EuroBioc 2026 Hackathon, Turku, Finland, 2026, Turku, Finland

  EuroBioc2026 

2026-06-01 - 2026-06-02
https://bioconductor.org/developers/bioccommits/

YAML instructions

biohackathon_name: "EuroBioc 2026 Hackathon, Turku, Finland, 2026"
biohackathon_url: "https://bioconductor.org/developers/bioccommits/"
biohackathon_location: "Turku, Finland"

Preprints

    Jul 8, 2026
    https://doi.org/10.37044/osf.io/cd9s6_v1

  • Maintaining and refining the Tidyomics ecosystem: enhancing core packages and interoperability for EuroBioc2026

    The Tidyomics ecosystem facilitates the manipulation of computational omics data structures by bringing the intuitive and consistent syntax of the tidy paradigm to R. During the EuroBioc2026 Tidyomics Hackathon, five bioinformatics researchers collaborated to strengthen this ecosystem across four areas. First, we introduce tidyAnnData, a new package that expands interoperability between the tidyverse and AnnData objects. Second, we updated and harmonized the accessibility of information across the core packages that form the current Tidyomics backbone. Third, we improved the stability of core packages by resolving critical bugs through targeted pull requests and implementing functional enhancements to the DFplyr and tidybulk packages. Fourth, we enhanced the documentation by producing a comprehensive and stable vignette for tidySingleCellExperiment covering typical single-cell analysis workflows. Together, these contributions lower the barrier to entry for new users, promote reproducibility, and support the continued transition from disparate scripts toward robust, unified omics workflows driven by community development. less than 1 minute read
    • Jun 19, 2026
    https://doi.org/10.37044/osf.io/ywsmq_v1

  • BiocExecute: Make package functions or workflows executable from the command line

    Bioconductor (Huber et al., 2015) is a collection of more than 2,400 open-source software packages, together accounting for about a million downloads per year (Bioconductor, 2026). The packages are thoroughly maintained and documented, and their quality is enforced through BiocCheck. Their reach, however, largely stops at the R console. The R and Bioconductor paradigm of interactivity through a responsive, informative REPL has served academic users well for a long time. But computational biology has grown more interdisciplinary, and increasingly runs on high-performance and high-throughput compute, large-scale experimentation, and the cloud. In these settings analyses are assembled from command-line tools and run under workflow managers, where an interactive R session does not fit. For Bioconductor and the work built on it to stay relevant, its tooling must be portable and scriptable as well as interactive. Some of this ground is already covered: R2G2 integrates R with Galaxy, and Rapp (r-lib,2024) lets an R script run as if it were a command-line program. What is missing is a path from a Bioconductor package to such tools that follows the project’s own packaging conventions. BiocExecute fills that gap. It is a package that wraps Rapp so that the functions and workflows inside any Bioconductor package can be called from the command line, with these command-line entry points declared and bundled as part of the package itself. Both users and developers gain from this. Users can run Bioconductor tools outside of Rscripts, combine them as modules with other command-line tools, and reuse them in workflows under any workflow manager; developers reach a wider range of users. More broadly, making Bioconductor packages executable improves their FAIRness (Barker et al., 2022; Wilkinson et al., 2016) and gives Bioconductor software visibility among a larger community of bioinformaticians. Longer term, the goal is to lay the groundwork for programmatic generation of command-line tooling from within Bioconductor packages, so that this tooling can be slotted into modern workflow management systems or interactive platforms such as Galaxy (Goecks et al., 2010). 1 minute read
    • Jun 15, 2026
    https://doi.org/10.37044/osf.io/acxky_v1

  • Eurobioc2026 BiocContainer Report

    Containers enhance reproducibility and provide an easy and convenient way to share the setups used to run an analysis. As part of the EuroBioc 2026 Hackathon, this working group got together with the aim of offering user-friendly and straightforward ways to create containers given the desired R packages, data and scripts, and importantly, coupled to the used Bioconductor release. This resulted in an R package called SimpleBiocContainer which offers a minimal set of functions to do this. less than 1 minute read