Colony: a framework for reproducible and easy-to-use data analysis pipelines for biomedical research with singularity containers

TL;DR

Colony is a user-friendly tool that allows biologists to use containerized software without needing command line skills, promoting reproducible biomedical research.

Contribution

The novelty is a graphical interface for Singularity containers, making containerized software accessible to non-programmers in biomedical research.

Findings

Colony provides a graphical user interface for interacting with Singularity containers.

The tool was evaluated for feasibility using software from the TRR156 project.

Colony is freely available and open-source for use and modification.

Abstract

Bioinformatics pipelines should meet the FAIR criteria to enable reproducible analysis. FAIR describes four key requirements for reproducible research: findability, accessibility, interoperability and reusability. Software containers such as Singularity are widely used tools that facilitate the reuse of software across different computing environments. However, many biologists and other researchers find command line tools such as Singularity unfamiliar and do not feel productive when using software via the command line. We present a graphical user interface that allows biologists without programming experience to interact with containerized software. We evaluate the feasibility of our approach with software used at the TRR156.

Colony can be freely downloaded on its project page: https://clipc-jpg.github.io/ColonyWebsite/. The Colony launcher’s code is MIT-licensed and freely available at: https://github.com/clipc-jpg/Colony. All related assets can be found at: https://doi.org/10.7910/DVN/Z3OTWY.

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