nodalpoint.org

It seems that most bioinformatics web services use SOAP, and the extent of their documentation is the accompanying WSDL file - not very helpful for anyone who wants to use them outside a workflow-type tool like Taverna, and even then often not descriptive enough to know what should go in each field.

The newest release of the Structured Blogging plugins might be of interest to anyone using Wordpress or Movable Type for keeping a digital record of their work, as it includes a template for writing reviews of journal articles. This provides a form for filling in standard fields (article and journal titles, volume, issue and page numbers, that sort of thing) and produces nicely formatted output as well as auto-generating COinS links so that anyone reading the article review can get directly to the full text of the paper.

I've been wondering how difficult it would be to prescribe a standard format for entering the methods and results of scientific experiments into a weblog...

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.

This month's Nature Immunology contains a Commentary article, 'Bioinformatics for the bench biologist: How to find regulatory regions in genomic DNA' and an extensive accompanying tutorial that works through all the steps involved.
[subscription required, probably]

I've put an early version of a tool for visualising networks of protein interactions online.

Here is an alternative front-end for PubMed, put together using Perl and the NCBI E-Utilities.