Wayne

RNA sequencing data with R/Bioconductor Online, 3-14 November 2025 To foster international participation, this course will be held online

🎓 Upcoming Online Course: RNA Sequencing Data with R/Bioconductor by Physalia Courses and Bioconductor Training

📅 November 3–14, 2025

Instructor: Dr Ludwig Geistlinger

👉 Register and learn more: www.physalia-courses.org/courses-work...

Snakemake Hackathon March 2026 We are excited to announce the Snakemake Hackathon 2026, to be held 9-13 March, 2026 at the Technical University Munich. This event will bring together passionate developers and data scientists to col...

Want to help shaping the future of #Snakemake? Then participate in the Snakemake hackathon 2026 in Munich! There's still room as the maximum number of participants is not yet reached. You can register here: indico.cern.ch/e/snakemake-...

#sciworkflows #reproducibility

Go from JupyterLab user to creator 🚀
At JupyterCon 2025, learn to build + publish custom extensions for real-world workflows — guided by experts in JupyterLab development.
🗓️ Nov 3 | San Diego
Details: sched.co/28H2m
Register: events.linuxfoundation.org/jupytercon/r...

Teaching workflow systems to new users: why is it so hard? I’ll discuss the challenges (and opportunities!) of teaching workflow systems to scientists, and present two concepts that I have found useful for guiding my teaching: (1) workflow systems as imperfec...

Join us!

workflows.community/talks/2025_0...

Schedule | LF Events View the O3DECon 2021 Schedule & Directory.

JupyterCon 2025 has an early-bird registration discount that ends October 3rd! Get your tickets now, and check out the schedule below

events.linuxfoundation.org/jupytercon/p...

Jupyter Community Workshops Are Back! The Jupyter Community Building Working Group is pleased to announce that the next call for proposals for Jupyter Community Workshops is now…

A reminder that there are two Call for Proposals out from the Jupyter Foundation!

👉 (deadline soon!) Jupyter Community Workshops: blog.jupyter.org/jupyter-comm...
👉 Jupyter Community Support funding: blog.jupyter.org/your-ideas-o...

Check them out and share the word!

Jupyter Community Workshops Are Back! The Jupyter Community Building Working Group is pleased to announce that the next call for proposals for Jupyter Community Workshops is now…

Jupyter Community Workshops are back! Workshops will be held through February 2026.

The call for proposals is open until September 7th! Learn more and submit your proposal here:

blog.jupyter.org/jupyter-comm...

👋 JupyterLab and Jupyter Notebook users:

What's one thing you'd love to see improved in JupyterLab, Jupyter Notebook, or JupyterLite?

The team is prepping the upcoming 4.5/7.5 releases and wants to tackle some usability issues.

Drop your feedback below, this will help prioritize what gets fixed!👇

Call For Proposals (CFP) | LF Events The Jupyter ecosystem has transformed data science, scientific research, and education. It has shaped the way a generation of developers and scientists develop their workflows.

🚨 the JupyterCon CFP closes on Sunday (in 2 days) at the end of the day! 🚨

Get your submissions in quickly!

events.linuxfoundation.org/jupytercon/p...

Learning from Each Other's Journeys: case studies from Open Initiatives

🔥 We are pleased to announce the The Turing Way Fireside Chat Series on Governance. This series brings together experts and community members to explore the many dimensions of governance in research and open science. Find out more about the events at:
www.software.ac.uk/news/turing-...

BiocPy: Facilitate Bioconductor Workflows in Python github.com/BiocPy

Victor Chang Cardiac Research Institute on X: "Our scientist @CarusL studies the malfunctioning of an important ion channel that keeps our heart beating. Using #cryoEM, he looks at how these ion channels function. https://t.co/joXxnvUnNH" / X Our scientist @CarusL studies the malfunctioning of an important ion channel that keeps our heart beating. Using #cryoEM, he looks at how these ion channels function. https://t.co/joXxnvUnNH

These two still seem to be working twitter.com/VictorChangI... x.com/DNA_RNA_Uni/...

For those of you who prefer R over Python — good news! 🎉

You can now try out and run R code directly right in your browser from the @jupyter.org website — all in just a couple of seconds 🚀

Huge thanks to Isabel Paredes and contributors for making this possible!

👉 jupyter.org/try

H/ACA snR30 snoRNP guides independent 18S rRNA subdomain formation - Nature Communications During synthesis, modification and maturation of the ribosomal RNA, correct subdomain folding without additional guidance poses a major challenge. Here, the authors observe the snR30 H/ACA snoRNP form...

Our results finally explain the essential role of snR30 snoRNA! Check out the details in www.nature.com/articles/s41...

The Turing Way - Github Workshop - May 2025 Date: Monday, 6 May, 15-16:30 UTC+1 (in your timezone) The Turing Way is a community-led resource for reproducible, open, collaborative, and inclusive data science. Created by over 400 contributors, T...

Join our Github training workshop - open to all (including people not signed up for Book Dash!)

⚒️ Learn how to use the Github platform
⚒️ Make your first Pull Request
⚒️ Find out how to contribute to The Turing Way project

📅 6 May
⏰ 5-5:30 UTC+1

forms.gle/GBrBmpbJ4DdT...

JupyterCon | LF Events Discover the future of data science with hands-on training, visionary keynotes, innovative tools, and insights from top Jupyter contributors.

