nodalpoint.org

Greg Tyrell recently remarked that there was no point in defending open-access publishing because its triumph is a foregone conclusion. I agree with him. However, for the younger guys out there, it may not be obvious why subscription science magazines is going the way of the Dodo. So I would like to offer some history.

I decided to jump on the bandwagon, the same Rosie Redfield jumped because of Pedro: Open Science.

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.

Football informatics, theory and practice: Germany 2006

The frenchman Pierre Bézier knew a thing or two about curves. But as World Cup fever tightens its grip around the globe, it is the footballers in Germany who are showing us just how much they know about the practical science of curving and bending the ball into the goal. Is there any essential curve-theory for World Cup stars like Beckham, Ronaldinho and Thierry Henry to read and brush-up on in their German hotels this summer?

Pedro mentioned it, I mentioned it but there's no harm in mentioning it again. BioPerl has a redesigned website built on MediaWiki and an associated news blog. Great stuff.

This week's Nature continues the "new Web technology" theme with a look at wikis - specifically a comparison of Wikipedia and Britannica (with an editorial here).

Nature are really pushing this web technology angle - This week's issue contains an editorial and four news features on "science in the web age". Once again, quotes from popular blogger PZ Myers of Pharyngula and our very own Greg Tyrelle.

As the web was invented some 15 years ago by physicists, perhaps it should be "life science in the web age" - you can't help but form the impression that it's mostly biologists who have been slow to catch on.

I've added a bit of stuff to the Nodalpoint wiki of late: some notes on using iprscan + OpenPBS and installing Manatee on Debian are the latest.

Just to remind you that the Wiki link is at the top right of this page and all registered users can contribute. I know that writing an article is a lot of work but if everyone contributed one item, we'd have a great source of documentation.

Enfold Systems just released a Open Source LIMS based on Zope 3 (written in Python) and the python Object/Relational module, SQLObject.

SIP's Project Page is at the enfold systems website. It has flash demo's, screenshots and a link to Sample Inventory Program's Sourceforge Prroject It uses Postgresql but should work on MySQL and on Windows, OSX or *BSD. Link to download 1.0.2

The SIP application requires the Zope 3.0.x release of the Zope application server, PostgreSQL or Sybase Relational Database Servers and the Python 2.3.5 language runtime. Many integration tests exist for various aspects of the SIP application ranging from command line importing of samples and project configuration to CSV web based importing of sample modifications.

I don't know if anyone here uses an electronic lab notebook (I'd be interested to hear if you do), but for the last couple of years I've been using a simple weblog-style notebook based on Wordpress.

Now, so that I had something to recommend to people who were interested in keeping an electronic log of their experiments, and to get feedback on the kind of tools people would like to be able to use, I've released NotePress: a package of Wordpress (slightly modified), a custom theme and some useful plugins.

It's free, open source and all that, and pretty obviously doesn't include the kind of electronic signature verification or data management tools that the big expensive commercial notebook packages do, but it's been good enough as a searchable archive of experiments.