Florian Huber

Bayerischer Landtag: Streit um Microsoft eskaliert Das bayerische Finanzministerium will weiterhin Microsoft-Produkte im Freistaat einsetzen und dafür einen millionenschweren Vertrag verlängern. Die Opposition will eine Abkehr vom Tech-Riesen und ford...

Das bayerische Finanzministerium will weiterhin Microsoft-Produkte einsetzen und dafür einen millionenschweren Vertrag verlängern. Die Opposition will eine Abkehr vom Tech-Riesen und fordert „digitale Souveränität“. Doch auch das könnte sich als Bumerang erweisen.

netzpolitik.org/2026/bayeris...

This is an excellent analogy, because my recollection from grade school is that the pen on the right looks fun and exciting, and then you play with it for a few minutes and realize it's not actually useful for anything and in fact makes some tasks more cumbersome, and never think about it again.

Abschied bis Herbst: Dänisches Digitalministerium kehrt Microsoft den Rücken Beim dänischen Digitalministerium sollen alle Angestellten ohne Microsoft auskommen. Stattdessen werde man Linux und LibreOffice nutzen, sagt die Ministerin.

The Danish Ministry of Digital Affairs is moving away from Microsoft and switching instead to Linux and LibreOffice
www.heise.de/news/Von-Wor...

Considering I again did not receive the Nobel Prize for Economics, I no longer feel an obligation to pay back my debts.

Not my core expertise, but nonetheless also my (and most people's) business: Dependency on non-European digital services and infrastructure. Two days ago, the German Federal Ministry of the Inter... Not my core expertise, but nonetheless also my (and most people's) business: Dependency on non-European digital services and infrastructure. Two days ago, the German Federal Ministry of the Interior ...

I sometimes wonder how many more signs we (Europeans) need before we go all-in on European-based digital infrastructure.

Well, here is yet another report telling us why we shouldn't feel too comfortable when fully relying on US-based services:

www.linkedin.com/posts/f-hube...

#DigitalSovereignty

#matchms #ms2query #ms2deepscore | Florian Huber I had an inspiring short trip to Wageningen University & Research at the end of November. First of all, to attend (and then celebrate!) the PhD defense of Niek de Jonge, and second, to join the Mini-S...

I had a fantastic short trip to @w-u-r.bsky.social at the end of November. First, to attend and celebrate the PhD defense of Niek de Jonge and second, to join the Mini-Symposium organized by @jjjvanderhooft.bsky.social !

See more on LinkedIn: www.linkedin.com/posts/f-hube...

xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem High-quality data preprocessing is essential for untargeted metabolomics experiments, where increasing data set scale and complexity demand adaptable, robust, and reproducible software solutions. Modern preprocessing tools must evolve to integrate seamlessly with downstream analysis platforms, ensuring efficient and streamlined workflows. Since its introduction in 2005, the xcms R package has become one of the most widely used tools for LC-MS data preprocessing. Developed through an open-source, community-driven approach, xcms maintains long-term stability while continuously expanding its capabilities and accessibility. We present recent advancements that position xcms as a central component of a modular and interoperable software ecosystem for metabolomics data analysis. Key improvements include enhanced scalability, enabling the processing of large-scale experiments with thousands of samples on standard computing hardware. These developments empower users to build comprehensive, customizable, and reproducible workflows tailored to diverse experimental designs and analytical needs. An expanding collection of tutorials, documentation, and teaching materials further supports both new and experienced users in leveraging broader R and Bioconductor ecosystems. These resources facilitate the integration of statistical modeling, visualization tools, and domain-specific packages, extending the reach and impact of xcms workflows. Together, these enhancements solidify xcms as a cornerstone of modern metabolomics research.

Out now! xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem doi.org/10.1021/acs....
with Phillipine and @jorainer.bsky.social (EURAC), @metabomichael.bsky.social, Hendrik and Norman from @ipbhalle.bsky.social, @janstanstrup.bsky.social, et al.

Digi-Health Heroes - die Zukunft digitaler Gesundheit | Zentrum für Digitalisierung und Digitalität (ZDD) Die ZZDenkanstöße gehen in die nächste Runde! Ab jetzt laden wir wieder wöchtenlich dazu ein, vor Ort oder online, unsere Forschenden und Projekte am ZDD kennenzulernen und über Themen der Digitalen T...

Relaunch unserer Vortragsreihe "ZDDenkanstöße". Zum Start mit Sabrina Großkopp --> www.linkedin.com/posts/zdd-du...

Über die nächsten Wochen folgen weitere Vorträge: zdd-duesseldorf.de

Kommt gerne vorbei!

Super useful new feature! I've started to recommend plotnine to everybody who does data analysis in python and needs a plotting solution, so this is very welcome.

We still can’t predict much of anything in biology Biology is hard. Yes, even for AI.

Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...

Impressive milestone by @europarl.europa.eu to ban "veggie-burger" and other great dangers to humanity. 100 millions of confused meat-eaters can now finally navigate the menus again.

GitHub - matchms/matchms: Python library for processing (tandem) mass spectrometry data and for computing spectral similarities. Python library for processing (tandem) mass spectrometry data and for computing spectral similarities. - matchms/matchms

Special thanks to @julianpollmann.bsky.social and Niek de Jonge for code and code reviews!

GitHub: github.com/matchms/matc...