JupyterCon 2025 is happening! Join us in San Diego, California, from November 3–6, 2025. CFP is open now. Learn more at bit.ly/jupytercon

The option to change console prompt position is available under the three dots button in the console toolbar, which is the last toolbar button

Toggling all the three new settings transforms the console into a single cell

The Import and Export buttons in the Settings Editor are the first two items in the toolbar panel

The workspace indicator in the open state

JupyterLab 4.4.0b1 and Notebook 7.4.0b1 are available for testing 🎉
- improved code console
- settings import/export
- better real time collaboration
- workspace indicator
- kernel subshells

Please test:

pip install --pre 'jupyterlab>=4.4.0b1'

or

pip install --pre 'notebook>=7.4.0b1'

Restore MyBInder badge to working state · Issue #7 · ramalho/jupyturtle At this point the launch badge on the main README page is pointing at an old version of the repo and doesn't work. However, launches from the current repo work fine. I suggest the following URL for...

Jupyturtle does work via MyBinder in more modern Jupyter as long as you use the correct MyBinder links, see github.com/ramalho/jupy... . Similar for Jupyturtle2 which uses ipycanvas (see bottom of my post at stackoverflow.com/a/78994855/8...).

Restore MyBinder working by pinning ipywidgets and installing Notebook 6 by fomightez · Pull Request #29 · takluyver/mobilechelonian This is relation to Issue #28 - Fix to keep working via MyBinder's NbClassic by pinning to old ipywidgets and very recent updates to MyBinder's default notebook. This edits environment.yml ...

(I have made a pull request at github.com/takluyver/mo...). And it looks like github.com/ramalho/jupy... could be made work possible with even more recent Jupyter.

Restore MyBinder working by pinning ipywidgets and installing Notebook 6 by fomightez · Pull Request #29 · takluyver/mobilechelonian This is relation to Issue #28 - Fix to keep working via MyBinder's NbClassic by pinning to old ipywidgets and very recent updates to MyBinder's default notebook. This edits environment.yml ...

Are you suggesting something that lets users not have to install anything or sign up to use it? I don't know if the implementations match what you are using, but I have updated mobilechelonian repo so it works in MyBinder-served sessions at github.com/fomightez/mo... ....

R in JupyterLite 💡 😍 🎉

Pythonistas, if you haven't already done this, give it a try! Run this in your terminal:

uvx textual-demo

Requires UV docs.astral.sh/uv/

Real-time collaboration and collaborative editing for GIS workflows with Jupyter and QGIS The QGIS open-source project is a cornerstone in the geosciences ecosystem, providing robust tools for spatial data analysis and…

Announcing JupyterGIS 🌍 🌐 🎉

Real-time collaboration for #GIS workflows with #Jupyter and #QGIS

@qgis.fosstodon.org.ap.brid.gy @jupyter.org

blog.jupyter.org/real-time-co...

The PR improving the JupyterLab code consoles has been merged, and is now available in the latest JupyterLab, Notebook and JupyterLite pre-releases!

➡️ pip install --pre jupyterlab notebook

💡We're working on making the new options available in the JupyterLite REPL, stay tuned! 💡

2i2c has officially become part of the mybinder.org federation, introducing a new, cost-effective, and faster approach. We hope to make it easier for more people to join the federation by contributing a single-node BinderHub at 2i2c.mybinder.org.

More in our blog: https://2i2c.org/blog/2025/binde…

U of A DataLab workshops: week of Feb 3rd. 2025.
Want to improve your skills with AI/ML tools, foundation models, and methods? Join our weekly workshops at the U of A DataLab.
#AI #ML #UArizona #UArizonaDataLab #DataScience #GenAI #Bioinformatics
ua-datalab.github.io/events/

GitHub: fomightez/SQUARNA-binder/main Click to run this interactive environment. From the Binder Project: Reproducible, sharable, interactive computing environments.

You can add use of MyBinder so that those wishing to try the software can do so in temporary Jupyter session in their browser without installing anything on their computer. No login or Google account needed. Try at mybinder.org/v2/gh/fomigh... Fork: github.com/fomightez/SQ...

GitHub: fomightez/genomenotebook-binder/main Click to run this interactive environment. From the Binder Project: Reproducible, sharable, interactive computing environments.

Or to do that using current Jupyter with everything already installed without need to login or a Google account you can use Jupyter sessions served via the MyBinder service as illustrated by launching via mybinder.org/v2/gh/fomigh... (fork: github.com/fomightez/ge...)

🚀 Prototyping launch buttons for JupyterHub & MyBinder by agoose77 · Pull Request #503 · jupyter-book/myst-theme To close jupyter-book/mystmd#1643 and jupyter-book/mystmd#1644, this PR prototypes a launch UI. We will want to move things around in time, but this PR is designed to start design conversations. Th...

I'm excited to get Binder / JupyterHub launch button functionality back into Jupyter Book 2!

Gets a little better every day!

github.com/jupyter-book...

Ribosomes hibernate on mitochondria during cellular stress Nature Communications - Cells adapt to low glucose by halting protein synthesis and altering organelle shape. Here the authors showed that hibernating ribosomes tether to mitochondria and form...

Yeast ribosomes adapt to glucose starvation by tethering to mitochondria in hibernation. Prolonged depletion halts protein synthesis and remodels ribosomes to create protective ribosome arrays. #ribosomes #RNASky #RNABiology #translation rdcu.be/d1xqj