There was some talk about the history of chemoinformatics toolkits by Noel and Andrew, which made me wonder on the exact history of Jmol and JChemPaint.

Via Carbon-Based Curiosities’s blogroll I found a number of new blogs (on top of the list I posted yesterday), and just added them to Chemical blogspace. This is something I found in Infiniflux!: Blog comments? No, Peer Reviews! Nice thought, Joel! I’ll copy that, if you don’t mind.

Two companies recently showed two things: open access and open data allow adding value adding value is easier by forking Rich’ MetaMolecular set up Chempedia which combines a substructure-searchable chemical Wikipedia. There is also a page to make links to new Wikipedia monographs.

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.

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): CC-BY 3.0 reads differently, but has similar aims. Let me make clear that I value machine readable publications much more than free (gratis, as-in-free-beer) publications.

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): This is the doctorate certificate Christoph mentioned, with also Karin and our kids: And, here (map) was the dinner in the evening:

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. With this blog item, I would to thank everyone who left a message, sent email, etc with good luck messages. Very much appreciated!

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): These kind of diagrams help us maintain the library, and apply some design goals, as explained in the first post on this.

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. I have to catch the train in about 15 minutes, so will not elaborate too much, but here are some Sesame 2.0.1 work: > create native. Please specify values for the following variables: Repository ID [native]: foafRepo Repository title [Native store]: FOAF Repository Triple indexes [spoc,posc]: Repository created >