#opensource #RSE #researchsoftwareengineering

New #matchms release (0.31)🚀

With functionalities that were on our TODO list for a looooong time: Flash Entropy and BLINK scores! The new "FlashSimilarity" allows computing modified cosine, spectral entropy etc., about 100x faster (or more if you use Linux).

#Python #opensource #massspec

Ready for the 4th International Summer 🌞 School on Non-Target Metabolomics at DTU - Technical University of Denmark #Copenhagen organized by Martin Hansen & Scott Jarmusch with a team of local and international helpers and instructors 😎
Thanks Lone Gram for opening the school 🙌
#CompMetabolomics

Today's #RDKit blog post is a heartfelt plea for clearer communication.
greglandrum.github.io/rdkit-blog/p...

Great post!

We also noted the same thing, which triggered us to point out some pitfalls of various fingerprints --> www.biorxiv.org/content/10.1...

BREAKING NEWS: AI coding may not be helping as much as you think Coding has been the strongest use case. But a new study from METR just dropped.

BREAKING NEWS: #AI coding may not be helping as much as you think

"But for now, the disconnnect between what coders thought they would get out of the tools efficiency-wise and what they actually did get out of them is cause for reevaluation." ~ @garymarcus.bsky.social

garymarcus.substack....

Paris cycling numbers double in one year thanks to massive investment and it's not stopping The report delves into the nuances of Parisian cycling culture, exploring the vibrant community of riders who navigate the city's streets

Paris cycling numbers double in one year thanks to massive investment and it’s not stopping.
A visionary urban policy lead by @annehidalgo.bsky.social 💫🫶🏻🙏🏻
momentummag.com/paris-cyclin...

Hier in @duesseldorf.bsky.social wird vorerst lieber noch jeder Parkplatz verteidigt...

(und leider nicht nur hier)

I don’t think anyone is prepared for what they just did w/ ICE.

This is not a simple budget increase. It is an explosion - making ICE bigger than the FBI, US Bureau of Prisons, DEA,& others combined.

It is setting up to make what’s happening now look like child’s play. And people are disappearing.

Verwaltung der Digitalisierung gestalten: Neue Arbeitsgruppe startet! | D64 – Zentrum für digitalen Fortschritt Wir gründen am 17. Juli 2025 eine neue Arbeitsgruppe zur Verwaltungsdigitalisierung. Hier bringen wir digitale Kompetenz und politische Gestaltung zusammen.

Hey Verwaltungs-Digitalisierer:innen! Am 17. Juli starten wir eine neue AG zur Verwaltungsdigitalisierung. Eure Expertise aus dem öffentlichen Dienst ist gefragt! Gemeinsam gestalten wir die Zukunft der öffentlichen, digitalen Verwaltung 💪

d-64.org/veranstaltun...

Effective data visualization strategies in untargeted metabolomics Covering: 2014 to 2023 for metabolomics, 2002 to 2023 for information visualization LC-MS/MS-based untargeted metabolomics is a rapidly developing research field spawning increasing numbers of…

🔓Read in our MS Metabolomics themed collection, a #OpenAccess review from Kevin Mildau, Henry Ehlers, @jjjvanderhooft.bsky.social et al. at @w-u-r.bsky.social‬ @tuwien.at‬ covering effective data visualization strategies in untargeted metabolomics #natprod

Find it here🔽

@jorainer.bsky.social and @philouail.bsky.social gave a great overview of the ecosystem around #RforMassSpectrometry and #XCMS!

#MetSoc25
I am super glad they now also provide options to combine with #Python and #matchms (thanks🙏)

📢 Poster 1001 at #MetSoc2025: Marilyn De Graeve on our #SpectriPy #rstats package to integrate #python and #rstats packages for #MassSpec data analysis . TODAY

Hi, in case your phone didn't pick up the QR code to the slides of my Hitch-Hikers Guide to Computational Metabolomics talk this morning at #Metabolomics2025, featuring #xcms, #massbank, not #metfrag but #CASMI and #MetFamily, please find them at doi.org/10.5281/zeno...

Slide from presentation of Steffen Neumann

Great keynote by @sneumann.bsky.social at #MetSoc25, strongly advocating for #opensource , data-sharing, and making things interoperable.

Glad to also spot #matchms in this universe :)

Proud of Niek de Jonge who did a fantastic job in presenting his work on cross-ion mode spectral similarity scoring! 😎 👏
Work with Florian Huber @me-datapoint.bsky.social

#metabolomics #CompMetabolomics #MetSoc25 #MS2DeepScore

Chemical Space Visualizations using UMAP and various molecular fingerprints.

4/4
We also highlight options for count fingerprints, such as log-counts and IDF weighted counts. The latter can be used to adjust the bit importance to a dataset of your choice.

An example use-case are chemical space visualizations.

Preprint: www.biorxiv.org/content/10.1...

3/4
A huge issue is bit collisions.
Fingerprints with a high bit occupation (RDKit, MAP4) often lead to (1) arbitrary misinterpretations, (2) shifts to high Tanimoto scores, (3) very different handling of small and large molecules.

--> Consider using sparse fingerprints!
--> Morgan >> MAP4 / RDKit

Benchmarking plot on fingerprint duplications.

2/4
We focused on weaknesses of the fingerprints.
Many show frequent duplicates, so same fingerprint for different compounds. Most problematic: this can include *very* different compounds ending up with identical fingerprints.

- MAP4 >> Morgan-type >> daylight
- count >> binary

#cheminformatics