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

Dapper

So Andrew has been talking about Dapper and Pedro about kapow, both screen scraping (sort of) services that let you extract data from websites. It's interesting and potentially useful stuff.

Here's my Dapped contribution: an RSS feed of advance access articles from Bioinformatics and NAR. I tried putting Nature advance publications in there but shamefully the nature.com markup isn't up to scratch or something and Dapper refuses to pull out the correct pieces of data consistently. Neh.

There's a little bit of custom PHP code involved to create links for each paper from the doi, to extract publication dates and to merge the two dap RSS feeds - this seems like the kind of thing Pipes was designed for but unfortunately it's not quite flexible enough yet.

I made the original bioinformatics and NAR daps public if you want to tweak them.