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/
@nf-co.re
Bioinformatics Engineer @seqera.io
https://link.edmundmiller.dev/
Reposted by 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
🧑💻Explore today: hubs.la/Q03P_Q8t0
October 24, 2025 at 11:07 AM
🚀 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
🧑💻Explore today: hubs.la/Q03P_Q8t0
Reposted by Edmund Miller
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
October 20, 2025 at 1:17 PM
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
Reposted by Edmund Miller
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🧵
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
August 5, 2025 at 6:31 AM
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🧵
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🧵
Reposted by Edmund Miller
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...
www.biorxiv.org/content/10.1...
August 16, 2025 at 5:07 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Edmund Miller
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...
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
August 17, 2025 at 4:52 AM
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...
doi.org/10.1101/2025...
Automatic identification and annotation of MYB gene family members in plants
doi.org/10.1101/2021...
Reposted by Edmund Miller
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
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
November 20, 2024 at 1:31 AM
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
arxiv.org/abs/2411.11158
Reposted by Edmund Miller
💡 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
July 10, 2025 at 12:29 PM
💡 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
Reposted by Edmund Miller
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
💻 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
June 24, 2025 at 9:53 AM
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
💻 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!
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
📖 Read now: hubs.la/Q03rQZx-0
June 12, 2025 at 6:18 PM
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!
Can’t wait to start implementing all of the benefits of gpu workflows across all of the @nf-co.re pipelines!
Reposted by Edmund Miller
🚀 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
📖 Read now: hubs.la/Q03rQZx-0
June 12, 2025 at 12:28 PM
🚀 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
📖 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!
So excited to see the Modern Data Stack and Modern Biotech Stack collide!
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
Databricks SQL support in @nextflow.io via the nf-databricks plugin! 🎉
🔗 Learn more: hubs.la/Q03rCjFY0
June 11, 2025 at 1:03 PM
What is This, a Crossover Episode?
So excited to see the Modern Data Stack and Modern Biotech Stack collide!
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?...
youtu.be/PTbiCVq0-sE?...
Nextflow Summit 2022 - Paolo di Tommaso
YouTube video by Nextflow
youtu.be
May 23, 2025 at 6:04 PM
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?...
youtu.be/PTbiCVq0-sE?...
Reposted by Edmund Miller
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
💡Learn more: hubs.la/Q03mQ2_10
May 15, 2025 at 6:25 PM
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
💡Learn more: hubs.la/Q03mQ2_10
Reposted by Edmund Miller
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! 🎉
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! 🎉
May 16, 2025 at 3:42 PM
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! 🎉
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! 🎉
Reposted by Edmund Miller
🚀 Introducing Seqera Compute: Managed, Optimized Compute for Scalable Bioinformatics
📕Read the blog post: hubs.la/Q03mKwMb0
🔍Discover Seqera Compute: hubs.la/Q03mKxyB0
📕Read the blog post: hubs.la/Q03mKwMb0
🔍Discover Seqera Compute: hubs.la/Q03mKxyB0
May 15, 2025 at 2:33 PM
🚀 Introducing Seqera Compute: Managed, Optimized Compute for Scalable Bioinformatics
📕Read the blog post: hubs.la/Q03mKwMb0
🔍Discover Seqera Compute: hubs.la/Q03mKxyB0
📕Read the blog post: hubs.la/Q03mKwMb0
🔍Discover Seqera Compute: hubs.la/Q03mKxyB0
Reposted by Edmund Miller
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
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
May 6, 2025 at 1:50 PM
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
Learn more: hubs.la/Q03lcmf20
Reposted by Edmund Miller
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!
🛠️ Build packages from source
📦 Cross-platform and cross-language
✨ Build backends for powerful standards!
Currently released as a preview feature, with improvements dropping daily!
March 26, 2025 at 2:33 PM
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!
🛠️ 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...
```
#!/usr/bin/env -S pixi exec --spec bat -- bash -e
```
pixi.sh/dev/advanced...
Shebang - Pixi by prefix.dev
None
pixi.sh
March 27, 2025 at 12:56 AM
Pixi has shebang support like uv now! 😍
```
#!/usr/bin/env -S pixi exec --spec bat -- bash -e
```
pixi.sh/dev/advanced...
```
#!/usr/bin/env -S pixi exec --spec bat -- bash -e
```
pixi.sh/dev/advanced...
Severance is just docker for brains🐳🧠
March 26, 2025 at 2:01 AM
Severance is just docker for brains🐳🧠
Reposted by Edmund Miller
New blog post! Spring cleaning 2025
https://nf-co.re/blog/2025/springcleaning/
https://nf-co.re/blog/2025/springcleaning/
March 20, 2025 at 12:02 PM
New blog post! Spring cleaning 2025
https://nf-co.re/blog/2025/springcleaning/
https://nf-co.re/blog/2025/springcleaning/
Reposted by Edmund Miller
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 👩🏻💻
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 👩🏻💻
March 21, 2025 at 8:28 PM
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 👩🏻💻
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 👩🏻💻
Reposted by Edmund Miller
@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...
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
February 21, 2025 at 3:10 PM
@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...
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...
Reposted by Edmund Miller
🎤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
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
February 12, 2025 at 7:20 PM
🎤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
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!
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
February 9, 2025 at 2:07 PM
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...
January 29, 2025 at 1:50 AM
Come hang out in the #arm64 Slack channel! join.slack.com/share/enQtOD...