Working through a data analysis on plant disease looking at weather's influence on the disease and recalled that some colleagues had done some interesting work in this area. Looked up the article and found that they had indeed included examples of #RStats code! Hooray for #ReproducibleResearch!
https://doi.org/10.1094/PHYTO-11-17-0386-R
cc @edelponte
Keeping track of your analyses just got easier!
Galaxy now integrates with RSpace, allowing you to send datasets and histories directly to your electronic lab notebook. No more jumping between tools or losing track of results.
Learn more: https://galaxyproject.org/news/2025-06-23-rspace-integration/
The #isc25 is over and I half-recovered from the weekend, too. Time to continue my thread summing up the #SnakemakeHackathon2025 !
To me, an important contribution was from Michael Jahn from the Charpentier Lab: A complete re-design of the workflow catalogue. Have a look: https://snakemake.github.io/snakemake-workflow-catalog/ - findability of ready-to-use workflows has greatly improved! Also, the description on how to contribute is now easy to find.
A detailed description has been published in the #researchequals collection https://www.researchequals.com/collections/hm1w-cg under https://doi.org/10.5281/zenodo.15574642
#Snakemake #ReproducibleComputing #ReproducibleResearch #OpenScience
Enabling #FAIR Research Data Management with #RDIs : a solution for marine and freshwater communities.
Markus Konkol explains the ins and outs of publishing readily-shareable reproducible workflows in #AquaINFRA. 👉 https://blog.52north.org/2025/06/12/hard-rock-aquainfra/
#reproducibleresearch #Galaxy #fairdata #workflows #hydrology
Oh! Here at the #isc25 I noticed, I got my first #nanopub PR merged: https://github.com/Nanopublication/nanopub-py/pull/193 🥳
Blog post: What Guix could offer in computational medical environments?
French national agency for secure drug and medicine (ANSM) requires for a medical device to have unambiguous identifications:
1. reference of the product
2. reference of the maker
3. serial number
Well, through my lenses applied to software, it reads:
1. #SoftwareHeritage identifier (#SWHID)
2. #Guix
and 3. is redundant. 😁
Well, a quick summary of a 30min talk I gave past week.
Thanks my previous colleague Sam from APHP to give me the opportunity to brainstorm on this topic. 🤩
https://simon.tournier.info/posts/2025-06-04-aphp-guix.html
#ReproducibleResearch #OpenScience #Debian #ReproducibleBuilds
On my way to Hamburg, #ISC25. The place where #HPC folks gather to learn about some new hardware trends.
Luckily, I will meet some like minded people, too. Those concerned about #usebility , #teaching , #ReproducibleResearch and so on.
On-Demand Data Science Support for Researchers! 📊🧪
Got valuable data but no time for deep analysis? 🕒
The #SUNDDataLab at the UCPH Center for Health Data Science (#HeaDS) connects you with expert Data Scientists—on demand!
We offer help with #DataCleaning, #Visualization, #Stats, and #ReproducibleResearch.
🌐 https://www.heads.ku.dk/datalab/
📧 datalab@sund.ku.dk
#Bioinformatics #AcademicResearch #DataScience #Collaboration
Did you know? During the #SnakemakeHackathon2025 we had a staggering 194 work items!
It took a while, but now we are gathering contribution reports and present them online as a ResearchEquals (https://fediscience.org/@ResearchEquals@akademienl.social) collection:
https://www.researchequals.com/collections/hm1w-cg
The first 10 are online and I will post some highlights in the coming weeks.
#Snakemake #ReproducibleComputing #ReproducibleResearch #OpenScience
+++ Update to LANDO +++
Small update for a niche corner of science 🧪
I’ve made my linked age-depth modeling tool (LANDO) Docker-ready 🐳
That means no more dependency hell — just pull & run.
Supports rbacon, Bchron, clam, hamstr, Undatable.
🔗 https://github.com/GPawi/LANDO
#OpenScience #Paleoclimatology #ReproducibleResearch #Docker #Geochronology
Asking for news from a colleague now in Univ. of Tours – long time, no see.
Nicolas pointed me a recent publication where… guess what? … they archived the source code in #SoftwareHeritage.
https://pubmed.ncbi.nlm.nih.gov/39487603/
Section « Open Research, data availability statement » reads:
« Anonymized raw data, the source code of the analyses, instructions to reproduce the computing environment, unformatted analysis reports and figures are available online (https://gitlab.com/nivall/car-lacates) and long term preserved at Software Heritage (https://archive.softwareheritage.org/swh:1:dir:a5c9b94421a6b5d6d0ab89e4aee752b540e7364f). »
And guess what else? The computational environment is managed using #Guix.
