nodalpoint.org - Test-drive the NAR web server issue - Comments

great tip

Neil — Mon, 24 Jul 2006 08:00:19 -0400

That's a great tip. Are there any neat web tricks that alf doesn't know ;)

mozex

alf — Mon, 24 Jul 2006 05:25:24 -0400

Mozex (Firefox extension) is worth a mention here too.

Marking nar tests

Neil — Sat, 22 Jul 2006 21:42:38 -0400

I thought about that (a column with a tick or something). I think it's easier if people just look for the "none yet" in the comments column. Also, there's no reason not to have >1 comment per service. Wiki editing is a freeform process - I think this troubles people who prefer a clean forms interface to a database, but I'd encourage people to give it a try. You need to get into the "wiki mindset" :)

wiki format is tricky

Neil — Sat, 22 Jul 2006 21:01:46 -0400

I just knew that someone would have this criticism :). You're quite right though - the people in my group have the same complaint about the lab wiki. I know that Twiki has a table editor plugin which provides a form interface for table editing - does dokuwiki have similar?

I did consider a forms/database solution, but wasn't sure if it was worth the time. If people are keen to contribute to this, leave comments and I'll cook something up. The good think about the wiki though, is that it's already setup for Nodal users.

In the meantime, you can always copy the wiki-formatted text to an editor and search for what you want, then paste back, I guess.

[s, |s and URLs

Stewb — Sat, 22 Jul 2006 18:42:29 -0400

You probably don't want to hear this after all that copy n' paste but the format on the wiki is a bit tricky: it's hard to find the program that you want to add a note to. :)

The wiki is a good starting

Greg — Sat, 22 Jul 2006 14:43:43 -0400

The wiki is a good starting point, but some kind of database listing these services would be better. Amazingly these resources now have a term: Resourseome. This comes from a recent perspective in PLOS compbio, Time to Organize the Bioinformatics Resourceome.

The article mentions the Bioinformatics Links Directory, which in fact has all the NAR web server issue links with categories. Of course there is no machine readable representation of the data to help avoid the copy-and-paste problem. Sigh.

Some more detail on the reasoning behind using a 'links directory' is available here. There is only one other effort I know of that catalogues biological resources: BiowareDB. I have previously toyed with using this kind of thing as a starting point for RDF descriptions of biological resources. Read more about that here.

As an aside, I find the use of "web server" annoying, it should be "web services". Maybe I'm just pedantic.

suggestion for NAR test

PedroBeltrao — Sat, 22 Jul 2006 11:13:03 -0400

Maybe we could mark the ones that we are testing so that we don't re-test stuff.

Test-drive the NAR web server issue

Neil — Sat, 22 Jul 2006 10:19:27 -0400

maximilianh and alf suggested that we should try out and rate the tools in the 2006 NAR web server issue.
I've trawled through the abstracts and created this wiki page. With that much copying and pasting there are sure to be errors - I counted 146 links on the page, but then I'm now almost blind.

Anyway, the idea is that you can go there, choose a link and try it out, then leave a comment as to how well it worked for you. If you haven't used the Nodalpoint wiki before, it's dead easy. Just login with your Nodal user/password and look at some pages to get an idea of wiki syntax. I'm fairly sure that all Nodal users should be able to edit this but if not, leave a comment and we'll sort it out.