One of the nice features of Google App Engine is you can easily view logs for your application to quickly see requests generating errors. Browsing the logs of ResolveRef, I’ve been able to identify an few classes of query which for one reason or another, weren’t working.
Author Archive for perry
David Baker’s lab and friends, have recently released a new ‘experiment’ in protein folding called FoldIt. Essentially, individuals or teams can compete online to manually fold protein structures, guided by the internal energy function within the game (it very likely uses code from the impressive ab initio folding software Rosetta under the hood). The interface is designed as a game to make it accessible to everyone, not just experts in protein folding. While it’s pretty simplified compared with your average molecular structure editing software, I think designers of scientific software (often scientists themselves) should take note; a good clean interface can really assist getting a specific job done painlessly. I haven’t played enough with it yet, but I get the feeling that FoldIt could be a nice way to introduce some protein structure concepts to undergraduates too.
There were the usual complaints on Slashdot that FoldIt doesn’t have a Linux version. Well, I’m happy to report that it seems to run alright using Wine (on Ubuntu Hardy Heron). I couldn’t log in to try the competitive puzzles, but I suspect the server is just in the midst of a Slashdotting. I’ll try later.
From the FoldIt FAQ:
Can humans really help computers fold proteins?
We’re collecting data to find out if humans’ pattern-recognition and puzzle-solving abilities make them more efficient than existing computer programs at pattern-folding tasks. If this turns out to be true, we can then teach human strategies to computers and fold proteins faster than ever!
Not sure where I saw it, but I remember reading an argument that the future of crowdsourcing would be to not just blindly trust the whole crowd, but also identify experts in the crowd and weight their predictions more strongly. I’d say this is will be the case with ‘manual’ protein folding - just like some players become l33t at first-person-shooters (like my favorite, RTCW: Enemy Territory which depsite enjoying, I’m not so l33t at), and could beat any AI player that doesn’t cheat… some people will probably become pretty good at folding up proteins. Maybe FoldIt will identify them, and they can make their gaming skills useful, and teach their tricks to software to automate the process. Or maybe it will just remain a fun-ish puzzle game 
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.
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.
Continue reading ‘Announcing ResolveRef on Google App Engine’
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
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