I just ran into BioSpider. Unlike ChemSpider, BioSpider crawls the internet (well, this list of sources really) to find information, and depending on what it finds it continues the search.

In this series I will introduce the technologies behind my FOAF network.

That must be a record!

A bit over two years I posted my first blog item, Chem-bla-ics , introducing the topic of my blog. In January this year I explained why I like blogging .

Bob has set up a new interface between the data model and the Jmol renderer, which allows him to define other types of export too. One of this is a POV-Ray export, which allows creating of high quality images for paper. Jmol has had POV-Ray export for a long time now, but never included the secondary structures or other more recent visual featues.

I added a Bioclipse plugin for JOELib (GPL, by Joerg) which comes with many QSAR descriptors, several of which are now available in the QSAR feature of Bioclipse :

The Open Data/ChemSpider debate is continuing, and Noel wondered in the ChemSpider Blog item on the Open Data spectra in ChemSpider. The spectra in ChemSpider come from four persons, two of which released their data as Open Data (Robert and Jean-Claude) and two as proprietary data.

On my way back from the Taverna workshop I visited Nature HQ, as Ian reported about on Nascent. It was a (too) short meeting, but very nice to meet Euan (finally;

A molecular structure without any properties in meaningless. Structure generators can easily build up a database of molecules of unlimited size. 30 million in CAS, 20 million in ChemSpider or 15 million in PubChem is nothing yet. The value comes in when linking those structures with experimental properties.

I value ODOSOS very high: they are a key component of science, and scientific research, though not every scientist sees these importance yet. I strongly believe that scientific progress is held back because of scientific results not being open; it’s putting us back into the days of alchemy, where experiments were like black boxes and procedures kept secretly.

CompLife 2007 was held 1.5 weeks ago in Utrecht, The Netherlands. The number of participants was much lower than last year in Cambridge. Ola and I gave a tutorial on Bioclipse, and Thorsten one on KNIME.