Lightnews — Scholar-powered news

Reposted by Edmund Miller

Yo Akiyama @yoakiyama.bsky.social · Aug 5

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

1 43 95

Reposted by Edmund Miller

Javier Santoyo @jsantoyo.bsky.social · Aug 16

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...

11 26

Reposted by Edmund Miller

plantgenomics.bsky.social @plantgenomics.bsky.social · Aug 17

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

2 3

Reposted by Edmund Miller

Pooja Kathail @poojakathail.bsky.social · Nov 20

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

1 13 34

Reposted by Edmund Miller

Seqera @seqera.io · Jul 10

💡 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

1 3 5

Reposted by Edmund Miller

Seqera @seqera.io · Jun 24

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

1 3 6

Edmund Miller @edmundmiller.dev · Jun 12

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 · Jun 12

🚀 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

4

Reposted by Edmund Miller

Seqera @seqera.io · Jun 12

🚀 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

1 4 3

Edmund Miller @edmundmiller.dev · Jun 11

What is This, a Crossover Episode?

So excited to see the Modern Data Stack and Modern Biotech Stack collide!

Nextflow @nextflow.io · Jun 11

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

3

Edmund Miller @edmundmiller.dev · May 23

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

5

Reposted by Edmund Miller

Seqera @seqera.io · May 15

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

1 4 4

Reposted by Edmund Miller

Seqera @seqera.io · May 16

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! 🎉

1 3 7

Reposted by Edmund Miller

Seqera @seqera.io · May 15

🚀 Introducing Seqera Compute: Managed, Optimized Compute for Scalable Bioinformatics

📕Read the blog post: hubs.la/Q03mKwMb0
🔍Discover Seqera Compute: hubs.la/Q03mKxyB0

1 3 4

Reposted by Edmund Miller

Seqera @seqera.io · May 6

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

1 7 13

Reposted by Edmund Miller

prefix.dev @prefix.dev · Mar 26

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!

1 1 7

Edmund Miller @edmundmiller.dev · Mar 27

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

1 4

Edmund Miller @edmundmiller.dev · Mar 26

Severance is just docker for brains🐳🧠

3

Reposted by Edmund Miller

nf-core @nf-co.re · Mar 20

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

1 1

Reposted by Edmund Miller

nf-core @nf-co.re · Mar 21

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 👩🏻‍💻

4 6

Reposted by Edmund Miller

Davis Vaughan @davisvaughan.bsky.social · Feb 21

@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.

www.tidyverse.org

21 120 360

Reposted by Edmund Miller

Seqera @seqera.io · Feb 12

🎤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

5 8

Edmund Miller @edmundmiller.dev · Feb 9

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

Gregor Sturm @grst.bsky.social · Feb 5

If you want to learn more, I'll be presenting this at a @nf-co.re bytesize talk: nf-co.re/events/2025/...

Bytesize: data science operations (DSO)

Gregor Sturm, Boehringer Ingelheim

nf-co.re

1 4

Edmund Miller @edmundmiller.dev · Jan 29

join.slack.com/share/enQtOD...

Slack

join.slack.com

1

Edmund Miller @edmundmiller.dev · Jan 29

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

7

Reposted by Edmund Miller

Seqera @seqera.io · Jan 28

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

1 2 3