Fuzzier Logic

5 Best Data Visualization Projects of the Year – 2009 | FlowingData

via flowingdata.com

The top visualization project of the year, according to FlowingData, is a project by Ben Fry, which shows changes to the theory of evolution over time. The project takes advantage of the publication of the full works of Darwin online to trace changes in the text of On the Origin of Species over time.
A deserved winner, and very apt, considering the batch of anniversaries that have gone by this year.

Posted via web from Simon’s posterous

Tags: data-visualization, posterous

Google Acquires AppJet – are there any live, functional alternatives to Etherpad?

Posted via web from Simon’s posterous

Tags: posterous, Software, web

Now that’s what I call microblogging

As noted previously, ISMB is underway, and the FriendFeeders present are working hard to keep the rest of us updated on what’s going on.

I just wanted to highlight the coverage of this morning’s keynote, which was absolutely exemplary.

Tags: friendfeed, microblog

ISMB – attending without travelling

It’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.

Tags: Conference, friendfeed, ISMB, microblog

MMR scaremongerer sicks the legal dogs on Ben Goldacre

Let the blogosphere and twittersphere spring to his defence!

See here for full details, but a London broadcaster had a half hour long rant on her show about the ‘dangers’ of the MMR jab on 7th January. Ben Goldacre subsequently posted the entire, repulsive, segment on his blog, to show this woman up for the scaremongerer she is. The radio station she works for has now set the lawyers on him, insisting he cease and disist.

So I am reposting his plea for help, and posting links to the relevant content (original post here, complain about the broadcast here). If you have the know-how to help him out, please do so.

EDIT – You can get the audio of the original broacast from YouTube or WikiLeaks… if you want your head to explode with frustration… Also note this graph, which illustrates the very real effect of irresponsible woo like this.

Tags: badscience, doom, MMR, weirdos

Twitter and Me

This is a bit of a follow-up to my post about FriendFeed. I registered for Twitter at the same time as FriendFeed, and while I immediately saw the value of FF for a long time I only saw Twitter as a tool to broadcast work-related ideas and thoughts to FriendFeed. I saw it as having little utility in it’s own right.

My follower/following count slowly increased, driven by FF, I tended to reciprocally follow people, and the few people who were following me found me there. Then, early this year, David Bradley posted his list of 100+ Scientwists, and I thought: ‘hey, I’m a scientist, and on Twitter… maybe I should be on that list”. So I got included, and then got a sudden upsurge in followers.

Not all these followers were on FF anymore, so I couldn’t follow my Twitter traffic on FF (without creating a whole bunch of imaginary friends, which I didn’t want to do). So I had to start following Twitter properly.

This has led to a more interesting conversation developing. I post more @replies, and am receiving a few more in return (though often from the desk next to me in the office), and though I don’t have any specific examples like I did for FF, I feel I am gaining more value from Twitter as a tool in its own right.

I have tried a number of apps to monitor Twitter traffic, but none of them quite fit into my workflow properly (though TweetDeck comes closest, and is much better than Twhirl). However, I got a 3G iPhone yesterday, the Twitterific App seems great, and in the future I suspect most of my Tweeting will be done on that platform.

Finally, there has been a lot written about Twitter in the last couple of weeks, and in particular about the number of ‘celebrities’ tweeting, both real and fake. For my part, I do follow a few, and get most value from @stephenfry (bonus linky), who really seems to ‘get it’ (as he does most things, though how he keeps track following over 30k people, I’ll never know), and @dave_gorman (bonus linky), who, like me, is just learning the value of the platform. But the real value of Twitter is again, like FF, in the quality of the science conversation on there, and how it makes me feel connected to a worldwide community of like-minded people.

Tags: microblog, science, twitter

Wordle

I’m a bit behind the zeitgeist here, I know, but Wordle is a pretty cool little tool. I think the cloud of my CiteULike tags fairly reflects my academic interests, and the fact that even after 5 years away from the lab, ‘wet’ techniques dominate, I really should make more of the bioinformatics involved in the papers I bookmark.

Wordle Tag Cloud of my CiteULike Library

Find it on Wordle here.

A few notes on technique. I extracted the tags from the RIS export of my CiteULike library using this Python script, I had to limit the represntation of words to 25, otherwise ‘proteomics’ would have dominated to such an extent that virtually none of the other tags would be visible (except maybe ‘protein-protein-interactions’). But then I am responsible for supporting proteomics researchers, and predicting and validating protein-protein interactions is my major personal research interest. So I guess this is fair enough.

Tags: citeulike, tag cloud, wordle

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, CiteULike.org, del.icio.us, 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.

Tags: friendfeed, lifefeed, microblog