texshade: useful, and still kickin’

I’ve been looking at doing an analysis with some protein subfamily sequence logos, using Eric Beitz’s texshade. While it’s a little strange that it does the actual analysis part (rather than just the rendering) using LaTeX, it’s the only implementation of the method I know of, and it beats reimplementing it from the paper.

Although it was published in 2006 (and earlier in 2000), with the original URLs now dead, I noticed the latest update for the version of texshade in CTAN (v1.18) was on 15th of April, 2008 … ie texshade was updated just 14 days ago !

It happens all to often that published bioinformatics tools cease to be updated or even disappear from the Web not long after the peer-review publication is released. Kudos to Eric for not abandoning his software.

Announcing ResolveRef on Google App Engine

About two weeks ago, tipped off by Neil, I heard about Google App Engine. I managed to get a beta account, and I’ve finally had a chance to do something (hopefully) useful with it.

In the absence of any quickly achievable ideas for a bioinformatics app, I ported over the OpenRef application I wrote on top of TurboGears a few months back.

Just like the original, the new app, ResolveRef, is essentially a RESTful way of doing PubMed queries.
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How do you describe your job as a scientist ?

I’ve always found it interesting how people describe their jobs, particularly scientists. Sometimes I find the “inevitable dinner party question” (“So, what do you do?”) difficult. The answer typically requires knowing the background of the inquirer … if your job description is too technical, it tends to freak people out, and can often cause the evenings conversation to disintegrate into too much science-talk (yes, sometimes it’s possible to have too much science-talk). The safer option, giving a simplified very high-level job description geared toward lay-people, is usually unsatisfying and can even sound a bit insulting if you are unknowingly speaking to someone with experience in your field.

Overall, I think it’s really good practice to be able to describe your job (or “role”, or “work”) as a scientist at many different levels. It certainly helps me understand “what I do”, and can really assist in having the right words on-hand when writing grants, fellowship applications, abstracts and maybe even (gasp) press-releases, each that could be aimed at widely differing audiences.

What got me thinking so philosophically this morning ? A tongue-in-cheek quote I noticed on a lab head’s page describing his role in the research group:

Gets the big pay check, sits around waiting for results, drinks coffee, helps write papers and tells people to work harder.

I’m sure he does a little more than that … but I suspect there’s also a bit of refreshing honesty in that description. Probably every part is true, except the “sits around waiting” part. I wouldn’t try using it to describe your role on a grant application though 🙂