Your bones got a little machine

Here’s a list of some of the publicly available web applications I’ve written. Many of them remain at the ‘incomplete but working stage’ (like the Web2.0 perpetual beta, but worse).

Recent stuff

• ResolveRef is a Google App Engine application. It is an attempt at making a RESTful and human readable URL identifier for any paper in PubMed. It is based on an earlier version written with the Turbogears framework (OpenRef resolver), which in turn was based on an idea by Noel O’Boyle. The ResolveRef source code is available here.
• I have other interests, outside science (“What a well rounded individual”, I hear you say !). WiiRSS is a news aggregator site for Nintendo Wii news sources. I can’t claim too much credit here, since it’s a customization of Gregarious, which I didn’t write.

Older stuff

• Here is a simple CGI application for estimating protein secondary structure content based on a circular dichroism (CD) spectrum, based on the method of Raussens et al, 2003. The Raussens method isn’t as advanced or accurate as some competing methods, but it is extremely useful if you need secondary structure estimates but cannot accurately measure the protein concentration of your sample (eg, due to the prescence of detergents). It also makes a nice sanity check to compare against the results from the CDPro suite or Dichroweb.
• I wrote a Quickchange(tm) mutagenesis primer design helper when I was doing some mutagenesis. It’s a bit ugly, but it works. It can help design primers based on the method of Zheng et al, 2004, which is supposed to be better than the method recommended by Stratagene. I wrote this before I discovered PrimerX.
• Here is a silly biotech company name generator. This one really needs to be prettied up, and could do with an update with some more recent buzzword prefixes and suffixes.

I also have one or two web applications in ’stealth mode’ … when they are ready they will emerge. Watch this space