Nothing much going to say about it, and just to report some progress: [Read more...]

Last Thursday, there was a UM library network drink. And as I see a library where knowledge is found, and libraries still rarely think of knowledge as ever being able to be stored outside books and papers, I was happy to see the library promoting the D... [Read more...]

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...]

[This article was first published on chem-bla-ics, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your [Read more...]

I just ran into this interesting post on the R-bloggers Planet. The described R functionality allows you to compile R code (to byte code) so that it will no longer be interpreted but actually run. That is a performance boost. I guess in due time we will see R use ... [Read more...]

I normally work with full numerical data, not categorical data. R, when using read.csv() seems to recognize such categories and marks the column as to have factor levels. This is useful indeed. However, I wanted to make a PCA biplot on this data, so wa... [Read more...]

We are using a Semantic MediaWiki (SMW) for the Gold Compound selection task by the ToxBank in the SEURAT-1 cluster, funded by Colipa and the EC. I do stress that despite being funded by Colipa, they have no control over my research; they just co-... [Read more...]

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Blog planets are websites that aggregate blog feeds around a particular topic or project. It is probably called after one of its first implementations, the Planet software. These planets are like conferences, rather than journals. Like conferences with... [Read more...]

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...]

Not so long ago I wrote about [i]mporting RDF input in R for analysis. I am collecting nanotoxicology data in a Semantic MediaWiki with the RDFIO extension installed (by Samuel), allowing me to SPARQL that data directly from R. There is nothing much structural to visualize at this moment, ... [Read more...]

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...]

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...]

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... [Read more...]

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...]

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... [Read more...]

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...]

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... [Read more...]

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...]

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...]