If pipettes could talk, oh the tales they could tell !

Occasionally impoverished University labs and early career researchers go looking for bargain priced lab equipment on Ebay ... sometimes hard to get but still very useful equipment also comes up. A colleague of mine found this entertaining auction for a P20 Gilson Pipette, much of it written from the pipettes perspective. Here's a quote:

For the purposes of full disclosure, this pipette has NOT resulted in data that has made it into Nature or Science (and in hindsight then the Cell paper may be considered to be a fluke). However, we choose to believe that that is the fault of both the editorial staff of these journals, and many a short-sighted peer-reviewer, rather than the pipette itself. Nonetheless, you may want to calibrate the pipette upon its arrival.

Fluke or not, a sentient pipette that produces Cell papers has got to be worth more than the mere $48 it's currently sitting at ! Sadly (or maybe happily for them), it looks like the seller is leaving bench science and selling up their gear. I've no idea who it is, but they live in the same suburb as me, so there's a good chance this is a fairly well-published senior scientist that I've crossed paths with at some stage. Also, don't miss the (*) footnote at the bottom of the auction info about impact factors ...

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 !!

Searching biological databases from the Firefox search bar

There is currently no "Google for Bioinformatics", and so biologists/bioinformaticians typically need to search a number of separate databases to find the data the desire. While the Biobar Firefox extension helps search for a dizzying array of biological databases (individually), I think sometimes it offers too much, and contains too many databases that I rarely if ever use. As useful as it is, most of the time I keep the Biobar toolbar hidden to reclaim the screen real-estate.

Instead, I prefer the more lightweight "search plugins" to fully fledged extentions (accessed via the little search box up near the URL location bar). Here are some Firefox search plugins for common 'bioinformatic' search engines which I found scattered across the far reaches of the web:

• HubMed is a clean and slick interface to search the PubMed database, with some features that the NCBI search doesn't have. You may already be familiar with it, but sadly the majority of life scientists appear not to know about it / use it. I prefer HubMed to the regular NCBI Entrez interface. You can install the HubMed Firefox search plugin at HubMed.
• In case you want the plain vanilla NCBI PubMed interface, the UCSF library provides a PubMed search plugin.
  
• The Mycroft project by Mozilla seems to be an official repository of firefox search plugins. On Mycroft, I found plugins for searching SwissProt, the Protein Data Bank (PDB).

I also wanted some that couldn't find, so I made them. Here are Firefox search plugins for Uniprot and Pfam:

Here is the code for the Pfam one, as an example:

