Facebook as a platform, pt 1

(The next couple of posts have very little to do with bioinformatics - sorry).

I've been trying out a whole bunch of online social networks this year in the name of research (no, really). LinkedIn is the most boring. Bebo, which has a widget that suggested that my celebrity lookie-likie is Whoopi Goldberg, is the weirdest. MySpace is just scary.

Facebook is pretty good, though. The design is grown up and so is the userbase (relatively speaking). Nature has a group there to help point young scientists towards some of the less obvious services that NPG provides (like free drinks at Nature Network meetups - if you're in London then come along). Facebook were the first big social network to release an API and now they've gone a step further and opened up Facebook as a platform.

I was pretty excited by this announcement. Facebook works brilliantly as a social platform - will 3rd parties add features that'll enable it to compete in the 'professional' social networking arena too?

Pg10k

OK, it's cheating because the figure includes books as well as papers, but Postgenomic has now tracked more than ten thousand citations in blog posts. As the majority of blogs either (a) don't supply fulltext RSS feeds, just excerpts or (b) strip out HTML and thus the links from feeds there must be a sizeable dark figure, too - how many citations are being missed by Postgenomic and Chemical Blogspace, I wonder?

Anyway, paper #10,000 was Mauro Costa-Mattioli's paper in Cell about stress induced translation regulation (conveniently the citing post from Gene Expression explains what that is and then goes into some interesting detail - an excellent advert for science blogging).

I'm pleased. Scientists write blogs and put science in them. They talk about recent papers. Their numbers are growing. Might blog trackbacks be a good or even necessary supplement to comments on a paper on a journal website?

It'd be interesting to take, say, BioMedCentral papers from the past twelve months and compare the number of comments on each to the number of citations from posts. I think that BMC does comments quite well, possibly better than any other STM publisher - PLoS included - not that that's necessarily saying much (also there's still no comment RSS feed, boo). Using comment data from PLoS One would be another option (was speaking about this with a colleague earlier today) but considering how new PLoS One is perhaps there isn't enough data in Postgenomic yet for any results to be meaningful.

Actually, it'd also be interesting to compare the number of blog citations to the number of 'real' citations recieved by each paper in the index. Is blog buzz a good indicator of impact?

A brief stats update: the site has been running for about fourteen months. The most popular book has been The God Delusion, with relevant posts from 15 different blogs. The most popular 'proper' paper (anything with a DOI in PubMed gets tracked, which includes some opinion pieces) was Ben Voight's a map of recent positive selection in the human genome, from PLoS Biology.

There are 735 blogs in the index, of which 341 were active in the past week. Usually ~2,500 posts are aggregated each week (a major exception being the last two weeks of December, when this number falls to 1,400). There are ~120,000 blog posts in the database.

I've been busy with other projects at NPG recently but plan on spending some more time on Postgenomic over the next few months. If you've got any ideas (or you'd like to help out with coding, documentation, design - it's an open source project, born from discussions in the comment threads of bioinformatics blogs) then please let me know. If you're interested in using data from Postgenomic in some way then that's cool too, I'm keen to help.

I was going to reiterate my thanks to people who have contributed so far but the list is too long and I'd forget people. You know who you all are - ta muchly. Science bloggers rock.

Genomic visualizations suck

I've written a blog post on Nascent about genomic visualizations (following on from the 'where's the AJAX?' thread on Nature Network). It turned into a bit of a rant, unfortunately. Anyway, if you've got any relevant links, comments or contacts then please add them there. I've been out of bioinformatics for a year so maybe I've just lost touch...

Quick notices

Some quick notices:

• One of the development servers at Nature went down and took some cgi-scripts with it - including the one that made the box.net / Connotea mashup work. Sorry if you noticed this. I'll fix things soon.


• Noel has written a Greasemonkey script based on Pedro's original work that pulls in comments from Postgenomic and Chemical Blogspace (Egon's chemisty blog aggregator which, amongst other things, tracks InChi mentions - very cool, I've been crap at applying the patches to the main code, sorry Egon). The script shows comments in a nifty little bubble. Here's a table of contents to try out the script on.