Lightnews — Scholar-powered news

Reposted by Johannes Rainer

Wolfgang Huber @wkhuber.bsky.social · 1d

My take: Engineering *is* important. Ideas are cheap. Novelty is overrated. "Hyperparameter tuning" is a cynically dismissive term for something that is in fact the real, difficult problem.

Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 1d

Sometimes I’ll see a paper that implements an idea I’ve had but implements it poorly for engineering reasons. But then it’s hard to write a follow up paper because it’s not “novel” anymore

1 6 28

Reposted by Johannes Rainer

Bioconductor @bioconductor.bsky.social · 13h

🚀 New on the Bioconductor Blog: GPU Support in Bioconductor

Bioconductor is building better support for GPU-accelerated package development for faster and more scalable analysis workflows
Learn how package maintainers can leverage this new GPU infrastructure: blog.bioconductor.org/posts/2025-1...

GPU Support in Bioconductor – Bioconductor community blog

Support GPU-accelerated Bioconductor packages

blog.bioconductor.org

5 7

Reposted by Johannes Rainer

HUMAN Doctoral Network @human-dn.bsky.social · 12h

New #HUMAN paper out! 🩸

Our partners from CEMBIO explored blood microsampling (DBS, qDBS, VAMS) for untargeted #lipidomics using high-throughput LC-MS.

Volumetric devices show plasma-like precision & recovery!

🔗bit.ly/476qWXw

1 1

Reposted by Johannes Rainer

Florian Huber @me-datapoint.bsky.social · 4d

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

1 2 4

Johannes Rainer @jorainer.bsky.social · 4d

Reminder 👇

Interested in improving our R tools for #MassSpectrometry data analysis and integrating them into Galaxy?

⏲️ 3 year position
📍 Bolzano, 🇮🇹

👉 apply if you like:

- #rstats SW development
- @bioconductor.bsky.social
- large-scale #metabolomics data analysis
- hiking ⛰️

🔗 bit.ly/46AMawx

1 6 7

Reposted by Johannes Rainer

Robert Castelo @robertclab.bsky.social · 21d

#EuroBioC2025 is over and it has been a blast! Thanks to all participants that came to @prbb.org for contributing to make such an enjoyable event and special thanks to the support from our sponsors, the organizing institutions @upf.edu @isglobal.org and the European @bioconductor.bsky.social Society

Group picture with all participants at EuroBioC2025

Vince Carey, Bioconductor project lead, giving the opening keynote lecture.

Audience carefully listening to Vince Carey in the Auditorium.

Christophe Vanderaa giving a workshop on msqrob2, a robust modelling workflow for mass spectrometry-based proteomics

3 10 26

Johannes Rainer @jorainer.bsky.social · 20d

Thanks Robert and the rest for the organizing committee for this great, and really well organized, conference!

3

Reposted by Johannes Rainer

Bioconductor @bioconductor.bsky.social · 22d

EuroBioC2025 is in full swing here in Barcelona!

Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!

#EuroBioC2025 #Bioconductor #OpenScience #Community

EuroBioC2025 group photo on PRBB terrace with sea in background.

EuroBioC2025 welcome in PRBB auditorium by host Robert Castelo, showing slides with conference sticker and sponsor logos.

EuroBioC2025 hexwall banner with the hexwall creator Kevin Rue-Albrecht standing beside it.

EuroBioC2025 carved wooden keyring, a gift for all participants, created by Annekathrin Nedwed.

7 19

Johannes Rainer @jorainer.bsky.social · 23d

and a preprint with some more info on the #Spectra infrastructure and #SpectriPy : doi.org/10.31219/osf...

OSF

doi.org

1 1

Johannes Rainer @jorainer.bsky.social · 23d

Was really fun to present our #SpectriPy @bioconductor.bsky.social package for combined #rstats & #Python analysis of #MassSpectrometry data today at #EuroBioC2025

also available on Zenodo: doi.org/10.5281/zeno...

SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python

Mass spectrometry (MS) is a key technology used across multiple fields, including biomedical research and life sciences. Technological advancements result in increasingly large and complex data sets a...

doi.org

1 2 14

Johannes Rainer @jorainer.bsky.social · 23d

thanks Wolfgang 😊

1

Reposted by Johannes Rainer

Wolfgang Huber @wkhuber.bsky.social · 23d

Dream job - research software engineer, in one of the most beautiful parts of the world

1 7 19

Johannes Rainer @jorainer.bsky.social · 23d

@philouail.bsky.social presenting the #Metabonaut tutorials for #metabolomics data analysis at #EuroBioC2025 @bioconductor.bsky.social conference.