<?xml version="1.0" encoding="UTF-8"?>
<OpenSearchDescription xmlns="http://a9.com/-/spec/opensearch/1.1/"
                      xmlns:moz="http://www.mozilla.org/2006/browser/search/">
 <shortname>Pfam</shortname>
 <description>Search the Pfam database</description>
 <image width="16" height="16">data:image/x-icon;base64,AAABAAEAICAAAAAAAACoCAAAFgAAACgAAAAgAAAAQAAAAAEACAAAAAAAgAQAAAAAAAAAAAAAAAAAAAAAAAAAAAAA%2F%2F%2F%2FAMWLMwDew54AjEcBAO22WwD658kAoWclAMSdbADYn0gA1LKBALiLVADt1rMA%2FffkAKp0PACcXQ0AtnomAMiXVwDxvmsA0ZY4ALuJQwDjqk8AzqZ3AKVoFQD27dkA2LuRAJJRFACVVAEA5s6lALyVYgCbXR0Aq3ElAPPhvwClbDIAzqBkAL2BLgDFkEAAtYJKAPS9YACQTwkA%2Fu3QALJxHgDZnD8A5bJfAMWTTwD%2B89cAnmIUAOiwVQDXtYkAl1gXAN6%2FlgDsuWYAxJpeAN6kTADoz60AwYg6AL6RWwDQrH0Ay6NwAMmPOQCNTgEAllcMAKVtIwDNlD4A9uPGAPfAZgCocjEAxp1mAJhYBQDZv5sAi0oLAKxvHgDUmkIAt4hIAJpeFACoaxoAn2EOAKBlGQDwuF4Aun8qALJ2JQCocDgA3KFEAJRSCAD%2B9twAjksFAJVWEQDt2rcAkFEOAMKVXQD57M4AklACAKBfGACkaigA%2BvDWAPXnyQDr068A7bNWALeHTQD24sEAu5NdAJlZCgDgxqEA6rZjALyOWADcvZIAzZE4ANi5jQDEmGIAj0oAAJVWBgDl0KoA67NaAMCELwDChzQA8%2BLDAJhZEgClbS4AqnM1AOSpSwDy3L4Ai0cFAJxfEQCiYxQAnWAbAJteIQChZikAx402ANyhSAD669EA8Ni2AJBNAgCXVwIAzqt6AOjTsACSUwUAl10WAKhpGADutl0A5a9UAMugbgCSUAwA1rB%2FAOCmSgD86s4A9ujGAI1MAgCbYBUApmoZAK9yHwCjai8AqHAmANWzhADFnm8Ajk8EAI9LCADlzasAk1MBAKBeDgCfZBYAm2AeAKpzOQDQlD0At4ROALuQXQD879QA%2BujLAJFPAACVVgMAmFcFAJRTFQCVVhgAmFsYAKVmFwDZtocA9L1jAPK7YQDLkDsAvJNdAMeVUAD77c8AkFEFAOGqUQDhqE8A3J9CAM2TOgD57NAA9OTHAPThwACPUAIAjk0HAOXNpwCWWAQA27uTAJ9jGACkZhUApmkbAKNsJADwul8A77dbAO60WQDRq38A67RYAOmxVwDPqXkA36ZNANmeRgC%2BlmEA%2FOvQAPvqzAD86MkA7di2AI1KAQCPTAEAjUoFAI9OAACOTQMA6NCrAJJOAgCRUQEAk1QDAJZVAwCTVQYAklENAJRWCACYWAcAmFcKAJtdDwCYWRkAnmMWANW0iQDyvWIA07ODAOu2XADnsFcAuHsmALh%2BKQDcpEsAtIJIALuTXACOSwMAkE0HAI9NCQCSUQUAkE8MAJhZAwCcXw8Anl8RAPK7XwDtuFwA7bVWAP745QD66s4A%2BebJAJBPAwCQUQMAPuWfn5%2Bfn5MfJIjln%2BWfLkIZgdGmwX0un5%2Bf5eWf9s%2FlwETAwMCp3EznUNjdRET1nY2jDLTROINERETARERE75%2FARMDARETdbgUmfz29wMCphNRWyV5v1sCERERERERkn8BEwMBERIT%2Bf7DGt5XznanARNvymdPx3cBERERERO%2BfwETAwMD1RBvgsbDHTj96kqjARKiNWd6oqUREREREZJ%2FARMDARERERNyHT3DHinBP4p2onaBJg4RERERERESyn8BEwMBERERERN08xM1O%2BcY1S5LkA5x5hERERERERLKfwETAwERERERERMCd8yMvxunGajQY6FWEREREREREsp%2FARMDAREREREREwMCoW%2FcTYQXHUhF1G4TARERERESyn8BEwMBERERERPVEwIQ8RguzKshOjw%2Fc9cBERERERO%2BfwETAwEREREREqYSd8UIy0LuOO8jnudj1REREREREsp%2FARMDAwMBERMCE1B7Mpga0kQhYieqLW4TARERERETvn8BEwMDAwMCEGydiV1rSWml1VRvblO2HqMBEREREwGSfwETAwEREqRsnjIHSkIJovoOEwIT%2FiYTAREREREREZJ%2FARMDAwETA2EO0kHMWdIOEhMCEW60C%2FoRERERERERkn8BEwMDARBtWYy1gDlUbhKlEhDzjtou9wERERERERLKfwETAwMBEW10NhZvahEREwJ1T7PmvooOERERERERE75%2FARMDARPWdSjlWnYTAwN3%2Fw87H%2BcutG%2FVERERERMDvn8BEwMDAwN1NfKeERIT%2B4jv5ik7LR9vARPVEREREwO%2BfwETAwETAW0JFqp2dtVAVTgXGCXvbwEREREREREREsp%2FARMDAwIRbB%2Ftrq2VI%2BIpOLxCH%2F4SERERERERERESyn8BEwMBEwBs9vKWGLLj6BQIPvahERESpREREREREwO%2BfwETAwEREhJKkugZACnJcg6jAwEREREREREREREREZJ%2FARMDAwETAWykiQP3ReEMa2oREqURERERERERERESyn8BEwMBE9dxuyncUYNAGKGZ28Bup9URE9URERERERO%2BfwETAwMD1G55BcdXfbCDQBrTM5NX1RKlEREREREREZJ%2FARMDARESo4euHGxvYljC6Bvy%2FIYOERERERERERMBkn0T1wMBERBsXR731RIRbBCXZgZBf7tepRMDAwMDAwLKfwET1RMDAncPplL2oRPXd2jE6IChzoZ3AwMDAwMDA759EwMBEREQbTEHLUJqdwITAnW1RHFSY1oTARERERERk5UTAwMDAhN29gPjGSHv%2F3UTAhL305jbWwITAwMBERGTFn%2BXln5%2Bf5UqXKzMSZzfC5eXCn0p%2Brqzl5Z%2Bfn5%2F2HQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 </image>
 <url type="text/html" method="GET" template="http://www.sanger.ac.uk/cgi-bin/Pfam/qquerypfam.pl?">
   <param name="terms" value="{searchTerms}">
 </url>
</opensearchdescription>

