Userscripts for the life sciences

Egon and Noel have a paper in BMC Bioinformatics this month describing userscripts for the life sciences... nice work, guys.

Last year there was a discussion over at Pedro's of the merits of publishing individual userscripts after Ben Good's paper about a Greasemonkey based iHOP enhancement appeared in BMC. This is more of a review.

We discussed the possibility of hosting a science mashups / web services wiki at NPG - sort of like ProgrammableWeb, but listing only the APIs, databases and tools relevant to science. This sort of ties in with the post over at Nodalpoint that Alf wrote about documenting bioinformatics APIs. There's enough stuff available nowadays for it to be a useful resource, I think.


Incidentally: I started writing this post BEFORE I read the paper properly and realised that I got a namecheck for Postgenomic. Now I definitely recommend it. ;p

Nature Network - add papers to profile by PMID

Nature Network v2 was launched on Valentines Day. Nature Network, in case you haven't heard of it before, is sort of like MySpace for scientists (except not crap). Previously it was restricted to scientists in the Boston area, but this new version allows anybody to sign up, network with others, post to blogs and forums, set up a profile... you get the idea.

There's space on your profile to enter the papers that you've authored, which is cool. Unfortunately for lazy people like me you have to enter the details of those papers manually (or at least you do for now).

Luckily the form HTML is of great semantic beauty. Thus: nnaddbypmid.user.js, a quick Greasemonkey script that fetches paper metadata from PubMed using the the EUtils. Follow the 'add publication' link on your Nature Network profile as normal, then fill in the PMID textbox and click on the new 'look up details' button. Voila! The other fields should get filled in automagically.

PLoS One / Postgenomic mashup

Chris Surridge has an interesting post over at the PLoS blog about the comments (or the lack thereof) on PLoS One papers. He mentions one paper in particular that has a long discussion thread associated with it on Gene Expression but no real comments on the actual PLoS One site.

As a temporary solution (?) to the problem of blog comments not being immediately accessible from the paper, summaries of notable manuscripts are going to be posted to the PLoS publishing blog with open comment threads. Based on the three posts already up I think this is a terrible idea.

Partly this is personal preference - I hate blogs that just replicate tables of contents - but more importantly I think that it misses the point.

People like the GNXP folks have taken the time and trouble to build up a loyal community that fosters debate and to create an environment in which visitors enjoy interacting with the site and with each other. Sticking up an abstract or two on your own blog just isn't going to compete with that, doesn't matter how much traffic you get.

Blog properly - engage your audience - or don't blog at all. It's a personal communication medium, that's one of the reasons why people feel more comfortable commenting in a blogging environment. A link and an abstract on a publisher's blog isn't personal, it's an advert. The PLoS One blogs are generally a good read at the moment, don't ruin them.

I'm not just PLoS bashing here: I like the ideas behind PLoS One and we do the same 'if we blog the abstract then people will comment!' thing at Nature on some blogs (the ones I don't read any more). The intention is good, it's just misguided, IMHO.

Anyway, I think that a better solution would be to embrace the existing science blogosphere and to explore ways of working with it more closely. As a proof of concept, here's a Greasemonkey script that adds science blog trackbacks to PLoS One.

It's doesn't look particularly nice, mainly because I didn't have time to style things very well. Feel free to do with it as you will, though (you could get it working with PLoS Two, for a start).