@human-dn.bsky.social #MassSpectrometry #ProudPI

2 5

Johannes Rainer @jorainer.bsky.social · 23d

Collaborative project with @sneumann.bsky.social , funded by @dfg.de and the Autonomous Province of Bolzano/Bozen South Tyrol

Johannes Rainer @jorainer.bsky.social · 23d

Interested in integrating our R tools into Galaxy?

👉 apply if you like:

- #rstats SW development
- contributing to @bioconductor.bsky.social and @galaxyproject.bsky.social
- large-scale #metabolomics data analysis
- hiking ⛰️

📍 Bolzano, 🇮🇹
⏲️ 3 year position

🔗 info and apply: bit.ly/46AMawx

1 5 11

Johannes Rainer @jorainer.bsky.social · Aug 18

Reminder 📣

still time to apply to the position in my team!

- statistical modeling
- large scale #metabolomics and #proteomics data
- #rstats , #python

📍 Bolzano, ⛰️, 🇮🇹

🔗https://eurac.onboard.org/jobs/Q4301nGV

6 11

Reposted by Johannes Rainer

Bioconductor @bioconductor.bsky.social · Jul 17

🌟 Bioconductor 2025 CAB & TAB nominations are open!

Join our advisory boards to support community growth or guide technical strategy.

📅 Apply by Aug 31
CAB: forms.gle/8NYxRGhprfuN...
TAB: forms.gle/eqef9ThpUypc...

#Bioconductor #RStats

Bioconductor nominations graphic with CAB and TAB illustrations and www.bioconductor.org

13 13

Johannes Rainer @jorainer.bsky.social · Jul 15

Interested in a #PostDoc / researcher position in my team at Eurac Research 🇮🇹?

👉 apply if you like

- analyzing large-scale #proteomics and #metabolomics data
- #rstats and/or #Python
- reproducible research
- hiking ⛰️ (on weekends!)

🔗 eurac.onboard.org/jobs/Q4301nGV

Post-Doc Researcher for the evaluation of external influences on blood proteomics and metabolomics data

Eurac Research · Bozen/Bolzano

eurac.onboard.org

7 9

Johannes Rainer @jorainer.bsky.social · Jun 26

Have added the slides to Zenodo: doi.org/10.5281/zeno...

RforMassSpectrometry: A Community-Driven Ecosystem for Reproducible and Scalable Mass Spectrometry Data Analysis in R

A common problem with scientific research software is the lack of support, maintenance and further development. In particular, development by a single researcher can easily result in orphaned and dysf...

doi.org

2

Johannes Rainer @jorainer.bsky.social · Jun 26

Added: doi.org/10.5281/zeno... 😊

RforMassSpectrometry: A Community-Driven Ecosystem for Reproducible and Scalable Mass Spectrometry Data Analysis in R

A common problem with scientific research software is the lack of support, maintenance and further development. In particular, development by a single researcher can easily result in orphaned and dysf...

doi.org

1 2

Johannes Rainer @jorainer.bsky.social · Jun 26

Combining #rstats and #Python for #MassSpectrometry data analysis is the way to go!

github.com/rformassspec...

supports (for now) #matchms and #spectrum_utils #Python libraries

GitHub - rformassspectrometry/SpectriPy: Interfacing R's Spectra package with the Python world.

Interfacing R's Spectra package with the Python world. - rformassspectrometry/SpectriPy

github.com

1 3 4

Reposted by Johannes Rainer

Michael Love @mikelove.bsky.social · Jun 26

Tuomas Borman from @antagomir.bsky.social lab demonstrating why data containers are so useful (book >> loose pages)

Online book for microbiome analysis:
microbiome.github.io/OMA/docs/dev...

#GBCC2025

Speaker at podium holding book in one hand and loose pages in another

3 6

Johannes Rainer @jorainer.bsky.social · Jun 26

I did not plan to - but will 😊. I'll post the link here once done

1

Reposted by Johannes Rainer

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🙏)

1 6 11

Johannes Rainer @jorainer.bsky.social · Jun 26

and BIG thanks to all contributors over the years! just tagging the ones I found here on bsky @sneumann.bsky.social @carlbrunius.bsky.social @janstanstrup.bsky.social