [1] 30

oldertweets

If we can't archive, how can anyone else?

30? Are we using twitteR properly? Running the same search at the Twitter website gives roughly the same results, plus this unhelpful message.

I like Twitter – as a real-time communication tool. As a data archive? Forget it.