Blog Archives

Importing RDF input in R for analysis

April 28, 2011
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August last year I asked on BioStar about how to import RDF into the R statistical package and at the time nothing seemed existing. Over the past few weeks I ported code I wrote for Bioclipse to create the rrdf package for R, which is now available fro...

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Chemometrics with R

March 15, 2011
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Chemometrics with R

I just heard that my supervisor's book Chemometrics with R was released, and I immediately requested our library to get a copy. Ron introduced me to R at a time that most at our department were still using Matlab. In fact, I had be maintaining Matlab s...

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Mapping BioStar users onto the world map

October 9, 2010
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Mapping BioStar users onto the world map

Neil is my new bioinformatics hero! (Sorry Pierre :)BioStar is a Q&A website for bioinformatics, just like the Blue Obelisk eXchange. Neil and Pierre have an ongoing struggle to gain the most karma, requiring Pierre to put in a formal complaint aga...

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QSPR modeling with signatures

June 20, 2010
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QSPR modeling with signatures

I had to dig deep to find posts on QSAR modeling. There are quite a few on QSAR in Bioclipse, but that focuses on the descriptor calculation. In a quick scan, I could only spot two modeling posts:The CDK/Metabolomics/Chemometrics Unconference resultsWh...

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The CDK/Metabolomics/Chemometrics Unconference results

April 7, 2008
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The CDK/Metabolomics/Chemometrics Unconference results

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.We u...

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Christmas presents…

December 21, 2007
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Our Christmas tree has not been decorated yet, but the presents are there: the BMC Bioinformatics paper on userscripts in life sciences, Bioclipse 1.2.0, a long list of blogs to rate, and a very nice overview from Wendy Warr on workflow environments, d...

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MetWare: metabolomics database project started on SourceForge

November 22, 2007
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The Applied Bioinformatics at PRI group where I now work in Wageningen and the group of Steffen Neumann in Halle have started the MetWare project on Sourceforge to develop opensource databases for metabolomics data.The databases design will be based on...

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An R-based genetic algorithm

November 19, 2007
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During my PhD I wrote a simple but effective genetic algorithm package for R. Because there was a bug recently found, and there is interest in extending the functionality, I have set up a SourceForge project called genalg.The package provides GA support for binary and real-value chromosomes (and integer chromosomes is something that will be...

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XCMS on Ubuntu Feisty

August 27, 2007
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I just installed XCMS 1.9.2 on my Ubuntu system. XCMS is a GPL-ed R package for metabolomics data analysis. Just for the record, you need to install the Feisty packages for NetCDF:sudo aptitude install netcdfg-dev libnetcdf3R CMD INSTALL --library=/usr...

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Further Bioclipse QSAR functionality development

July 26, 2007
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Further Bioclipse QSAR functionality development

I had some time to work some more on the QSAR functionality in Bioclipse. There is still much to do, but it is getting there. The calculation of a QSAR descriptor data matrixThis screenshot shows that multi-resource selection is now working, and that t...

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