Software review: producing two dimensional diagrams of membrane proteins

E. coli LamB, presented using TMRPres2D. Not that the cytoplasmic/extracellular labels are incorrect, and should say extracellular/periplasmic.

I recently needed to make a simple, two dimensional figure of a beta-barrel membrane protein. I went hunting for programs that might take a sequence and/or structure and produce a pretty looking diagram to save me constructing everything by hand. Here are two I found and tried.

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ResolveRef updated : now with auto-suggest and source code

I updated ResolveRef last night and checked in the most current sourcecode to svn at Google Code.

New features include:

ResolveRef, now prettier, with comments box by disqus.

  • Suggest/autocomplete for journal title field, using the journal title lists provided by PubMed.
  • A “Verify” button. Allows a ResolveRef URL to be constructed with the web form and verified as working and valid without actually forwarding the user to the article.
  • Some bugfixes (handled the case where there is no DOI in the PubMed record, handled network timeouts to PubMed)
  • Refreshed visuals
  • Disqus comments box for feedback

In the interest of just getting something working quickly, I implemented the suggest feature in the laziest, possibly most RAM and CPU hungry way possible (the “JQuery Suggest” code queries the web app with substrings as you type each character. At the server side, the app uses a regex to scan a ~1.5 Mb list of journal titles held in RAM). I’ve already noticed a few “This request used a high amount of CPU” warnings in the logs, with the threat “High CPU requests have a small quota, and if you exceed this quota, your app will be temporarily disabled“. If my nasty hack starts heating up Google’s datacentre too much, I might have to disable the ‘suggest’ feature until I can implement it “properly”.

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ResolveRef : looking at the logs

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.

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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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Information R/evolution

I just stumbled upon this great little short film by Michael Wesch of Kansas State University (it’s a year old now, it could be that everyone else has seen it but me). It highlights the way that the organization and retrieval of information has been changing since the growth of the Web. I’m sure the question “Exactly what is Web2.0 ?” has been debated around in circles for the last couple of years … well, beyond the flashy web-based
UIs and ‘social’ aspects, this film exposes nicely one of the more important parts of Web2.0 in my opinion – the change in the way many of us organize and find information.