Lightnews — Scholar-powered news

Genomics to Notebook (g2nb): extending the computational notebook

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 10h

An environment that integrates Jupyter with Galaxy, allowing tools to be added as notebook cells, and providing access to thousands of bioinformatics tools from within a notebook interface.
http://galaxyproject.org/news/2025-04-11-galaxy-to-notebook-g2nb/

##UseGalaxy ##GalaxyProject ##EOSC (1/2)

An environment that integrates Jupyter with Galaxy, allowing tools to be added as notebook cells, and providing access to thousands of bioinformatics tools from within a notebook interface.

1 2 3

Reposted by Hans-Rudolf Hotz

Swiss Reproducibility Network @swissrn.bsky.social · 1d

🚨 Update on the SwissRN Annual Meeting
Find the complete program of our 4th annual meeting now here:
www.swissrn.org/contents/new...
📅 December 05, 2025, 09:30-17:00, Hybrid format
📌 Universität Basel, Spitalstrasse 41, 4056, room U1.101

Please register by 31 October 2025.

Microbial Genes Recovery in Galaxy

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 1d

New workflow from the Galaxy Community!
A reproducible workflow for microbial gene analysis (open, FAIR, and ready to explore). Explore the power of Galaxy for microbiome and genomics research: https://galaxyproject.org/news/2025-09-26-microbial-gene-workflow/

##Bioinformatics (1/2)

A new Galaxy workflow enables researchers to recover and analyze microbial genes from metagenomic data.

EuroScienceGateway Project: Testing the deployment of Galaxy and Pulsa

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 1d

Galaxy isn’t just for genomics — it’s powering new discoveries in materials science too. This μSR study on redox-active metal hydrides used Galaxy to explore hydrogen radical chemistry in {2Fe2S} centers — a fine example of cross-disciplinary ##OpenScience. (1/3)

1 1 1

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 1d

Nearly a year ago, the EuroScienceGateway project showed how Galaxy + Pulsar could run on the EOSC EU Node — a major leap for federated ##OpenScience. Still worth revisiting as we keep building FAIR, scalable research infrastructure.

https://galaxyproject.org/news/2025-01-29-esg-eosc/ (1/2)

Deploy your own Galaxy and Pulsar instances on the EOSC EU Node

DNA rhythms orchestrate gene activity across development

1 1 3

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 1d

Galaxy 25.0 steps up the game in data management. Now you can set up and manage InvenioRDM / Zenodo (or S3, Dropbox, etc.) integrations from a dedicated section in User Preferences — clean UI, prioritized sources, and true “Export datasets” support.

Read more: (1/2)

1 2 2

Reposted by Hans-Rudolf Hotz

FMI science @fmiscience.bsky.social · 1d

🎥 FMI scientists discovered that thousands of C. elegans genes switch on and off in rhythmic patterns controlled by chromatin, revealing how gene timing shapes development & offering clues to human biological clocks. @labgrosshans.bsky.social www.youtube.com/watch?v=Dibw...

YouTube video by The Friedrich Miescher Institute for Biomedical Research

www.youtube.com

4 4

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 2d

From public-health genomics to hibernating hedgehogs (and even turtle conservation), discover what’s new in Galaxy. Plus upcoming events, workshops, and fresh GTN highlights!
https://galaxyproject.org/news/2025-09-29-galaxy-newsletter-sep2025/

##GalaxyProject ##Bioinformatics ##OpenScience (1/2)

September 2025 Galaxy Newsletter

From public-health genomics to hibernating hedgehogs (and even turtle conservation), discover whatâs new in Galaxy. Plus upcoming events, workshops, and fresh GTN highlights!

1 1 3

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 2d

The Galaxy Tool Development Workshop kicked off a new series of events to strengthen our tool ecosystem!
This inaugural session, held for the Galaxy EU team, focused on best practices, collaboration, and reproducible development.

Catch the recap: (1/2)

1 2 2

Reposted by Hans-Rudolf Hotz

twist-basel.bsky.social @twist-basel.bsky.social · 23d

🚀 Alternative Careers Beyond the Bench

Join TWIST for an inspiring Panel discussion about alternative career paths beyond academia
Date: Wednesday, 15th October 2025
Time: 16:30
Location: Friedrich Miescher Institute (FMI), Novartis Campus, Basel
Register now at www.twistbasel.com/events-1/alt...

Empowering Wet Lab Scientists with NGS Analysis Skills Without Coding

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 2d

Teaching NGS to wet lab scientists got a whole lot easier once I discovered TIaaS and the Galaxy platform.
https://galaxyproject.org/news/2025-05-05-empowering-wet-lab-scientists-with-ngs-analysis-skills-without-coding-barriers/

##eurosciencegateway ##galaxyproject ##teaching ##infrastructure (1/2)

Teaching NGS to wet lab scientists got a whole lot easier once I discovered TIaaS and the Galaxy platform.

