Articles by Egon Willighagen

New paper: “SPLASH, a hashed identifier for mass spectra”

November 11, 2016 | Egon Willighagen

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...]

Using the WikiPathways API in R

December 22, 2015 | Egon Willighagen

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...]

Using the WikiPathways API in R

December 22, 2015 | Egon Willighagen

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...]

Twitter at conferences

November 22, 2015 | Egon Willighagen

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...]

Twitter at conferences

November 22, 2015 | Egon Willighagen

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...]

RRegrs: exploring the space of possible regression models

November 22, 2015 | Egon Willighagen

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...]

#Altmetrics on CiteULike entries in R

September 19, 2015 | Egon Willighagen

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...]

#Altmetrics on CiteULike entries in R

September 19, 2015 | Egon Willighagen

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...]

CDK Literature #8

July 11, 2015 | Egon Willighagen

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...]

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...]
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