Bioinformatics Zen

Science, biology in particular, lags behind in the uptake of new web technologies. For example blogging is still regarded in the mainstream as a frivolous, self-indulgent activity. While, in business, blogs have been embraced as an effective method of communicating with customers - have a look at these wired articles, here and here.

However, the adoption of web technologies in science is inevitable. In 5-10 years time, your group will be behind if it doesn’t have a blog. It may even be the case that there will be an option on grant applications to enter your blog - the reviewers can read about your most recent thoughts on the field and how you manage your research. As an example of how serious journals consider this, guess how many blogs the journal Nature has. The answer is here. This is direction the web has gone, and where science is heading. But blogging is only part of this, one of the key technologies driving the change is RSS.

If you’re reading this article, there’s a good chance that you know what RSS is. If you’re unfamiliar and want an introduction, have a look at this. This post goes through three reasons why RSS feeds would be of interest to you as a scientist.

Updates on websites you’re interested in
The most common use of RSS is keeping up to date on websites that you’re interested in. Often a blog. Where ever you see this button:

or the text “RSS”, “Atom”, or “Feed” this means that the website has an RSS feed that you can subscribe to. Put the link to this website into your feed reader, and whenever the website has new content added, you’ll be updated.

But the alternative to this is, checking back to the website every so often, while tedious is not life threatening; so what is all the fuss about? Well, read on…

Creating content you’re interested in

The RSS stuff that’s creating a buzz, is when you create a feed for the content you want. Here’s a real world example. You’re interested in a particular researcher, because his work is very similar to yours. So how do you keep up to date on what they’re publishing? Go to Pubmed every-so-often, and do an author search? Well you could. Or instead you could go to Hubmed, and run the same search. When the results are returned, click on the feed button. This generates an RSS feed of all the authors papers. Which is updated when a new paper is published. You can generate this type of RSS feed for any type of literature feed you can think of. For example articles in nature and science containing the keywords “systems biology”.

But custom RSS are is a niche technology confined to a few esoteric websites. There’s a good chance that anything that returns a set of results may have an a similar RSS feed. Another example: I’m interested in all the delicious bookmarks that are tagged with the word “bioinformatics”. You guessed it, delicious has an RSS feed that gets updated when new bioinformatics bookmarks are added.

RSS is only going to get bigger too. Yahoo released a toolbox called Pipes that allows you to customise and create RSS feeds further. Pedro has written an article on this.

Monitoring stuff you’re interested in

My third, and final point, is that RSS can be used to keep an eye on pretty much anything you’re untested in. Another example, using this website, when I’m not writing a post for Bioinformatics Zen, I’m interested in two things. Who is writing comments on posts, and who is linking to this website from their website. BZ runs off a content management system called Wordpress, every time I log in, the first page tells me this. But this means I have to log in every so often to keep up to date. Which is a bit of a pain. You can tell what I’m going to write next - instead I use RSS feeds for both these things. The comments feed is produced by the code running the website. The link feed is produced by technorati, a website that monitors blogs. Go on kids, link to my blog from yours, and your name will, by RSS magic, appear in the feed!

But on a more serious tone, there’s no reason that everything you have to monitor, or wait for, can’t have an RSS feed. What if your sequencing facility, or computing cluster, produced an RSS feed for completed jobs. All you’d have to do is filter this for your job id, and you’d know as soon as the job was done. The possibilities of RSS can take us in any direction we can think of.

Where to get started

All you need to use RSS feeds, is a feed reader. I use Google Reader, all that’s required is a Google log in.