#reproducibleresearch — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #reproducibleresearch, aggregated by home.social.
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Our contribution "Open-Source Quantitative MRI: Full Implementation of Acquisition and Reconstruction in BART" by Daniel Mackner et al. received the 1st price of the Open & Reproducible Research Study Group
#MRI #reproducibleresearch #imaging #radiology #openscience -
Our contribution "Open-Source Quantitative MRI: Full Implementation of Acquisition and Reconstruction in BART" by Daniel Mackner et al. received the 1st price of the Open & Reproducible Research Study Group
#MRI #reproducibleresearch #imaging #radiology #openscience -
Our contribution "Open-Source Quantitative MRI: Full Implementation of Acquisition and Reconstruction in BART" by Daniel Mackner et al. received the 1st price of the Open & Reproducible Research Study Group
#MRI #reproducibleresearch #imaging #radiology #openscience -
Our contribution "Open-Source Quantitative MRI: Full Implementation of Acquisition and Reconstruction in BART" by Daniel Mackner et al. received the 1st price of the Open & Reproducible Research Study Group
#MRI #reproducibleresearch #imaging #radiology #openscience -
Our contribution "Open-Source Quantitative MRI: Full Implementation of Acquisition and Reconstruction in BART" by Daniel Mackner et al. received the 1st price of the Open & Reproducible Research Study Group
#MRI #reproducibleresearch #imaging #radiology #openscience -
#Guix at the annual French #ReproducibleResearch Network conference, May 19–21 👇
https://hpc.guix.info/blog/2026/05/guix-at-the-french-reproducible-research-network-conference/ -
💁♂️ Want to know how to make computational research more reusable❓
👍 Join our short course on Supporting the understanding and reuse of #reproducible analysis workflows.📅 Friday, May 8
🕓 8:30-10:15Check out the #NFDI4Earth poster:
From Data Rocks to #FAIR Peaks: With NFDI4Earth’s services towards Harmonized Metadata and User-Centered Tools for Earth System Research.📅 Friday, May 8
🕓 16:15–18:00 -
💁♂️ Want to know how to make computational research more reusable❓
👍 Join our short course on Supporting the understanding and reuse of #reproducible analysis workflows.📅 Friday, May 8
🕓 8:30-10:15Check out the #NFDI4Earth poster:
From Data Rocks to #FAIR Peaks: With NFDI4Earth’s services towards Harmonized Metadata and User-Centered Tools for Earth System Research.📅 Friday, May 8
🕓 16:15–18:00 -
💁♂️ Want to know how to make computational research more reusable❓
👍 Join our short course on Supporting the understanding and reuse of #reproducible analysis workflows.📅 Friday, May 8
🕓 8:30-10:15Check out the #NFDI4Earth poster:
From Data Rocks to #FAIR Peaks: With NFDI4Earth’s services towards Harmonized Metadata and User-Centered Tools for Earth System Research.📅 Friday, May 8
🕓 16:15–18:00 -
💁♂️ Want to know how to make computational research more reusable❓
👍 Join our short course on Supporting the understanding and reuse of #reproducible analysis workflows.📅 Friday, May 8
🕓 8:30-10:15Check out the #NFDI4Earth poster:
From Data Rocks to #FAIR Peaks: With NFDI4Earth’s services towards Harmonized Metadata and User-Centered Tools for Earth System Research.📅 Friday, May 8
🕓 16:15–18:00 -
💁♂️ Want to know how to make computational research more reusable❓
👍 Join our short course on Supporting the understanding and reuse of #reproducible analysis workflows.📅 Friday, May 8
🕓 8:30-10:15Check out the #NFDI4Earth poster:
From Data Rocks to #FAIR Peaks: With NFDI4Earth’s services towards Harmonized Metadata and User-Centered Tools for Earth System Research.📅 Friday, May 8
🕓 16:15–18:00 -
RE: https://fediscience.org/@biohackrxiv/116477505622903440
Today, we published the summary (as a #BioHackrXiv preprint) of the #SnakemakeHackathon2026 . All the accomplishments which contribute once more to improve the #Snakemake "ecosystem" for #reproducibleResearch & #Dataanalysis .
Many thanks to @egonw from BioHackrXiv for helping us!
