Tagging, thesauri or ontologies?

Controlled vocabularies, hierarchies, microformats, RDF. Nico Adams pointed me to this excellent video:

2 minute read

Open Source, Open Data at the European Bioinformatics Institute

I was pleased to hear that Christoph will move to the EBI early next year. Christoph has been working on Open Source and Open Data chemoinformatics since at least 1997. I first got in contact with Christoph when I wrote code for JChemPaint (which Christoph developed) to be able to read Chemical Markup Languages (CML). This also got me into contact with Dan Gezelter who is the original author of Jmol, to which I also added CML support. And, of course, with Henry and Peter, who first developed CML. This was before XML was an official recommendation, and I have worked with CML files which you would no longer recognize. It was in Dan’s office that the CDK was founded, where Christoph, Dan and I designed data classes to replace the JChemPaint and Jmol data classes. Both JChemPaint and Jmol were rewritten afterwards, but for Jmol it was later decided that more tuned classes were needed to achieve to required performance for the live rendering of tens of thousands of atoms.

1 minute read

My Open Laboratory 2007 submissions

As promised , here is my list of submission for the Open Laboratory 2007:

less than 1 minute read

Web2O, Open Chemistry, and Chemblaics

Chemistry World December issue features a nice item on the future of data in chemistry: Surfing Web2O; Peter gave an excerpt, and Peter commented on it.

less than 1 minute read

Be in my Advisory Board #1: being a good Open Science citizen

I recently saw that blogger.com blogs gained a poll feature. From now on, I will try to be a bit more Open Science, in addition to Open Source. From now on, you can be in my Advisory Board. To do so, vote on my next chemblaics (aka Open Source Chemoinformatics) project. The poll can be found on the left side of this blog. Associated which each poll, which I may run more or less frequently depending on the time of year, will be one blog post where I introduce the options. Options not mentioned, or completely different things, you would like to suggest me to do, can be left as comments to these items.

1 minute read

Metabolomics workflows in Taverna

My current jobs description is to speed up metabolomics data analysis, and finally got around to making a first relevant workflow for Taverna, using the webservices just posted over at ChemSpider:

1 minute read

MetWare: metabolomics database project started on SourceForge

The Applied Bioinformatics at PRI group where I now work in Wageningen and the group of Steffen Neumann in Halle have started the MetWare project on Sourceforge to develop opensource databases for metabolomics data.

less than 1 minute read