Quantifying Electrophoresis Gel Bands with QuPath and Galaxy

1 1 4

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 2d

New tutorial from the Galaxy Training Network! Learn how to quantify gel electrophoresis bands using QuPath + Galaxy. Fully open, reproducible, and beginner-friendly.
https://training.galaxyproject.org/training-material/news/2025/08/18/bands_image_analysis.html

##Bioinformatics (1/2)

Gel Electrophoresis is a staple of molecular biology, providing a way to separate DNA, RNA, or proteins by size and charge. While gels are usually interpreted visually, the ability to quantify band intensities offers much richer insights—allowing researchers to estimate product yields, verify PCR amplification, or assess protein purity.

training.galaxyproject.org

Reposted by Hans-Rudolf Hotz

de.NBI & ELIXIR Germany @denbi.bsky.social · 2d

🛠️🌌 Join the @galaxyproject.bsky.social Admin Workshop 2025!
📆 Nov 24–28 | 📍 Brno, Czechia
Learn to install, configure & manage your own high-performance Galaxy server, hands-on with community experts.
🔗 Info & registration: www.denbi.de/training-cou...
#usegalaxy #Bioinformatics #AdminWorkshop

blog posts: RO-Crate and WorkflowHub at the European Galaxy Days 2025 | Research Object Crate (RO-Crate)

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 2d

From the RO-Crate blog: RO-Crate and WorkflowHub at the European Galaxy Days 2025

https://www.researchobject.org/ro-crate/blog/2025-10-09/ro-crate-at-european-galaxy-days-2025

##OpenScience ##ReproducibleResearch ##GalaxyProject ##ROCrate ##WorkflowHub ##Bioinformatics ##FAIRData ##ResearchTools (1/2)

The European Galaxy Days took place from 1-3 October 2025 in Freiburg im Breisgau, Germany. Users, developers, teachers, and administrators of Galaxy in Europe gathered to discuss new developments in...

www.researchobject.org

BellaVista interactive tool now available in Galaxy

Reposted by Hans-Rudolf Hotz

GTN @galaxytraining.bsky.social · 7d

GTN joined the TEACH V to talk about education across Communities at Helmholtz

Read more at https://training.galaxyproject.org/training-material/news/2025/10/08/joined-teachV.html

@galaxyproject.bsky.social

1 1

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 6d

🌋 Save the date! GCC2026 is coming to Clermont-Ferrand, France 🇫🇷, June 22–24, 2026
Join the global Galaxy community for talks, training, posters & collaboration in the heart of the French volcanoes!

Sign up for our GCC2026 mailing list, here: gaggle.email/join/gcc2026...

3 2

Reposted by Hans-Rudolf Hotz

Rob Patro @robp.bsky.social · 6d

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

Rob Patro @robp.bsky.social · 8d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

37 29

Reposted by Hans-Rudolf Hotz

Grosshans Lab @labgrosshans.bsky.social · 6d

Paper alert! doi.org/10.1038/s443... - "A scheduler for rhythmic gene expression". We show how 9 txn factors suffice for rhythmic gene expression of thousands of genes with any phase or amplitude in #Celegans larvae (and also look at the tissues where oscillations happen) 1/n

2 11 22

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 3d

Open-Source Visualization for Imaging-Based Spatial Transcriptomics
http://galaxyproject.org/news/2025-04-26-bellavista-it/

##UseGalaxy ##GalaxyProject ##EOSC ##EuroScienceGateway

Open-Source Visualization for Imaging-Based Spatial Transcriptomics

LLM Hub: Large Language Models Made Easy in Galaxy

1 3

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 3d

Access powerful Large Language Models in Galaxy easily
https://galaxyproject.org/news/2025-10-10-llm-hub/

##UseGalaxy ##GalaxyProject ##EOSC ##ai ##machine_learning ##llm ##large_language_model ##open_ai ##deepseek ##mistral ##meta ##image_models ##multimodal_models ##gpt

Access powerful Large Language Models in Galaxy easily

Galaxy Workshop for Humanities and Social Sciences in Freiburg

2 5

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 3d

Introducing Galaxy and Digital Humanities on site
https://galaxyproject.org/news/2025-05-19-dh-lab/

##UseGalaxy ##GalaxyProject ##EOSC ##digital_humanities ##social_science

Introducing Galaxy and Digital Humanities on site

Training Infrastructure as a service (TIaaS) Feedback from Dr. Janne M

1 2

Reposted by Hans-Rudolf Hotz

Galaxy Project @galaxyproject.bsky.social · 3d

Thanks to TIaaS, our RNA-Seq workshops run smoothly—no more delays, just effective hands-on learning.
https://galaxyproject.org/news/2025-05-23-tiaas-success-story-toivonen/

##UseGalaxy ##GalaxyProject ##EOSC ##EuroScienceGateway ##training ##infrastructure ##teaching

Thanks to TIaaS, our RNA-Seq workshops run smoothlyâno more delays, just effective hands-on learning.

1 2

Reposted by Hans-Rudolf Hotz

Ensembl @ensembl.org · 3d

Notice for users of Ensembl Rapid Release - this site has been archived and is now accessible at rapid-archive.ensembl.org. Any saved URLs will now redirect to the latest data on our new site- beta.ensembl.org

Learn more on our blog: www.ensembl.info/2025/10/13/...