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RE: https://fediscience.org/@biohackrxiv/116477505622903440
Today, we published the summary (as a #BioHackrXiv preprint) of the #SnakemakeHackathon2026 . All the accomplishments which contribute once more to improve the #Snakemake "ecosystem" for #reproducibleResearch & #Dataanalysis .
Many thanks to @egonw from BioHackrXiv for helping us!
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RE: https://fediscience.org/@biohackrxiv/116477505622903440
Today, we published the summary (as a #BioHackrXiv preprint) of the #SnakemakeHackathon2026 . All the accomplishments which contribute once more to improve the #Snakemake "ecosystem" for #reproducibleResearch & #Dataanalysis .
Many thanks to @egonw from BioHackrXiv for helping us!
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RE: https://fediscience.org/@biohackrxiv/116477505622903440
Today, we published the summary (as a #BioHackrXiv preprint) of the #SnakemakeHackathon2026 . All the accomplishments which contribute once more to improve the #Snakemake "ecosystem" for #reproducibleResearch & #Dataanalysis .
Many thanks to @egonw from BioHackrXiv for helping us!
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RE: https://fediscience.org/@biohackrxiv/116477505622903440
Today, we published the summary (as a #BioHackrXiv preprint) of the #SnakemakeHackathon2026 . All the accomplishments which contribute once more to improve the #Snakemake "ecosystem" for #reproducibleResearch & #Dataanalysis .
Many thanks to @egonw from BioHackrXiv for helping us!
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Would anyone have advice on FOSS tooling for reproducible biomedical literature searches? What I'd want to do specifically is to document the *absence* of case reports of exceptional responses to drugs that got FDA accelerated approval. (As for why, see https://osf.io/59sya/files/q6trp.) These would start with automated searches of EuropePMC, then annotation of manual review results. Since a new case report could be published at any time, I would need these to be update-able. I'm guessing an approach built on #orgmode #make and other #root technologies could work well. @lukascbossert @jameshowell
#reproducibleresearch -
Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊
Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.
📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)🔗Registration form link: https://lnkd.in/gQcHggGF
#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats
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Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊
Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.
📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)🔗Registration form link: https://lnkd.in/gQcHggGF
#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats
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Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊
Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.
📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)🔗Registration form link: https://lnkd.in/gQcHggGF
#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats
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Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊
Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.
📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)🔗Registration form link: https://lnkd.in/gQcHggGF
#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats
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Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊
Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.
📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)🔗Registration form link: https://lnkd.in/gQcHggGF
#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats
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Save the date for the next NLRN Symposium!
We will meet on 25 January 2027 in Utrecht.Thanks to OSNL for awarding an OS meeting grant! We are looking forward to seeing many of you to discuss the implementation of #research policies and how those affect the daily work of researchers and supporters.
We have a newsletter if you prefer receiving news in your inbox: https://reproducibilitynetwork.nl/newsletter/
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Hackathon kicking off! ✨
(Pre-event for #OSR26UK)@priyasilverstein and Ruth Davies facilitating the day of updating the #UKRN resource "Open Research Across Disciplines" - "How the principles of open research can be applied to your discipline":
ukrn.org/disciplines/
Intro slides: https://docs.google.com/presentation/d/1WASJvGs0nUsNOaRo64fERyKw0tvfrLMmL7sdAQ4eT6A/mobilepresent#slide=id.p
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Why publish your research data in a proper repository like Zenodo, not a on a fancy institutional website?
I was looking to access the UN Peace Missions Mandate dataset for some analysis. When I checked https://www.peacemissions.info it was gone. Timed out.
I have no idea if it's temporarily down or down forever or what has happened.
It's not accessible elsewhere as far as I can tell, so the analysis is not happening.
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First Keynote Announcement for uRos2026
We are excited to reveal our first keynote speaker for the Use of R in Official Statistics Conference 2026 (uRos2026):
🎤 Rebecca Killick
Professor & Director of Research, Lancaster University
Rebecca Killick is a leading expert in statistical methodology, with a strong focus on nonstationary time series analysis and applications across domains such as energy, finance, health, and official statistics.
Her work bridges real-world problems and innovative methodology, always with a strong commitment to open-source software and reproducible research.
