nodalpoint.org

We had some serious comment spam today (1389 to be exact), so as a short term solution I've turned off anonymous comments.

The Scriptome is a cookbook of perl one liners for bioinformatics data processing tasks. Designed for you non-coding-biologists friend, the Scriptome is available in Unix and Windows versions. The concept is introduced in the following article: Data Munging for Non-Programming Biologists.

One of my greatest concerns in talking to people about biologists' data munging is that people don't even realize that there's a problem, or they think it's already been solved. Biologists--who happily pipette things over and over and over again--don't realize that computers could save them lots of time.

Nice work, and I hope that they are successful with the project, however I'm doubtful. Read on for the rant...

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.

As a slightly delayed announcement, I'd just like to mention that I have finally handed in my thesis, entitled "The genetics of variation in gene expression". I have been on holiday for the last three weeks or so, and I'm now feeling human again after a period of social dysfunction and catatonia that I am informed is par for the course. Fortunately, I'm still waiting for my visa so I can work here with this group for the next X years.

Everyone knows what DNA is these days. Hm. Just stumbled over today's article in Nature about Z-DNA and B-DNA with some nice pictures (see also the free Figure S8)

Frankly, I completely forgot about left-handed DNA. That brings me to a topic where I'm clearly lacking keywords: What is there on DNA apart from the raw sequence? I seems to be really similar to a normal cord. What can you do with a piece of cord? Similar things as with DNA. I remember...

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.

I'm not sure "how scared we should be" - rather less than the commercial news networks would have us believe, I suspect. If you're looking to inform yourself about avian influenza (aka 'bird flu'), Flu Wiki is a good place to start.

Update: I just can't resist The Onion's Nation's Leading Alarmists Excited About Bird Flu.

I'm skimming through the latest TOC of the journal Bioinformatics and making a few observations.

Can it be IgNobel time already? Seems like only yesterday I was posting about the 2004 awards.

See all the winners here or summary in the Guardian here. The penguins have to be the highlight.

CSIRO, Australia's governmental science organisation, is to host the local W3C office. There's a short, uninformed and generally poor summary at ABC News and an official press release at CSIRO.