Data mining talks

As a molecular biophysicist I often hear talks (and see posters) given by bioinformaticists.* I am struck by how these are almost uniformly abysmal. I'm not necessarily referring to the data, but rather the presentation as a whole. This has reached the point where I don't think I can bring myself to sit through another bioinformatics talk (or poster presentation) for at least the next three months.

Why has the quality of the now dozens of such talks I've suffered through been so low?

In the majority of cases I posit it's a combination, in varying degrees, of a lack of imagination and a disconnection from the underlying biology. Too many of these presenters regale their audiences with interminable laundry lists of how property X is over-represented in sequences of class A, and under-represented in sequences of class B. Ummmm... So what? Why should I care? Often such presenters either don't know or are too lazy to spend the time connecting their data with known biology. As an example, I recently sat through a talk where the speaker made a big deal about the prevalence of glutamine-rich sequences in proteins involved in transcription. Not once did he refer to the fairly substantial body of experimental data on these very same sequences. In fact, when asked, he couldn't offer up any explanation for this observation.** Major fail.

I can't explain why this happens. Obviously it shouldn't. Perhaps it's a function of the relatively immature nature of bioinformatics as a field. It's still at a stage where method development trumps method application. Application of the intelligent kind.

I remember when macromolecular crystallography talks suffered from similar issues. They would often be these long detailed descriptions of the structure(s) just solved by the crystallographer. No connection to the biology, just the details of the structure. Listen, I don't give a rat's arse that there's a type VIIb turn between helices 7 and 8. What I want to know is what the structure tells us about the biology. Nowadays most crystallographers do make the connections. One can't get a grant for simply solving structures any more.***

I've heard through the grapevine that getting a grant to do bioinformatics has become increasingly difficult. More so than would be expected from the downturn in science funding. Perhaps we'll see the field forced to mature more rapidly and presentations improve.








* By "bioinformatics" I mean the data-mining thing. A colleague once defined it thusly: "Bioinformatics is the mining of biological databases for profit (not necessarily of the monetary kind)." This is distinct from computational biology which, at least at the molecular level, tends to employ an energy function of sorts.

** Glutamine-rich regions can be involved in DNA binding - the glutamine side chain is quite good at making hydrogen bonds with nucleic acids.

*** Not when I'm reviewing the grant. :-)

Re that stolen iPhone...

The Daily Show With Jon Stewart	Mon - Thurs 11p / 10c
Appholes
www.thedailyshow.com
Daily Show Full Episodes Political Humor Tea Party

End of an (old) era

This week I sent three of these off to surplus.

A 13-year old Unix workstation...
Kind of cute really.

I had bought them out of my start up funds when I first started here. I hadn't turned them on for at least five years. I felt kind of sad getting rid of them.

iPhone apps

I have a question for my iPhone-wielding compadres: what apps do you find truly useful? Other than the ones that come standard.

I've grown partial to the following:

Evernote - particularly useful since it automagically syncs with my laptop via the internet. Good for recording notes, saving web pages etc. A useful catchall and organizer for information.

TripIt - useful as long as you're comfortable with them potentially having access to your travel info. It's also available on LinkedIn if you happen to have an account there. I like the built-in flight status and map features.

UrbanSpoon - for when you're traveling and have a need for good Thai food...

Windows, windows, everywhere

This is kind of a scary read:

Top Ten Worst Uses for Windows.