Lightnews — Scholar-powered news

Florian Huber @me-datapoint.bsky.social · 11h

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.

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Florian Huber @me-datapoint.bsky.social · 2d

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

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

#opensource #RSE #researchsoftwareengineering

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

github.com

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Florian Huber @me-datapoint.bsky.social · 2d

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

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Reposted by Florian Huber

Justin J.J. van der Hooft @jjjvanderhooft.bsky.social · Aug 18

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

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Reposted by Florian Huber

Greg Landrum @greglandrum.bsky.social · Jul 17

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

Please stop saying “The Tanimoto similarity is” – RDKit blog

A simple tip to explain what you actually did

greglandrum.github.io

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Florian Huber @me-datapoint.bsky.social · Jul 17

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...

www.biorxiv.org

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Reposted by Florian Huber

Bob E Hayes @bobehayes.bsky.social · Jul 10

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....

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.

garymarcus.substack.com

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Reposted by Florian Huber

Pr Carlos Moreno - IAE Paris1 Sorbonne University @carlosmorenofr.bsky.social · Jul 12

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...

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

momentummag.com

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Florian Huber @me-datapoint.bsky.social · Jul 3

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

(und leider nicht nur hier)

Annika Joeres @annikajoeres.bsky.social · Jul 3

Paris setzt auf grüne Dächer, weniger Parkplätze und Stadtwälder – und verzeichnet dort während Hitzewellen deutlich kühlere Temperaturen.
Stadtchefin Anne Hidalogo rettet Leben, weil sie die Klimakrise ernst nimmt.
Ist so.
www.derstandard.at/story/300000...

Paris kühlt sich während der Hitzewelle dank der Begrünung ab

Die Vegetalisierung von Paris durch Bürgermeisterin Anne Hidalgo vermag die Temperaturen deutlich zu senken, wie sich vor allem während der sommerlichen Hitze zeigt

www.derstandard.at

Reposted by Florian Huber

Alexandria Ocasio-Cortez @aoc.bsky.social · Jul 3

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.

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Reposted by Florian Huber

D64 @d-64.org · Jul 1

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...

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.

d-64.org

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Reposted by Florian Huber

Natural Product Reports @natprodreports.rsc.org · Jun 26

🔓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🔽

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…

pubs.rsc.org

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Florian Huber @me-datapoint.bsky.social · Jun 26

@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🙏)

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Reposted by Florian Huber

Johannes Rainer @jorainer.bsky.social · Jun 23

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

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Reposted by Florian Huber

Steffen Neumann @sneumann.bsky.social · Jun 25

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...

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Florian Huber @me-datapoint.bsky.social · Jun 25

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 :)

Slide from presentation of Steffen Neumann

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Reposted by Florian Huber

Justin J.J. van der Hooft @jjjvanderhooft.bsky.social · Jun 23

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

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Florian Huber @me-datapoint.bsky.social · Jun 23

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...

Chemical Space Visualizations using UMAP and various molecular fingerprints.

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Florian Huber @me-datapoint.bsky.social · Jun 23

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

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Florian Huber @me-datapoint.bsky.social · Jun 23

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

Benchmarking plot on fingerprint duplications.

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Florian Huber @me-datapoint.bsky.social · Jun 23

New preprint out!
1/4

@julianpollmann.bsky.social and I went down several rabbit holes to assess some commonly used molecular fingerprints.

Bottom line: For large datasets, make an effort to select suitable settings. "We used Tanimoto" is not good enough.

--> www.biorxiv.org/content/10.1...

Sketch of count/binary fingerprints and weighing options.

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Florian Huber @me-datapoint.bsky.social · Jun 23

Good start for me at #metabolomics2025 with a hands-on workshop on MS2LDA by Jonas Dietrich, Rosina Torres Ortega and @jjjvanderhooft.bsky.social.

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Florian Huber @me-datapoint.bsky.social · Jun 22

Went by train to #Prague for #metabolomics2025.

These are the kind of moments that remind me how great the European project is. No border controls, no visas. Just a train following a river to the neighboring country.

Elbe river seen from a train somewhere after Dresden.

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Reposted by Florian Huber

Gary Marcus @garymarcus.bsky.social · Jun 22

Orwell’s 1984, but with LLMs

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Florian Huber @me-datapoint.bsky.social · Jun 17

Hier alle Ergebnisse: fahrradklima-test.adfc.de/ergebnisse

(Besonders von Ruhrpott bis Köln ist es leider ziemlich traurig)

Ergebnisse

fahrradklima-test.adfc.de