To add this to your list of search engines, you also need to put the appropriate "link" tag in the head of an html page that you want the search plugin to be detected from, like this:

<link rel="search" href="opensearch_uniprot.xml"
   type="application/opensearchdescription+xml"
   title="Uniprot" />
<link rel="search" href="opensearch_pfam.xml"
   type="application/opensearchdescription+xml"
   title="Pfam" />

OpenSearch plugins are also partially supported by some versions of Internet Explorer, but I haven't tested it (there is no POST support for OpenSearch plugins in IE 7). [insert obligatory Firefox fanboy stab at IE here].

Chances are, you'd like to make one to search your favorite database. Here is the documentation I used for creating OpenSearch plugins for Firefox:

• "Creating OpenSearch plugins for Firefox" at the Mozilla Developer Centre, and some blog posts here and here.
• "The data: URI kitchen" is a useful web-based tool for encoding images a base64 (you need this to embed icons using the Image tag).
• There is also this "add to search bar" extension, which I didn't use in the end.
  

---

Edit: Argghh .. looks like this code is showing up fine on the web page, but is a bit broken when displayed from the RSS feed in akregator .. I assume other feed readers may also be having trouble .. Anyone know a reliable way to post code in Blogger ? Wordpress is starting to look attractive ...

A simple but useful application for Google Co-op On-the-fly Custom Search

My del.icio.us linkstream is a bit like a window into my stream of consciousness.

I've always wanted to be able to 'search outward' from just my delicious links ... a recent post from Alf about Google Co-op 'on-the-fly' search engines just triggered a simple but really useful idea; make a Google Co-op search of my delicious linkstream ... this way I can search just within pages I've deemed worthy of bookmarking.

After a bit of wrangling with the various ways of getting data out of delicious (see my own comments to this post), I found this script for generating an html page of links from delicious. This page contains all my delicious links, not just the most recent ones (it seems you can only get a subset of the most recent links without authenticating with delicious, hence the PHP script using the delicious API).

So, after hosting the PHP script revealing all my links, I can point the Google Co-op Custom Search Engine to that page, and search away ! It's a nice way of using search to 'retrace' my steps, since it should generally restrict results to the parts of the web I've already seen and rated as worthy of re-examination.

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).