« 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/

#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.

https://anil.recoil.org/notes/deprecating-ocaml-408

« 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 )

https://www.elysee.fr/emmanuel-macron/2025/05/05/lancement-de-choose-europe-for-science-a-la-sorbonne

#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?

@academicchatter #openscience #reproducibleresearch

« If open science is done transparently, it doesn’t have to be done perfectly. You can always refine as you go. »

https://www.nature.com/articles/d41586-025-00944-0

Last year at the Open Science Retreat (#OSR24NL) I have been introduced to nanopubs by @egonw and created my first nanopub declaring citations for a paper using CiTOs (citation ontologies).

Now, travelling to #OSR25CH, due to issues with the train network foreseen with plenty of time, I use the opportunity and created a new one ( https://w3id.org/np/RAicq7k9QHX8EG8ho7Baib9GxHsU18O0tyFCZ4tbbGGPA ) for my latest publication on teaching #Snakemake on #HPC systems.

The teaching material is — again — in desperate need of additions and overhaul, but that is for another day.

If you’re into #ReproducibleResearch & #OpenScience, don’t miss this MOOC
https://scholar.social/@khinsen/114314471616473600

Lots of practical tools for computational reproducibility, including the unequaled #Guix :-), all this brought to you by experts in the field, starting with @khinsen.

Do you know Stata?

« a general-purpose statistical proprietary software package developed by StataCorp for data manipulation, visualization, statistics, and automated reporting. It is used by researchers in many fields, including biomedicine, economics, epidemiology, and sociology. »

Guess how much does it cost? $USD ~1000 per year! Option government/nonprofit single-user. Bang!

And guess what?

For this price, you have only the “fast“ option, not “twice as fast”, neither “almost four times as fast” or neither even “even faster”. Ahah!

Crazy to read we’re still there in 2025 about #ReproducibleResearch and #OpenScience in some academic fields…

https://en.wikipedia.org/wiki/Stata
https://www.stata.com/order/new/gov/single-user-licenses/dl/

As of 2019, less than 25% of the papers in ecology & evolution came with their data; less than 20% came with their code. Ouch.

Content d’être à Lyon pour les journées du Réseau Français de la Recherche Reproductible.

Riche programme !

https://jrfrr-2025.sciencesconf.org/?lang=fr
#ReproducibleResearch #OpenScience

I recently did a live demo of a "reproducibility audit" for @us_rse. Check it out: https://www.youtube.com/watch?v=Q2ZsLbBkWrk

Ugh, #SnakeMake apparently has a hard requirement of all input (and previously-made output-) files to be present on-disk. Can't even do a dry-run `snakemake -n`.

#SnakemakeHackathon2025 ! We started!

At the CERN for better #ReproducibleComputing and #ReproducibleResearch .