Articles by Egon Willighagen

Triples, stores, and SPARQL in R

November 27, 2012 | Egon Willighagen

For some time I have been stealing an hour here and there for the rrdf package for R. This package is based on Apache Jena and allows reading and writing of RDF triples, as well as doing local and remote SPARQL querying. BTW, rrdf is not only R pa... [Read more...]


August 7, 2011 | Egon Willighagen

Usability. I am not an expert in Human-Computer Interaction (HCI) at all. Worse, I make the crappiest looking interfaces, typically. So, that's said. Usability. Wikipedia writes that "[U]sability is the ease of use and learnability of a ... [Read more...]

Importing RDF input in R for analysis

April 28, 2011 | Egon Willighagen

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... [Read more...]

Chemometrics with R

March 15, 2011 | Egon Willighagen

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... [Read more...]

QSPR modeling with signatures

June 20, 2010 | Egon Willighagen

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... [Read more...]

Christmas presents…

December 21, 2007 | Egon Willighagen

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... [Read more...]

An R-based genetic algorithm

November 19, 2007 | Egon Willighagen

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 ... [Read more...]

XCMS on Ubuntu Feisty

August 27, 2007 | Egon Willighagen

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... [Read more...]
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