While I do not agree in details on the statement made by Klaus, I agree with his intentions, and happy to propagate the mantra, like others did before me:

Today starts the MetWare developers meeting, hosted by Steffen Neumann, at the Leibniz-Institut für Pflanzenbiochemie. Steffen’s group and the Applied Bioinformatics group where I now work, are co-developing an opensource platform for metabolomics data management.

As announced earlier, Miguel, Velitchka, Christoph and I held a small CDK/Metabolomics/Chemometrics unconference. We started late, and did not have an evening program, resulting in not overly much results. However, we did do molecular chemometrics.

In reply to Peter’s news that the NIH’s PubMed Central (PMC) does not allow machine retrieval of content, I was wondering about this section in the CC license of much of the PMC content, such as our paper on userscripts (section 4a of the CC-BY 2.0):

I normally do not do these kinds of blog items, but, in reply to Christoph’s blog, here’s an overview of the ceremony (see also T-26 and T+18):

I am doctor now; I shall now be addressed as weledelzeergeleerde Egon; translating to something like quite-noble-very-knowledgeable, hahahaha. I’ll put up a few photo’s of the ceremony, which is actually quite formal at the Radboud University, later.

In about 26 hours from now, I will be defending my PhD thesis. Follow that link to read the summary; I was thinking if publishing my introduction and discussion (the rest has been published in peer-reviewed journals) on Nature Precedings; would that be a good idea? Otherwise, I’ll post it in my blog.

A bit over 2 years ago I published a UML diagram showing the dependencies between CDK modules . Since then I lot of new modules have been defined, added or factored out from the extra module (click to zoom):

As promised, I am working on JChemPaint. I have progressed in cleaning up the CDK trunk/ repository by removing traces of the old JChemPaint applet and application. And, importantly, removed the GeometryTools class that took rendering coordinates. The history here is that the original GeometryTools was renamed to GeometryToolsInternalCoordinates, but is now available as GeometryTools again. I still have to merge Niels’ additions with it, though.

FOAF rulez: it’s RDF. With RDF comes SPARQL. SPARQL needs a query engine, however. And there comes OpenRDF which created Sesame.

Richard informed me (via Planet RDF) about N3 support in Tabulator. N3 is a more compressed version of RDF/XML, which I have been using so far, but both are RDF. Now, I don’t plan to use N3 for my FOAF experimenting, but two things caught my eye in the nice blog item.