Carl M. Kobel

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. #MicrobialGenomes #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...

Finally got my tool published!

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes www.biorxiv.org/content/10.1... #jcampubs

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes academic.oup.com/bioinformati... #jcampubs

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes www.biorxiv.org/content/10.1... 🧬🖥️ github.com/cmkobel/comp...

👏Today our new Section Head Thomas Pontén officially takes over after Head of Section Morten Limborg!

Thanks to Morten for all his work and welcome Thomas in your new important role!🤩

At today’s meeting Ostaizka introduces @hologen.bsky.social and Carl his #hologenomics tool CompareM2! 🦠💡
@dg.dk

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve.

Preprint 📝: biorxiv.org/content/10.1...

🧵 1/n

I want to expand on the extent to which IDEAA materials have been purged: I wrote an article last year for women’s history month on the history of women in antimicrobial development….DELETED.

Congratulations DR @cmkobel.bsky.social on the successful defense of your thesis 🙌🏼 Massive thanks to @hairyllama.bsky.social and @manuelkleiner.bsky.social for the time and your style which made the day all the more entertaining.

Coining the term "rumen community types" (RCT)

New preprint out from @cmkobel.bsky.social, @velma-te-a.bsky.social, @microbesrule.bsky.social and many others! 📄

It's been very cool to follow and play a small part in this story: Carl and Velma found two distinct community types across omics layers in the cow rumen that are driven by protozoa 🐮👾

Hi Bluesky! 🦋

I am transitioning to this platform and will start posting here about my own and others' cool science! 🤩

Sad to say goodbye to science Twitter, but I can't keep using a platform that is being used to destroy democracy...

I'll be moving my old Twitter posts here in the coming days.

My supervisor, @velma-te-a.bsky.social, is so cool!!!

Check out her talk on ciliate multi-omics, taking you through a history of science.

jams.org.au/index.php/ja...

Wow what a cool preprint!

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes https://www.biorxiv.org/content/10.1101/2024.07.12.603264v1 Here, we present CompareM2, a genomes-to-report pipeline for comparative analysis of bacterial and a

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes https://www.biorxiv.org/content/10.1101/2024.07.12.603264v1

Dreaming of a one-stop-shop for analysing microbial genomes using all your favorite tools? Look no further, CompareM2 is out 🤩

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

And now the preprint is out!

www.biorxiv.org/content/10.1...

Release v2.8.2 · cmkobel/CompareM2 What's Changed Update README.md by @wwood in #102 New Contributors @wwood made their first contribution in #102 Full Changelog: v2.8.1...v2.8.2 2.8.2 Add --cite parameter to executable. New mo...

Yay new version of CompareM2 (v2.8.2)
github.com/cmkobel/Comp...

- New "passthrough argument" feature to address any command line argument to any rule in the workflow.

#microbiology #bioinformatics #opensource #science #genomics

Microflora Danica: the atlas of Danish environmental microbiomes

10,686 shotgun metagenomes from a variety of environments across Denmark

www.biorxiv.org/content/10.1...

So strange this doesn't get any attention. Anyhow, maybe adding an illustration works. This is the exact same model

Holo-omics review is out!

There are no animals - Only holobionts.

link: doi.org/10.1039/D4MO...

@oveoyas.bsky.social @microbesrule.bsky.social @jennymerkesvik.bsky.social @velma-te-a.bsky.social
#symbiosis #microbiology #holoomics #bioinformatics #science #openaccess

Innsbruck, Austria

Currently, we have the following open positions in the Rinke Group for Microbial MultiOmics and Biorecycling (MMOB) @ the University of Innsbruck, Austria:

1x postdoc
3x PhD
1x RA

More info @ rinkelab.org/index.php/op...

Which style is better?

data %>%
mutate(type = "significant")

or

data %>%
mutate(type = "significant")

Wouldn't it be better if R had a non-vector data type, then there would be no doubt distinguishing vectorized and non-vectorized functions?

Data science:
Is it bad if I have more comments than code?

S2 Ep 9 - Carl Bergstrom on Science and Disinformation - The HPS Podcast - Conversations from Histor... Today's guest is Professor Carl Bergstrom from the University of Washington. Carl has been touring Australia over the last few weeks and we were delighted when he agreed to join us while he was in Mel...

Our latest episode is with the amazing @carlbergstrom.com talking all things science studies and 'Calling Bullshit' on mis- and disinformation.

Thanks so much to Carl for joining us on the podcast while he was in Melbourne!

#STS #MetasSci #HistSTM #PhilSci #SciComm #SocialPsyc🧪

Updated the Kraken 2 index collection to include an updated nt index: benlangmead.github.io/aws-indexes/k2 . It's getting big, folks: tarball is 550 GB and hash.k2d file is 710 GB.

A striking brushturkey with powerful beak, bare red head, and yellow neck collar.

Australian brushturkeys may be common to the point of being a nuisance, but they're stunning to look at and amazing in how they brood their eggs. Rather than sitting on them, they make incubation mounds—compost piles, essentially—the size of VW bugs and regulate the temperature therein carefully.

Found these sunglasses on the bottom of a lake. They will have a new life on BS.

The clade of ridiculous stuffies- that’s what came to me in class. Super useful PVC pipe rotating nodes to teach tree thinking and how to read ancestry