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Hans-Rudolf Hotz

@hrhotz.bsky.social
293 followers 157 following 119 posts

Molecular Biologist turned Bioinformatician working in the Computational Biology facility at the Friedrich Miescher Institute in Basel Open Science, Training/Mentoring, #UseGalaxy, Bioconductor

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Reposted by Hans-Rudolf Hotz
Rob Patro @robp.bsky.social · 14/10/2026
Got to share some recent (& ongoing) work with folks at @fulcrumgenomics.com yesterday! Instead of my normal style (go deep on 1 project), I covered 3 recent projects: github.com/COMBINE-lab/... github.com/COMBINE-lab/... github.com/zrudnick/bra... Thanks for inviting me to meet with the team!
github.com
GitHub - COMBINE-lab/gravlax: Annotation-independent molecular-evidence archives for single-cell RNA-seq
Annotation-independent molecular-evidence archives for single-cell RNA-seq - COMBINE-lab/gravlax
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Reposted by Hans-Rudolf Hotz
Galaxy Project @galaxyproject.bsky.social · 15/10/2026
🌊 Galaxy Europe is diving into Ocean Hackathon 2026! From October 16–18, teams across 11 cities will turn marine data into innovative solutions, with Galaxy for Earth System Sciences supporting accessible, reproducible analysis. 🌐 galaxyproject.org/news/2026-10... #usegalaxy
galaxyproject.org
Galaxy Europe Goes Ocean: Ready for Ocean Hackathon 2026!
48 hours, ocean data and fresh ideas! Galaxy Europe's Earth System Sciences platform joins the Ocean Hackathon adventure.
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Reposted by Hans-Rudolf Hotz
Galaxy Project @galaxyproject.bsky.social · 15/10/2026
48 hours, ocean data and fresh ideas! Galaxy Europe's Earth System Sciences platform joins the Ocean Hackathon adventure. galaxyproject.org/news/2026-10-13-g… #UseGalaxy #GalaxyProject #EOSC
Ocean Hackathon 2026Galaxy for Earth System SciencesExample of a marine data analysis workflow using Galaxy Europe
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FMI science @fmiscience.bsky.social · 15/10/2026
Congrats to @anupamahl.bsky.social & Selma Dahmane on their @snsf.ch grants, totalling nearly CHF 2 million! Hemalatha's team will explore how metabolism shapes the fate of cancer-causing mutations in skin. Dahmane's group will investigate how immune cells detect Zika virus and trigger inflammation.
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Rfam @rfamdb.bsky.social · 15/10/2026
Check out the latest news from Rfam and scan the QR codes on the poster to discover the new Rfam website, with more interactive features to explore RNA families. #EESRNA @emblebi.bsky.social
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Galaxy Project @galaxyproject.bsky.social · 14/10/2026
📣 Workflow4Experimenters 2027 Analyze your data with Galaxy and the Workflow4Metabolomics infrastructure! During this one-week-long on-site course (preceded by half-a-week of webinars), you will learn how to use the W4M-promoted Galaxy tools for metabolomics, (1/2)
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EU-LIFE @eu-life.bsky.social · 14/10/2026
We are highlighting voices from EU-LIFE member institutes that embody the alliance's priorities. Today, we showcase #Internationality with Anupama Hemalatha, Junior Group Leader at @fmiscience.bsky.social in #Basel ➡️ www.linkedin.com/feed/update/... #WeAreEULIFE
linkedin.com
#fmi #basel #internationality #weareeulife | EU-LIFE
Anupama Hemalatha 𝗵𝗮𝘀 𝗮𝗹𝘄𝗮𝘆𝘀 𝗯𝗲𝗲𝗻 𝗳𝗮𝘀𝗰𝗶𝗻𝗮𝘁𝗲𝗱 𝗯𝘆 𝗱𝗶𝘀𝗰𝗼𝘃𝗲𝗿𝘆. Growing up in India, she devoured books on science and language, even though no one in her family had a research background. During her zoolo...
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InterPro @interprodb.bsky.social · 13/10/2026
Check out our latest blogpost with all the updates included in InterPro 110.0 and the release of InterProScan 6 🥳 www.ebi.ac.uk/about/news/u...
ebi.ac.uk
InterPro 110.0 and InterProScan 6: a re-engineered pipeline and AI-ready access to the protein universe
A rebuilt InterProScan, InterPro-N predictions for your own sequences, a new Matches API and an MCP server bring faster, self-service and AI-ready protein classification
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Biozentrum, University of Basel @biozentrum.unibas.ch · 13/10/2026
Bacterial Viruses – From Basic Biology to Phage Therapy #EinblickeBiozentrum: October 27, 2026 Prof. Yuping Li explores how viruses infect bacteria, overcome their defenses, and could offer new ways to fight antibiotic-resistant infections. www.biozentrum.unibas.ch/events/bioze...
