Blog Archives

The Dutch Dataverse Network: a host for the ChEMBL-RDF v13.5 data, and some thoughts in workflow integration

August 31, 2013
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The Dutch Dataverse Network: a host for the ChEMBL-RDF v13.5 data, and some thoughts in workflow integration

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...

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Triples, stores, and SPARQL in R

November 27, 2012
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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...

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My #ACSPhilly #skolnik2012 slides for “Semantic pipelines to molecular properties”

August 21, 2012
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(This article was first published on chem-bla-ics, and kindly contributed to R-bloggers) To leave a comment for the author, please follow the link and comment on their blog: chem-bla-ics. R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL,...

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Compiling R code, and speed up your computation

May 5, 2012
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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 JIT technologies, so that the difference will...

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Tricks I learned today #1: as.integer() on factor levels

October 12, 2011
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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...

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rrdf 1.5: Accessing SMW SPARQL end points behind LDAP authentication

September 25, 2011
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rrdf 1.5: Accessing SMW SPARQL end points behind LDAP authentication

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-...

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Plotting molecular properties for (sub)sets

August 10, 2011
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Plotting molecular properties for (sub)sets

For a toxicology paper we are writing up, I need to create a few plots showing how the toxic and non-toxic molecules differ (or not) with respect to a few molecular properties, such as logP or the molecular weight. The rcdk package provides all, of cou...

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Blog planets are like conferences… (aka R-bloggers.com)

August 8, 2011
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Blog planets are like conferences… (aka R-bloggers.com)

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...

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Usability

August 7, 2011
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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 "sability is the ease of use and learnability of a ...

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Importing Nanotoxicity Data with SPARQL into R for analysis

June 14, 2011
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Not so long ago I wrote about 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, so I'm skipping the Bioclipse...

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