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Reposted by Ken Brewer

Nextflow @nextflow.io · Jun 18

Nextflow Training Week is Back on June 23-27, 2025! 🎉

This free, self-paced training is perfect for newcomers looking to get started with Nextflow

Sign up now: hubs.la/Q03sDmpr0

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Reposted by Ken Brewer

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

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Reposted by Ken Brewer

Nextflow @nextflow.io · Apr 4

🎉Episode 50 of the @nextflow.io Podcast is here!

Host @ewels.bsky.social sits down with @kbestak.bsky.social, a PhD student and active contributor to the @nf-co.re community, working at the cutting edge of #SpatialOmics and #microscopy.

🎧Catch it here: hubs.la/Q03fVPNx0

Imaging pipelines and analysis, with Krešimir Beštak | The Nextflow Podcast by Seqera

Seqera | The Home for Open Science | From the creators of Nextflow, Wave, and MultiQC

hubs.la

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Ken Brewer @kenibrewer.bsky.social · Mar 10

I'll be speaking in the session "Managing Data Analyses with Nextflow and nf-core in Bioinformatics Core Facilities" on Monday, March 24 chaired by Charlie Whittaker along with @lopantano.bsky.social and Ramiro Barrantes-Reynolds.

More details about the event here: web.cvent.com/event/924ddc...

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Ken Brewer @kenibrewer.bsky.social · Mar 10

I’m excited to share I will be speaking at #ABRF2025’s Annual Meeting in Las Vegas in March. This meeting brings together scientific leaders of biomolecular and bioinformatics core facilities to discuss how we can maximize the impact these valuable groups have within their institutions.

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Ken Brewer @kenibrewer.bsky.social · Mar 7

We've been working really hard on the new Nextflow training materials and they've turned out great. Take advantage of them on your own or by doing a watch party with a group next week during our Nextflow training week. 🚀

Nextflow @nextflow.io · Mar 7

🚀 Next week is #Nextflow #Training Week!

We’ve got fresh new material ✨ including “Hello Nextflow”, premiering on the @nextflow.io YouTube channel 🎬

Got questions? The #Nextflow #Ambassadors are ready, standing-by on the Community Forum all week 💬

Sign up here:
community.seqera.io/t/nextflow-t...

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Ken Brewer @kenibrewer.bsky.social · Feb 20

I'm doing a webinar next week about instrument-to-analysis automation of bioinformatics data processing!

Seqera @seqera.io · Feb 18

Just as robotics revolutionized wet lab experiments, automation is transforming bioinformatics. 💻

Join us next week as we demonstrate how to automate and scale event-driven bioinformatics workflows using @nextflow.io and Seqera. 🧵

👉 Register now: hubs.la/Q0375dwt0

Automating Event-Driven Data Analysis with Nextflow and Seqera

We are witnessing an explosive growth in omics data, where rapid data generation is outpacing our ability to derive meaningful insights—making analytics the bottleneck in research. But how can bioin...

hubs.la

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Ken Brewer @kenibrewer.bsky.social · Feb 4

Super excited for the distributed nf-core hackathon! We've got 36+ local sites being organized in over 20 countries! Registration is now open!

nf-core @nf-co.re · Feb 3

Calling all bioinformatics enthusiasts! Join a global network of @nextflow.io ninjas for the @nf-co.re hackathon from March 24-26, 2025 🎉

Collaborate remotely or at one of the 36+ local sites worldwide (🇦🇷🇦🇺🇧🇪🇧🇷🇨🇦🇨🇴🇨🇿🇩🇰🇪🇹🇫🇷🇩🇪🇬🇭🇬🇷🇮🇳🇮🇹🇳🇱🇳🇿🇵🇰🇵🇱🇿🇦🇪🇸🇸🇪🇨🇭🇹🇷🇬🇧🇺🇸).

Registration is now open! 🎟

nf-co.re/events/2025/...

