Ken Brewer
@kenibrewer.bsky.social
Open-source x Science - Dev Advocate @ Seqera
Bioimaging enthusiast
Bioimaging enthusiast
Reposted by Ken Brewer
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
This free, self-paced training is perfect for newcomers looking to get started with Nextflow
Sign up now: hubs.la/Q03sDmpr0
June 18, 2025 at 1:46 PM
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
This free, self-paced training is perfect for newcomers looking to get started with Nextflow
Sign up now: hubs.la/Q03sDmpr0
Reposted by Ken Brewer
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 Ken Brewer
🎉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
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
April 4, 2025 at 12:55 PM
🎉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
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
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.
March 10, 2025 at 9:16 AM
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.
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. 🚀
🚀 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...
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...
March 7, 2025 at 9:59 PM
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. 🚀
I'm doing a webinar next week about instrument-to-analysis automation of bioinformatics data processing!
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
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
February 20, 2025 at 12:08 AM
I'm doing a webinar next week about instrument-to-analysis automation of bioinformatics data processing!
Super excited for the distributed nf-core hackathon! We've got 36+ local sites being organized in over 20 countries! Registration is now open!
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/...
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
February 4, 2025 at 2:26 PM
Super excited for the distributed nf-core hackathon! We've got 36+ local sites being organized in over 20 countries! Registration is now open!
Reposted by Ken Brewer
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 ...
Spot price for c8g.16xlarge (Graviton4) and it is below 60¢/hr. Or < 1¢ per physical CPU if your application supports Arm ...
January 28, 2025 at 6:12 PM
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 ...
Spot price for c8g.16xlarge (Graviton4) and it is below 60¢/hr. Or < 1¢ per physical CPU if your application supports Arm ...
Reposted by Ken Brewer
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
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
January 28, 2025 at 4:17 PM
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
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
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!
Heading to SLAS2025 in San Diego? ✨
Stop by Seqera’s booth #2850 for live demos, expert chats, and a chance to win AirPods!
Stop by Seqera’s booth #2850 for live demos, expert chats, and a chance to win AirPods!
January 10, 2025 at 5:08 PM
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!
Reposted by Ken Brewer
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
January 2, 2025 at 1:30 PM
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...
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...
Read or watch however you prefer!
www.youtube.com/watch?v=Pn_B...
January 7, 2025 at 4:29 PM
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...
Read or watch however you prefer!
www.youtube.com/watch?v=Pn_B...
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.
#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...
www.biorxiv.org/content/10.1...
December 31, 2024 at 9:25 PM
Reposted by Ken Brewer
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/...
- 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
December 19, 2024 at 12:04 AM
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/...
- 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/...
Reposted by Ken Brewer
Know someone looking for a new start in 2025? 🔍
Colleagues of #BlueSci, help flex this new social muscle! 🦾
Colleagues of #BlueSci, help flex this new social muscle! 🦾
🚀 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
💻 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
December 13, 2024 at 5:04 PM
Know someone looking for a new start in 2025? 🔍
Colleagues of #BlueSci, help flex this new social muscle! 🦾
Colleagues of #BlueSci, help flex this new social muscle! 🦾
Reposted by Ken Brewer
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...
👉 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
December 10, 2024 at 1:19 PM
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...
👉 Check it out: github.com/seqeralabs/n...
Reposted by Ken Brewer
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
December 5, 2024 at 5:35 PM
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!
Reposted by Ken Brewer
📍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
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
December 5, 2024 at 10:05 AM
📍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
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
Really exciting seeing the results from this incredible effort come out!
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”
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
December 5, 2024 at 7:49 PM
Really exciting seeing the results from this incredible effort come out!
Reposted by Ken Brewer
Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. 👇 #Jobs #Opportunities
December 3, 2024 at 6:08 PM
Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. 👇 #Jobs #Opportunities
Reposted by Ken Brewer
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.
📦🔒✨
The magic here for me is being able to automatically halt pipeline runs if new container CVEs are released. Totally hands off but safe.
November 26, 2024 at 10:55 PM
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.
📦🔒✨
The magic here for me is being able to automatically halt pipeline runs if new container CVEs are released. Totally hands off but safe.
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
#OpenScience
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...
Harness the power of QM data with a single line of code: www.openqdc.io
Read the blog: www.valencelabs.com/blog-posts/o...
November 26, 2024 at 7:16 PM
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
#OpenScience
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
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
November 26, 2024 at 6:13 PM
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
https://x.com/kamens/status/1858585137690407038
Reposted by Ken Brewer
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...
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
November 23, 2024 at 3:44 PM
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...
Great little blog post by Lorena! 🎉
lpantano.github.io/post/2024/ne...
If you already have the Nextflow VSCode extension installed be sure to update to the latest version because it is 🔥🔥🔥.
The language server that the extension includes has other cool implications for the future of Nextflow tooling. Attend the webinar for details!
The language server that the extension includes has other cool implications for the future of Nextflow tooling. Attend the webinar for details!
💻Webinar: A new era for @nextflow.io!
Join us on Dec 10 to explore the latest major version of the Nextflow VS Code extension, now powered by a new language server that elevates Nextflow into a first-class language in its own right!
👉 Register now: hubs.la/Q02Z0R0q0
Join us on Dec 10 to explore the latest major version of the Nextflow VS Code extension, now powered by a new language server that elevates Nextflow into a first-class language in its own right!
👉 Register now: hubs.la/Q02Z0R0q0
November 21, 2024 at 3:00 PM
If you already have the Nextflow VSCode extension installed be sure to update to the latest version because it is 🔥🔥🔥.
The language server that the extension includes has other cool implications for the future of Nextflow tooling. Attend the webinar for details!
The language server that the extension includes has other cool implications for the future of Nextflow tooling. Attend the webinar for details!