Bioinformatics & Firefox

My spare time at the moment is taken up with writing an extension for Firefox, which with any luck I'll talk more about next week. OK, that and Railroad Tycoon 3 which I picked up for £10 (about $6) in the budget section of my local video game store. Oh, the shame...

Anyway, considering that Firefox is only supposed to have about 10% of the browser market it's maybe remarkable that the web logs for this site and of the departmental web site at my work suggest that, actually, in bioinformatics the figure is a lot higher. Closer to 60% in fact, which is pretty good going (I'm not a hater; if you want to use IE go right ahead. Personally I just find Firefox a lot more productive).

Maybe it's not all that surprising; you gotta figure that for the internet as a whole a lot of the 90% using Internet Explorer are working stiffs on corporate managed desktops or people who just want to surf the web without worrying about any of that technical stuff. Bioinformatics is a computer science-y discipline: no doubt if this was a hardcore CS blog then the alternative browser share would be a lot higher.

To get back to the point: Firefox and bioinformatics. I was planning to do a rundown of some of the more interesting science related extensions at this point but then I discovered that Jawahar Swaminathan has already done something very similar over at Nodalpoint a couple of months ago. Jawahar is the clever chappie behind Biobar and he knows what he's talking about: check it out if you haven't already.

One interesting looking extension that isn't specifically geared towards science is Piggy Bank, which is described as:

an extension to the Firefox Web browser that turns it into a “Semantic Web browser”, letting you make use of existing information on the Web in more useful and flexible ways.

Piggy Bank was created by a collaboration between W3C and MIT called SIMILE and is released under an open source licence. Essentially it's a way of scraping data from different web sites (i.e. parsing out the useful bits), organising it using ontologies and then collating it all together in some useful form. It's data mashups made easy.

One of the potential uses they give is of somebody moving house who wants to combine the apartment for rent notices from one web site with the addresses of local schools, subway stations etc. on the same map. Piggy Bank can scrape the relevant data from the different sites and then display it all on Google Maps.

Obviously screen scraping isn't the way forward - see Greg's Nodalpoint post the other day to read more about the standards which formalize things - but it's an interesting halfway house. I'd be interested to hear if anybody has had any experiences with Piggy Bank (good or bad) in the life sciences domain.