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de.NBI & ELIXIR Germany @denbi.bsky.social · 13/10/2026
🧬 Spontaneous event tomorrow: Join our online session to Update Galaxy Tools for Microbiome Research! Meet the community, learn the tools, and get hands-on experience updating them together. 🗓️ Tomorrow, 14 Oct 2026, 10:00 CEST (Open End) 📍 Online www.denbi.de/training-cou... #Galaxy #Microbiome
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The Turing Way @turingway.bsky.social · 13/10/2026
🚀 Interested in joining The Turing Way Book Dash this November? Application form here: forms.gle/kcyJ2fJ9Qzb9... 📅 Key dates: - Book Dash Week = 30 Nov to 4 Dec 2026 • Application deadline: 28 Oct (Midnight Anywhere on Earth) #TheTuringWay #OpenScience #OpenResearch #ResearchCulture
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Galaxy Project @galaxyproject.bsky.social · 13/10/2026
Efficient start of the ESG4Stars project with kick-off meeting, general assembly and first collaborative working days all in one week galaxyproject.org/news/2026-10-12-e… #UseGalaxy #GalaxyProject
Opening presentation of the kick-off meetingGroup photo of participants taken in front of the main building of the Faculty of Engineering at the University of Freiburg on the very sunny October afternoon of day 1The five high-level objectives of ESG4Stars: track smarter, transfer less, store less, compute less and drive change printed in the style of an energy label together with short catch phrases - Make energy use visible, measurable and FAIR; Move only the necessary data; Optimise storage footprints with storage classes and modern file formats; Reduce redundant processing and allocate right-sized resources; Raise awareness and drive adoption into European research infrastructures - explaining each objective
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Galaxy Project @galaxyproject.bsky.social · 13/10/2026
Workshop on high-throughput sequencing data analysis with Galaxy This course introduces scientists to the data analysis platform Galaxy Freiburg im Breisgau, Germany 1 March 2027 Info: training.galaxyproject.org/training…
training.galaxyproject.org
Workshop on high-throughput sequencing data analysis with Galaxy
This course introduces scientists to the data analysis platform Galaxy. The course is designed for beginners; no prior programming skills are required.
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Reposted by Hans-Rudolf Hotz
Galaxy Project @galaxyproject.bsky.social · 12/10/2026
📣 microGalaxy Hackathon for Tool Development Join the microGalaxy community on October 14th to update outdated metagenomics tools in the IUC repository! 📍 Online 📅 14 October 2026 🔗 More info & registration: galaxyproject.org/events/2026-10-14… #UseGalaxy (1/2)
galaxyproject.org
microGalaxy Hackathon for Tool Development
Join the microGalaxy community on October 14th to update outdated metagenomics tools in the IUC repository!
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Ilya Flyamer @phlya.bsky.social · 12/10/2026
Join us for the 5th season of Sci.STEPS! We are looking for mentors in all fields of science (academia or not, everyone is welcome!) to help their junior colleagues consciously plan and develop their career.
