Johannes Rainer @jorainer.bsky.social · 06/10/2026please open issues at the GitHub repo in case something is not working as expected - or you want to contribute 😊 010
Johannes Rainer @jorainer.bsky.social · 05/10/2026The up-and-coming default infrastructure for chromatographic mass spectrometry data in @bioconductor.bsky.social / #rstats 💪 great work @philouail.bsky.social ! 020
Reposted by Johannes RainerPhili @philouail.bsky.social · 05/10/2026Chromatograms 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 #MassSpecdoi.orgChromatograms: A Modular Infrastructure for Scalable Chromatographic Data Handling in RAbstract. Chromatographic traces are central to LC-MS analysis, yet most software treats them as transient intermediates inside a fixed pipeline rather tha 052
Johannes Rainer @jorainer.bsky.social · 05/10/2026big thanks to: Marilyn De Graeve, Alexandru Mahmoud, Daniel Marques de Sá e Silva, @kozo2.bsky.social , Vilhelm Suksi, Anna Tagliaferri, Gabriele Tomè, Vinicius Verri Hernandes and the whole #RforMassSpectrometry community! ... and 🇪🇺 @human-dn.bsky.social for funding! 010
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.lyExploring and Analyzing LC-MS DataThis resource hosts tutorials and end-to-end workflows describing how to analyze LC-MS/MS data, from raw files to annotation, using Bioconductor packages. 144
Reposted by Johannes RainerBioconductor @bioconductor.bsky.social · 06/08/2026🎉 Introducing the Bioconductor Student-ECR Council! The Council will support students and ECRs with mentorship, networking, professional development & opportunities to contribute to Bioconductor. Learn more: bit.ly/4giOlJ1 Interested in joining? Connect on Zulip: bit.ly/4yYVxT0 054
Johannes Rainer @jorainer.bsky.social · 06/08/2026Our RmzTabM package is now included in @bioconductor.bsky.social (devel version)! ℹ️ core #rstats API for the HUPO-PSI mzTab-M 2.1 standard for reporting #metabolomics and #lipidomics results. 🙏 Gabriele Tomè, @philouail.bsky.social + mzTab-M working group! 🔗https://bit.ly/3RLHIGN 050
Johannes Rainer @jorainer.bsky.social · 06/06/2026For those not at @bioconductor.bsky.social #EuroBioc2026 : our workflow for 🔀 interactive and reproducible combined #rstats + 🐍 #Python #MassSpectrometry data analysis is available here: jorainer.github.io/SpectriPyWor...jorainer.github.ioCriss-crossing R and Python for Powerful MS Data Analysis WorkflowsThis workshop explains how R and Python can be combined in a single interactive workflow through the SpectriPy package. The SpectriPy package takes care of translating the MS data structures from the ... 0144
Johannes Rainer @jorainer.bsky.social · 06/06/2026... and I forgot: also great local food and drinks 😋 010
Johannes Rainer @jorainer.bsky.social · 06/06/2026well done Tuomas! was a very welcoming and entertaining conference! ❤️🇫🇮 110
Reposted by Johannes RainerBioconductor @bioconductor.bsky.social · 05/06/2026What an amazing few days in Turku at #EuroBioC2026! 🇫🇮 This year's conference brought together 147 participants from 23 countries, showcasing the diversity of the Bioconductor community. A huge thank you to everyone who made EuroBioC2026 memorable. See you in Basel for EuroBioC2027! 0154
Johannes Rainer @jorainer.bsky.social · 25/05/2026and already the first group activity 😊 - 5 minutes into the lecture 020
Johannes Rainer @jorainer.bsky.social · 25/05/2026Vince Carey kicking off the 22nd edition of the #CSAMA @bioconductor.bsky.social summer school in Brixen 🇮🇹 #CSAMA2026 183
Johannes Rainer @jorainer.bsky.social · 20/05/2026Today @philouail.bsky.social received the Open Research Award from Eurac Research for her contributions to open and collaborative #metabolomics . Very well deserved! 💪🥳 #proudPI 092
Reposted by Johannes Rainerde.NBI & ELIXIR Germany @denbi.bsky.social · 08/05/2026🚀 Registration is OPEN for the de.NBI Summer School 2026 - Bioinformatics for Proteomics! 🧬 🙌 Fully Supported: There are no fees for the event and we will provide accommodation and local travel tickets for the selected candidates 📅 7-11 September 📍 Bochum, Germany 🔗 www.denbi.de/training-cou... 021
Johannes Rainer @jorainer.bsky.social · 18/04/2026framework is just great! I have this one since 4-5 years now. changed/upgraded the mainboard once and now the lid. if anything is broken, simply repair it. have them also for my family, so I could reuse my old mainboard in my son's framwork 😊 100
Johannes Rainer @jorainer.bsky.social · 18/04/2026bought a new lid for my @frame.work notebook - now I have to start over again adding #stickers 😊 - and to decide what to do with the old one (on top). 451
