2-year Postdoc Position: Evolution and Organization of Ant Olfactory Systems

– in Carlotta Martelli's lab at Johannes Gutenberg University Mainz, Germany.

https://mrtlllab.uni-mainz.de/wp-content/uploads/2025/01/PostDoc-Position-Neuro-Ants-150125.pdf

"The ideal candidate should have a strong background in bioinformatics, ideally with practical or theoretical experience in single-cell transcriptomics or comparative genomics. A keen interest in neurobiology is essential. Additional skills in evolutionary biology, insect handling, and programming (preferably in Python) would be advantageous, but are not mandatory."

Position still open!

Question for #archaea #microbiology #bioinformatics folks: I'm looking at a specific contig in an Archaeal genome with repeat elements that remain difficult to resolve even with 100~1000x coverage and minimum 10k read length.

Anyone else dealt with something similar? What could I even be looking at?

GBCC2025 Poster Abstracts

There’s still time to submit your abstract for a poster presentation at GBCC2025! Submit by May 1st to join us at Cold Spring Harbor, June 23–26.

We’re looking forward to seeing your work!

Submit here: https://gbcc2025.bioconductor.org/abstracts/submission_guidelines/

Menghadiri seminar hasil an. Hotma Hutapea di prodi S3 Epidemiologi FKM University of Indonesia dengan topik penelitian mengenai long COVID. Berfoto dengan Prof Mako, Dekan FKM UI, dengan jajarannya. Juga ada prof Sunarno , dari BRIN & Pak Adi Yulandi dari Universitas Atmajaya Jakarta
Sebagai ko-promotor, saya sangat puas dengan upaya Bu Hotma untuk mengintegrasikan Epidemiologi dengan Biologi molekuler dan Bioinformatika.
#COVID19 #epidemiology #bioinformatics #biomedicine

Abstract submitted with hours to spare - fingers crossed for #BOSC2025 / #ISMB2025 / #ECCB2025 and plenty of interesting #OpenSource #Bioinformatics presentations!

https://www.open-bio.org/events/bosc-2025/submit/

Excited to share our latest preprint about CoExpPhylo:
https://doi.org/10.1101/2025.04.03.647051.

Not long ago, Nele excelled at a #Python course for life scientists and acquired crucial skills for this work
#Bioinformatics #DataScience
@PuckerLab

Running RStudio in a rootless container on Linux.

This approach avoids dealing with compiling basic packages or adding extra repositories to your main OS, and it's targeted for running the container on your computer and not somewhere else.

1. Get Podman (make sure it works rootless)
2. Run the following command in a terminal (see "man podman-run" for details on what it does)

podman run --rm -it -p 8787:8787 -e PASSWORD=baa -v $HOME:/root/home -v $HOME/.config/rstudio:/root/.config/rstudio docker.io/rocker/verse

Cloud computing: where you're not just a bioinformatician, you’re also the finance manager, compliance officer, and IT support, all while carrying a hefty dose of mental fatigue. I miss those PhD days with a inhouse HPC when all you had to do was sbatch every parameter combo under the sun to test your research question… then complain about queue times and who was clogging the damn cluster with their BLAST jobs
#bioinformatics

@bgeedb was used to design stem-cell based vaccines against #cancer in mouse models, opening a door to a potential application with humans.

This is an example of the impact that #bioinformatics databases and tools developed by SIB groups have. Researchers use them to make sense of their data and tackle essential societal challenges.

Learn more: https://www.sib.swiss/services/open-software-and-databases/impact#designing-stem-cell-based-vaccines-against-cancer

@marcrr @fbastian

#Genetic data repo #OpenSNP to self-destruct before authoritarians weaponize it
The reason, according to #bioinformatics researcher Bastian Greshake Tzovaras, one of the founders of the project, is the dissolution of genetic testing biz #23andMe and the potential weaponization of genetic data by #farright #authoritarian regimes.
https://www.theregister.com/2025/04/01/opensnp_shutdown/

asking for a friend: do you know any database/framework to visualize RNAseq data ? (just like https://github.com/broadinstitute/gnomad-browser for WGS)

The programme for the #bc2basel tutorials & workshops is out! From #geneexpression analysis to #machinelearning or #datavisualization, beginner or advanced: boost your #bioinformatics skills!

Register to make sure to secure your spot (limited seats): https://tinyurl.com/3y8ay2d6

Busy year:

- Workflow programming for Data Analysis on #HPC Systems (Course in Mainz in January):
- Same Course in Dresden (February)
- #SnakemakeHackathon2025 at the CERN in March:
- upcoming: #OpenScience Retreat (no hashtag, yet?) in April
- International Supercomputing Conference in June (so, @boegel, I will be there, after all and hope to meet people from @irods, too ; will you be there folks from #iRODS ?)
- German Conference for #Bioinformatics and NHR Conference in September

And I do not know whether this will be all. I have a nagging feeling there is more to come

Big shoutout to the folks at NCBI GEO. They have been doing an incredible job managing enormous amounts of gene expression and related biomedical data for many, many years They do it efficiently and very, very well. I am so grateful: both when I download data published by others and when I submit my own data. You are true #bioinformatics heroes doing priceless and highly impactful work! #NCBI #nih

#Genomics
#Bioinformatics
#Academia

Beware US academic coders. If you have collaborators contributing code from a sanctioned region, your repos may be locked.

See https://mastodon.social/@organicmaps/114155428924741370

The kicker is that the US is leaning authoritarian and all in on censorship. If Canada or Mexico become sanction targets and you have code pushes from there, Microsoft will lock you out of your GitHub accounts.

The #SnakemakeHackathon2025 just induced another collaboration for me!

It is always good to work along with like-minded people, interested in #ReproducibleComputing, #HPC and #Bioinformatics

Alexandros Stamatakis' annual EMBO satellite #bioinformatics workshop in Crete is open again for registration (free-of-charge, first-come-first-serve)

This year: #biodiversity #genomics tools

https://forms.gle/GRvPxCp2TnYdo8Po8

As Alexi is keen to point out: "... a good excuse to visit Crete?"

"BWA-0.7.19 released with a fix to the internal HD-line bug introduced in 0.7.18"

https://github.com/lh3/bwa/releases/tag/v0.7.19

Yikes modkit likes to eat up ram when making summaries of methylation called bams.

Subsampled bam with 100k reads still requires close to 50gb of ram, which for me is cutting it way too close. I'm beginning to envy those real lab people with monster rigs.

I like to remind people, if you want less of my human rights, future, open science, and other opiniatied posts, follow my #cheminformatics and #bioinformatics account at @egonw@social.edu.nl

Of course, I love you to stay here too, because I honestly believe in a better future and am hopeful. But hoping is not enough, hence my posts here.