Keynote Talk: “R and Open-Source: A love story”
In this keynote, Rebecca will reflect on over 20 years of working with R and open-source.📅 Stay tuned for more speakers and details!
#uRos2026 #OfficialStatistics #RStats #OpenSource #DataScience #Statistics #rOpenSci #ReproducibleResearch -
If you’re into #Rstats and/or #bioinformatics, if you care about #ReproducibleResearch, consider helping out fellow #Guix hackers!
https://codeberg.org/guix-science/guix-cran-scripts/The scripts above are what powers the automated imports of CRAN and Bioconductor as Guix channels, and they need ❤
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RE: https://fosstodon.org/@robinlovelace/116136723310374275
It's great to log-on to #Mastodon to find not only my work being discussed and put out there with enlightening comments (thanks @AntoninDanalet ), but also that quote reposts are now a thing, when did that happen?! In any case check it out when you get a chance and join the conversation of openness (including open publications, code, data and accessible communities) in research! #OpenSource #dataScience for #reproducibleresearch in the public interest 🚀
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#AcademicChatter Hello, fellow academic chatters. I'm an experimental scientist. And I regularly have the problem of how to organize acquired data by different participants to a same experiment. I'd like to have some feedback of how other people do this. Not necessarily specific computer programmes (such as digital labbooks), but rather how-tos based on robust, basic things, such as text and csv files, folder structures etc. I'm often battling with the workflow which is including handwritten measurements, their digital counterparts, metadata for the measurements, codes for samples, all of these done by different people, but all will have to end in one final dataset, where I would like to be able to trace data back to the paper files, and their metadata. And all of this with not too much additional effort by everybody ;-) Have done this usually with some shared server space, but usually it ends up as something a bit difficult to get through. I'm now rather thinking about a system involving perhaps something based on #MarkDown or even #RMarkdown or #knitr etc. Any feedback much welcome 😁
#ReproducibleResearch -
Read on #Guix science channel about #Bazel:
« The offending upstream commit is here: github.com/tensorflow/tensorflow@e85860e838
There is no way to build Tensorflow without a bundled Python toolchain. The only way I see is to trick it into "downloading" our provided Python toolchain from a file:// URL.
I find this battle against upstream's approach towards reproducibility exhausting. »
🤔 Could you stop to say: “yeah Guix is great but I don’t use because it doesn’t provide what I need”…
…and instead explicitly say: “my research outcome is more important than doing it correctly”.
https://codeberg.org/guix-science/guix-science/issues/593#issuecomment-11048234
#ReproducibleResearch #OpenScience -
📣 Looking for tutorials and other references about containers!
In the context of #ReproducibleResearch [1], we’re writing “cards” gathering resources for more robust scientific outcomes.
You want to help?
Easy: mention one tutorial or some reference that already helped you!
• Either a practical getting started;
• Either something that helped you to get how containers can boost your research by being more reproducible.Checkout: https://gt-env-logiciels.gricad-pages.univ-grenoble-alpes.fr/sandbox-notecards/cards/containers
Thanks
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Personne qui interviewe : « Cela prend du temps et les chercheurs en manquent cruellement… »
🤔 Et si on réduisait la bureaucratie, euh, compétitivité, euh, de mettre des couches de labels d’excellence, euh… bah peut-être que le temps manquerait moins, non ?
Sarah Cohen-Boulakia : « Aujourd’hui, on publie trop et trop vite. Il faudrait évaluer les chercheurs davantage sur la qualité et la transparence plutôt que sur la quantité.
La peur du “décrochage de la France” en termes de publications scientifiques terrorise beaucoup de décideurs alors que la transparence nous permettrait d’avoir des résultats plus solides et de regagner la confiance du grand public en ces temps de désinformation. »
👍 😍
https://themeta.news/sarah-cohen-boulakia
#ReproducibleResearch #OpenScience -
« Il faut expliquer le mieux possible comment un résultat a été obtenu, rendre les plus traçables possibles les conditions de son obtention.
C’est d’abord ce manque d’information qui crée la crise.
On parle de crise de la reproductibilité mais en réalité c’est la transparence qui compte et qui permettra de la résoudre. Chacun a un rôle à jouer : décideurs, éditeurs, chercheurs… »
🤔 D’ailleurs, peut-être que la crise est une crise de confiance, et dont la transparence est un moyen pour la résoudre.
https://themeta.news/sarah-cohen-boulakia
#ReproducibleResearch #OpenScience -
Story: when colleagues realize #Guix rocks!
