nodalpoint.org - Hubmed in NAR - Comments

Why even have a web server issue?

Neil — Sun, 23 Jul 2006 20:32:43 -0400

I find myself wondering - what exactly is the point of a web server issue? Given that most people locate web services via search engines or other web pages that point to them. Given also that the web is in a constant state of flux, with services appearing and disappearing all the time. My conclusion is that its sole purpose is to provide a publication opportunity for people who have set up a web service.

I think this really reflects the disconnect between the current state of publishing and what we've started to call Web 2.0/Science 2.0. Pedro has more to say about this in a recent post, as does the OpenWetWare community.

NAR should rigorously review these web server papers

firefox77 — Sun, 23 Jul 2006 18:59:46 -0400

I am wondering what's the median citation # for articles in the webserver issue...

NAR tools test

Neil — Sat, 22 Jul 2006 07:06:15 -0400

This is a good idea. The way things are in bioinformatics journals just now, we could probably write a paper: "User experiences of the NAR web server issue" :) Or at least, a letter to NAR.

I'll probably regret this, but I'll volunteer to create a page on the Nodalpoint wiki with a link to each resource in the NAR webserver issue and space for users to leave their comments. Unless anyone has a better plan?

writing about NAR

maximilianh — Thu, 20 Jul 2006 09:31:25 -0400

how about grouping together, everyone describes the tools that he tried? I volunteer for anything related to regulation of transcription (around 10 tools). Anyone else?

Taverna etc

Duncan — Mon, 17 Jul 2006 14:17:48 -0400

I'm obviously biased but there is a paper on Taverna, which is a useful tool that works...

I was a little disappointed to find there don't seem to be many new tools described this year (unless someone can correct me). I did find the bit about using ontologies to describe the bioinformatics links directory in the first paper of the issue quite interesting though.

“We are also investigating the development of an ontology and/or meta-tags to aid in the functional classification of servers listed in this Bioinformatics Links Directory as well as others, as was recently suggested by Cannata and colleagues. We look forward to working with the community on this exciting development.”

I wonder how far they will take this? Perhaps they will go for OBO status?

I think this is some well

Greg — Mon, 17 Jul 2006 13:37:29 -0400

I think this is some well deserved recognition for Hubmed (dare I say, main stream ?), well done Alf! And also Congratulations on the new job.

Nature seem to be making a habit of smart moves e.g. Connotea (acquisitions now) in the area of Science 2.0 (or the new new science, what ever takes your fancy).

Thanks Chris. I was actually

alf — Mon, 17 Jul 2006 12:57:52 -0400

Thanks Chris. I was actually going to post about the web server issue here anyway, seeing as so much of it is bioinformatics tools. Has anyone picked out any interesting papers about tools that actually work?

Hubmed in NAR

chris — Mon, 17 Jul 2006 11:24:13 -0400

Alf has a paper in the NAR web-server special issue, descibing HubMed. He also has a new job. Well done Alf!

via HubLog