🚀 Introducing the @nextflow.io Plugins Registry: a centralized repository for discovering, sharing, and managing #Nextflow plugins. We've streamlined the entire plugin lifecycle for the bioinformatics community. 🧑‍💻Explore today: hubs.la/Q03P_Q8t0

Attending SBI2 2025 in Boston next week? Join Ken Brewer (Scientific Solutions Lead) for the @nextflow.io for bioimaging workshop!🔬Sign up for the workshop when you register for the conference: hubs.la/Q03Ph_d10

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction. #Genomics #Rust #GenomeAnnotation #GFF #GenomicFeatures @biorxiv-bioinfo.bsky.social 🧬 🖥️ www.biorxiv.org/content/10.1...

nf-core/proteinfamilies: A scalable pipeline for the generation of protein families doi.org/10.1101/2025... Automatic identification and annotation of MYB gene family members in plants doi.org/10.1101/2021...

Super excited to share our review on genomic deep learning models for non-coding variant effect prediction, with Ayesha Bajwa and Nilah Ioannidis. We’d like this review to be a useful resource, and welcome any feedback, comments, or questions! 1/4 arxiv.org/abs/2411.11158

💡 Run custom applications on the same infrastructure as your @nextflow.io pipelines with Studios 🧵Read the blog to find out how! hubs.la/Q03wC-3p0

Don't miss our webinar with @bigomics.bsky.social tomorrow! Join us to discover how the integration of Omics Playground into Seqera Studios is supporting faster, scalable end-to-end omics analysis. 💻 Register now: hubs.la/Q03tjp-50

We got some amazing results from combining @seqera.io Fusion and NVIDIA Healthcare Parabricks! Can’t wait to start implementing all of the benefits of gpu workflows across all of the @nf-co.re pipelines!

🚀 We’ve teamed up with #NVIDIA to help bioinformatics teams scale faster, analyze more efficiently, and simplify cloud operations 🧵 📖 Read now: hubs.la/Q03rQZx-0

What is This, a Crossover Episode? So excited to see the Modern Data Stack and Modern Biotech Stack collide!

Maybe it was just the post-pandemic travel or finally meeting the @nextflow.io community in person, but @paoloditommaso.bsky.social blew my mind with Wave that day. 😂 youtu.be/PTbiCVq0-sE?...

We’ve just dropped some powerful new @nextflow.io features as part of the 25.04 release, all designed to enhance clarity, control, and collaboration in workflow development. 🎉 💡Learn more: hubs.la/Q03mQ2_10

Supporting Community at the Core of Innovation 🌍🙌 We were honored to provide space at the #NextflowSummit Boston for the incredible Boston Women in Bioinformatics group to gather, connect, and celebrate a major milestone: becoming a 501(c)(3) nonprofit! 🎉

🚀 Introducing Seqera Compute: Managed, Optimized Compute for Scalable Bioinformatics 📕Read the blog post: hubs.la/Q03mKwMb0 🔍Discover Seqera Compute: hubs.la/Q03mKxyB0

To continue advancing the vision that scientific innovation runs on software, we are thrilled to announce that Seqera has closed it’s Series B funding, led by Addition, with participation from Speedinvest, Talis, Amino Collective, BoxOne, and SNR! Learn more: hubs.la/Q03lcmf20

Dive into Pixi Packages! 🛠️ Build packages from source 📦 Cross-platform and cross-language ✨ Build backends for powerful standards! Currently released as a preview feature, with improvements dropping daily!

Pixi has shebang support like uv now! 😍 ``` #!/usr/bin/env -S pixi exec --spec bat -- bash -e ``` pixi.sh/dev/advanced...

Severance is just docker for brains🐳🧠

New blog post! Spring cleaning 2025 https://nf-co.re/blog/2025/springcleaning/

Next week is the March 2025 @nf-co.re #hackathon! 🎉 With 44 local sites across 27 countries, this event is truly global 🌏🌏🌎 We have 992 people registered - so close to 1000! Register here: nf-co.re/events/2025/... 🎟 ✍️ If you still need convincing, here's a little video to whet your appetite 👩🏻‍💻

@lionelhenry.bsky.social and I are so excited to finally announce Air - an extremely fast R code formatter! 🎉 With Air, you'll never need to worry about styling your #rstats code ever again. All you need to do is save, and Air takes care of the rest. www.tidyverse.org/blog/2025/02...

