🚀 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
Edmund Miller
@edmundmiller.dev
PhD Candidate @ UT Dallas in the Functional Genomics Lab working on Nascent RNA identification @nf-co.re Bioinformatics Engineer @seqera.io https://link.edmundmiller.dev/
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🧵
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
biorxiv.org
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...
nf-core/proteinfamilies: A scalable pipeline for the generation of protein families
The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity and evolutionary relationships. However, the vast majority of the...
doi.org
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
Leveraging genomic deep learning models for non-coding variant effect prediction
The majority of genetic variants identified in genome-wide association studies of complex traits are non-coding, and characterizing their function remains an important challenge in human genetics. Gen...
arxiv.org
💡 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
Powering Interactive Omics Analysis with BigOmics Analytics and Studios | Seqera
Join us for an insightful webinar with BigOmics Analytics as we showcase the integration of Omics Playground into Studios as a powerful new way to interactively explore RNA-Seq and proteomics results ...
hubs.la
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!
Seqera@seqera.io · last yr.🚀 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
🚀 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!
Nextflow@nextflow.io · last yr.We’ve thrilled to announce a powerful new capability: native Databricks SQL support in @nextflow.io via the nf-databricks plugin! 🎉 🔗 Learn more: hubs.la/Q03rCjFY0
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?...
Nextflow Summit 2022 - Paolo di Tommaso
YouTube video by Nextflow
youtu.be
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
Scaling the Future of Scientific Software: Seqera Raises $26M Series B
Today, we're ecstatic to announce that Seqera has raised $26 million in Series B funding, led by Addition with participation from Speedinvest, Talis, Amino Collective, BoxOne, and SNR. This milestone ...
hubs.la
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...
Shebang - Pixi by prefix.dev
None
pixi.sh
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...
Air, an extremely fast R formatter
We are thrilled to announce Air, a new R formatter.
tidyverse.org
🎤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
Come hang out in the #arm64 Slack channel! join.slack.com/share/enQtOD...
Slack
join.slack.com
Angel Pizarro@angelp.bsky.social · 2y agoThis is a call out to bioinformatics developers that we are working to get all of NF-Core pipelines (and by extension most of Bioconda) to support Arm. Spot price for c8g.16xlarge (Graviton4) and it is below 60¢/hr. Or < 1¢ per physical CPU if your application supports Arm ...
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/
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