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Reposted by Hans-Rudolf Hotz
Galaxy Project @galaxyproject.bsky.social · 12/10/2026
Are you at ASM-BIG? Stop by the Galaxy table during the poster sessions to chat about microbial workflows, ask questions, grab some CANDY, or just say hi! galaxyproject.org/events/2026-10-11… #UseGalaxy #ASMBIG
BRC Analytics logo
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de.NBI & ELIXIR Germany @denbi.bsky.social · 06/10/2026
Service of the week: Infrastructure for training events not just Galaxy, but R, Python, & more. TIaaS is provided by usegalaxy.eu and offers stable, dedicated resources for bioinformatics and data science courses of all sizes. Free for academic life scientists. Provided by RBC 👉 usegalaxy.eu/tiaas
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Galaxy Project @galaxyproject.bsky.social · 06/10/2026
📄 Long text + LLM context limits? Galaxy can help. The new LangChain Text Splitters tool breaks long texts into manageable chunks for tasks like summarization, translation & RAG, all within Galaxy workflows. 🤖✨ Learn more: galaxyproject.org/news/2026-10... #usegalaxy #LLM #OpenScience
galaxyproject.org
LangChain Text Splitters, the Missing Link when Processing Long Texts with LLMs
Circumvent context window limits of LLMs by splitting long texts into manageable chunks
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Reposted by Hans-Rudolf Hotz
Galaxy Project @galaxyproject.bsky.social · 07/10/2026
Circumvent context window limits of LLMs by splitting long texts into manageable chunks galaxyproject.org/news/2026-10-02-l… #UseGalaxy #GalaxyProject #EOSC
Demo of LangChain Text Splitters in Galaxy
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Bioconductor @bioconductor.bsky.social · 08/10/2026
How can Bioconductor methods become more reusable across different workflow ecosystems? Our latest blog explores how Bioconductor, Galaxy & nf-core contributors used a single-cell workflow to test the BiocJobs approach & advance research software interoperability. Read the full post: bit.ly/4y4ZuUB
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Reposted by Hans-Rudolf Hotz
BF Francis Ouellette @bffo.bsky.social · 11/10/2026
From kerstinhowe.bsky.social and colleagues in @qbiogn-bot.bsky.social | Generating eukaryotic reference genome assemblies: Earth BioGenome Project quality #Standards and #Recommendations | #OpenScience #Bioinformatics #Genomics #EarthBioGenomeProject | 🧬🖥️🧪🔓 ⬇️ arxiv.org/abs/2610.03075
arxiv.org
Generating eukaryotic reference genome assemblies: Earth BioGenome Project quality standards and recommendations
Reference genome assemblies are foundational resources across the biological sciences as they begin to expose the fundamental building blocks of each species and the molecular toolkits vital for adapt...
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Hans-Rudolf Hotz @hrhotz.bsky.social · 12/10/2026
This week, the small scale @galaxyproject.bsky.social admins will meet on Thursday (October 15th): galaxyproject.org/events/2026-...
galaxyproject.org
Small Scale Galaxy Admins Meeting
Galaxy Community Hub
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Reposted by Hans-Rudolf Hotz
Phili @philouail.bsky.social · 05/10/2026
Chromatograms is out in Analytical Chemistry! Chromatographic data in R, in memory, on disk or computed on demand, now part of xcms and tested on 4,000+ LC-MS files. Thanks to my amazing co-authors and specifically @jorainer.bsky.social doi.org/10.1021/acs.... #RStats #Bioconductor #MassSpec
doi.org
Chromatograms: A Modular Infrastructure for Scalable Chromatographic Data Handling in R
Abstract. Chromatographic traces are central to LC-MS analysis, yet most software treats them as transient intermediates inside a fixed pipeline rather tha
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Reposted by Hans-Rudolf Hotz
Friedemann Zenke @fzenke.bsky.social · 05/10/2026
1/9 New paper led by Michael Hauri & Peter Buttaroni: “Learning Commute-Time-Preserving World Models for Planning.” We show how to shape a world model's latent space so its distances mean something for planning.🧵 📄 arxiv.org/abs/2610.01373 💻 github.com/fmi-basel/co... 🌐 ctwm-website.github.io
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Galaxy Project @galaxyproject.bsky.social · 04/10/2026
Across 160 bioinformatics tasks, agents using Galaxy achieved accuracy comparable to agents writing custom code. galaxyproject.org/news/2026-09-21-a… #UseGalaxy #GalaxyProject
Local image
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Reposted by Hans-Rudolf Hotz
Johannes Rainer @jorainer.bsky.social · 05/10/2026
🚨our educational resource for #reproducible #metabolomics data analysis using @bioconductor.bsky.social and #rstats integrating #Python and #SIRIUS6 is now published! 👉 #Metabonaut bit.ly/4z9WaYZ 📄 doi.org/10.1007/s113... Great work from @philouail.bsky.social and big thanks to all contributors! 🙌
bit.ly
Exploring and Analyzing LC-MS Data
This resource hosts tutorials and end-to-end workflows describing how to analyze LC-MS/MS data, from raw files to annotation, using Bioconductor packages.
