T Grébert 🌊🦠🔬🧬

Very happy to share our latest findings on how the marine cyanobacteria Synechococcus gets its crazy colors! 🦠🌊🌈 (image from @L_Garczarek) A thread 🧵👇 (1/n)

Le Monarque a tranché : ce sera 49.3. Ils écrasent la démocratie comme ils écrasent la France qui travaille. C’est le jour de leur défaite : après avoir perdu pied dans le pays, ils perdent pied à l’Assemblée. Le problème de la Nation, c’est Macron. #DirectAN

🔴 DERNIERE MINUTE Réforme des retraites : le gouvernement va recourir au 49.3 à l’Assemblée #Echobox=1678974568-1" target="_blank" rel="nofollow noopener">liberation.fr/politique/refo…

En recourant au 49.3 le gouvernement fait la démonstration qu’il n’ a pas de majorité pour approuver le report de deux ans de l’âge légal de départ en retraite. Le compromis politique a échoué. Ce sont les travailleurs qu’il faut écouter quand on prétend agir sur leur travail.

Donc ce texte sur les retraites : -Passe par un PFLSSR (pas fait pour cela) -Fait l'objet d'un débat raccourci (50 jours) : art 47.1 -N'est pas voté en 1ère lecture à l'AN -Fait l'objet d'un vote bloqué au Sénat -Fait l'objet d'un 49.3 (absence de vote à l'AN) J'en oublie ?

«Je ne souhaite pas que le 49.3 soit utilisé» (@olivierdussopt, 22 nov) «Je n’envisage pas l’hypothèse d’un 49.3» (@Elisabeth_Borne, 2 fév) «Nous ne voulons pas du 49.3» (@olivierveran, 12 mars) «Je ne vois pas pourquoi il faudrait utiliser le 49.3» (@GabrielAttal, 13 mars)

@bessonmarc They also just released a global shutter camera for tracking fast-moving objects raspberrypi.com/products/raspb…

@bessonmarc Raspberry camera module v3 ? raspberrypi.com/products/camer… 12 MP, exists in wide (120°) and standard (75°) FOV, w. or w/o IR filter

Hi fish sci friends. Planning to invest in new cameras 🎥 to record fish behavior videos (🐠 1-5cm SL) from above. Looking for lab cameras (plugged), fully programmable (ideally Python 🖥️), with high res, large FOV, maybe IR. What camera would you recommend? #fishscience #fishsci

@NetanyaMarquis @nsegata Looks very promising, thanks for the feedback!

@T_Greb @nsegata If I remember correctly - got mamba to install 2.5.0 - it was a very weird process because it kept insisting on older versions. And yeah - AVX2 is why I upgraded in the first place. The results I had where bit-same even though there were allegedly some bug fixes

More than ten years after the first version, I'm so glad to see the MetaPhlAn concept further developed and improved. Now with SGBs, massive integration of MAGs, higher taxonomic consistency, better coverage of non-human microbiomes. Looking forward to hear users' feedback!

@NetanyaMarquis @nsegata Very interesting! Did you install Bowtie from a repo or manually compiled it? Curious to hear if the speed increase comes from the added AVX2 instructions.

@nsegata Super interesting paper + It runs pretty well - If it helps - I'm running it with a newer version of bowtie (2.5.0+) which saves me like 10% of the time

@PierreDdeG @rmsothebys En plus de contrevenir aux recommandations de l'ARPP, les photos ne sont même pas originales (Honda a fait les mêmes il y a tout juste un an, et s'est fait taper sur les doigts) ... twitter.com/HondaFrancePR/…

Les photos officielles du modèle unique de la Profilée, dernière Bugatti Chiron qui sera mise en vente chez @rmsothebys demain, avec une belle dédicace à la team #velotaf parisienne.

@aldertzomer @bioinformer @savetonotion #thread #metagenomics #tools #pipeline

@bioinformer kraken2+bracken. Sometimes centrifuge as the 2016 nt database can be useful and doesn't require massive amounts of ram

Back in 2013, I started maintaining a GoogleDoc of published #metagenomics pipelines. By 2018, 100+ pipelines existed, so I stopped Today: ~180+ pipelines _just_ for taxonomic profiling of shotgun data…😐 What are you using for your metagenomics / microbiome analysis?

@svpino @SaveToNotion #thread #chatgpt #python #programming

Next time, I'll show you how to build an end-to-end deep learning model using ChatGPT. I'll only ask questions. It'll blow your mind. Follow me @svpino to ensure you don't miss it. 16 of 16

11 ways ChatGPT saves me hours of work every day, and why you'll never outcompete those who use AI effectively. A list for those who write code: 1 of 16

@SunagawaLab @SaveToNotion #thread #metagenomics #motus #metaphlan

To demonstrate the utility of mOTUs3, we reanalyzed rumen metagenomes from high- and low-methane-emitting (HME and LME) sheep. mOTUs3 was able to identify 131 differentially abundant species, while MetaPhlAn and Bracken were able to identify only 10 and 30 respectively. 6/6

We are very happy to announce that mOTUs3 is out today in @MicrobiomeJ, now allowing everyone to profile unknown species from more than 23 environments. Congratulations to @hjruscheweyh, @alessio_mila, @BorkLab, @pangenomics & @ZellerGroup. microbiomejournal.biomedcentral.com/articles/10.11… 1/6

@pangenomepapers @savetonotion #tweet #genotyping #metagenomics #intrastrain

Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables dlvr.it/SdvwT4

@WeAreRLadies @savetonotion #thread #R #dataviz #ggtext

@tangming2005 @jokergoo_gu @savetonotion #thread #heatmap #dataviz

@jokergoo_gu That's a wrap! If you enjoyed this thread: 1. Follow me @tangming2005 for more of these 2. RT the tweet below to share this thread with your audience 3. I dedicated a chapter on heatmap in my coming book: from cell line to command line divingintogeneticsandgenomics.ck.page sign up!

Making a heatmap is an essential skill for a bioinformatician. But you probably do not understand heatmap. 7 reading resources to understand heatmap!👇🧵 compiled at crazyhottommy.blogspot.com/2022/11/7-link…

@razoralign @SaveToNotion #tweet #rnaseq #nanopore #computational #tool #integrative

NanoTrans: an integrated computational framework for comprehensive transcriptome analyses with Nanopore direct-RNA sequencing biorxiv.org/content/10.110…

@WeAreRLadies @glyphe @Datawrapper @yjunechoe @quarto_pub as it changes some graphical parameters from defaults (in particular it messes device resolution if I recall correctly), making it a sub-optimal solution. Did you face such problems? From your thread it doesn't look like you had to use additional libraries for fonts? 2/2

@WeAreRLadies @glyphe @Datawrapper @yjunechoe @quarto_pub Thx for sharing, for many of the reasons you explain, I went with developping a package containing my custom colors and ggplots themes. However, changing the font was particularly difficult and I had to use sysfonts and showtext, but am not satisfied with the result ... 1/2

@rpetit3 @savetonotion #tweet #tool #bacteria #genomics #annotation #assembly

🎉 Bactopia v2.2.0 is out!🎉 This version brings more Bactopia Tools (47 total!), better cloud support, bug fixes, and contributions to other open-source projects Learn more at: bactopia.github.io/v2.2.0/ #bioinformatics #microbiology #nextflow #bacteria