Is reproducibility practical?

Ludovic Courtès — July 21, 2022

Our attention was recently caught by a nice slide deck on the methods and tools for reproducible research in R. Among those, the talk mentions Guix, stating that it is “for professional, sensitive applications that require ultimate reproducibility”, which is “probably a bit overkill for Reproducible Research”. While we were flattered to see Guix suggested as good tool for reproducibility, the very notion that there’s a kind of “reproducibility” that is “ultimate” and, essentially, impractical, is something that left us wondering: What kind of reproducibility do scientists need, if not the “ultimate” kind? Is “reproducibility” practical at all, or is it more of a horizon?

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ccwl for concise and painless CWL workflows

Arun Isaac — January 10, 2022

In modern science, analysis is required to process data. When the data-flow is linear, such a process is easily represented by tools such as the standard Unix pipeline. However, this data-flow is often modeled by a directed graph: each processing node may have one or more inputs and the outputs may be directed to different processing nodes. This directed graph, mainly used in the fields of bioinformatics, medical imaging and astronomy, among many others, is called a workflow.

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When Docker images become fixed-point

Simon Tournier — October 22, 2021

We like to say that Docker images are like smoothies: you can immediately tell whether it’s your liking, but you can hardly guess what the ingredients are. Although containers are an efficient way to ship things, the core question is how these things are produced.

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What’s in a package

Ludovic Courtès — September 20, 2021

There is no shortage of package managers. Each tool makes its own set of tradeoffs regarding speed, ease of use, customizability, and reproducibility. Guix occupies a sweet spot, providing reproducibility by design as pioneered by Nix, package customization à la Spack from the command line, the ability to create container images without hassle, and more.

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Guix-Jupyter 0.2.1 released!

Ludovic Courtès — January 25, 2021

We are pleased to announce Guix-Jupyter 0.2.1, a new release of our Guix-powered Jupyter kernel for self-contained and reproducible notebooks.

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Reproducible research hackathon: experience report

Simon Tournier, Ludovic Courtès — July 10, 2020

Last week, on July 3rd, we held an on-line hackathon on reproducible research issues. This hackathon was a collaborative effort to bring GNU Guix to concrete examples inspired by to contributions the recent Ten Years Reproducibility Challenge organized by ReScience.

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Reproducible Research Hackathon

Simon Tournier — June 30, 2020

Several submissions to the recent Ten Years Reproducibility Challenge organized by ReScience took advantage of GNU Guix, as discussed earlier.

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Reproducible research articles, from source code to PDF

Ludovic Courtès — June 16, 2020

Early this year, ReScience, which is concerned with publishing replications (successful or not) of previously-published articles, organized the Ten Years Reproducibility Challenge. The idea is simple: pick a paper of yours that is at least ten years old, and try to replicate its results. The first difficulty is usually to get the source code of the software used to produce the results and to get that code to build and run. This challenge helped highlight again ways in which research practices can and must be improved. We took it as an opportunity to devise new practices and tools to ensure reproducibility and provenance tracking for articles, end-to-end: from source code to PDF.

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Reproducible computations with Guix

Konrad Hinsen — January 14, 2020

This post is about reproducible computations, so let's start with a computation. A short, though rather uninteresting, C program is a good starting point. It computes π in three different ways:

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Towards reproducible Jupyter notebooks

Ludovic Courtès — October 10, 2019

Jupyter Notebooks are becoming a key component of the researcher’s toolbox when it comes to sharing and reproducing computational experiments. Jupyter notebooks allow users to not only intermingle a narrative with supporting code in a way reminiscent of literate programming, they also make it easy to interact with the code and, thus, build on the work of each other.

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Chapter of “Evolutionary Genomics” on workflow tools and Guix

Ludovic Courtès — September 9, 2019

The book Evolutionary Genomics was published in July this year. Of particular interest to Guix-HPC is the chapter entitled “Scalable Workflows and Reproducible Data Analysis for Genomics”, by Francesco Strozzi et al.:

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Connecting reproducible deployment to a long-term source code archive

Ludovic Courtès — March 29, 2019

GNU Guix can be used as a “package manager” to install and upgrade software packages as is familiar to GNU/Linux users, or as an environment manager, but it can also provision containers or virtual machines, and manage the operating system running on your machine.

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Creating a reproducible workflow with CWL

Pjotr Prins — January 21, 2019

In the quest for truly reproducible workflows I set out to create an example of a reproducible workflow using GNU Guix, IPFS, and CWL. GNU Guix provides content-addressable, reproducible, and verifiable software deployment. IPFS provides content-addressable storage, and CWL describes workflows that can run on specifically supported backend hardware system. In principle, this combination of tools should be enough to provide reproducibility with provenance and improved security.

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PiGx paper awarded at the International Conference on Genomics (ICG-13)

Ricardo Wurmus — January 11, 2019

December 2018 the Akalin lab at the Berlin Institute of Medical Systems Biology (BIMSB) published a paper about a collection of reproducible genomics pipelines called PiGx that are made available through GNU Guix. The article was awarded third place in the GigaScience ICG-13 Prize. Representing the authors, Ricardo Wurmus was invited to present the work on PiGx and Guix in Shenzhen, China at ICG-13.

Ricardo Wurmus presenting at ICG-13.

Ricardo urged the audience of wet lab scientists and bioinformaticians to apply the same rigorous standards of experimental design to experiments involving software: all variables need to be captured and constrained. To demonstrate that this does not need to be complicated, Ricardo reported the experiences of the Akalin lab in building a collection of reproducibly built automated genomics workflows using GNU Guix.

Due to technical difficulties the recording of the talk was lost, so Ricardo re-recorded the talk a few weeks later.

Paper on reproducible bioinformatics pipelines with Guix

Ricardo Wurmus — May 9, 2018

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.

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Reproducibility vs. root privileges

Ludovic Courtès — September 22, 2017

Guix is a good fit for multi-user environments such as clusters: it allows non-root users to install packages at will without interfering with each other. However, a common complaint is that installing Guix requires administrator privileges. More precisely, guix-daemon, the system-wide daemon that spawns package builds and downloads on behalf of users, must be running as root. This is not much of a problem on one's laptop but it surely makes it harder to adopt Guix on an HPC cluster.

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Guix-HPC debut!

Ludovic Courtès, Roel Janssen, Pjotr Prins, Ricardo Wurmus — September 5, 2017

This post marks the debut of Guix-HPC, an effort to optimize GNU Guix for reproducible scientific workflows in high-performance computing (HPC). Guix-HPC is a joint effort between Inria, the Max Delbrück Center for Molecular Medicine (MDC), and the Utrecht Bioinformatics Center (UBC). Ludovic Courtès, Ricardo Wurmus, Roel Janssen, and Pjotr Prins are driving the effort in each of these institutes, each one focusing specific areas of interest within this overall Guix-HPC effort. Our institutes have in common that they are users of HPC, and that, as scientific research institutes, they have an interest in using reproducible methodologies to carry out their research.

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  • MDC
  • Inria
  • UBC
  • UTHSC