– Please help me! a colleague said.
– What’s wrong? I answered.
– My R stuff worked and now it crashes!
– Ah, so what’s changed in between?
– Nothing!
– Maybe an update?
– Indeed, apt update and upgrade, but packages were unrelated!
– Maybe not?
– I’ve double-checked:
• it still works on this other machine but crashed on this one.
• all the versions between the both machines are the sames.
Damned! I’m lost…
– Maybe it’s not the same versions?
– Look, 1.2.3-xzy and 1.2.3-xyz etc.
– Look, folder checksum are different so it’s not the same.
– …
– Please, give me the list of R packages you need.…half hour later…
Thanks #Guix and guix-science, guix-cran and guix-bioc channels, only one R package needs to be freshly packaged.
The command:
guix time-machine -C channels.scm -- shell -m manifest.scm
and tandam the same computational environment is running on the both machines.
Nothing more.
First conclusion: APT and Ubuntu are poorly designed for #ReproducibleResearch and one needs wizard skills to avoid the bitter bite.
Second conclusion: Some people in my lab are realizing the hard way: « Aaah maybe starting a project with Guix might be slower at first but then it frees from some painful burden. »
Third conclusion: let wait the end of some pending computations. 😁
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ReproducibiliTea Copenhagen is back with the first journal club of the year!
When: Feb 27, 10:30 am
Where: https://lnkd.in/dUTDkWSW
#ReproducibiliTeaCopenhagen #JournalClub #OpenScience #ReproducibleResearch #ResearchReproducibility
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« this discrepancy is a root cause of the #ReproducibilityCrisis. »
Please do not hide 🫣 behind technical means!
As scientific practitioners, it’s simple (but not easy!):
(1) Degrowth our outcome; for a better quality and a lower quantity
(2) Adopt and promote current practises that already help
The rule of thumb:
If our grandchildren cannot verify in the future our findings of today, then such findings aren’t scientific findings but findings of alchemists, wizards, sorcerers, occultists or warlocks.
https://scholarlykitchen.sspnet.org/2026/02/05/back-to-the-article-of-the-future-an-interview-with-sami-benchekroun-and-rod-cookson/
#ReproducibleResearch #OpenScience
3/3 -
« there are the systemic drivers:
• FAIR data mandates from funders
• Open-lab notebook movements
• Persistent Identifier (PID) expansion into every layer of research
• Preprint-to-publication workflows that treat research as a continuumAll of these point toward a future where the “unit of science” is no longer a PDF but a rich, evolving digital object grounded in data, workflows, and provenance. »
🧐 Guess what?
‣ #Guix and #Nix are designed around Persistent IDentifier (PID) for dealing with reproducible computational environments.
‣ Software Hash IDentifier (#SWHID) proposed by #SoftwareHeritage folk provides a Persistent IDentifier (PID) for source code.
https://scholarlykitchen.sspnet.org/2026/02/05/back-to-the-article-of-the-future-an-interview-with-sami-benchekroun-and-rod-cookson/
#ReproducibleResearch #OpenScience
2/3 -
« At the same time, we continue to invest enormous effort in perfecting the presentation of the final PDF like typesetting, formatting, and version-freezing, while under-investing in the earlier stages of the research journey where quality, integrity, and reuse are actually shaped. That imbalance is not a failure of intent, but a misalignment of effort driven by legacy workflows. »
🤔 Misalignment raised to power of “Publish or Perish”?
https://scholarlykitchen.sspnet.org/2026/02/05/back-to-the-article-of-the-future-an-interview-with-sami-benchekroun-and-rod-cookson/
#ReproducibleResearch #OpenScience
1/3 -
« La leçon principale de ce projet est donc : on ne peut pas bâtir une plate-forme de calcul reproductible sur une fondation instable comme Python. »
Et la personne qui écrit cela est mentionnée dans “The Story of Python and how it took over the world” (Python: The Documentary).
