Edmund Miller

🚀 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...

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/...

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...