Blog Archives

Using the WikiPathways API in R

December 22, 2015
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Using the WikiPathways API in R

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...

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Twitter at conferences

November 22, 2015
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Twitter at conferences

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...

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RRegrs: exploring the space of possible regression models

November 22, 2015
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RRegrs: exploring the space of possible regression models

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...

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#Altmetrics on CiteULike entries in R

September 19, 2015
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#Altmetrics on CiteULike entries in R

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...

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CDK Literature #8

July 11, 2015
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CDK Literature #8

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 by the training set. The paper indirectly uses...

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“What You’re Doing Is Rather Desperate”

March 22, 2015
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“What You’re Doing Is Rather Desperate”

Self-protrait by Gustave Courbet.Source: WikiMedia Commons.One blog that I have been (occasionally but repeatedly) reading for a long time is the What You're Doing Is Rather Desperate blog by Neil Saunders. HT to WoW!ter for po...

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rrdf 2.0: Updates, some fixes, and a preprint

January 3, 2014
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rrdf 2.0: Updates, some fixes, and a preprint

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...

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Pharmacology data from Open PHACTS in R

December 22, 2013
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Where I reported yesterday the initial steps of an client R package for Open PHACTS, I can now report the first pharmacology data import:

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Open PHACTS from R

December 21, 2013
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Nothing much going to say about it, and just to report some progress:

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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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