egonw

[egonw]

Model of gene regulation in bixin biosynthesis, created in PathVisio. Bixin (annatto) is a commercially important natural orange-red pigment derived from lycopene, produced and stored in seeds of Bixa orellana. This paper presents a hypothetical model for bixin biosynthesis, to provide a better understanding of the mechanisms regulating these pathways and to facilitate the genetic improvement of B. orellana.

De novo transcriptome sequencing in Bixa orellana to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis. Cárdenas-Conejo et al, BMC Genomics. 2015.

[egonw]

Elsevier insists on double dip

The original Dutch text:

Elsevier: geen onderhandelingen De onderhandelingen met Elsevier liggen stil. Elsevier wil alleen stappen maken richting open access wanneer de universiteiten daar dubbel voor betalen. Universiteiten moeten dan zowel voor het lezen als voor het publiceren betalen, dat budget is er niet.

My translation:

Elsevier: no negotiations The negotiations are on hold. Elsevier only wants to come forward if the universities pay twice. Universities must then pay for both reading access and for the submission; that budget is not available.

Source: http://www.vsnu.nl/files/documenten/Domeinen/Onderzoek/Open%20access/Nieuwsbrief_open_access_05_20150312.pdf 

[egonw]

I am closing this feed. Not that it hasn't been fun, but I realized last week that my chem-bla-ics blog is getting too little attention, and originally I would also just blog the kind of short posts that I do here. Nothing wrong with doing both again in my main blog.

[egonw]

Provenance in Wikidata about a statement that diamond has a particular CAS registry number.

Now I wonder if it even lists that I added that reference... Provenance all the way down?

[egonw]

Markus updated the Wikidata-ToolKit to accommodate for the updated HTML download page of JSON dumps. Also, he explained the expected data structure so that I can use the manually downloaded JSON. We here see the processing of a JSON dump file in Bioclipse, and the other screenshot shows the JSON content dumped by the entity document processor to STDOUT.

[egonw]

Mmm... is this the game changer we were waiting for?

[egonw]

Wikidata edits per day over a period of a bit more than two years.

Willighagen, Egon; Hoch, Marius (2015): Wikidata edits per day (2012-2014). figshare. http://dx.doi.org/10.6084/m9.figshare.1286885 Retrieved 10:35, Jan 10, 2015 (GMT)

[egonw]

What if we crowdsource knowledge with 7B people?

[egonw]

WikiData thinks Linked Data is the same as Linked Open Data... if only...

[egonw]

Because CDK 1.5.x is getting the standard, my updated book is not yet out, while considering the current version is still relevant, the 1.4.x is now available at a reduced price. 

[egonw]

3. Op welke tijdschriften heeft de deal met Springer betrekking? [...] Tijdschriften / publicaties in Springer Open en Biomed Central (ongeveer 400 tijdschriften). Dit zijn collecties die al volledig open access zijn. Publicaties zijn voor Nederlandse onderzoekers dus volledig vrij toegankelijk (lezen) maar voor publicatie in deze titels moeten APC’s betaald worden

Translation:

3. To which journals does the Springer deal apply?

[...]

Journals / publications by Springer Open and Biomed Central (about 400 journals). These are collections that are already fully open access. Therefore, for Dutch researchers publications are  fully freely accessible (reading) but for publication in these titles APCs need to be paid.

Source: http://www.vsnu.nl/files/documenten/Domeinen/Onderzoek/Open%20access/Veelgestelde%20vragen%20open%20access.pdf 

[egonw]

Last night I could no longer resist looking at the CiteULike plugin systems, and with some guidance and pointers from @citeulike on Twitter, and some great eco system they wrote, I managed to write in a few hours two plugins, one for figshare and the other for ZENODO. They are just first drafts, and hope to get some more feedback soon. Of course, it doesn't address the fact that CiteULike doesn't have a DataSet or Software types, so they are currently stored as GEN (aka @misc{}). But that is fine, because the citation consists of title, authors, year, and a link normally anyway.

The patches:

https://github.com/egonw/citeulike/compare/feature/zenodoPlugin?expand=1

https://github.com/egonw/citeulike/compare/feature/figsharePlugin?expand=1

If you like to have a go at plugins too, look out for the HOWTO.txt in the plugins/ folder in their source code repository.

[egonw]

Is this acceptable Nature/ReadCube use?

[egonw]

"All Maastricht University tweets collected" (Dutch)

[egonw]

Nature's ReadCube doesn't mean no one can copy the paper; they just made it more difficult, but the content is all in the HTML you download. Of course, it has to be! How else would your browser know how to display it. The images/figures are easy, but the text is there too.

As a proof of principle, check this screenshot (claiming fair use; and grayed out most of the text). Here I changed both the text and the placement of a bit of the text.

[egonw]

One hour HTML+ops.js+d3.js hack! I love good libraries!

[egonw]

Fixed the Open PHACTS / d3.js examples. This one showing a pie chart of activity units for all measurements in the ChEMBL data in the cache for paracetamol.