It makes my day! 😎
I’m happy to see #Guix and #SoftwarHeritage mentioned in the European Journal Of Clinical Investigation.
#ReproducibleResearch #OpenScience #EuropeanJournalOfClinicalInvestigation
« The integration of #Guix and #SoftwareHeritage paves the way for more transparency and verification of the whole computational environment involved in scientific research.
Scientific production should be robust to external service failures; for example, being able to audit or reuse scientific findings should not depend on the availability of platforms hosting source code.
That’s why backing package managers with Software Heritage appears vitally important. »
Thanks @swheritage for the spotlight! 😀
https://www.softwareheritage.org/2025/05/21/software-heritage-guix-deployment/
Hey “Choose Europe for Science”!
Do not only promote « public money, public code », make it an obligation!
Make an obligation that projects funded by Europe only rely on software that people all around the world are allowed to modify, distribute and make derivatives.
This would be a real measure which concretely claims: Science is a pillar for Democracy! There is no other Science than #OpenScience.
Yet another example.
This morning, a colleague of mine: Can you install https://mixcr.com/mixcr/about ?
1. It’s far to be trivial to be able to audit/verify the correspondence between the source code and the distributed binary. Who trust who? https://github.com/milaboratory/mixcr
2. It’s not based on the scientific principles! Because the LICENSE reads: « The User is not authorized by this License to modify, distribute or make derivatives of the Software. » https://github.com/milaboratory/mixcr/blob/1bbe28cf71bc294bcac2149c54d72f02467c28c9/LICENSE
About 1. ok that’s a difficult topic. It’s big and deep in our (technical) society.
About 2. hey it’s easy: « public money, public code ». Researchers paid by public money must only use free software (not gratis software!).
#OpenScience and #ReproducibleResearch, are they really making concrete progress?
Aside a ridiculous small set of people trying to do their best, the other are well-informed and deeply aware but they just don’t care!
Many researchers and communities hide behind « we cannot do otherwise »… 🤔 If *you* – paid by public money with a permanent position in a public institute – cannot do otherwise, who can?!? Damned!
Somehow I’m tired… Back from holidays one week ago and I already feel empty. 🤯
1/3
Reading « Are you still using OCaml 4.08 or earlier? », as a scientific practitioner I ask myself:
Well, 5 years is an eternity in the computing world – OCaml 4.08 is from 2019 and OCaml 4.07 from 2018, IIRC – but it’s peanuts when we speak about being able to audit and verify some scientific papers relying on these versions.
And there is the balance with the carbon footprint.
The question does not seem to retain 4.08 but to be able to rebuild from scratch 4.08, i.e., being able to rebuild all its dependencies. Thus it asks about the #bootstrap of the compiler and how we preserve it.
Et en plus ces identifiants #SWHID sont maintenant une norme ISO. Plus d’excuse ! 😉
https://www.iso.org/standard/89985.html
#ReproducibleResearch #OpenScience #Softwareheritage
3/3
#SoftwareHeritage ouvre un chemin…
Hop! Allez on utilise collectivement des identifiants intrinsèques dans nos papiers de recherche. Qu’est-ce que c’est ? Par exemple, petite explication là :
https://www.softwareheritage.org/2020/07/09/intrinsic-vs-extrinsic-identifiers
#ReproducibleResearch #OpenScience
2/3
« Réfléchissons collectivement à la lourde tâche d'archivage de certains savoirs spécifiques. Je pense aux travaux aussi de #SoftwareHeritage, qui, en France, archive l'ensemble des logiciels créés dans le monde, avec une initiative européenne à construire sur le sujet. Je souhaite, au-delà de la question de notre capacité, à attirer chercheurs, enseignants-chercheurs, que nous ayons aussi une capacité à préserver, consolider, attirer plateformes de collaboration et données au service de l'intérêt général. »
Bravo @swheritage !
(peu importe ce qu’il y a avant et après ce petit passage 😀)
#ReproducibleResearch #OpenScience
1/3
Reading an interesting paper with experimental results, but find some of the findings conflicting. I went to check the data, only to find the data availability statement reads: "Data sharing is not applicable as no datasets were generated or analyzed." I mean, what!? How would you handle this?
