#Tag
Using Guix for Reproducible Research—a guide in 4 steps 👇
https://guix.gnu.org/cookbook/en/html_node/Reproducible-Research.html
Cc: @swheritage
Using Guix for Reproducible Research—a guide in 4 steps 👇
https://guix.gnu.org/cookbook/en/html_node/Reproducible-Research.html
Cc: @swheritage
In 2020, I reran computational experiments made in 2006 for my PhD, and packaged the whole analysis-to-paper-production pipeline with Guix:
https://gitlab.inria.fr/lcourtes-phd/edcc-2006-redone
https://dx.doi.org/10.5281/zenodo.3886739
A fellow #Guix hacker reran this Guixified pipeline days ago and it still works as intended.
That’s good news and something to celebrate in my view, as someone who knows well about the speed of the software bitrot process and the work it took to achieve this.
But still, that’s just 5 years. What’s a success for us in the field (5 years was a long time ago on the software time scale!) probably looks like a very small time frame to anyone outside.
But here we are. The promise of reproducible research can only be upheld if one can re-deploy software years
later.
People working in #ReproducibleResearch and #OpenScience should realize how bad the situation is, what solutions
exist, and what promises they can make.
In 2020, I reran computational experiments made in 2006 for my PhD, and packaged the whole analysis-to-paper-production pipeline with Guix:
https://gitlab.inria.fr/lcourtes-phd/edcc-2006-redone
https://dx.doi.org/10.5281/zenodo.3886739
A fellow #Guix hacker reran this Guixified pipeline days ago and it still works as intended.
In 2020, I reran computational experiments made in 2006 for my PhD, and packaged the whole analysis-to-paper-production pipeline with Guix:
https://gitlab.inria.fr/lcourtes-phd/edcc-2006-redone
https://dx.doi.org/10.5281/zenodo.3886739
A fellow #Guix hacker reran this Guixified pipeline days ago and it still works as intended.
New server, new #introduction:
👋 Hi! I'm Eric! I'm a scientific programmer & educator who writes mostly 
code. I currently work part time at #UniversityOfArizona where I help researchers by making R packages, #Shiny apps, automated data workflows, and training them on #ReproducibleResearch practices. I also mentor data scientists for @Posit Academy. I am #OpenToWork as a contractor if any of those skills sound useful to you.
My background is in plant chemical ecology and population ecology and for my PhD I studied #tea and did field work in China. I love tea (although I've been drinking coffee more and more lately) and practice #GongFuCha when I can. I love #foraging and tasting new things.
I currently live in #Tucson but the #BayArea will always be my home.
#rstats #rse #datascience #dataviz #ecology #chemistry #statistics
New server, new #introduction:
👋 Hi! I'm Eric! I'm a scientific programmer & educator who writes mostly code. I currently work part time at #UniversityOfArizona where I help researchers by making R packages, #Shiny apps, automated data workflows, and training them on #ReproducibleResearch practices. I also mentor data scientists for @Posit Academy. I am #OpenToWork as a contractor if any of those skills sound useful to you.
My background is in plant chemical ecology and population ecology and for my PhD I studied #tea and did field work in China. I love tea (although I've been drinking coffee more and more lately) and practice #GongFuCha when I can. I love #foraging and tasting new things.
I currently live in #Tucson but the #BayArea will always be my home.
#rstats #rse #datascience #dataviz #ecology #chemistry #statistics
« 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/
#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
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
« 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
#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
Petr Knoth (Knowledge Media Institute, The Open University) talks about the reproducibility crisis, the role of software in science, and how source code availability is the very first prerequisite to address the crisis.
A space for Bonfire maintainers and contributors to communicate
