Blog Archives

Winter solstice challenge #3: the winner is Bianca Kramer!

January 20, 2018
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Winter solstice challenge #3: the winner is Bianca Kramer!

Part of the winning submission in the category 'best tool'. A bit later than intended, but I am pleased to announce the winner of the Winter solstice challenge: Bianca Kramer! Of course, she was the only contender, but her solution is awesome! In fact, I am surprised no one took her took, ran it on their own data and just submit...

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

November 11, 2016
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New paper: “SPLASH, a hashed identifier for mass spectra”

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 lead author on this paper. It provides an implementation of the...

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Aggregating data on nanomaterials: eNanoMapper is getting closer to critical mass

February 14, 2016
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Aggregating data on nanomaterials: eNanoMapper is getting closer to critical mass

Nanosafety data for silver nanoparticlesin data.enanomapper.net visualizedwith ambit.js and d3.js.The last three weeks featured two meetings around data infrastructures for the NanoSafety Cluster. The first maating was on January 25-26 in Bru...

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Aggregating data on nanomaterials: eNanoMapper is getting closer to critical mass

February 14, 2016
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Aggregating data on nanomaterials: eNanoMapper is getting closer to critical mass

Nanosafety data for silver nanoparticlesin data.enanomapper.net visualizedwith ambit.js and d3.js. The last three weeks featured two meetings around data infrastructures for the NanoSafety Cluster. The first meeting was on January 25-26 in Brussels, and last week the eNanoMapper project held its second year meeting with a subsequent workshop in Basel (see the program with links to course material). Here are some personal reflections...

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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 you can use them from basically any environment. Still, some...

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Using the WikiPathways API in R

December 22, 2015
By
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 you can use them from basically any environment. Still, some...

Read more »

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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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 the recent paper by Ekins et al (doi:10.1371/journal.pcbi.1003789).The backchannel discussions only get better when more and more people join,...

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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 PhD studies the interaction between the statistics and machine learning with how you computationally (numerically) represent the question. The right combination is not...

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RRegrs: exploring the space of possible regression models

November 22, 2015
By
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...

Read more »

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