Mais qui est-ce donc ? 😉
Un indice ? Aujourd’hui elle promeut (Common) Lisp. 😁
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Check out the Spring 2026 ReproducibiliTea
Program by Center for Reproducible Science and Research Synthesis - UZH
Register here: https://crs.uzh.ch/en/training/ReproducibiliTea.html#Reproducibility #ReproducibleResearch #OpenScience #OpenResearch #ResearchIntegrity #OpenData #ResearchMethods
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Check out the Spring 2026 ReproducibiliTea
Program by Center for Reproducible Science and Research Synthesis - UZH
Register here: https://crs.uzh.ch/en/training/ReproducibiliTea.html#Reproducibility #ReproducibleResearch #OpenScience #OpenResearch #ResearchIntegrity #OpenData #ResearchMethods
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Check out the Spring 2026 ReproducibiliTea
Program by Center for Reproducible Science and Research Synthesis - UZH
Register here: https://crs.uzh.ch/en/training/ReproducibiliTea.html#Reproducibility #ReproducibleResearch #OpenScience #OpenResearch #ResearchIntegrity #OpenData #ResearchMethods
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Check out the Spring 2026 ReproducibiliTea
Program by Center for Reproducible Science and Research Synthesis - UZH
Register here: https://crs.uzh.ch/en/training/ReproducibiliTea.html#Reproducibility #ReproducibleResearch #OpenScience #OpenResearch #ResearchIntegrity #OpenData #ResearchMethods
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Check out the Spring 2026 ReproducibiliTea
Program by Center for Reproducible Science and Research Synthesis - UZH
Register here: https://crs.uzh.ch/en/training/ReproducibiliTea.html#Reproducibility #ReproducibleResearch #OpenScience #OpenResearch #ResearchIntegrity #OpenData #ResearchMethods
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📣 Upcoming talk with R-NVSU
I’ll be giving a session on Git & GitHub in RStudio: Practical Version Control for Data Work for the R-NVSU community.
We’ll focus on:
• Git fundamentals as they appear in RStudio
• using the Git pane safely
• when to use the GUI vs the terminal
• practical workflows for R projects🗓️ Event & registration:
👉 https://www.meetup.com/r-nvsu/events/313201432#RStats #Git #GitHub #RStudio #VersionControl #ReproducibleResearch #RCommunity
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📣 Upcoming talk with R-NVSU
I’ll be giving a session on Git & GitHub in RStudio: Practical Version Control for Data Work for the R-NVSU community.
We’ll focus on:
• Git fundamentals as they appear in RStudio
• using the Git pane safely
• when to use the GUI vs the terminal
• practical workflows for R projects🗓️ Event & registration:
👉 https://www.meetup.com/r-nvsu/events/313201432#RStats #Git #GitHub #RStudio #VersionControl #ReproducibleResearch #RCommunity
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📣 Upcoming talk with R-NVSU
I’ll be giving a session on Git & GitHub in RStudio: Practical Version Control for Data Work for the R-NVSU community.
We’ll focus on:
• Git fundamentals as they appear in RStudio
• using the Git pane safely
• when to use the GUI vs the terminal
• practical workflows for R projects🗓️ Event & registration:
👉 https://www.meetup.com/r-nvsu/events/313201432#RStats #Git #GitHub #RStudio #VersionControl #ReproducibleResearch #RCommunity
-
📣 Upcoming talk with R-NVSU
I’ll be giving a session on Git & GitHub in RStudio: Practical Version Control for Data Work for the R-NVSU community.
We’ll focus on:
• Git fundamentals as they appear in RStudio
• using the Git pane safely
• when to use the GUI vs the terminal
• practical workflows for R projects🗓️ Event & registration:
👉 https://www.meetup.com/r-nvsu/events/313201432#RStats #Git #GitHub #RStudio #VersionControl #ReproducibleResearch #RCommunity
-
📣 Upcoming talk with R-NVSU
I’ll be giving a session on Git & GitHub in RStudio: Practical Version Control for Data Work for the R-NVSU community.
We’ll focus on:
• Git fundamentals as they appear in RStudio
• using the Git pane safely
• when to use the GUI vs the terminal
• practical workflows for R projects🗓️ Event & registration:
👉 https://www.meetup.com/r-nvsu/events/313201432#RStats #Git #GitHub #RStudio #VersionControl #ReproducibleResearch #RCommunity