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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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DefenseCheminfChemometricsPhdChemieEnglisch
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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.

CheminfChemometricsPhdChemieEnglisch
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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.

JchempaintBioclipseChemieEnglisch
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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.

DrugdiscoveryBlogChemieEnglisch
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Two things I like blogging: 1. the turn-over of information; 2. the informal nature. There are more . The turn-over is optimized by commonly: 1. short blog items; 2. easily allows scanning tons of headlines; 3. often full of links if you want to know the details.

FoafChemieEnglisch
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As promised , I’ll write a bit about using Bibliographic Ontology Specification (BIBO) over as bibliontology.com. I have written a basic XSLT to create a HTML GUI (open the RDF source in e.g. Firefox). Really basic: it only converts articles, and even assumes some conventions I found in examples in the BIBO wiki. I have not spotted a BIBO validator yet, so guessing a bit.

CasCheminfChemieEnglisch
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IUPAC chemical names, SMILES and InChIs are too long. InChIKeys are not unique enough because of safety reasons (you have a 1 in 10 billion chance of blowing up your building; well, odds are actually much, much lower than getting hit by Osama or friends, let alone a car). Wikipedia URIs do not cover enough chemical space.

BioclipseMetwareOntologySemwebOwlChemieEnglisch
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The MetWare project is going to make use of ontology technologies to control the content of the database, and a first step is to convert our MetWare database design into something using a formal ontology language. I have played with OWL in the past (see for example its use in Bioclipse ), but was not overly happy with it in all situations.