This is more like the update interval I had originally in mind: one month per version. In fact, this is the first edition for the same CDK release as the previous edition, and thus is edition 1.4.7-1. Still, this release adds 12 new pages, consisting mostly of a new Chapter 14, about molecular descriptors, and the CDK API for descriptor calculation:

Other new content includes a short code example for generating 3D coordinates.

The paperbak is available from Lulu.com, an on-demand publisher, as well as this ebook version.

I reported yesterday about MathJax support by Chemistry Central, Bryan informed me a cool Springer project:

LaTeXSearch lets you search for mathematical equations in literature, and also is helpful in providing the LaTeX source of those equations. For example, in the above screenshot I searched for RMSE. But there are more interesting queries, like all equations with ħ or with Q2.

The Blue Obelisk Descriptor Ontology has been using MathML for a long time, and it is good to see that MathJax for visualization of mathematically equations is getting mainstream.

Readers of my blog know I have been using the Citation Typing Ontology, CiTO (doi:10.1186/2041-1480-1-S1-S6). I allows me to see how the CDK is cited and used. CiteULike is currently adding more CiTO more functionality, which they started doing almost one and a half years ago.

One of the things, is that the CiTO data added via a certain account, can be downloaded as triples:

The second is that they are improving the graphics of how it is visualized. E.g.

I am happy that the Chemical blogspace is back in business. There were issues with the database earlier this week, but the website is back up. I am happy because if the pointers to interesting discussions and papers. For example, this funny entry in PubChem:

Really interesting too, is the difference in InChI between the Chemical blogspace and the PubChem entry.

Oh, and welcome back ChemBark! Check that URL; ChemBark is one of the oldest blogs on Chemical blogspace.

Below are the slides of the Chemical Interoperability presentation I gave this morning in Utrecht in a parallel meeting of the NBIC. The name was copied from the suggestion by Christine, who invited me. Chemical Interoperability - Utrecht / NBIC View more presentations from Egon Willighagen

Most of the cited papers can be found on my Google Scholar profile. But also on Mendeley and CiteULike.

I joined the Bioinformatics group at Maastricht University (BiGCaT) at the start of this year. I have been using the semantic web in the past years in drug discovery (doi:10.1186/2041-1480-2-S1-S6) and toxicology (doi:10.1186/1756-0500-4-487), and organized a conference at the ACS meeting in Boston in 2010 (the matching article collection in the J. Cheminformatics). Here in Maastricht I’ll be working on BridgeDB and putting that to use in the Open PHACTS projects (and more).

Change is scary. Submitting your application paper to a new journal certainly. When that journal requires your have a strategy for code testing and maintenance even more.

Hence, the Open Research Computation dillema.

We you may or may not know, I'm on the editorial board of the yet-to-kick-of journal Open Research Computation (ORC, official website). People are scared to submit, and even the editors are reluctant with submitting work.

Since we are getting more and more in trouble with SourceForge :( I started looking into the more standard git code review environment, called Gerrit, so that we can use that for the CDK. With some huge learning curve, lurking, googling, and seeing what Avagadro was doing (resulting in my first ever, trivial Avogadro patch), and a major headache. This is what my patch looks like in Avogadro's Gerrit install:

As you can see, Marcus reviewed my patch, and approved it.
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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!
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