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chem-bla-ics

chem-bla-ics
Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
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InchiChemistryJmolKimya Bilimleriİngilizce
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Nature Chemistry just released the first issue with a few free papers, like Asymmetric total syntheses of (+)- and (-)-versicolamide B and biosynthetic implications by Miller et al. (DOI:10.1038/nchem.110). Now, we’ve seen the Royal Society of Chemistry’s Project Prospect (see RSC: the first publisher to go semantic!) and ChemSpiders recent ChemMantis system which enriches the papers with machine readable representations of the

BlogKimya Bilimleriİngilizce
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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.

PubmedPmcCopyrightKimya Bilimleriİngilizce
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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.

DefenseCheminfChemometricsPhdKimya Bilimleriİngilizce
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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!

CheminfChemometricsPhdKimya Bilimleriİngilizce
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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.

CdkKimya Bilimleriİngilizce
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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.

JchempaintBioclipseKimya Bilimleriİngilizce
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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.