Reposted by Johannes RainerJulien Roux @julienroux.bsky.social · 12/02/2026We have a 3-years position open in our facility. Come join us to do great science in a nice team! jobs.unibas.ch/offene-stell...jobs.unibas.chUniversität Basel: Bioinformatician (100%)The Department of Biomedicine (DBM) is a joint effort between the University of Basel and the University Hospitals Basel. It unites basic and clinical scientists to advance our understanding of health... 087
Reposted by Johannes RainerBioconductor @bioconductor.bsky.social · 12/02/2026🎉 Speaker Reveal – EuroBioC 2026 We’re excited to announce Dr Aura Raulo as a keynote speaker at EuroBioC2026! 🚨Have work to share? Abstract submission is open! Submit here: openreview.net/group?id=bio... Learn more about EuroBioC2026 here: eurobioc2026.bioconductor.org #EuroBioC2026 063
Reposted by Johannes RainerDavide Risso @davi1893.bsky.social · 06/02/2026Registration is now open! See: csama2026.bioconductor.eu/registration...csama2026.bioconductor.euCSAMA 2026 Biological Data Science 023
Reposted by Johannes RainerBioconductor @bioconductor.bsky.social · 05/02/2026🔔 The Bioconductor Developers’ Forum is back! This monthly forum is for developers & users to discuss infrastructure, future tools, and community-driven changes. 🗓 When: Last Thursday of every month ⏰ Time: 4pm GMT First session: Feb 26, 2026 More info: bioconductor.org/developers/d... 063
Reposted by Johannes RainerHelena Lucia Crowell @helucro.bsky.social · 02/02/2026Registration now open for CSAMA! 📜 csama2026.bioconductor.eu Highly recommend for learning data science with a scenery, plus a fantastic crowd of students and faculty alike! 📸 from the traditional mid-week hike during last year’s edition. 065
Johannes Rainer @jorainer.bsky.social · 07/01/2026let's get the community rolling 💪! Thanks to Vilhelm Suksi from @antagomir.bsky.social 's group for the contribution of the notame vignette 🙌 043
Reposted by Johannes RainerPhili @philouail.bsky.social · 07/01/2026🚀 New release: Metabonaut v1.4.0 is here! 1️⃣ New integration with the notame package for robust feature selection. 2️⃣ Added GNPS2 FBMN export for molecular networking. Explore the updates: rformassspectrometry.github.io/Metabonaut/ #Metabolomics #RStats #OpenScience #MassSpec #Bioconductorrformassspectrometry.github.ioExploring and Analyzing LC-MS DataThis resource hosts tutorials and end-to-end workflows describing how to analyze LC-MS/MS data, from raw files to annotation, using Bioconductor packages. 0104
Reposted by Johannes RainerTuomas Borman @tuomasborman.bsky.social · 23/12/2025Little over a month left to submit an abstract to #EuroBioC2026 (eurobioc2026.bioconductor.org/pages/submis...), which will be held in Turku, Finland. Here are a couple of Finnish Christmas traditions that you might not know: 334
Reposted by Johannes RainerDavide Risso @davi1893.bsky.social · 23/12/2025This year's CSAMA Biological Data Science Summer School in Brixen takes place 24-29 May 2026. Topics: single-cell and spatial omics, statistics, multi-omics, ML/AI, all very hands-on using R / Bioconductor! More info: csama2026.bioconductor.eu Registration: 1 Feb 2026! @bioconductor.bsky.socialcsama2026.bioconductor.euCSAMA 2026 Biological Data Science – CSAMA 2026 Biological Data Science22nd Edition Bressanone-Brixen, Italy 24-29 May 2026 143
Johannes Rainer @jorainer.bsky.social · 18/12/2025and there will also be lectures and workshops for #MassSpectrometry - based #proteomics and #metabolomics analysis in #rstats with @bioconductor.bsky.social 😎 0113
Reposted by Johannes RainerWolfgang Huber @wkhuber.bsky.social · 17/12/2025CSAMA 2026 - Biological Data Science Summer School Bressanone-Brixen, South Tyrol / Italy 24-29 May 2026 csama2026.bioconductor.eu Statistical & computational methods for single cell and spatial omics, with lectures and hands-on exercises in R/Bioconductor. 02212
Johannes Rainer @jorainer.bsky.social · 16/12/2025aaaah, it's Matthijs Vynck (with a y not i as in the original post) - sorry for that 🫣🙏 010
Johannes Rainer @jorainer.bsky.social · 16/12/2025my workshop is available here: jorainer.github.io/xcms4gnps2/ - with contribution from @philouail.bsky.socialjorainer.github.ioxcms-based data preprocessing for FBMN with GNPS2xcms *for* GNPS2 provides an example workflow for preprocessing and preparation of an LC-MS/MS data set for feature-based molecular networking (FBMN) with GNPS2 on the example of a publicly available ... 143
Johannes Rainer @jorainer.bsky.social · 16/12/2025was a great #computational #metabolomics seminar yesterday in Ghent with @jjjvanderhooft.bsky.social Matthijs Vinck and myself! thanks @lynnvanhaecke.bsky.social for inviting us 🙏 261