Hackathon - March 2025 (Online / Distributed)

A virtual hackathon with local sites to develop nf-core together

nf-co.re

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Reposted by Ken Brewer

Angel Pizarro @angelp.bsky.social · Jan 28

This 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 ...

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Reposted by Ken Brewer

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

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Ken Brewer @kenibrewer.bsky.social · Jan 10

I'm attending SLAS! Come find me at our booth if you want to chat about anything Nextflow-related. I'll also be presenting a tutorial about setting up event-driven bioinformatics automation using Nextflow and Seqera Platform. I hope to see some of you there!

Seqera @seqera.io · Jan 10

Heading to SLAS2025 in San Diego? ✨

Stop by Seqera’s booth #2850 for live demos, expert chats, and a chance to win AirPods!

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Reposted by Ken Brewer

Stephen Turner @stephenturner.us · Jan 2

One of my favorite talks at the @nextflow.io summit was @kenibrewer.bsky.social's talk on how to NOT contribute to nf-core (using nf-core in your organization). He wrote a nice post on the @nf-co.re blog on building an nf-core style modules library for your organization seqera.io/blog/buildin...

Building an nf-core style modules library for your organization | Seqera

If you would like to bring nf-core’s approach to enabling code within your own organization, you can!

seqera.io

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Ken Brewer @kenibrewer.bsky.social · Jan 7

I wrote a blog article about some of the best parts of nf-core's modular tooling and how to use it within your own organization. This was an extension of a talk I gave at the Nextflow Summit late last year.

Read or watch however you prefer!

www.youtube.com/watch?v=Pn_B...

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Ken Brewer @kenibrewer.bsky.social · Dec 31

I didn't do any work directly on the OLE project during my time in the Breaker Lab, but I'm convinced that OLE is one of the most exciting bacterial #ncRNA to be discovered in recent years. Definitely check out this preprint if you'd like to see some really exciting RNA #cryoEM structures.

Ronald Breaker @ronbreaker.bsky.social · Dec 31

#ncRNA molecules are far stranger than you think. We propose that OLE RNA is bacteria's functional mimic of #mTOR, and the Das lab at Stanford proposes OLE RNA penetrates cell membranes! They also find that RNAs we called ROOL and GOLLD form 8-membered nanocages.
www.biorxiv.org/content/10.1...

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Reposted by Ken Brewer

nf-core @nf-co.re · Dec 19

Our next hackathon is rapidly approaching! 🚀

- March 24-26, 2025
- Online / local distributed sites

For the distributed sites, WE NEED YOU! 🎯

If you're able to book a meeting room and host a local site, fill in the local site registration form:

nf-co.re/events/2025/...

Hackathon - March 2025 (Online / Distributed)

A virtual hackathon with local sites to develop nf-core together

nf-co.re

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Reposted by Ken Brewer

Josh Moore @joshmoore.bsky.social · Dec 13

Know someone looking for a new start in 2025? 🔍

Colleagues of #BlueSci, help flex this new social muscle! 🦾

German BioImaging @gerbi-gmb.de · Dec 13

🚀 We're hiring! Join the German BioImaging Team as a Software Developer!
💻 Build scalable #bioimaging solutions
🌍 Collaborate globally
🎯 Contribute to open science through #OMEZarr @openmicroscopy.org
Remote, full-time. Apply by 31 Jan 2025: bit.ly/3Zrd4SR

Software Developer Wanted – Join the German BioImaging Team!

German BioImaging e.V. invites applications by 31. January for a remote position as Software Developer (m/f/d) (100 %, pay grade 13-14 TVöD depending on experience) Are you an enthusiastic open-...

bit.ly

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Reposted by Ken Brewer

Seqera @seqera.io · Dec 10

Exciting news! 🎉You can now try Chai-1, the SOTA model for biomolecular structure prediction by Chai Discovery, with Seqera!

👉 Check it out: github.com/seqeralabs/n...

