Lazy post: a Life Scientists best-of

When stuck for ideas or pressed for time, a blogger can always fall back on a round-up of activity from elsewhere on the web. Yes, it’s time for a “best of the past 14 days” from the FriendFeed Life Scientists group.

Just a slight twist to make it more exciting (?) – we’ll automate the process using the API and a little Ruby.

Analysing the ISMB 2010 meeting using R

The colossus of bioinformatics meetings, ISMB, convened in Boston this year from July 9 – 13. As in recent years, the meeting was covered online at its website, FriendFeed and Twitter.

I thought it would be fun to run a quick analysis of activity at the FriendFeed room using R.

How many monotypic genera?

During all the recent discussion around Neandertals and modern humans, it’s often pointed out that Homo sapiens is the sole extant representative of the genus Homo. I began to wonder “how unusual is this?” in a FriendFeed comment thread. What resources exist that could help us to answer this question?

Genera that contain only one species are termed monotypic. Wikipedia even has a category page for this topic but their lists are limited, since Wikipedia is not a comprehensive taxonomy resource.

Taxonomy is not my specialty but once in a while, I enjoy challenging myself with unfamiliar resources and data types. I figured initially that we could get some way towards an answer using BioSQL and the NCBI taxonomy database. As it turned out I was completely wrong, but it was an interesting educational exercise. I turned instead to a “real” taxonomy resource, the Integrated Taxonomic Information System, or ITIS.