Ola has been doing a good job of integrating BioMoby support into Bioclipse. Earlier he completed a GUI for running BioMOBY services, and added more recently a JavaScript wrapper too, using the Rhino plugin developed by Johannes. For example: console = Packages.net.bioclipse.util.BioclipseConsole; moby = Packages.net.bioclipse.biomoby.ui.scripts.MobyServiceScripting; biojava = Packages.net.bioclipse.biojava.scripts.BioJavaScripting;

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. Below is a screenshot of an intermediate point after starting with the InChI of methane: After the search it generates a long HTML page with all the information it found on the molecule you queried for.

In this series I will introduce the technologies behind my FOAF network. FOAF means Friend-of-a-Friend and My FOAF file (draft) will give you details on who I am, who I collaborate with (and other types of friends), which conferences I am attending, what I published etc. That is, I’ll try to keep it updated. BTW, FOAF is a RDF language.

That must be a record! Eric Jain wrote on public-semweb-lifesci: I surely hope this is not the last we hear of this huge RDF collection.

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 : Meanwhile, the Bioclipse team in Uppsala has set up the obligatory scatter plot functionality, but leave that screenshot for them to show. Therefore, time for integration with R.

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.

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.