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Hans-Rudolf Hotz @hrhotz.bsky.social · 02/10/2026
(finally) on my way to Freiburg to catch up with the latest development on @galaxyproject.bsky.social @galaxytraining.bsky.social
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Reposted by Hans-Rudolf Hotz
Daniela Schneider @schnda.fedihum.org.ap.brid.gy · 01/10/2026
Today was the kickoff of our new #EU project on #AI Readiness for Social Impact #ai4social We from @galaxyfreiburg are excited to be part of this #EOSC project with more than 10 partners. During the next years we will mostly contribute to developing an AI-ready infrastructure platform and […]
fedihum.org
Original post on fedihum.org
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Reposted by Hans-Rudolf Hotz
Bioconductor @bioconductor.bsky.social · 02/10/2026
#BioC2026 brought the Bioconductor community together in Seattle for three days of science, software and community building. From inspiring talks & posters to workshops, package demos, and the hackathon, it was a great celebration of 25 years of Bioconductor. Read the full recap: bit.ly/4e9Kopr
blog.bioconductor.org
BioC2026 conference recap – Bioconductor community blog
Highlights from the 2026 North American Bioconductor Conference in Seattle, Washington
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Galaxy Project @galaxyproject.bsky.social · 30/09/2026
🧬 New on the GTN: explore how protein structure can influence ligand-binding site predictions using SIMORGH, ColabFold, and structural ensembles. See how deep learning and Galaxy can help account for protein dynamics in binding-site analysis. training.galaxyproject.org/training-mat...
training.galaxyproject.org
Statistics and Machine Learning / Comparing ligand-binding site predictions across different protein structure modalities using SIMORGH / Hands-on: Comparing ligand-binding site predictions across dif...
Statistical Analyses for omics data and machine learning using Galaxy tools
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Hans-Rudolf Hotz @hrhotz.bsky.social · 30/09/2026
unfortunately, no mention of @galaxyproject.bsky.social 😞
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ELIXIR Europe @elixir-europe.org · 30/09/2026
🔬The second #ELIXIR_STEERS policy brief, Better software, better research, sets out 5️⃣ recommendations to strengthen Europe’s research software ecosystem. Read the news release and discover the recommendations: loom.ly/hCUxzds #FP10
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Galaxy Project @galaxyproject.bsky.social · 25/09/2026
🔬 Lab data 🤝 Galaxy analysis A new openBIS integration lets you browse and import lab files directly into Galaxy, run your analyses, and send results back to openBIS. Fewer manual file transfers, smoother workflows. galaxyproject.org/news/2026-09... #usegalaxy #OpenScience
galaxyproject.org
Connecting openBIS and Galaxy: from lab data to analysis and back
Browse openBIS files in Galaxy, analyse them, and return results to your lab notebook
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Galaxy Project @galaxyproject.bsky.social · 23/09/2026
🦠🛠️ Join the **microGalaxy Tool Development Hackathon** on October 14! Help update highly used metagenomics tools in Galaxy’s IUC repository and contribute alongside the microGalaxy community. 🌐 Online + free to participate 🔗 galaxyproject.org/news/2026-09... #usegalaxy #microGalaxy #Metagenomics
galaxyproject.org
microGalaxy Hackathon for Tool Development
Join the microGalaxy community on October 14th to update outdated metagenomics tools in the IUC repository!
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Reposted by Hans-Rudolf Hotz
#SingleCell preprints @prepub-singlecell.bsky.social · 21/09/2026
Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…
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Rob Patro @robp.bsky.social · 21/09/2026
It's here! new preprint: Gravlax, an annotation-independent molecular evidence archive for scRNA-seq. A count matrix freezes one annotation. Molecules never change. Instead, gravlax keeps the evidence. Requantify, query, and discover under any annotation. 🧵 www.biorxiv.org/content/10.6...
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Joel Lüthi @joelluethi.bsky.social · 21/09/2026
I'm happy to announce the fall 2026 Open Bioimaging Practices Meetup schedule. We'll have 3 exciting meetings about developments in the OME-Zarr space: - OME-Zarr viewers - Multiplexed Image analysis in OME-Zarr - Spatial OMICs in OME-Zarr See www.biovisioncenter.uzh.ch/en/events/Op... (🧵 1/10)
biovisioncenter.uzh.ch
Open Bioimaging Practices Meetups
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Bioinformatics Advances @bioinfoadv.bsky.social · 18/09/2026
We lost a giant of our field this March and we are happy to be able to share this tribute: "Phil Bourne (1953–2026): From small molecules to big data—the journey of a multifaceted visionary".  Read the tribute here: doi.org/10.1093/bioadv/vbag239
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Galaxy Project @galaxyproject.bsky.social · 17/09/2026
The Image Analysis in Galaxy community is happy to share the first publication on bioimage data analysis, management and community practices in Galaxy galaxyproject.org/news/2026-09-16-b… #UseGalaxy #GalaxyProject #EOSC
Galaxy single-cell and spatial omics graphical abstract
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Reposted by Hans-Rudolf Hotz
BF Francis Ouellette @bffo.bsky.social · 17/09/2026
From Thomas Sharpton (at @oregonstate.edu ) in @plos.org #Computational #Biology | A practical risk framework for large language model use in life science research | #Bioinformatics #Education #LLM #PromptDesign #Framework #Research #LifeSciences | 🧬 🖥️ 🧪 🔓 ⬇️ journals.plos.org/ploscompbiol...
journals.plos.org
A practical risk framework for large language model use in life science research
Responsible use of large language models (LLMs) in life science research demands a unified approach to risk, yet existing guidance treats prompting and verification as separate topics rather than as i...
