ISMB – attending without travelling

ismb2009It’s ISMB time again, and as colleagues jet off to Stockholm, I can’t help but feel that twinge of envy. Lucky then, that the conference organisers have a fantastic attitude towards live- and micro-bloggers, and after the success of last year’s efforts (see the FriendFeed room, and the paper), they are positively encouraging more of the same this year. There’s a FriendFeed room again, where a new thread will be posted 10 minutes before each talk, and with a number of dedicated FFers present, there’s sure to be some fantastic live coverage. I’ll be following along.

FriendFeed and Me

Apparently its bad for a blog to be introspective, and always about the author. But I’m unrepentant. What do people write about if not themselves, even indirectly? So here’s another post about me, and about my participation in a small web revolution.

Next week marks 6 months since I registered my account at FriendFeed (and simultaneously, Twitter). Ally posted yesterday about her moment of epiphany with the ‘lifestreaming’ site, and I know other people have blogged about it’s impact on their online lives, and I thought I’d do the same as a bit of a retrospective.

Briefly, FriendFeed is a site that aggregates information from other sites, and shares it with the world. I collate the feeds from this blog, Twitter,,, Flickr, Google Reader and a few others there. People can subscribe to this amalgamated feed, and get an idea of my interests and what I am upto.

I try to limit my activity on FF (and, consequently, Twitter) to stuff that’s purely work-related (although real life does occasionally creep in), and because of this ‘work-stream’ approach, it has become an increasingly indispensable tool in the pipeline of information discovery and my scientific ‘social life’.

The following are a (direct or indirect) result of my participation at FF:

  • I have finally learnt Python, and made it my programming language of choice
  • I have adopted Git for version control, and have several repos on GitHub
  • I bought this domain, and set up this blog
  • Found countless papers and blogs I may have missed

As a more concrete example of the power of FF, I am currently involved in a project looking at co-evolution of bacterial proteins, and am employing Statistical Coupling Analysis to score multiple sequence alignments. This method produced thousands of scores across an alignment, and the best way of viewing them is by constructing a sort of heatmap. I was using Gnuplot to do this, and my maps looked something like this:

This is not terribly useful, because you keep having to check the legend to see whether red is ‘hotter’ or ‘colder’ than yellow, etc. Then, one morning last week, I saw a link on FriendFeed to this blog post, and following the very wise suggestions in that post, I worked out how to redraw my plots so they now look like this:

This makes it much easier to tell at a glance where the hotspots are to be found in the alignment. It is just one blog post, but I would never have found it without FF, and it is a useful illustration of how this new workflow has changed my productivity.

So, for the next six months, and on into the more distant future, what role do I see for FF in my work life? Well, for a start I need to participate more. I am constantly aware that I should comment more, and even just ‘like’ more stuff. Contribution should also take the form of propogating things to FF for others to see. Most of my Feed consists of articles at CiteULike and Tweets. By posting more stuff to FF directly, and by sharing interesting articles on Google Reader, I’ll be providing more grist to the mill of conversation than I currently do. And I want to be an active member of this community, I like the people, I’ve got a lot out of the last 6 months of (relatively) passive interaction, and want that to continue, but I should no longer be a passenger.

A blog about the blog

This is, home to this blog, and my research wiki. I have yet to decide what I will blog about, or how often, though my spare online time tends to be spent microblogging these days, so activity may be limited… or I may surprise myself.

You can find more about me hereabouts, you are also welcome to follow me on Twitter or FriendFeed (or both).