Bioinformatics Zen

Deepak, Neil, and Cameron have set up life streams which aggregate the feeds from services from sites like Last.fm and Flickr into a single set of posts. I’m a bit wary of this doing this because I already get easily distracted by Ruby and bioinformatics blogs, but Neil gave me an idea when he wrote about using these technologies to track research. I currently use Subversion to back up my project files, and I noticed Twitter status updates are very similar in length to subversion log messages. I created a short script so that every time I do a subversion repository check in, the message is also sent to Twitter.

#!/bin/sh
#Inspired by tinyurl.com/yt4ssq
 
# Scrub weird characters
MSG=`echo $@|tr ' ' '+'`
 
# Send twitter request
curl --basic --user "username:password" --data-ascii "status=$MSG" "http://twitter.com/statuses/update.json"
 
# Send SVN request
svn ci -m $MSG

Combined with an RSS Wordpress plugin, my most recent research activity from Twitter is displayed as a stream on my blog. Taking this a step further I included feeds for my research tagged Figures on Flickr, my paper bibliography on CiteULike, and discussion of my research on my blog. This stream is available on www.michaelbarton.me.uk/research-stream/, and shows the general idea of what I’m trying to do. I like this because in bioinformatics its sometimes difficult to know what other people are doing, but, now I hope that other people in my group can have a quick glance to see what I’ve been up to. Furthermore this all works passively, where I’m already using these services in my research anyway, and the only thing I had to do, was use yahoo pipes to aggregate the already existing information.

Because bioinformatics work is amenable to being displayed, shared, and edited on the web I think that the field should be at the bleeding edge of using Web 2.0 services like this. Of course many other bloggers before me, in particular Deepak, are already discussing this. Compared to most mashups what I’ve created is a rather shoddy as I’m cobbling together various services and trying to use Wordpress plugins to create something not exactly what they were intended for. However I don’t have much time in my PhD to spend experimenting, and I think this would be true for most scientists. Therefore the more that existing services can be used, the better. As a further example, I think Flickr has a lot of potential, and I would like to create a group for my lab, so everyone can upload and tag their figures, as they are producing them. Then the group’s pictures can be browsed and organise by tag to visualise what everyone is working on. The only effort required is for people to upload and tag their photos as they are making them.

In a previous post I wrote about how great new web tools are making it easier for scientists to collaborate, find information, and share information. This light-hearted introduction was rather popular, so heres’s a tongue-in-cheek video version.

Collaborating on the same document

Tom, Dick, and Harry are collaborating on a paper. Tom, being the PhD student, does all the work and then writes the paper. Tom then sends a copy to Dick and Harry who edit it with their opinions. Unfortunately Dick completely removes the second paragraph of the discussion, while Harry expands it. Both then send their edited copies back to Tom.

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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.

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Neil Saunders has posted a great tip on using the new iGoogle page to synchronise your internet paraphernalia across computers. I definitely agree with his points. Having to “mark as read” the blog posts you read at home, in your work RSS reader, is a bit of a pain. Online tools, as opposed to installed, are where things are going, and iGoogle is an example of this.

One cool thing that google also offers is a new personalised search. Search results tailored to what you’re interested in, based on previous searches. Does this work with google scholar? It would be cool if you could upload your bibliographic database to google and it weighted your searches based on your article interests.