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Reposted by Hans-Rudolf Hotz
Galaxy Project @galaxyproject.bsky.social · 17/09/2026
📣 Introduction to the Data Analysis Platform Galaxy (in German) 📍 Freiburg, Germany 📅 2 December 2026 🔗 More info & registration: galaxyproject.org/events/2026-12-02… #UseGalaxy #GalaxyProject #EOSC #EuroScienceGateway
galaxyproject.org
Introduction to the Data Analysis Platform Galaxy (in German)
Galaxy Community Hub
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Paul Gardner @ppgardne.bsky.social · 18/09/2026
How not to build a lncRNA annotation tool: 1. assume the genome & transcriptome consists of only lncRNAs and mRNAs:
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Reposted by Hans-Rudolf Hotz
Paul Gardner @ppgardne.bsky.social · 18/09/2026
You can read more about why these approaches universally perform terribly here: rnajournal.cshlp.org/content/31/9...
rnajournal.cshlp.org
Evaluating computational tools for protein-coding sequence detection: Are they up to the task?
A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms
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Hans-Rudolf Hotz @hrhotz.bsky.social · 17/09/2026
by @bebatut.bsky.social on @galaxyproject.bsky.social
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BF Francis Ouellette @bffo.bsky.social · 17/09/2026
From the @bioinfoadv.bsky.social journal | Phil Bourne (1953–2026): from small molecules to big data—the journey of a multifaceted visionary | #Bioinformatics #Pioneer @rcsbpdb.bsky.social @iscb.bsky.social #PLOSCBTSR #OpenScience #OpenAccess #DataScience |🧬🖥️🧪🔓❤️ ⬇️ academic.oup.com/bioinformati...
academic.oup.com
Phil Bourne (1953–2026): from small molecules to big data—the journey of a multifaceted visionary
Abstract. Born in London in 1953 and raised in Australia, Phil Bourne spent over four decades in science moving across scales: from crystal structures to t
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Scott C Edmunds @scedmunds.bsky.social · 16/09/2026
Just realised its #PeerReviewWeek, so I thought I'd re-share my piece from last year on why we need a FAIR Principles for Peer Review doi.org/10.59350/dpr...
FAIR principles of peer review infographic
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BF Francis Ouellette @bffo.bsky.social · 16/09/2026
From @plos.org #Computational #Biology | Ten quick tips for spatial transcriptomics analysis | #Bioinformatics #Education #PLOSCBQT #Histology #Genomics #Transcriptomics #OpenScience | 🧬🖥️🧪🔓 ⬇️ journals.plos.org/ploscompbiol...
journals.plos.org
Ten quick tips for spatial transcriptomics analysis
Author summary Spatial transcriptomics (ST) lets researchers measure gene expression while preserving the tissue location of each measurement. Where a cell sits, and which cells surround it, shape how...
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Hans-Rudolf Hotz @hrhotz.bsky.social · 16/09/2026
we have an opening in our group at @fmiscience.bsky.social - contact @mbstadler.bsky.social or me to get more details: www.fmi.ch/education-ca...
fmi.ch
Friedrich Miescher Institute, open position
Friedrich Miescher Institute, open position
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Jalview @jalview.bsky.social · 15/09/2026
👓 Visualising sequence alignments in 3D? Jalview enables multiple structures to be visualised with Chimera, ChimeraX, PyMOL and Jmol — helping scientists and educators bring biology to life. 📺 Explore the editor's functionality: www.youtube.com/watch?v=pbms... www.youtube.com/watch?v=yRBL...
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FMI science @fmiscience.bsky.social · 15/09/2026
Now in @natneuro.nature.com: work from @rainerfriedrichlab.bsky.social shows that, in zebrafish, learning to tell smells apart reshapes activity across groups of neurons, making key odors easier to distinguish and offering clues to how the brain may organize memories. www.fmi.ch/news-events/...
fmi.ch
Learning reshapes the brain’s map of smell
The brain is constantly taking in sights, sounds and smells, and learning helps it decide which ones matter. Working in zebrafish, FMI neuroscientists have found that learning to tell smells apart cha...
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