In an ideal world, all bioinformatics tools would be made available via the Web as a web service with an API, as well as a standalone package to download for local use. This is rarely the case and sometimes, even where one or the other is available, factors such as cost come into play. So 
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 
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 
The wordcloud package is word clouds for R with a difference: they look great. Of course, having just analysed online coverage of the ISMB conference, I had to run all 6 906 comments from the 2008-2011 meetings through some code. If you followed along via the Sweave code, I went as far as generating the 
ISMB/ECCB 2011 was held between July 15-19 this year and as in previous years, FriendFeed was used to cover the meeting. Last year, I wrote a post about how to use R to analyse the coverage. I was planning something similar for 2011 when I thought: we have 4 years of ISMB at FriendFeed now 
Ask anyone how much time has elapsed since September last year and they’ll probably start counting on their fingers: “October, November…” and tell you “just over 9 months.” So, when faced as I was today with a data frame (named dates) like this: How to add a 7th column, with the number of months between 
If your WordPress blog is hosted at WordPress.com (like this one), you may know that source code in posts is formatted and highlighted using a shortcode, as explained here. Until recently, R was not on the list of supported languages (neither was Perl), but I noticed today that both of them are now supported. This 
Some years ago, Google discovered that when people are concerned about influenza, they search for flu-related information and that to some extent, search traffic is an indicator of flu activity. Google Flu Trends was born. Illness is sweeping through our department this week and I have succumbed. It’s not flu but at one point, I 
What’s a “Friday fun project”? It’s a small computing project, perfect for a Friday afternoon, which serves the dual purpose of (1) keeping your programming/data analysis skills sharp and (2) providing a mental break from the grind of your day job. Ideally, the skills learned on the project are useful and transferable to your work 
If you: use Linux have just upgraded your R installation from 2.12 to 2.13 installed some/all of your packages in your home area (e.g. ~/R/i486-pc-linux-gnu-library/2.12) and… …are wondering why R can’t see them any more just do this: # at a shell prompt cp ~/R/i486-pc-linux-gnu-library/2.12 ~/R/i486-pc-linux-gnu-library/2.13 # in R console update.packages(checkBuilt=TRUE, ask=FALSE) # back to 
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