GitHub - seqeralabs/nf-chai: POC Nextflow pipeline to run the Chai-1, SOTA model for biomolecular structure prediction

POC Nextflow pipeline to run the Chai-1, SOTA model for biomolecular structure prediction - seqeralabs/nf-chai

github.com

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Reposted by Ken Brewer

Srijit Seal 🇺🇸🇬🇧🇩🇪🇯🇵🇮🇳 @srijitseal.com · Dec 5

We’re thrilled to share our Nature Methods review on #CellPainting — your go-to resource for mastering Cell Painting! From MOA and toxicity prediction to contributing to candidate drugs in clinical trials, we’ve distilled 10 years of insights!

Cell Painting: a decade of discovery and innovation in cellular imaging - Nature Methods

This Review synthesizes the literature from over 10 years of Cell Painting for image-based profiling and highlights how advances in this technology enable new biological discovery of cellular phenotyp...

www.nature.com

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Reposted by Ken Brewer

Stephen Turner @stephenturner.us · Dec 5

📍Pinned Post: Welcome to the papers with code feed!
bsky.app/profile/did:...

Papers from PubMed, bioRxiv, Bature, PLoS, etc, with links to GitHub will be included here. Anyone can post to this feed.

See also: blog.stephenturner.us

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Ken Brewer @kenibrewer.bsky.social · Dec 5

Really exciting seeing the results from this incredible effort come out!

Anne Carpenter @drannecarpenter.bsky.social · Dec 4

Now on biorxiv! The JUMP-Cell Painting Consortium’s paper:

“Morphological map of under- and over-expression of genes in human cells”

This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months
www.biorxiv.org/content/10.1...

Morphological map of under- and over-expression of genes in human cells

Cell Painting images offer valuable insights into the state of a cell and enable many biological applications, but publicly available arrayed datasets only include hundreds of genes perturbed. The JUM...

www.biorxiv.org

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Reposted by Ken Brewer

Nextflow @nextflow.io · Dec 3

Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. 👇 #Jobs #Opportunities

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Reposted by Ken Brewer

Phil Ewels @ewels.bsky.social · Nov 26

This is really cool, definitely worth a look for anyone running in environments where container security is of concern (which should be.. everywhere, right?)

📦🔒✨

The magic here for me is being able to automatically halt pipeline runs if new container CVEs are released. Totally hands off but safe.

Seqera @seqera.io · Nov 26

Enhancing security in data pipelines with @nextflow.io and Wave!

👉 Read now: hubs.la/Q02ZxVW90

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Ken Brewer @kenibrewer.bsky.social · Nov 26

Really exciting to see @valenceai.bsky.social open-sourcing a large, curated, FAIR resource for #QuantumMechanics datasets. Pre-computing missing values needed to train #ML models is also fantastic from a #GreenAlgorithms perspective.

#OpenScience

Valence Labs @valenceai.bsky.social · Nov 26

We curated 40+ quantum mechanics datasets, covering 250+ quantum methods & 1.5B geometries. All of this is easily accessible through the OpenQDC library. 🧵

Harness the power of QM data with a single line of code: www.openqdc.io

Read the blog: www.valencelabs.com/blog-posts/o...

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Ken Brewer @kenibrewer.bsky.social · Nov 26

I'm really sad to see Spring Science winding down. Having worked closely with them in a previous role during a software evaluation, I was incredibly impressed by the quality of their tooling and the caliber of their team.

https://x.com/kamens/status/1858585137690407038

Ben Kamens on LinkedIn: Spring Science | 24 comments

Spring’s AI tools are loved by scientists. But we do not make enough money to continue running the company. Our tech gives ground-breaking new superpowers to… | 24 comments on LinkedIn

buff.ly

Reposted by Ken Brewer

Phil Ewels @ewels.bsky.social · Nov 23

Love seeing the new @seqera.io AI starting to be used for real-world uses, after we've been testing it with toy examples for so long.. 🧪

Great little blog post by Lorena! 🎉
lpantano.github.io/post/2024/ne...

Showcase: My Quick Dive into Pipeline Automation with Seqera AI | My bits

Example of automation with miniaml investment but good results

lpantano.github.io

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