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Charles Plessy @charles_plessy@mastodon.technology

By the way, avoid to click on the "R" link if you are at work: it leads to unexpected contents; sorry for this.

looks like being the appropriate hashtag for the R programming language.

Memo on how to use the `paste` function in .

```{r}
> paste("apple", "pen", sep="-")

[1] "apple-pen"

> paste(c("apple", "pineapple"), "pen", sep="-")

[1] "apple-pen" "pineapple-pen"

> paste(c("pen", "apple"), c("pineapple", "pen"), sep="-", collapse = "-")

[1] "pen-pineapple-apple-pen"
```

Take home message: `paste()` is vectorized, recycles its arguments if too short, and accepts a `collapse` argument which is not the same as the `sep` argument.

I did not get a talk but a poster.

- The negative viewpoint -> my abstract was not so good in the end.

- The positive viewpoint -> If all the talks are better than my research (which I of course do really like), the conference will be very exciting.

It was long overdue but I created a page on the website of my laboratory at to announce the publication the latest update of our method "nanoCAGE" for and analysis (gene activity, so to speak).

population-transcriptomics.org

Next: analyse the data that we produced with this method, at single-molecule resolution.

Mind-blowing article showing a pipeline cracked by a specially designed, synthesised and sequenced molecule. To make their proof or principle, the authors actually had to insert a specific weakness in one of the programs, but their manuscript concludes by an overview on how the of bioinformatics software is often very low. Thanks for the link.

Ney, Koscher, Organick, Ceze & Kohno, University of Washington:, <dnasec.cs.washington.edu>

zdnet.com/article/worlds-first

[EN/FR]

The open-source software collection for using is migrating to Git this August 16th!

stat.ethz.ch/pipermail/bioc-de

La collection « Bioconductor » d'outils libres pour la avec R migre à Git le 16 août prochain !

Intel a lancé très récemment le Movidius Neural Compute Stick petite machine d'apprentissage qui fut réalisée grâce à l'entreprise Movidius qui a mis au point le VPU, pour Visual Processing Unit. Cette puce, appelée Myriad 2, est capable de balancer 100 GFLOPS de puissante brute dans un TDP de seulement 1 W ! Une petite vidéo expliquant comment démarrer avec une carte Raspberry Pi 3 => youtube.com/watch?v=f39NFuZAj6 mastodon.etalab.gouv.fr/media/

Just read an article with 14 authors and more than 25 acknowlegements. is more and more fragmented...

A movie recorded in the genome of bacteria! In last week's Nature, Shipman and coll. (Church lab) encoded a 5-frame animated picture in collections of short molecules, used to sequentially populate arrays (a system use by bacteria to record signatures of viruses they encountered). Thus, frame order was solely recorded by the order in which the CRISPRs were introduced in the bacteria. This opens mind-blowing ways to log temporal information in DNA. doi.org/10.1038/nature23017

Ca laisse rêveur : tu demandes à Google "why we should own our data" et il te corrige en "why we should own YOUR data"(sur Google.com et Google.fr) framapiaf.org/media/J80v7L_Ws9 framapiaf.org/media/P7qQ-a-Sng

Following up on "registered reports", (where peer review starts during experimental design, before implementation): an editorial announces the availability of this format in Biology.

bmcbiol.biomedcentral.com/arti

The scientific journals Nature Genetics and Scientific Data are calling for the use of formats (such as RDF) in replacement for the supplementary tables produced by spreadsheet software.

nature.com/ng/journal/v49/n7/f

A RDF export wizard for or would definitely give them an edge in the scientific community.

jivarahasya.blogspot.jp/2017/0

Striking blog article showing a case where editors and the system failed to notice that authors conveniently ignored prior art in the literature.

"Towards a perceptive understanding of size in cellular biology" (Monica Zoppè, Nature Methods, 2017). To provide intuition for the size and scale of a biological object (ATP molecule, microtubule, ribosome, virus particle, etc...) show a daily-world example that has 10 million times the size. For instance, the nucleus is as big as the Colosseum and an ATP molecule is as small as the paw of a cat. Great idea for teaching ... and for adding plenty of cat pictures in publications!

has receptors!

is never short of surprises... In a study just published in Nature Neuroscience (<doi.org/10.1038/nn.4575>), Dhruv Zocchi, Gunther Wennemuth and Yuki Oka used advanced methods to show that stimulating the water receptors induces drinking behaviours, but only in thirsty animals, and that conversely the animals without the receptors have difficulty into discriminating water and other fluids.

Am I the only one who has difficulty to parse things like "a SH2 domain-targeting STAT3 inhibitor"? I would much prefer to read "an inhibitor of STAT3 that targets its SH2 domain". Do people write this because there are strict word counts in scientific publications, or is it proper English and I only have difficulties reading it because I am French and therefore heavily rely on glue words such as "the" "of" "that", etc. ?