Mike Schatz

This popped up in my feed today: adele.pollux.casa/gemlog/2025-...

Just started! openai.com/live/

Individual academics probably don’t have enough clout to apply any real pressure although if we band together we maybe do. This could be a good topic for GA4GH or another society to address

Another dimension to this is when code should be directly interacting with files vs leveraging an API. As datasets get increasingly large I see API based access becoming more popular, especially for data in the cloud

And as much as I hate fastq, at least it doesnt have vendor lock in. As recently as yesterday I was fighting with cbcl files that could only be converted by bcl-convert (closed source/closed binary from Illumina)

The Sequence Alignment/Map format and SAMtools Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by diff...

But in this spirit if we see "specialized" code being stretched into "production" use, then we should encourage the development of harden tools and formats to use and work with it. This can also be incredibly successful as a publication, e.g. SAMTools has been cited 60k times

For "production" code that runs many times / with many samples, then of course this is the right approach. But we should also acknowledge a lot of code is highly specialized for a given dataset in which transparency and programming efficiency are paramount

Galaxy and Bioconductor Community Conference 2025 - YouTube Cold Spring Harbor Laboratory, New York June 23–26, 2025

Missed GBCC2025? Want to rewatch your favorite talks?
All session recordings (including Galaxy Live!) are now available on our YouTube channel. Revisit the presentations, explore new tools and workflows, and catch up on sessions you may have missed.
Watch here: youtube.com/playlist?lis...

Just failed a CAPTCHA challenge to join a MS Teams call, but I cant decide if this is a feature or a bug

Congratulations @benlangmead.bsky.social!

Ben Langmead promoted to full professor. Computer science.

Congratulations to @benlangmead.bsky.social on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational and life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access and use DNA sequencing data. 🧬

Bioconductor: Planning a third decade of comprehensive support for genomic data science This opinion piece discusses the Bioconductor project for open-source bioinformatics and the engineering concepts underlying its effectiveness to date. Since the inception of Bioconductor in 2002 with...

www.cell.com/patterns/ful...

#bioconductor #rstats

Bioconductor and ggplot2 4.0.0: What’s Changing and How to Prepare – Bioconductor community blog Preparing for the upcoming update - key changes, potential breakages, and what developers and users can do

ggplot2 4.0.0 is coming soon, and is moving some of the internals from S3 to the new S7 OOP system. This is worth a read if you're developing packages with ggplot2 (bioconductor or otherwise) blog.bioconductor.org/posts/2025-0... #Rstats

Love this CoFest energy!
Great to see Galaxy and Bioconductor developers working side-by-side at #GBCC2025, exploring, coding, and learning from each other 💻💙

@galaxyproject.bsky.social @bioconductor.bsky.social

Awesome time closing out GBCC with our hands on CoFest! Lots of fun writing code, updating trainings and building out the ecosystems- I submitted my first PR to the core Galaxy repo. Special thanks to Chris Mason for hosting us at Weill Cornell. @galaxyproject.bsky.social @bioconductor.bsky.social

And here is to the next 20 years of Galaxy and beyond! Now on to CoFest for some hands on hacking.

That’s a wrap on GBCC2025! It was incredible to see all the awesome developments, science, and training coming from the community - the future is bright for Galaxy and Bioconductor! @galaxyproject.bsky.social @bioconductor.bsky.social @cshlnews.bsky.social

Getting into computational biology this summer? 🏖️ 📖 Check out “Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References” by @arun-das.bsky.social‬, @mikeschatz.bsky.social, and more for a great introduction to the field:

The first Galaxy / Bioconductor joint conference #GBCC2025 starts next week at CSHL! If anyone wants to connect feel free to reach out here.

Lightning talks signup form coming soon...

JXTX Foundation Awards Scholarships for GBCC2025 JXTX: The James P. Taylor Foundation for Open Science is pleased to announce the 2025 GBCC scholarship recipients.

Also huge congratulations to the JXTX fellowship winners selected for their commitments to open science! jxtxfoundation.org/news/2025-6-...

The whole room cheered for the grand finale using the GalaxyMCP server through Claude (in English!) to automate the analysis and even write up the methods descriptions! @galaxyproject.bsky.social

Awesome first night of the Galaxy and Bioconductor community conference at CSHL. The GBCC Live demo was the star showing off how to connect the communities through a detailed spatial omics tumor analysis. #GBCC2025 @galaxyproject.bsky.social @bioconductor.bsky.social @cshlmeetings.bsky.social

🎉 GBCC2025 kicks off today!

We’re gathering at Cold Spring Harbor to welcome attendees, reconnect with colleagues, and gear up for an exciting week of science, training, and community.

Stay tuned!

gbcc2025.bioconductor.org

Kicking off the GRADS-4C symposium to advance genomics and genomic data science for all! @ncatsuaggies.bsky.social @blueyedgenes.bsky.social

Very excited to share I’ll be starting my own group at University of Utah in the Department of Human Genetics in the new year! Reach out if you are interested! vollgerlab.com

Congratulations! Utah is super lucky to get you!

These are not just grants. This is thousands of people who devoted their lives and careers - taking pay cuts, working long hours, living with uncertainty - all for the chance to try to make people's lives a bit better for you and your loved ones. This breaks my heart.

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

MLCB The 20th Machine Learning in Computational Biology (MLCB) meeting will be a two-day hybrid conference, September 10-11, 9am-5pm ET, with the in-person component at the New York Genome Center, NYC. Reg...

The #MLCB deadline has been extended to June 3 (AOE)! Still time to submit your cutting-edge work on machine learning in biology. Don’t miss out! 👉 www.mlcb.org #ComputationalBiology #ML4Bio

Today (June 1) marks the 20th anniversary of Galaxy! Thanks to all the developers, admins, researchers, trainers, educators, students and more that have made up this amazing community. Here is to the next 20 years! @galaxyproject.bsky.social @jxtxfoundation.bsky.social galaxyproject.org