🎤Call for Speakers! The @nextflow.io Summit returns to Boston this May! We’re looking for speakers to showcase groundbreaking research, innovative solutions, and real-world success stories. 👉 Submit your abstract by March 14 to be part of the lineup: hubs.la/Q036sG6T0

Been looking forward to this talk since @alexpeltzer.bsky.social told me about DSO in October!

Come hang out in the #arm64 Slack channel! join.slack.com/share/enQtOD...

Attending #SLAS2025? Don't miss our exclusive Exhibitor Tutorial at 2:00 PM today in Room 24C! In this talk, we will discuss how @nextflow.io and Seqera are simplifying the analysis of large-scale sequencing and cell imaging data! 🔗 Can't attend? Get the recording instead: hubs.la/Q034lfYZ0

Genetic coupling of enhancer activity and connectivity in gene expression control https://www.nature.com/articles/s41467-025-55900-3 🧬🖥️🧪 ...beautiful plots made with #Rstats plotgardner https://phanstiellab.github.io/plotgardener/

Stop by and say hello if you’re there!

There's been a rapid growth in Australian researchers utilizing @nextflow.io for developing workflows, aswell as already implemented workflows from @nf-co.re and other open-source resources. In response, @ausbiocommons.bsky.social established the Australian Nextflow Seqera Service 🧵

Bluesky’s science takeover: 70% of Nature poll respondents use platform https://www.nature.com/articles/d41586-025-00177-1

At Stockholm University, we are now starting a 2-year Master’s programme in Evolutionary Genomics! Topics include population genetics, phylogenetics, molecular & genome evolution, DNA sequencing, bioinformatics, and palaeogenetics. Please spread the word! www.su.se/english/sear...

Went down a rabbit hole this weekend and wrote my first Python package that I published end to end! It's just a package of a wonderful Jupyter notebook for making UpSet plots in Altair! github.com/hms-dbmi/ups...

This meme picture made me laugh... #NextFlow #CWL #SnakeMake #Galaxy

Congrats to Johannes Linder, David Kelley et al. on the journal publication of Borzoi - a long context sequence models of RNA-seq coverage profiles with many nice applications for transcriptional & post-transcriptional regulation & variant effect prediction. www.nature.com/articles/s41... 1/

Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/ www.encodeproject.org/single-cell/...

another example is scale bio's ScaleMethyl, they released a public @nextflow.io pipeline alongside their product to process the raw reads. github.com/ScaleBio/Sca...

Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography–Mass Spectrometry Metabolomics Data Processing #JASMS pubs.acs.org/doi/10.1021/...

Another little uv trick I learned yesterday: ``` uvx --from git+https://github.com/httpie/cli httpie ``` You can just run #Python scripts from any git repo, no need for them to publish on PyPI.

Made a snippet for a uv run shebang because I got tired of hunting it down everytime I wanted to add it to a new script: github.com/edmundmiller...

Something that had been on my wishlist for a long time was a #Visidata plugin for common tabular #bioinformatics formats. I got by with just telling Visidata they were TSVs. Finally got around to writing a GFF plugin asciinema.org/a/Nt0AlgvxsX... 🧬🖥️

www.nature.com/articles/s43... we made The Matrix for worms

Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

This summer, @lukfor.bsky.social and I migrated the Michigan Imputation Server to Nextflow. 2M genomes later, we can say it was a big success. As a Christmas gift, we’re excited to show you how to set up your own local server in under 10 minutes. ##freeimputation genepi.github.io/michigan-imp...

it's big, and it's a review of 601 papers on the topic - but here's an update on Neuroinflammation in Alzheimer's Disease www.nature.com/articles/s41... led by Michael Heneka, published in @natrevimmunol.bsky.social today (MANY more authors listed and linked below)

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨 We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research! Read more: bmcgenomics.biomedcentral.com/articles/10.... 1/8

Achieving consistent results with Conda and Docker, both now and over time, is easier than ever! 🎉Wave now generates Conda lockfiles alongside containers, locking every dependency for precise reproducibility. 👉 Learn more: hubs.la/Q02-l2--0

There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research. A Place of Joy.

'But a new systematic analysis of what some call the “dark proteome” suggests scientists have missed thousands of nontraditional genes that lurk in previously overlooked stretches of the genome and make smaller than average proteins.' www.science.org/content/arti...