Paper on reproducible bioinformatics pipelines with Guix
I’m happy to announce that the bioinformatics group at the Max Delbrück Center that I’m working with has released a preprint of a paper on reproducibility with the title Reproducible genomics analysis pipelines with GNU Guix.
We built a collection of bioinformatics pipelines called "PiGx" ("Pipelines in Genomix") and packaged them as first-class packages with GNU Guix. Then we looked at the degree to which the software achieves bit-reproducibility, analysed sources of non-determinism (e.g. time stamps), discussed experimental reproducibility at runtime (e.g. random number generators, the interface provided by the kernel and the GNU C library, etc) and commented on the practice of using “containers” (or application bundles) instead.
Reproducible builds is a crucial foundation for computational experiments. We hope that PiGx and the reproducibility analysis we presented in the paper can serve as a useful case study demonstrating the importance of a principled approach to computational reproducibility and the effectiveness of Guix in the pursuit of reproducible software management.
Sauf indication contraire, les billets de blog de ce site sont la propriété de leurs auteurs respectifs et publiés sous les termes de la licence CC-BY-SA 4.0 et ceux de la GNU Free Documentation License (version 1.3 ou supérieur, sans section invariante, sans texte de préface ni de postface).