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I'm excited to have contributed to this important (IMHO) interoperability paper around metabolomics data: "SPLASH, a hashed identifier for mass spectra" (doi:10.1038/nbt.3689, readcube:msZj). A huge thanks to all involved in the great collaborative project! The source code project is fully open source and coordinated by Gert Wolgemuth, the ... [Read more...]

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Colored pathways created withthe new R package.Earlier this week there was a question on the WikiPathways mailing list about the webservices. There are older SOAP webservices and newer REST-like webservices, which come with this nice Swagger webfront set up by Nuno. Of course, both approaches are pretty standard and ... [Read more...]

Colored pathways created withthe new R package. Earlier this week there was a question on the WikiPathways mailing list about the webservices. There are older SOAP webservices and newer REST-like webservices, which come with this nice Swagger webfront set up by Nuno. Of course, both approaches are pretty standard and ... [Read more...]

I have been happily tweeting the BioMedBridges meeting in Hinxton last week using the #lifesciencedata hashtag, along with more than 100 others, though a small subset was really active. A lot has been published about using Twitter at conference, like t... [Read more...]

I have been happily tweeting the BioMedBridges meeting in Hinxton last week using the #lifesciencedata hashtag, along with more than 100 others, though a small subset was really active. A lot has been published about using Twitter at conference, like the recent paper by Ekins et al (doi:10.1371/journal.pcbi.1003789).The ... [Read more...]

Machine learning is a field of science that focusses on mathematically describing patterns in data. Chemometrics does this for chemical data. Examples are (nano)QSAR where structural information is related to biological activity. I studied during my Ph... [Read more...]

Machine learning is a field of science that focusses on mathematically describing patterns in data. Chemometrics does this for chemical data. Examples are (nano)QSAR where structural information is related to biological activity. I studied during my PhD studies the interaction between the statistics and machine learning with how you ... [Read more...]

I wanted to know when a set of publications I was aggregating on CiteULike was published. The number of publications per year, for example. I did a quick Google but could not find an R package to client to the CiteULike API, and because I wanted to pla... [Read more...]

I wanted to know when a set of publications I was aggregating on CiteULike was published. The number of publications per year, for example. I did a quick Google but could not find an R package to client to the CiteULike API, and because I wanted to play with JSON ... [Read more...]

Tool validationThe first paper this week is a QSAR paper. In fact, it does some interesting benchmarking of a few tools with a data set of about 6000 compounds. It includes looking into the applicability domain, and studies the error of prediction for compounds inside and outside the chemical space defined ... [Read more...]

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It all started 3.5 years ago with a question on BioStar: how can one import RDF into R and because lack of an answer, I hacked up rrdf. Previously, I showed two examples and a vignette. Apparently, it was a niche, and I received good feedback. And... [Read more...]

Where I reported yesterday the initial steps of an client R package for Open PHACTS, I can now report the first pharmacology data import: [Read more...]