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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Qutemol using Cedega

Pawel over at Freelancing Science recently highlighted Qutemol, a nice looking molecular viewer that does real-time ambient occlusion rendering. There isn’t any official Linux version, but I found that the Windows version runs okay on Linux using Cedega (a version of Wine that has better DirectX support, especially for games). Since Cedega is based on the Open Source Wine code, you can compile your own command line version … but it’s a good idea to buy a maintenance subscription from Transgaming and support it’s further development, if you can afford it.

Here’s a screenshot of Qutemol running under Cedega on Ubuntu Gutsy Gibbon, just to prove it.

Qutemol running under Cedega

No, it’s not Photoshopped … (or GIMPed) … 🙂

ARIA verson 2.2 released

I don’t usually post about NMR (Nuclear Magnetic Resonance) and structural biology related stuff, but I’ve always intended to. In this post I’m pulling out all the stops on specialist lingo and assumed background knowledge, so hopefully it isn’t too incomprehensible to the non-structural biology crowd :).

ARIA version 2.2 has been released in the last few weeks. ARIA is an automated NOE assignment and structure calculation package, which (in theory) takes some of the pain and slowness out of producing protein (and DNA and/or RNA) structures from Nuclear Magnetic Resonance data. I’ll say up front; I haven’t tried this version yet, but some of the improvements look exciting.

Here are two new features worth noting … followed by what I think it all means:

  • The assignment method has been improved with the introduction of a network-anchoring analysis (Herrmann et al., 2002) for filtering of the initial assignments.
  • The integration of the CCPN has been completed. The imported CCPN distance constraints lists can enter the ARIA process for calibration, violation analysis and network-anchoring analysis. The final constraint lists can be exported as well.

In the past I have done some quick and dirty tests comparing the quality of protein structures produced using Aria 2.1 vs. Peter Gunterts CYANA 1.07 and 2.1, using the exact same NMR peak input lists (with slightly noisy data containing a number of incorrectly picked peaks). CYANA always won hands down, assigning more NOE crosspeaks correctly and producing an ensemble of model structures with much lower RMSD and generally better protein structure quality scores (ie using pretty much any decent pairwise pseudo-energy potential, and Procheck). Also, ARIA produced ‘knotted’ structures which were almost certainly incorrect, while CYANA did not. Other postdocs and students in my former lab had done similar independent tests with ARIA 1.2 vs. CYANA 1.0.7, and had come to similar conclusions.

The disclaimer: It should be noted here that assessment of the quality of an ensemble of NMR structure coordinates can be problematic, and is really the topic of another long post (and probably tens if not hundreds of peer-reviewed journal articles). So saying “CYANA version X is better then ARIA version X” based on the RMSD of the final calculated ensemble is a bit unfair … in fact using RMSD of the ensemble to gauge structure quality is just plain wrong in this context. In my (unpublished, non-peer reviewed) tests, it is possible that ARIA could be producing high RMSD but essentially ‘correct’ structures, while CYANA could be producing tightly defined but ‘incorrect’ structures, but I doubt it. The gap between the output of each program was wide enough to suggest that under real-world conditions where the input peak list contained a number of ‘noise’ peaks, ARIA was failing to give a set of consistent solutions (probably due to lack of NOE assignments), while CYANA was giving a set of tightly defined structures (which may or may not have represented the ‘correct’ solution). Other evaluations (protein structure quality measures, Procheck, comparison to known structures of similar proteins) indicated that the CYANA structures were not grossly ‘incorrect’, so I’d say CYANA was just giving a better defined (ie lower ensemble RMSD) set of plausible solutions.

My gut feeling is that ARIA 2.2 will perform much better than past versions, due to one key feature that has been ‘borrowed’ from CYANA; the introduction of a network-anchoring analysis. In a nutshell, network-anchoring scores essentially weight distance constraints (or NOE assignments) based on how ‘connected’ that constraint is within the graph formed by other constraints. This means that in effect a single, isolated constraint pulling two residues on opposite sides of a protein together is down-weighted, while if multiple constraints link those residues (or their neighboring residues) then those constraints are considered more trusted and hence weighted heavier. For better or worse (usually better), this score simulates what the human NMR spectroscopist would do when assigning NOE crosspeaks manually … usually two residues in contact will show multiple NOE crosspeaks connecting them and involve multiple different nuclei, however a single lonely NOE between two nuclei which are distant from eachother in the primary protein sequence is heavily scrutinized and regarded with suspicion since it is likely to be mis-assigned. I’m very keen to test ARIA 2.2 on my old data set and see if I’m actually right (I may be able to try it with network anchoring turned on, and off, and see just what sort of contribution that score is making).

Another completed feature, the integration between ARIA and the CCPN libraries/analysis package should also be a big plus. I haven’t used the CCPN analysis software yet, but a few years ago I wrote some code to help make CYANA and the Sparky NMR assignment program work together better. The result was functional, but very hackish (and I’m probably the only person in the world who understands how it was intended to be used, since I still haven’t got around to writing any documentation. Naughty, naughty). CCPN + ARIA may turn out to be the better option for spectral analysis and structure calculation in the future, as opposed to my currently preferred Sparky + CYANA combination.

I’m really itching to find a good reason to do an NMR structure project now … back to work !!

Google Desktop for Linux Released

Google Desktop for Linux has been officially released. It’s a real-honest-to-god native linux application, and doesn’t use Wine like the Linux version of Picasa.

I’ve just installed it on Ubuntu Feisty Fawn from the Google Linux software repositories, and while it’s currently only indexed about 1 % of my files, my initial tests suggest it is pretty slick … a quick Ctrl-Ctrl, and up pops the search box. Apart from all the things I’d expect, like indexing the content of pdf files, directories like “/usr/man” are included on the default path list, so I presume it also looks inside man pages. One problem I’ve noticed so far in my very quick testing is that it seems to not follow symlinks to directories and won’t let me add them as paths to index. The effect is that my “/home/perry/documents”, which is actually a symlink to a larger partition, does not get indexed unless I add it to the path list with it’s real path.

While there are already similar offerings for Gnome (eg Beagle) and KDE (eg Kat), my gut feeling is that Google Desktop will be my preferred option for the moment. Maybe one day we will get lucky, and Google will even make it FOSS (not holding my breath though).

Flash Player 9 for Linux released : Quick install for Ubuntu Dapper

Adobe Flash Player 9 is finally out of beta ! No more feeling like a second class netizen on “flashy” sites !

Here’s how I installed it on Ubuntu Dapper (the package is for Debian Sarge, but seems to work fine):

Download flashplugin-nonfree.

Use right-click, “Save Link As …” and save it to \tmp.

$ cd /tmp

$ sudo dpkg -i flashplugin-nonfree_9.

(you’ll be prompted for your password, and once you provide it, the install should happen)

You can check if it worked by typing about:plugins into the URL box in Firefox. You should see something like “Shockwave Flash 9.0 d78″ on that page.

Now go view some F-F-F-Flash cartoons 🙂 (I don’t think Homerstarrunner requires Flash 9, but it’s the only Flash site I use on any regular basis)