Postgenomic update

Sorry I haven't been writing any general bioinformatics posts recently...

I've made quite a few changes to the code for Postgenomic over the last week or so - to the extent that I feel it's relatively stable, though still very much in beta. I've also been able to document the code a little (domain is a bit flaky; hit reload if you get a "page not found" error) and set up a Subversion repository on Sourceforge.

You can check out the code with Subversion using

svn co https://svn.sourceforge.net/svnroot/postgenomic postgenomic

The directory structure that results is explained in marginally more detail in the docs. Basically, there are three main parts to Postgenomic: the database, the pipeline (blogs => parsed data) and the web interface. The pipeline and web interface are independent of one another, so if you wanted to make any interface improvements (or speed it up) you can do that without getting mixed up in Perl and Python.

Vague future plans include prettifying the pipeline output, implementing a REST API for browser extensions / other web apps and picking out gene and protein names from the text.

Along the latter lines, Egon is doing some great work adding support for InChIs to the code.

There're more development bits and pieces at postgenomic.org (see flaky domain notice above) including mailing list details (postgenomic.org will also always have a dump of the latest database at this link, if you just want to get your hands on the raw data). From now on I'll post Postgenomic announcements and updates there rather than on F&L.

Well, most of the time.