Johannes Rainer @jorainer.bsky.social · 12/12/2025Thanks Gary! Also, we have to thank you for keeping #xcms open-source and for adding it to @bioconductor.bsky.social back in 2006 🙌 130
Reposted by Johannes RainerStefano Mangiola @stemang.bsky.social · 07/12/2025It's official! The #tidyomics blog is up! 🚀 Here, the introductory post tidyomics.github.io/tidyomicsBlo... This blog aims to publish not only news about our community but also anything related to tidy interfaces, opinions, events, and more. Plz share! 🙏 @bioconductor.bsky.social #rstatstidyomics.github.ioThe Tidyomics Ecosystem – tidyomicsBlogAn introduction to the tidyomics ecosystem, including principles, core packages, publications, and community resources for tidy omic analysis. 02713
Johannes Rainer @jorainer.bsky.social · 09/12/2025and of course also big thanks to @metabomichael.bsky.social and @human-dn.bsky.social ☺️ 030
Johannes Rainer @jorainer.bsky.social · 09/12/2025Great work from @philouail.bsky.social 🙌 #xcms now fully integrated into @bioconductor.bsky.social 💪 👉 #metabolomics #MassSpectrometry #rstats 2136
Johannes Rainer @jorainer.bsky.social · 03/12/2025was a bit too fast - DOI not yet available. preprint link in @medrxivpreprint.bsky.social is www.medrxiv.org/content/10.6...medrxiv.orgMolecular characterization of liver steatosis through circulating proteins, metabolites and lipidsBackground: Metabolic dysfunction-associated steatotic liver disease (MASLD) is among the most prevalent liver disorders in Western countries. While steatosis is prevalent, molecular mechanisms associ... 100
Johannes Rainer @jorainer.bsky.social · 03/12/2025New preprint 📃: doi.org/10.64898/202... 👉 characterization of liver steatosis through blood #metabolomics and #proteomics Great work from Marilyn! and big thanks to all co-authors 🙌doi.org 141
Reposted by Johannes RainerWolfgang Huber @wkhuber.bsky.social · 01/12/2025Join EMBL's Interdisciplinary Postdoc Programme! 3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states. In particular: AI&Theory, use mathem. models, physics principles and AI www.embl.org/about/info/p...embl.orgEIPOD-LinC Fellowship Programme – Postdoctoral Programme 22021
Reposted by Johannes RainerTuomas Borman @tuomasborman.bsky.social · 25/11/2025Representing EuroBioC2026 at the @abacbs.bsky.social Conference this week. The next European @bioconductor.bsky.social Conference will be in Turku, Finland! #ABACBS2025 #EuroBioC2026 0158
Reposted by Johannes RainerBioconductor @bioconductor.bsky.social · 27/11/2025🚀 EuroBioC2026 – Call for Abstracts is Now Open! We invite submissions for short talks, posters, and workshops for EuroBioC2026 by Jan 30, 2026. 👉 Submit here: openreview.net/group?id=bio... ⚠️ Note: Register on OpenReview at least two weeks before the abstract deadline to be able to submit. 065
Reposted by Johannes RainerStefano Mangiola @stemang.bsky.social · 27/11/2025The Euro Bioc 2026 in Turku is official! 1115
Johannes Rainer @jorainer.bsky.social · 17/11/2025📣 join in my team 🤗! 👇 - #rstats software development - contribute to @bioconductor.bsky.social and @galaxyproject.bsky.social - large-scale #MassSpectrometry #metabolomics and #proteomics data analysis - hiking ⛰️ 📍 Bolzano, 🇮🇹 ⏲️ 3 year position 🔗 full description: bit.ly/4pyXi3V please sharebit.lyResearcher in Software Development for Large-Scale Mass Spectrometry Data Analysis (MetaRbolomics4Galaxy)Eurac Research · Bozen/Bolzano 086
Johannes Rainer @jorainer.bsky.social · 07/11/2025yey! also spotted hackathon co-lead @philouail.bsky.social - I was only virtually attending 😔 - and very likely missed a lot of fun 031
Johannes Rainer @jorainer.bsky.social · 31/10/2025Happy to announce that also our #SpectriPy package for cross-language #Rstats - #Python #MassSpectrometry data analysis is part of the just released @bioconductor.bsky.social release 3.22 🥳 This was a great collaborative effort! Thanks to all contributors! 💪 040
Reposted by Johannes RainerBioconductor @bioconductor.bsky.social · 31/10/2025🚀 Bioconductor 3.22 is released! Thanks to all developers and community members for contributing to the project! 🔗 Please see the full release announcement here: bioconductor.org/news/bioc_3_...bioconductor.orgBioconductor - Bioconductor 3.22 ReleasedThe Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and… 0105
Reposted by Johannes RainerBioconductor @bioconductor.bsky.social · 29/10/2025🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026! Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology. 👉 More details soon at eurobioc2026.bioconductor.org 01211